I: pbuilder: network access will be disabled during build I: Current time: Tue Jul 2 11:11:28 +14 2024 I: pbuilder-time-stamp: 1719868288 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [picard-tools_2.24.1+dfsg-1.dsc] I: copying [./picard-tools_2.24.1+dfsg.orig.tar.xz] I: copying [./picard-tools_2.24.1+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.kRvJo5Sp/trustedkeys.kbx': General error gpgv: Signature made Thu Jan 28 21:02:08 2021 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./picard-tools_2.24.1+dfsg-1.dsc dpkg-source: info: extracting picard-tools in picard-tools-2.24.1+dfsg dpkg-source: info: unpacking picard-tools_2.24.1+dfsg.orig.tar.xz dpkg-source: info: unpacking picard-tools_2.24.1+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 10-build.xml.patch dpkg-source: info: applying 20-shadowjar.patch dpkg-source: info: applying 30-tests-fix-dataprovider.patch dpkg-source: info: applying 40-tests-fix-testng.patch dpkg-source: info: applying 50-tests-exclude-Barclay.patch dpkg-source: info: applying remove_google_nio.patch dpkg-source: info: applying fix_unreadabletests.patch dpkg-source: info: applying 60-tests-exclude-network.patch dpkg-source: info: applying non-intel-skip-intel-tests dpkg-source: info: applying correct_dataprovider_TestDontMergeAbuttingData.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3151990/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jul 2 11:12 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/3151990/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3151990/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=20 ' DIRSTACK=() DISTRIBUTION=bullseye EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=625bbad73aac45e587f16253f7b7bdaa LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3151990 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.o0vBACIx/pbuilderrc_dGAD --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.o0vBACIx/b2 --logfile b2/build.log picard-tools_2.24.1+dfsg-1.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-22-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.94-1 (2024-06-21) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 28 2022 bash -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash -rwxr-xr-x 1 root root 113664 Sep 24 2020 date -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd -rwxr-xr-x 1 root root 93936 Sep 24 2020 df -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir -rwxr-xr-x 1 root root 84440 Mar 29 00:09 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep -rwxr-xr-x 1 root root 39680 Sep 24 2020 false -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 69032 Mar 29 00:09 findmnt -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 203072 Jan 25 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98048 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln -rwxr-xr-x 1 root root 56952 Feb 8 2020 login -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls -rwxr-xr-x 1 root root 149736 Mar 29 00:09 lsblk -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp -rwxr-xr-x 1 root root 59632 Mar 29 00:09 more -rwsr-xr-x 1 root root 55528 Mar 29 00:09 mount -rwxr-xr-x 1 root root 18664 Mar 29 00:09 mountpoint -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 17 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd lrwxrwxrwx 1 root root 4 Mar 28 2022 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 9 Jul 2 11:12 sh -> /bin/bash -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty -rwsr-xr-x 1 root root 71912 Mar 29 00:09 su -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync -rwxr-xr-x 1 root root 531928 Jan 20 23:59 tar -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch -rwxr-xr-x 1 root root 39680 Sep 24 2020 true -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Mar 29 00:09 umount -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir -rwxr-xr-x 1 root root 63744 Mar 29 00:09 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/3151990/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: default-jdk (>= 2:1.9~), debhelper-compat (= 13), javahelper, gradle-debian-helper, maven-repo-helper, libguava-java, libcommons-collections4-java, libcommons-io-java, libcommons-lang3-java, libcommons-math3-java, libbarclay-java, libgkl-java (>= 0.8.6+dfsg-2), libgkl-jni, libgatk-native-bindings-java, libhtsjdk-java (>= 2.22.0~), testng (>= 6.9.10), r-base-core, default-jdk-doc, libhtsjdk-java-doc, libjs-jquery dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19711 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on default-jdk (>= 2:1.9~); however: Package default-jdk is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on javahelper; however: Package javahelper is not installed. pbuilder-satisfydepends-dummy depends on gradle-debian-helper; however: Package gradle-debian-helper is not installed. pbuilder-satisfydepends-dummy depends on maven-repo-helper; however: Package maven-repo-helper is not installed. pbuilder-satisfydepends-dummy depends on libguava-java; however: Package libguava-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-collections4-java; however: Package libcommons-collections4-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-io-java; however: Package libcommons-io-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-lang3-java; however: Package libcommons-lang3-java is not installed. pbuilder-satisfydepends-dummy depends on libcommons-math3-java; however: Package libcommons-math3-java is not installed. pbuilder-satisfydepends-dummy depends on libbarclay-java; however: Package libbarclay-java is not installed. pbuilder-satisfydepends-dummy depends on libgkl-java (>= 0.8.6+dfsg-2); however: Package libgkl-java is not installed. pbuilder-satisfydepends-dummy depends on libgkl-jni; however: Package libgkl-jni is not installed. pbuilder-satisfydepends-dummy depends on libgatk-native-bindings-java; however: Package libgatk-native-bindings-java is not installed. pbuilder-satisfydepends-dummy depends on libhtsjdk-java (>= 2.22.0~); however: Package libhtsjdk-java is not installed. pbuilder-satisfydepends-dummy depends on testng (>= 6.9.10); however: Package testng is not installed. pbuilder-satisfydepends-dummy depends on r-base-core; however: Package r-base-core is not installed. pbuilder-satisfydepends-dummy depends on default-jdk-doc; however: Package default-jdk-doc is not installed. pbuilder-satisfydepends-dummy depends on libhtsjdk-java-doc; however: Package libhtsjdk-java-doc is not installed. pbuilder-satisfydepends-dummy depends on libjs-jquery; however: Package libjs-jquery is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: ant{a} ant-optional{a} antlr{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bnd{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} dctrl-tools{a} debhelper{a} default-jdk{a} default-jdk-doc{a} default-jdk-headless{a} default-jre{a} default-jre-headless{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gnupg-utils{a} gpg{a} gpg-agent{a} gpg-wks-client{a} gpg-wks-server{a} gpgconf{a} gpgsm{a} gradle{a} gradle-debian-helper{a} groff-base{a} groovy{a} intltool-debian{a} ivy{a} java-common{a} java-wrappers{a} javahelper{a} junit4{a} libactivation-java{a} libantlr-java{a} libaopalliance-java{a} libapache-pom-java{a} libarchive-zip-perl{a} libargs4j-java{a} libasm-java{a} libasound2{a} libasound2-data{a} libassuan0{a} libatinject-jsr330-api-java{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libb-hooks-op-check-perl{a} libbarclay-java{a} libbcel-java{a} libbcpg-java{a} libbcprov-java{a} libblas3{a} libbrotli1{a} libbsd0{a} libbsf-java{a} libbsh-java{a} libcairo2{a} libcdi-api-java{a} libclass-method-modifiers-perl{a} libcodemodel-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-collections4-java{a} libcommons-compress-java{a} libcommons-io-java{a} libcommons-jexl2-java{a} libcommons-lang-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-math3-java{a} libcommons-parent-java{a} libcups2{a} libcurl4{a} libdatrie1{a} libdbus-1-3{a} libdd-plist-java{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdom4j-java{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libdtd-parser-java{a} libdynaloader-functions-perl{a} libeclipse-jdt-annotation-java{a} libedit2{a} libel-api-java{a} libelf1{a} libencode-locale-perl{a} libexpat1{a} libfastinfoset-java{a} libfelix-framework-java{a} libfelix-gogo-runtime-java{a} libfelix-resolver-java{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} libfindbugs-java{a} libfontconfig1{a} libfreemarker-java{a} libfreetype6{a} libfribidi0{a} libgatk-native-bindings-java{a} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libgfortran5{a} libgif7{a} libgkl-java{a} libgkl-jni{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgoogle-gson-java{a} libgradle-core-java{a} libgradle-plugins-java{a} libgraphite2-3{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{a} libhawtjni-runtime-java{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhtsjdk-java{a} libhtsjdk-java-doc{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libhttpclient-java{a} libhttpcore-java{a} libice6{a} libicu67{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libistack-commons-java{a} libjansi-java{a} libjansi-native-java{a} libjarjar-java{a} libjatl-java{a} libjavaewah-java{a} libjaxb-api-java{a} libjaxb-java{a} libjaxen-java{a} libjbig0{a} libjcifs-java{a} libjcip-annotations-java{a} libjcommander-java{a} libjetty9-java{a} libjformatstring-java{a} libjgit-java{a} libjline2-java{a} libjna-java{a} libjna-jni{a} libjoptsimple-java{a} libjpeg62-turbo{a} libjs-jquery{a} libjsch-java{a} libjsoup-java{a} libjsp-api-java{a} libjsr305-java{a} libjzlib-java{a} libkryo-java{a} libksba8{a} liblapack3{a} liblcms2-2{a} libldap-2.4-2{a} liblightcouch-java{a} libllvm11{a} liblog4j2-java{a} liblogback-java{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1{a} libmaven-file-management-java{a} libmaven-parent-java{a} libmaven-resolver-java{a} libmaven-shared-io-java{a} libmaven-shared-utils-java{a} libmaven3-core-java{a} libmd0{a} libminlog-java{a} libmodule-runtime-perl{a} libmongodb-java{a} libmoo-perl{a} libmpdec3{a} libnative-platform-java{a} libnative-platform-jni{a} libncurses6{a} libnekohtml-java{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnghttp2-14{a} libngs-java{a} libngs-sdk-dev{a} libngs-sdk2{a} libnpth0{a} libnspr4{a} libnss3{a} libobjenesis-java{a} libosgi-annotation-java{a} libosgi-compendium-java{a} libosgi-core-java{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libparams-classify-perl{a} libpciaccess0{a} libpcsclite1{a} libpipeline1{a} libpixman-1-0{a} libplexus-archiver-java{a} libplexus-cipher-java{a} libplexus-classworlds-java{a} libplexus-component-annotations-java{a} libplexus-container-default-java{a} libplexus-interpolation-java{a} libplexus-io-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libpng16-16{a} libpolyglot-maven-java{a} libpsl5{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libqdox-java{a} libreadline8{a} libreflectasm-java{a} librelaxng-datatype-java{a} librhino-java{a} librngom-java{a} librole-tiny-perl{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libservlet-api-java{a} libservlet3.1-java{a} libsigsegv2{a} libsimple-http-java{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsm6{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libssh2-1{a} libstax-ex-java{a} libstreambuffer-java{a} libstrictures-perl{a} libsub-override-perl{a} libsub-quote-perl{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff5{a} libtimedate-perl{a} libtk8.6{a} libtool{a} libtry-tiny-perl{a} libtxw2-java{a} libuchardet0{a} liburi-perl{a} libvulkan1{a} libwagon-file-java{a} libwagon-http-java{a} libwagon-provider-api-java{a} libwebp6{a} libwebsocket-api-java{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxbean-reflect-java{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxdamage1{a} libxdmcp6{a} libxerces2-java{a} libxext6{a} libxfixes3{a} libxft2{a} libxi6{a} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxpp3-java{a} libxrender1{a} libxshmfence1{a} libxsom-java{a} libxss1{a} libxstream-java{a} libxt6{a} libxtst6{a} libxxf86vm1{a} libxz-java{a} libyaml-snake-java{a} libz3-4{a} m4{a} man-db{a} maven-repo-helper{a} media-types{a} netbase{a} openjdk-11-doc{a} openjdk-11-jdk{a} openjdk-11-jdk-headless{a} openjdk-11-jre{a} openjdk-11-jre-headless{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} python3{a} python3-minimal{a} python3.9{a} python3.9-minimal{a} r-base-core{a} readline-common{a} sensible-utils{a} testng{a} ucf{a} unzip{a} wdiff{a} x11-common{a} xdg-utils{a} zip{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf curl dbus debian-keyring dput dput-ng dupload equivs fonts-dejavu-extra javascript-common libarchive-cpio-perl libatk-wrapper-java-jni libbindex-java libclass-xsaccessor-perl libclone-perl libdata-dump-perl libdistro-info-perl libfile-mimeinfo-perl libgit-wrapper-perl libgitlab-api-v4-perl libglib2.0-data libgpars-groovy-java libgpm2 libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl libnet-dbus-perl libsasl2-modules libsoap-lite-perl libstring-shellquote-perl libsub-name-perl libx11-protocol-perl libxt-dev licensecheck lintian lynx mesa-vulkan-drivers pristine-tar publicsuffix python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg r-base-dev r-doc-html r-recommended shared-mime-info strace wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 374 newly installed, 0 to remove and 0 not upgraded. Need to get 337 MB of archives. After unpacking 1064 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8+deb11u2 [146 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 netbase all 6.3 [19.9 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 openssl amd64 1.1.1w-0+deb11u1 [859 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 ca-certificates all 20210119 [158 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3+deb11u1 [273 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3+deb11u1 [128 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3+deb11u1 [69.2 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 ucf all 3.0043 [74.0 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 libnspr4 amd64 2:4.29-1 [112 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 libnss3 amd64 2:3.61-1+deb11u3 [1305 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 ca-certificates-java all 20190909+deb11u1 [15.9 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 java-common all 0.72 [14.5 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 libavahi-common-data amd64 0.8-5+deb11u2 [124 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 libavahi-common3 amd64 0.8-5+deb11u2 [58.7 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libdbus-1-3 amd64 1.12.28-0+deb11u1 [223 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libavahi-client3 amd64 0.8-5+deb11u2 [62.6 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libcups2 amd64 2.3.3op2-3+deb11u6 [351 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.4+dfsg-1+deb11u1 [418 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 fonts-dejavu-core all 2.37-2 [1069 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libfontconfig1 amd64 2.13.1-4.2 [347 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 liblcms2-2 amd64 2.12~rc1-2 [150 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 libasound2-data all 1.2.4-1.1 [38.2 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libasound2 amd64 1.2.4-1.1 [356 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.66.8-1+deb11u4 [1377 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 libharfbuzz0b amd64 2.7.4-1 [1471 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 libpcsclite1 amd64 1.9.1-1 [60.2 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 openjdk-11-jre-headless amd64 11.0.23+9-1~deb11u1 [38.2 MB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 default-jre-headless amd64 2:1.11-72 [10.9 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 ant all 1.10.9-4 [2118 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 ant-optional all 1.10.9-4 [381 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 libantlr-java all 2.7.7+dfsg-10 [458 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 antlr all 2.7.7+dfsg-10 [14.0 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 unzip amd64 6.0-26+deb11u1 [172 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 java-wrappers all 0.3 [10.9 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 libhamcrest-java all 1.3-9 [388 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 junit4 all 4.13.1-2 [347 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 libfelix-framework-java all 4.6.1-2.1 [569 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 libfelix-gogo-runtime-java all 0.16.2-1.1 [114 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 libosgi-annotation-java all 7.0.0-2 [10.1 kB] Get: 69 http://deb.debian.org/debian bullseye/main amd64 libosgi-core-java all 7.0.0-2 [157 kB] Get: 70 http://deb.debian.org/debian bullseye/main amd64 libfelix-resolver-java all 1.16.0-1 [180 kB] Get: 71 http://deb.debian.org/debian bullseye/main amd64 libhawtjni-runtime-java all 1.17-1 [35.3 kB] Get: 72 http://deb.debian.org/debian bullseye/main amd64 libjansi-native-java all 1.8-1 [26.0 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 libjansi-java all 1.18-1 [66.6 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 libjline2-java all 2.14.6-4 [151 kB] Get: 75 http://deb.debian.org/debian bullseye/main amd64 libosgi-compendium-java all 7.0.0-1 [477 kB] Get: 76 http://deb.debian.org/debian bullseye/main amd64 libslf4j-java all 1.7.30-1 [144 kB] Get: 77 http://deb.debian.org/debian bullseye/main amd64 libxz-java all 1.8-2 [141 kB] Get: 78 http://deb.debian.org/debian bullseye/main amd64 libyaml-snake-java all 1.28-1+deb11u2 [314 kB] Get: 79 http://deb.debian.org/debian bullseye/main amd64 bnd all 5.0.1-3 [9915 kB] Get: 80 http://deb.debian.org/debian bullseye/main amd64 dctrl-tools amd64 2.24-3+b1 [104 kB] Get: 81 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 82 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 83 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 84 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 85 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 86 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 87 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 88 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 89 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 90 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 91 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get: 92 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 93 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 94 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 95 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 96 http://deb.debian.org/debian bullseye/main amd64 libglvnd0 amd64 1.3.2-1 [53.6 kB] Get: 97 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 98 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get: 99 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1+deb11u1 [108 kB] Get: 100 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 101 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get: 102 http://deb.debian.org/debian bullseye/main amd64 libx11-data all 2:1.7.2-1+deb11u2 [311 kB] Get: 103 http://deb.debian.org/debian bullseye/main amd64 libx11-6 amd64 2:1.7.2-1+deb11u2 [772 kB] Get: 104 http://deb.debian.org/debian bullseye/main amd64 libdrm-common all 2.4.104-1 [14.9 kB] Get: 105 http://deb.debian.org/debian bullseye/main amd64 libdrm2 amd64 2.4.104-1 [41.5 kB] Get: 106 http://deb.debian.org/debian bullseye/main amd64 libglapi-mesa amd64 20.3.5-1 [71.7 kB] Get: 107 http://deb.debian.org/debian bullseye/main amd64 libx11-xcb1 amd64 2:1.7.2-1+deb11u2 [204 kB] Get: 108 http://deb.debian.org/debian bullseye/main amd64 libxcb-dri2-0 amd64 1.14-3 [103 kB] Get: 109 http://deb.debian.org/debian bullseye/main amd64 libxcb-dri3-0 amd64 1.14-3 [102 kB] Get: 110 http://deb.debian.org/debian bullseye/main amd64 libxcb-glx0 amd64 1.14-3 [118 kB] Get: 111 http://deb.debian.org/debian bullseye/main amd64 libxcb-present0 amd64 1.14-3 [101 kB] Get: 112 http://deb.debian.org/debian bullseye/main amd64 libxcb-shm0 amd64 1.14-3 [101 kB] Get: 113 http://deb.debian.org/debian bullseye/main amd64 libxcb-sync1 amd64 1.14-3 [105 kB] Get: 114 http://deb.debian.org/debian bullseye/main amd64 libxcb-xfixes0 amd64 1.14-3 [105 kB] Get: 115 http://deb.debian.org/debian bullseye/main amd64 libxdamage1 amd64 1:1.1.5-2 [15.7 kB] Get: 116 http://deb.debian.org/debian bullseye/main amd64 libxext6 amd64 2:1.3.3-1.1 [52.7 kB] Get: 117 http://deb.debian.org/debian bullseye/main amd64 libxfixes3 amd64 1:5.0.3-2 [22.1 kB] Get: 118 http://deb.debian.org/debian bullseye/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get: 119 http://deb.debian.org/debian bullseye/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get: 120 http://deb.debian.org/debian bullseye/main amd64 libdrm-amdgpu1 amd64 2.4.104-1 [28.5 kB] Get: 121 http://deb.debian.org/debian bullseye/main amd64 libpciaccess0 amd64 0.16-1 [53.6 kB] Get: 122 http://deb.debian.org/debian bullseye/main amd64 libdrm-intel1 amd64 2.4.104-1 [71.8 kB] Get: 123 http://deb.debian.org/debian bullseye/main amd64 libdrm-nouveau2 amd64 2.4.104-1 [26.8 kB] Get: 124 http://deb.debian.org/debian bullseye/main amd64 libdrm-radeon1 amd64 2.4.104-1 [30.2 kB] Get: 125 http://deb.debian.org/debian bullseye/main amd64 libedit2 amd64 3.1-20191231-2+b1 [96.7 kB] Get: 126 http://deb.debian.org/debian bullseye/main amd64 libz3-4 amd64 4.8.10-1 [6949 kB] Get: 127 http://deb.debian.org/debian bullseye/main amd64 libllvm11 amd64 1:11.0.1-2 [17.9 MB] Get: 128 http://deb.debian.org/debian bullseye/main amd64 libsensors-config all 1:3.6.0-7 [32.3 kB] Get: 129 http://deb.debian.org/debian bullseye/main amd64 libsensors5 amd64 1:3.6.0-7 [52.3 kB] Get: 130 http://deb.debian.org/debian bullseye/main amd64 libvulkan1 amd64 1.2.162.0-1 [103 kB] Get: 131 http://deb.debian.org/debian bullseye/main amd64 libgl1-mesa-dri amd64 20.3.5-1 [9633 kB] Get: 132 http://deb.debian.org/debian bullseye/main amd64 libglx-mesa0 amd64 20.3.5-1 [186 kB] Get: 133 http://deb.debian.org/debian bullseye/main amd64 libglx0 amd64 1.3.2-1 [35.7 kB] Get: 134 http://deb.debian.org/debian bullseye/main amd64 libgl1 amd64 1.3.2-1 [89.5 kB] Get: 135 http://deb.debian.org/debian bullseye/main amd64 libgif7 amd64 5.1.9-2 [45.1 kB] Get: 136 http://deb.debian.org/debian bullseye/main amd64 libxi6 amd64 2:1.7.10-1 [83.4 kB] Get: 137 http://deb.debian.org/debian bullseye/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get: 138 http://deb.debian.org/debian bullseye/main amd64 x11-common all 1:7.7+22 [252 kB] Get: 139 http://deb.debian.org/debian bullseye/main amd64 libxtst6 amd64 2:1.2.3-1 [27.8 kB] Get: 140 http://deb.debian.org/debian bullseye/main amd64 openjdk-11-jre amd64 11.0.23+9-1~deb11u1 [194 kB] Get: 141 http://deb.debian.org/debian bullseye/main amd64 default-jre amd64 2:1.11-72 [1044 B] Get: 142 http://deb.debian.org/debian bullseye/main amd64 openjdk-11-jdk-headless amd64 11.0.23+9-1~deb11u1 [73.6 MB] Get: 143 http://deb.debian.org/debian bullseye/main amd64 default-jdk-headless amd64 2:1.11-72 [1100 B] Get: 144 http://deb.debian.org/debian bullseye/main amd64 openjdk-11-jdk amd64 11.0.23+9-1~deb11u1 [13.5 kB] Get: 145 http://deb.debian.org/debian bullseye/main amd64 default-jdk amd64 2:1.11-72 [1056 B] Get: 146 http://deb.debian.org/debian bullseye/main amd64 openjdk-11-doc all 11.0.23+9-1~deb11u1 [13.5 MB] Get: 147 http://deb.debian.org/debian bullseye/main amd64 default-jdk-doc amd64 2:1.11-72 [11.0 kB] Get: 148 http://deb.debian.org/debian bullseye/main amd64 libassuan0 amd64 2.5.3-7.1 [50.5 kB] Get: 149 http://deb.debian.org/debian bullseye/main amd64 gpgconf amd64 2.2.27-2+deb11u2 [548 kB] Get: 150 http://deb.debian.org/debian bullseye/main amd64 libksba8 amd64 1.5.0-3+deb11u2 [123 kB] Get: 151 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1+deb11u1 [69.1 kB] Get: 152 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1+deb11u1 [106 kB] Get: 153 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3+deb11u1 [232 kB] Get: 154 http://deb.debian.org/debian bullseye/main amd64 libnpth0 amd64 1.6-3 [19.0 kB] Get: 155 http://deb.debian.org/debian bullseye/main amd64 dirmngr amd64 2.2.27-2+deb11u2 [763 kB] Get: 156 http://deb.debian.org/debian bullseye/main amd64 gnupg-l10n all 2.2.27-2+deb11u2 [1086 kB] Get: 157 http://deb.debian.org/debian bullseye/main amd64 gnupg-utils amd64 2.2.27-2+deb11u2 [905 kB] Get: 158 http://deb.debian.org/debian bullseye/main amd64 gpg amd64 2.2.27-2+deb11u2 [928 kB] Get: 159 http://deb.debian.org/debian bullseye/main amd64 pinentry-curses amd64 1.1.0-4 [64.9 kB] Get: 160 http://deb.debian.org/debian bullseye/main amd64 gpg-agent amd64 2.2.27-2+deb11u2 [669 kB] Get: 161 http://deb.debian.org/debian bullseye/main amd64 gpg-wks-client amd64 2.2.27-2+deb11u2 [524 kB] Get: 162 http://deb.debian.org/debian bullseye/main amd64 gpg-wks-server amd64 2.2.27-2+deb11u2 [516 kB] Get: 163 http://deb.debian.org/debian bullseye/main amd64 gpgsm amd64 2.2.27-2+deb11u2 [645 kB] Get: 164 http://deb.debian.org/debian bullseye/main amd64 gnupg all 2.2.27-2+deb11u2 [825 kB] Get: 165 http://deb.debian.org/debian bullseye/main amd64 libfile-dirlist-perl all 0.05-2 [7444 B] Get: 166 http://deb.debian.org/debian bullseye/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get: 167 http://deb.debian.org/debian bullseye/main amd64 libfile-homedir-perl all 1.006-1 [43.8 kB] Get: 168 http://deb.debian.org/debian bullseye/main amd64 libfile-touch-perl all 0.11-1 [9254 B] Get: 169 http://deb.debian.org/debian bullseye/main amd64 libio-pty-perl amd64 1:1.15-2 [37.0 kB] Get: 170 http://deb.debian.org/debian bullseye/main amd64 libipc-run-perl all 20200505.0-1 [102 kB] Get: 171 http://deb.debian.org/debian bullseye/main amd64 libclass-method-modifiers-perl all 2.13-1 [19.2 kB] Get: 172 http://deb.debian.org/debian bullseye/main amd64 libb-hooks-op-check-perl amd64 0.22-1+b3 [11.3 kB] Get: 173 http://deb.debian.org/debian bullseye/main amd64 libdynaloader-functions-perl all 0.003-1.1 [12.7 kB] Get: 174 http://deb.debian.org/debian bullseye/main amd64 libdevel-callchecker-perl amd64 0.008-1+b2 [15.9 kB] Get: 175 http://deb.debian.org/debian bullseye/main amd64 libparams-classify-perl amd64 0.015-1+b3 [25.7 kB] Get: 176 http://deb.debian.org/debian bullseye/main amd64 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get: 177 http://deb.debian.org/debian bullseye/main amd64 libimport-into-perl all 1.002005-1 [11.6 kB] Get: 178 http://deb.debian.org/debian bullseye/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 179 http://deb.debian.org/debian bullseye/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get: 180 http://deb.debian.org/debian bullseye/main amd64 libsub-quote-perl all 2.006006-1 [21.0 kB] Get: 181 http://deb.debian.org/debian bullseye/main amd64 libmoo-perl all 2.004004-1 [59.9 kB] Get: 182 http://deb.debian.org/debian bullseye/main amd64 libencode-locale-perl all 1.05-1.1 [13.2 kB] Get: 183 http://deb.debian.org/debian bullseye/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 184 http://deb.debian.org/debian bullseye/main amd64 libhttp-date-perl all 6.05-1 [10.4 kB] Get: 185 http://deb.debian.org/debian bullseye/main amd64 libfile-listing-perl all 6.14-1 [12.4 kB] Get: 186 http://deb.debian.org/debian bullseye/main amd64 libhtml-tagset-perl all 3.20-4 [13.0 kB] Get: 187 http://deb.debian.org/debian bullseye/main amd64 liburi-perl all 5.08-1 [90.6 kB] Get: 188 http://deb.debian.org/debian bullseye/main amd64 libhtml-parser-perl amd64 3.75-1+b1 [105 kB] Get: 189 http://deb.debian.org/debian bullseye/main amd64 libhtml-tree-perl all 5.07-2 [213 kB] Get: 190 http://deb.debian.org/debian bullseye/main amd64 libio-html-perl all 1.004-2 [16.1 kB] Get: 191 http://deb.debian.org/debian bullseye/main amd64 liblwp-mediatypes-perl all 6.04-1 [19.9 kB] Get: 192 http://deb.debian.org/debian bullseye/main amd64 libhttp-message-perl all 6.28-1 [79.6 kB] Get: 193 http://deb.debian.org/debian bullseye/main amd64 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get: 194 http://deb.debian.org/debian bullseye/main amd64 libhttp-negotiate-perl all 6.01-1 [12.8 kB] Get: 195 http://deb.debian.org/debian bullseye/main amd64 perl-openssl-defaults amd64 5 [7360 B] Get: 196 http://deb.debian.org/debian bullseye/main amd64 libnet-ssleay-perl amd64 1.88-3+b1 [321 kB] Get: 197 http://deb.debian.org/debian bullseye/main amd64 libio-socket-ssl-perl all 2.069-1 [215 kB] Get: 198 http://deb.debian.org/debian bullseye/main amd64 libnet-http-perl all 6.20-1 [25.1 kB] Get: 199 http://deb.debian.org/debian bullseye/main amd64 liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get: 200 http://deb.debian.org/debian bullseye/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get: 201 http://deb.debian.org/debian bullseye/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 202 http://deb.debian.org/debian bullseye/main amd64 libwww-perl all 6.52-1 [192 kB] Get: 203 http://deb.debian.org/debian bullseye/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get: 204 http://deb.debian.org/debian bullseye/main amd64 wdiff amd64 1.2.2-2+b1 [122 kB] Get: 205 http://deb.debian.org/debian bullseye/main amd64 devscripts amd64 2.21.3+deb11u1 [1093 kB] Get: 206 http://deb.debian.org/debian bullseye/main amd64 fontconfig amd64 2.13.1-4.2 [417 kB] Get: 207 http://deb.debian.org/debian bullseye/main amd64 ivy all 2.5.0-1 [1268 kB] Get: 208 http://deb.debian.org/debian bullseye/main amd64 libasm-java all 9.1-1 [379 kB] Get: 209 http://deb.debian.org/debian bullseye/main amd64 libbsf-java all 1:2.4.0-8 [76.3 kB] Get: 210 http://deb.debian.org/debian bullseye/main amd64 libcommons-cli-java all 1.4-2 [57.3 kB] Get: 211 http://deb.debian.org/debian bullseye/main amd64 libapache-pom-java all 18-1 [4676 B] Get: 212 http://deb.debian.org/debian bullseye/main amd64 libcommons-parent-java all 43-1 [10.8 kB] Get: 213 http://deb.debian.org/debian bullseye/main amd64 libcommons-logging-java all 1.2-2 [62.2 kB] Get: 214 http://deb.debian.org/debian bullseye/main amd64 libqdox-java all 1.12.1-3 [172 kB] Get: 215 http://deb.debian.org/debian bullseye/main amd64 libservlet-api-java all 4.0.1-2 [81.0 kB] Get: 216 http://deb.debian.org/debian bullseye/main amd64 libjsp-api-java all 2.3.4-3 [53.7 kB] Get: 217 http://deb.debian.org/debian bullseye/main amd64 libel-api-java all 3.0.0-3 [64.9 kB] Get: 218 http://deb.debian.org/debian bullseye/main amd64 libwebsocket-api-java all 1.1-2 [40.1 kB] Get: 219 http://deb.debian.org/debian bullseye/main amd64 libservlet3.1-java all 1:4.0.1-2 [9516 B] Get: 220 http://deb.debian.org/debian bullseye/main amd64 libxpp3-java all 1.1.4c-3 [292 kB] Get: 221 http://deb.debian.org/debian bullseye/main amd64 libxstream-java all 1.4.15-3+deb11u2 [546 kB] Get: 222 http://deb.debian.org/debian bullseye/main amd64 groovy all 2.4.21-1 [12.9 MB] Get: 223 http://deb.debian.org/debian bullseye/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get: 224 http://deb.debian.org/debian bullseye/main amd64 libcommons-collections3-java all 3.2.2-2 [526 kB] Get: 225 http://deb.debian.org/debian bullseye/main amd64 libcommons-compress-java all 1.20-1 [574 kB] Get: 226 http://deb.debian.org/debian bullseye/main amd64 libcommons-io-java all 2.8.0-1 [279 kB] Get: 227 http://deb.debian.org/debian bullseye/main amd64 libcommons-lang-java all 2.6-9 [273 kB] Get: 228 http://deb.debian.org/debian bullseye/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get: 229 http://deb.debian.org/debian bullseye/main amd64 libguava-java all 29.0-6 [2419 kB] Get: 230 http://deb.debian.org/debian bullseye/main amd64 libcommons-codec-java all 1.15-1 [292 kB] Get: 231 http://deb.debian.org/debian bullseye/main amd64 libhttpcore-java all 4.4.14-1 [631 kB] Get: 232 http://deb.debian.org/debian bullseye/main amd64 libhttpclient-java all 4.5.13-2 [1233 kB] Get: 233 http://deb.debian.org/debian bullseye/main amd64 libjarjar-java all 1.4+svn142-10 [192 kB] Get: 234 http://deb.debian.org/debian bullseye/main amd64 libjcip-annotations-java all 20060626-6 [11.8 kB] Get: 235 http://deb.debian.org/debian bullseye/main amd64 libjna-jni amd64 5.6.0-1 [60.9 kB] Get: 236 http://deb.debian.org/debian bullseye/main amd64 libjna-java all 5.6.0-1 [223 kB] Get: 237 http://deb.debian.org/debian bullseye/main amd64 libjzlib-java all 1.1.3-2 [80.0 kB] Get: 238 http://deb.debian.org/debian bullseye/main amd64 libjsch-java all 0.1.55-1 [298 kB] Get: 239 http://deb.debian.org/debian bullseye/main amd64 libminlog-java all 1.3.0-1.1 [7928 B] Get: 240 http://deb.debian.org/debian bullseye/main amd64 libobjenesis-java all 3.1-1 [52.6 kB] Get: 241 http://deb.debian.org/debian bullseye/main amd64 libreflectasm-java all 1.05-4.1 [18.4 kB] Get: 242 http://deb.debian.org/debian bullseye/main amd64 libkryo-java all 2.20-6.2 [157 kB] Get: 243 http://deb.debian.org/debian bullseye/main amd64 liblogback-java all 1:1.2.3-6 [763 kB] Get: 244 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2+deb11u2 [102 kB] Get: 245 http://deb.debian.org/debian bullseye/main amd64 libnative-platform-jni amd64 0.14-5 [13.0 kB] Get: 246 http://deb.debian.org/debian bullseye/main amd64 libnative-platform-java all 0.14-5 [71.0 kB] Get: 247 http://deb.debian.org/debian bullseye/main amd64 libxml-commons-external-java all 1.4.01-5 [240 kB] Get: 248 http://deb.debian.org/debian bullseye/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get: 249 http://deb.debian.org/debian bullseye/main amd64 libxerces2-java all 2.12.1-1 [1440 kB] Get: 250 http://deb.debian.org/debian bullseye/main amd64 libnekohtml-java all 1.9.22-1.1 [124 kB] Get: 251 http://deb.debian.org/debian bullseye/main amd64 libxbean-reflect-java all 4.5-8 [133 kB] Get: 252 http://deb.debian.org/debian bullseye/main amd64 libgradle-core-java all 4.4.1-13 [4246 kB] Get: 253 http://deb.debian.org/debian bullseye/main amd64 libbcprov-java all 1.68-2 [3512 kB] Get: 254 http://deb.debian.org/debian bullseye/main amd64 libbcpg-java all 1.68-2 [323 kB] Get: 255 http://deb.debian.org/debian bullseye/main amd64 libbsh-java all 2.0b4-20 [291 kB] Get: 256 http://deb.debian.org/debian bullseye/main amd64 libdd-plist-java all 1.20-1.1 [72.6 kB] Get: 257 http://deb.debian.org/debian bullseye/main amd64 libjaxen-java all 1.1.6-4 [214 kB] Get: 258 http://deb.debian.org/debian bullseye/main amd64 libdom4j-java all 2.1.3-1 [310 kB] Get: 259 http://deb.debian.org/debian bullseye/main amd64 libbcel-java all 6.5.0-1+deb11u1 [637 kB] Get: 260 http://deb.debian.org/debian bullseye/main amd64 libjformatstring-java all 0.10~20131207-2.1 [34.5 kB] Get: 261 http://deb.debian.org/debian bullseye/main amd64 libfindbugs-java all 3.1.0~preview2-3 [3502 kB] Get: 262 http://deb.debian.org/debian bullseye/main amd64 libgoogle-gson-java all 2.8.6-1+deb11u1 [225 kB] Get: 263 http://deb.debian.org/debian bullseye/main amd64 libaopalliance-java all 20070526-6 [9048 B] Get: 264 http://deb.debian.org/debian bullseye/main amd64 libguice-java all 4.2.3-2 [1435 kB] Get: 265 http://deb.debian.org/debian bullseye/main amd64 libjatl-java all 0.2.3-1.1 [29.0 kB] Get: 266 http://deb.debian.org/debian bullseye/main amd64 libjcifs-java all 1.3.19-2 [394 kB] Get: 267 http://deb.debian.org/debian bullseye/main amd64 libeclipse-jdt-annotation-java all 2.2.600+eclipse4.18-1 [25.1 kB] Get: 268 http://deb.debian.org/debian bullseye/main amd64 libjavaewah-java all 1.1.7-1 [156 kB] Get: 269 http://deb.debian.org/debian bullseye/main amd64 libjetty9-java all 9.4.50-4+deb11u2 [2954 kB] Get: 270 http://deb.debian.org/debian bullseye/main amd64 libjgit-java all 4.11.9-1 [2502 kB] Get: 271 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 272 http://deb.debian.org/debian bullseye/main amd64 libplexus-utils2-java all 3.3.0-1 [250 kB] Get: 273 http://deb.debian.org/debian bullseye/main amd64 libwagon-provider-api-java all 3.3.4-1 [50.2 kB] Get: 274 http://deb.debian.org/debian bullseye/main amd64 libmaven-resolver-java all 1.4.2-3 [556 kB] Get: 275 http://deb.debian.org/debian bullseye/main amd64 libcommons-lang3-java all 3.11-1 [550 kB] Get: 276 http://deb.debian.org/debian bullseye/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB] Get: 277 http://deb.debian.org/debian bullseye/main amd64 libmaven-parent-java all 31-2 [5100 B] Get: 278 http://deb.debian.org/debian bullseye/main amd64 libmaven-shared-utils-java all 3.3.0-1+deb11u1 [149 kB] Get: 279 http://deb.debian.org/debian bullseye/main amd64 libplexus-cipher-java all 1.8-2 [15.0 kB] Get: 280 http://deb.debian.org/debian bullseye/main amd64 libplexus-classworlds-java all 2.6.0-1 [49.4 kB] Get: 281 http://deb.debian.org/debian bullseye/main amd64 libplexus-component-annotations-java all 2.1.0-1 [7620 B] Get: 282 http://deb.debian.org/debian bullseye/main amd64 libplexus-interpolation-java all 1.26-1 [76.8 kB] Get: 283 http://deb.debian.org/debian bullseye/main amd64 libplexus-sec-dispatcher-java all 1.4-4 [28.1 kB] Get: 284 http://deb.debian.org/debian bullseye/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B] Get: 285 http://deb.debian.org/debian bullseye/main amd64 libcdi-api-java all 1.2-3 [54.3 kB] Get: 286 http://deb.debian.org/debian bullseye/main amd64 libsisu-inject-java all 0.3.4-2 [347 kB] Get: 287 http://deb.debian.org/debian bullseye/main amd64 libsisu-plexus-java all 0.3.4-3 [181 kB] Get: 288 http://deb.debian.org/debian bullseye/main amd64 libmaven3-core-java all 3.6.3-5 [1538 kB] Get: 289 http://deb.debian.org/debian bullseye/main amd64 libplexus-container-default-java all 2.1.0-1 [193 kB] Get: 290 http://deb.debian.org/debian bullseye/main amd64 libpolyglot-maven-java all 0.8~tobrien+git20120905-10 [74.9 kB] Get: 291 http://deb.debian.org/debian bullseye/main amd64 librhino-java all 1.7.7.2-3 [1200 kB] Get: 292 http://deb.debian.org/debian bullseye/main amd64 libsimple-http-java all 4.1.21-1.1 [211 kB] Get: 293 http://deb.debian.org/debian bullseye/main amd64 libwagon-file-java all 3.3.4-1 [10.8 kB] Get: 294 http://deb.debian.org/debian bullseye/main amd64 libjsoup-java all 1.10.2-2 [350 kB] Get: 295 http://deb.debian.org/debian bullseye/main amd64 libwagon-http-java all 3.3.4-1 [53.9 kB] Get: 296 http://deb.debian.org/debian bullseye/main amd64 libjcommander-java all 1.71-3 [72.7 kB] Get: 297 http://deb.debian.org/debian bullseye/main amd64 testng all 6.9.12-4 [795 kB] Get: 298 http://deb.debian.org/debian bullseye/main amd64 libgradle-plugins-java all 4.4.1-13 [5158 kB] Get: 299 http://deb.debian.org/debian bullseye/main amd64 gradle all 4.4.1-13 [401 kB] Get: 300 http://deb.debian.org/debian bullseye/main amd64 maven-repo-helper all 1.10 [142 kB] Get: 301 http://deb.debian.org/debian bullseye/main amd64 gradle-debian-helper all 2.1 [25.3 kB] Get: 302 http://deb.debian.org/debian bullseye/main amd64 javahelper all 0.78 [97.2 kB] Get: 303 http://deb.debian.org/debian bullseye/main amd64 libactivation-java all 1.2.0-2 [84.7 kB] Get: 304 http://deb.debian.org/debian bullseye/main amd64 libargs4j-java all 2.33-1.1 [137 kB] Get: 305 http://deb.debian.org/debian bullseye/main amd64 libfreemarker-java all 2.3.23-11 [1221 kB] Get: 306 http://deb.debian.org/debian bullseye/main amd64 libjoptsimple-java all 5.0.4-4 [73.1 kB] Get: 307 http://deb.debian.org/debian bullseye/main amd64 liblightcouch-java all 0.0.6-1.1 [65.2 kB] Get: 308 http://deb.debian.org/debian bullseye/main amd64 libmongodb-java all 3.6.3-2 [1901 kB] Get: 309 http://deb.debian.org/debian bullseye/main amd64 liblog4j2-java all 2.17.1-1~deb11u1 [2081 kB] Get: 310 http://deb.debian.org/debian bullseye/main amd64 libbarclay-java all 2.1.0-3.1 [116 kB] Get: 311 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3+deb11u1 [153 kB] Get: 312 http://deb.debian.org/debian bullseye/main amd64 libpixman-1-0 amd64 0.40.0-1.1~deb11u1 [543 kB] Get: 313 http://deb.debian.org/debian bullseye/main amd64 libxcb-render0 amd64 1.14-3 [111 kB] Get: 314 http://deb.debian.org/debian bullseye/main amd64 libcairo2 amd64 1.16.0-5 [694 kB] Get: 315 http://deb.debian.org/debian bullseye/main amd64 libmaven-shared-io-java all 3.0.0-3 [33.3 kB] Get: 316 http://deb.debian.org/debian bullseye/main amd64 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get: 317 http://deb.debian.org/debian bullseye/main amd64 libplexus-io-java all 3.2.0-1.1 [65.0 kB] Get: 318 http://deb.debian.org/debian bullseye/main amd64 libsnappy1v5 amd64 1.1.8-1 [17.9 kB] Get: 319 http://deb.debian.org/debian bullseye/main amd64 libsnappy-jni amd64 1.1.8.3-1 [7152 B] Get: 320 http://deb.debian.org/debian bullseye/main amd64 libsnappy-java all 1.1.8.3-1 [98.9 kB] Get: 321 http://deb.debian.org/debian bullseye/main amd64 libplexus-archiver-java all 3.6.0-2 [171 kB] Get: 322 http://deb.debian.org/debian bullseye/main amd64 libistack-commons-java all 3.0.6-5 [145 kB] Get: 323 http://deb.debian.org/debian bullseye/main amd64 libcodemodel-java all 2.6+jaxb2.3.0.1-10 [163 kB] Get: 324 http://deb.debian.org/debian bullseye/main amd64 libcommons-collections4-java all 4.2-1 [662 kB] Get: 325 http://deb.debian.org/debian bullseye/main amd64 libcommons-jexl2-java all 2.1.1-5 [256 kB] Get: 326 http://deb.debian.org/debian bullseye/main amd64 libcommons-math3-java all 3.6.1-3 [2018 kB] Get: 327 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1+deb11u1 [77.2 kB] Get: 328 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get: 329 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 330 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2+deb11u1 [156 kB] Get: 331 http://deb.debian.org/debian bullseye/main amd64 libcurl4 amd64 7.74.0-1.3+deb11u12 [347 kB] Get: 332 http://deb.debian.org/debian bullseye/main amd64 libdatrie1 amd64 0.2.13-1 [42.7 kB] Get: 333 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get: 334 http://deb.debian.org/debian bullseye/main amd64 libdtd-parser-java all 1.2-1 [64.9 kB] Get: 335 http://deb.debian.org/debian bullseye/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB] Get: 336 http://deb.debian.org/debian bullseye/main amd64 libstax-ex-java all 1.7.8-3 [40.9 kB] Get: 337 http://deb.debian.org/debian bullseye/main amd64 libstreambuffer-java all 1.5.4-1.1 [74.0 kB] Get: 338 http://deb.debian.org/debian bullseye/main amd64 librelaxng-datatype-java all 1.0+ds1-3.1 [11.7 kB] Get: 339 http://deb.debian.org/debian bullseye/main amd64 libxsom-java all 2.3.0.1-10 [396 kB] Get: 340 http://deb.debian.org/debian bullseye/main amd64 libfastinfoset-java all 1.2.12-3 [343 kB] Get: 341 http://deb.debian.org/debian bullseye/main amd64 libfribidi0 amd64 1.0.8-2+deb11u1 [64.9 kB] Get: 342 http://deb.debian.org/debian bullseye/main amd64 libgatk-native-bindings-java all 1.0.0-2.1 [7344 B] Get: 343 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get: 344 http://deb.debian.org/debian bullseye/main amd64 libgkl-java all 0.8.7+dfsg-1 [998 kB] Get: 345 http://deb.debian.org/debian bullseye/main amd64 libgkl-jni amd64 0.8.7+dfsg-1 [203 kB] Get: 346 http://deb.debian.org/debian bullseye/main amd64 librngom-java all 2.3.0.1-10 [288 kB] Get: 347 http://deb.debian.org/debian bullseye/main amd64 libtxw2-java all 2.3.0.1-10 [134 kB] Get: 348 http://deb.debian.org/debian bullseye/main amd64 libjaxb-java all 2.3.0.1-10 [1954 kB] Get: 349 http://deb.debian.org/debian bullseye/main amd64 libngs-sdk2 amd64 2.10.9-1 [59.2 kB] Get: 350 http://deb.debian.org/debian bullseye/main amd64 libngs-sdk-dev amd64 2.10.9-1 [104 kB] Get: 351 http://deb.debian.org/debian bullseye/main amd64 libngs-java amd64 2.10.9-1 [80.4 kB] Get: 352 http://deb.debian.org/debian bullseye/main amd64 libhtsjdk-java all 2.23.0+dfsg-2 [1607 kB] Get: 353 http://deb.debian.org/debian bullseye/main amd64 libhtsjdk-java-doc all 2.23.0+dfsg-2 [1167 kB] Get: 354 http://deb.debian.org/debian bullseye/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get: 355 http://deb.debian.org/debian bullseye/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get: 356 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3+deb11u1 [2166 kB] Get: 357 http://deb.debian.org/debian bullseye/main amd64 libthai-data all 0.1.28-3 [170 kB] Get: 358 http://deb.debian.org/debian bullseye/main amd64 libthai0 amd64 0.1.28-3 [54.2 kB] Get: 359 http://deb.debian.org/debian bullseye/main amd64 libpango-1.0-0 amd64 1.46.2-3 [191 kB] Get: 360 http://deb.debian.org/debian bullseye/main amd64 libpangoft2-1.0-0 amd64 1.46.2-3 [62.2 kB] Get: 361 http://deb.debian.org/debian bullseye/main amd64 libpangocairo-1.0-0 amd64 1.46.2-3 [50.6 kB] Get: 362 http://deb.debian.org/debian bullseye/main amd64 libpaper1 amd64 1.1.28+b1 [21.6 kB] Get: 363 http://deb.debian.org/debian bullseye/main amd64 libpaper-utils amd64 1.1.28+b1 [18.3 kB] Get: 364 http://deb.debian.org/debian bullseye/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get: 365 http://deb.debian.org/debian bullseye/main amd64 libtcl8.6 amd64 8.6.11+dfsg-1 [1018 kB] Get: 366 http://deb.debian.org/debian bullseye/main amd64 libwebp6 amd64 0.6.1-2.1+deb11u2 [259 kB] Get: 367 http://deb.debian.org/debian bullseye/main amd64 libtiff5 amd64 4.2.0-1+deb11u5 [290 kB] Get: 368 http://deb.debian.org/debian bullseye/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB] Get: 369 http://deb.debian.org/debian bullseye/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get: 370 http://deb.debian.org/debian bullseye/main amd64 libtk8.6 amd64 8.6.11-2 [780 kB] Get: 371 http://deb.debian.org/debian bullseye/main amd64 libxt6 amd64 1:1.2.0-1 [189 kB] Get: 372 http://deb.debian.org/debian bullseye/main amd64 zip amd64 3.0-12 [232 kB] Get: 373 http://deb.debian.org/debian bullseye/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 374 http://deb.debian.org/debian bullseye/main amd64 r-base-core amd64 4.0.4-1 [25.1 MB] Fetched 337 MB in 26s (13.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. 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Setting up autopoint (0.21-4) ... Setting up libwebp6:amd64 (0.6.1-2.1+deb11u2) ... Setting up libb-hooks-op-check-perl (0.22-1+b3) ... Setting up fonts-dejavu-core (2.37-2) ... Setting up libfelix-framework-java (4.6.1-2.1) ... Setting up libngs-sdk-dev:amd64 (2.10.9-1) ... Setting up libipc-run-perl (20200505.0-1) ... Setting up libpcsclite1:amd64 (1.9.1-1) ... Setting up libsensors5:amd64 (1:3.6.0-7) ... Setting up libmongodb-java (3.6.3-2) ... Setting up libactivation-java (1.2.0-2) ... Setting up libhamcrest-java (1.3-9) ... Setting up libglapi-mesa:amd64 (20.3.5-1) ... Setting up libbsh-java (2.0b4-20) ... Setting up libjsp-api-java (2.3.4-3) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up libgfortran5:amd64 (10.2.1-6) ... Setting up libvulkan1:amd64 (1.2.162.0-1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libgif7:amd64 (5.1.9-2) ... Setting up libjarjar-java (1.4+svn142-10) ... Setting up libmd0:amd64 (1.0.3-3) ... Setting up libfreemarker-java (2.3.23-11) ... Setting up sensible-utils (0.0.14) ... Setting up libxshmfence1:amd64 (1.3-1) ... Setting up libjsoup-java (1.10.2-2) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libxml-commons-external-java (1.4.01-5) ... Setting up libjna-java (5.6.0-1) ... Setting up libxbean-reflect-java (4.5-8) ... Setting up libasound2:amd64 (1.2.4-1.1) ... Setting up libservlet-api-java (4.0.1-2) ... Setting up libmpdec3:amd64 (2.5.1-1) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libplexus-sec-dispatcher-java (1.4-4) ... Setting up libthai-data (0.1.28-3) ... Setting up libssh2-1:amd64 (1.9.0-2+deb11u1) ... Setting up netbase (6.3) ... Setting up libcommons-math3-java (3.6.1-3) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006006-1) ... Setting up libnative-platform-jni (0.14-5) ... Setting up libtiff5:amd64 (4.2.0-1+deb11u5) ... Setting up libhttpcore-java (4.4.14-1) ... Setting up libjoptsimple-java (5.0.4-4) ... Setting up libbcpg-java (1.68-2) ... Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Setting up libngs-java:amd64 (2.10.9-1) ... Setting up libxerces2-java (2.12.1-1) ... Setting up libfile-dirlist-perl (0.05-2) ... Setting up libfile-homedir-perl (1.006-1) ... Setting up librelaxng-datatype-java (1.0+ds1-3.1) ... Setting up libantlr-java (2.7.7+dfsg-10) ... Setting up libyaml-snake-java (1.28-1+deb11u2) ... Setting up openssl (1.1.1w-0+deb11u1) ... Setting up libbsd0:amd64 (0.11.3-1+deb11u1) ... Setting up libdrm-common (2.4.104-1) ... Setting up libcdi-api-java (1.2-3) ... Setting up libelf1:amd64 (0.183-1) ... Setting up libsnappy-jni (1.1.8.3-1) ... Setting up readline-common (8.1-1) ... Setting up libhawtjni-runtime-java (1.17-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up liburi-perl (5.08-1) ... Setting up libargs4j-java (2.33-1.1) ... Setting up libfile-touch-perl (0.11-1) ... Setting up dctrl-tools (2.24-3+b1) ... Setting up libservlet3.1-java (1:4.0.1-2) ... Setting up libjatl-java (0.2.3-1.1) ... Setting up libnet-ssleay-perl (1.88-3+b1) ... Setting up pinentry-curses (1.1.0-4) ... Setting up libdom4j-java (2.1.3-1) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libwagon-provider-api-java (3.3.4-1) ... Setting up libnative-platform-java (0.14-5) ... Setting up libosgi-core-java (7.0.0-2) ... Setting up libice6:amd64 (2:1.0.10-1) ... Setting up libhttp-date-perl (6.05-1) ... Setting up libxstream-java (1.4.15-3+deb11u2) ... Setting up libnekohtml-java (1.9.22-1.1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.9.0-3+deb11u1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.14-3) ... Setting up gettext (0.21-4) ... Setting up libjetty9-java (9.4.50-4+deb11u2) ... Setting up libxcb-xfixes0:amd64 (1.14-3) ... Setting up java-wrappers (0.3) ... Setting up libfile-listing-perl (6.14-1) ... Setting up libosgi-compendium-java (7.0.0-1) ... Setting up libtool (2.4.6-15) ... Setting up libxcb-render0:amd64 (1.14-3) ... Setting up libstax-ex-java (1.7.8-3) ... Setting up libxcb-glx0:amd64 (1.14-3) ... Setting up libmaven-parent-java (31-2) ... Setting up libedit2:amd64 (3.1-20191231-2+b1) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up libcommons-parent-java (43-1) ... Setting up libavahi-common3:amd64 (0.8-5+deb11u2) ... Setting up libcommons-logging-java (1.2-2) ... Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Setting up libnet-http-perl (6.20-1) ... Setting up m4 (1.4.18-5) ... Setting up libsisu-inject-java (0.3.4-2) ... Setting up libnss3:amd64 (2:3.61-1+deb11u3) ... Setting up libxcb-shm0:amd64 (1.14-3) ... Setting up default-jdk-doc (2:1.11-72) ... Setting up libdevel-callchecker-perl (0.008-1+b2) ... Setting up libcommons-lang-java (2.6-9) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxcb-present0:amd64 (1.14-3) ... Setting up patchutils (0.4.2-1) ... Setting up libcommons-jexl2-java (2.1.1-5) ... Setting up libthai0:amd64 (0.1.28-3) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libsisu-plexus-java (0.3.4-3) ... Setting up libmaven-resolver-java (1.4.2-3) ... Setting up libbcel-java (6.5.0-1+deb11u1) ... Setting up libllvm11:amd64 (1:11.0.1-2) ... Setting up libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Setting up libguava-java (29.0-6) ... Setting up libxcb-sync1:amd64 (1.14-3) ... Setting up testng (6.9.12-4) ... Setting up libstreambuffer-java (1.5.4-1.1) ... Setting up libcommons-collections4-java (4.2-1) ... Setting up ucf (3.0043) ... Setting up libcommons-lang3-java (3.11-1) ... Setting up autoconf (2.69-14) ... Setting up libxcb-dri2-0:amd64 (1.14-3) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libfelix-resolver-java (1.16.0-1) ... Setting up librngom-java (2.3.0.1-10) ... Setting up libdrm2:amd64 (2.4.104-1) ... Setting up dwz (0.13+20210201-1) ... Setting up libjansi-native-java (1.8-1) ... Setting up groff-base (1.22.4-6) ... Setting up libhtml-parser-perl (3.75-1+b1) ... Setting up gpgconf (2.2.27-2+deb11u2) ... Setting up libcurl4:amd64 (7.74.0-1.3+deb11u12) ... Setting up libx11-6:amd64 (2:1.7.2-1+deb11u2) ... Setting up libharfbuzz0b:amd64 (2.7.4-1) ... Setting up libsnappy-java (1.1.8.3-1) ... Setting up libxsom-java (2.3.0.1-10) ... Setting up libwagon-file-java (3.3.4-1) ... Setting up libcommons-codec-java (1.15-1) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libavahi-client3:amd64 (0.8-5+deb11u2) ... Setting up libio-socket-ssl-perl (2.069-1) ... Setting up libplexus-container-default-java (2.1.0-1) ... Setting up gpg (2.2.27-2+deb11u2) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up gnupg-utils (2.2.27-2+deb11u2) ... Setting up libhttp-message-perl (6.28-1) ... Setting up libdrm-amdgpu1:amd64 (2.4.104-1) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libxcb-dri3-0:amd64 (1.14-3) ... Setting up libpaper1:amd64 (1.1.28+b1) ... Creating config file /etc/papersize with new version Setting up libx11-xcb1:amd64 (2:1.7.2-1+deb11u2) ... Setting up libhttp-negotiate-perl (6.01-1) ... Setting up libdrm-nouveau2:amd64 (2.4.104-1) ... Setting up libfindbugs-java (3.1.0~preview2-3) ... Setting up libxdamage1:amd64 (1:1.1.5-2) ... Setting up gpg-agent (2.2.27-2+deb11u2) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libcommons-compress-java (1.20-1) ... Setting up libhttp-cookies-perl (6.10-1) ... Setting up libcommons-io-java (2.8.0-1) ... Setting up libdrm-radeon1:amd64 (2.4.104-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-2) ... Setting up libparams-classify-perl (0.015-1+b3) ... Setting up gpgsm (2.2.27-2+deb11u2) ... Setting up libdrm-intel1:amd64 (2.4.104-1) ... Setting up libgl1-mesa-dri:amd64 (20.3.5-1) ... Setting up libxext6:amd64 (2:1.3.3-1.1) ... Setting up libpaper-utils (1.1.28+b1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libguice-java (4.2.3-2) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up dh-autoreconf (20) ... Setting up dirmngr (2.2.27-2+deb11u2) ... Setting up libmodule-runtime-perl (0.016-1) ... Setting up libxfixes3:amd64 (1:5.0.3-2) ... Setting up libjansi-java (1.18-1) ... Setting up libxt6:amd64 (1:1.2.0-1) ... Setting up gpg-wks-server (2.2.27-2+deb11u2) ... Setting up libcups2:amd64 (2.3.3op2-3+deb11u6) ... Setting up libhttpclient-java (4.5.13-2) ... Setting up liblightcouch-java (0.0.6-1.1) ... Setting up libwagon-http-java (3.3.4-1) ... Setting up libmaven-shared-utils-java (3.3.0-1+deb11u1) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libfontconfig1:amd64 (2.13.1-4.2) ... Setting up libfastinfoset-java (1.2.12-3) ... Setting up libjline2-java (2.14.6-4) ... Setting up python3.9 (3.9.2-1) ... Setting up libjgit-java (4.11.9-1) ... Setting up fontconfig (2.13.1-4.2) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.2-2) ... Setting up libplexus-io-java (3.2.0-1.1) ... Setting up libglx-mesa0:amd64 (20.3.5-1) ... Setting up libxi6:amd64 (2:1.7.10-1) ... Setting up gpg-wks-client (2.2.27-2+deb11u2) ... Setting up libglx0:amd64 (1.3.2-1) ... Setting up libmaven3-core-java (3.6.3-5) ... Setting up libmaven-shared-io-java (3.0.0-3) ... Setting up libimport-into-perl (1.002005-1) ... Setting up libxtst6:amd64 (2:1.2.3-1) ... Setting up libmoo-perl (2.004004-1) ... Setting up liblog4j2-java (2.17.1-1~deb11u1) ... Setting up libtk8.6:amd64 (8.6.11-2) ... Setting up libpango-1.0-0:amd64 (1.46.2-3) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up libcairo2:amd64 (1.16.0-5) ... Setting up libgl1:amd64 (1.3.2-1) ... Setting up libmaven-file-management-java (3.0.0-1) ... Setting up gnupg (2.2.27-2+deb11u2) ... Setting up libplexus-archiver-java (3.6.0-2) ... Setting up libpangoft2-1.0-0:amd64 (1.46.2-3) ... Setting up libbarclay-java (2.1.0-3.1) ... Setting up libpangocairo-1.0-0:amd64 (1.46.2-3) ... Setting up r-base-core (4.0.4-1) ... Creating config file /etc/R/Renviron with new version Setting up default-jre-headless (2:1.11-72) ... Setting up libwww-perl (6.52-1) ... Setting up openjdk-11-jre-headless:amd64 (11.0.23+9-1~deb11u1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up openjdk-11-jre:amd64 (11.0.23+9-1~deb11u1) ... Setting up maven-repo-helper (1.10) ... Setting up openjdk-11-jdk-headless:amd64 (11.0.23+9-1~deb11u1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jaotc to provide /usr/bin/jaotc (jaotc) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jre (2:1.11-72) ... Setting up antlr (2.7.7+dfsg-10) ... Setting up default-jdk-headless (2:1.11-72) ... Setting up devscripts (2.21.3+deb11u1) ... Setting up ivy (2.5.0-1) ... Setting up ant (1.10.9-4) ... Setting up openjdk-11-jdk:amd64 (11.0.23+9-1~deb11u1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up javahelper (0.78) ... Setting up ca-certificates-java (20190909+deb11u1) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:GTS_Root_R1.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:ACCVRAIZ1.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Certigna.pem Adding debian:Secure_Global_CA.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:GTS_Root_R3.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:ISRG_Root_X1.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:SecureSign_RootCA11.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Izenpe.com.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:EC-ACC.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:DST_Root_CA_X3.pem Adding debian:GTS_Root_R2.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:Certigna_Root_CA.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:GTS_Root_R4.pem Adding debian:AffirmTrust_Premium.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:SecureTrust_CA.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:AffirmTrust_Networking.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:TrustCor_ECA-1.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem done. Setting up junit4 (4.13.1-2) ... Setting up liblwp-protocol-https-perl (6.10-1) ... Setting up groovy (2.4.21-1) ... update-alternatives: using /usr/share/groovy/bin/groovy to provide /usr/bin/groovy (groovy) in auto mode update-alternatives: using /usr/share/groovy/bin/groovyc to provide /usr/bin/groovyc (groovyc) in auto mode update-alternatives: using /usr/share/groovy/bin/grape to provide /usr/bin/grape (grape) in auto mode update-alternatives: using /usr/share/groovy/bin/startGroovy to provide /usr/bin/startGroovy (startGroovy) in auto mode update-alternatives: using /usr/share/groovy/bin/groovysh to provide /usr/bin/groovysh (groovysh) in auto mode update-alternatives: using /usr/share/groovy/bin/java2groovy to provide /usr/bin/java2groovy (java2groovy) in auto mode update-alternatives: using /usr/share/groovy/bin/groovyConsole to provide /usr/bin/groovyConsole (groovyConsole) in auto mode update-alternatives: using /usr/share/groovy/bin/groovydoc to provide /usr/bin/groovydoc (groovydoc) in auto mode Setting up default-jdk (2:1.11-72) ... Setting up ant-optional (1.10.9-4) ... Setting up bnd (5.0.1-3) ... Setting up libgradle-core-java (4.4.1-13) ... Setting up libgradle-plugins-java (4.4.1-13) ... Setting up gradle (4.4.1-13) ... Setting up libistack-commons-java (3.0.6-5) ... Setting up libcodemodel-java (2.6+jaxb2.3.0.1-10) ... Setting up gradle-debian-helper (2.1) ... Setting up libtxw2-java (2.3.0.1-10) ... Setting up libjaxb-java (2.3.0.1-10) ... Setting up libhtsjdk-java (2.23.0+dfsg-2) ... Processing triggers for libc-bin (2.31-13+deb11u10) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/3151990/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for bullseye I: user script /srv/workspace/pbuilder/3151990/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/picard-tools-2.24.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../picard-tools_2.24.1+dfsg-1_source.changes dpkg-buildpackage: info: source package picard-tools dpkg-buildpackage: info: source version 2.24.1+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=gradle --with javahelper,jh_maven_repo_helper dh_auto_clean -O--buildsystem=gradle install -d /build/reproducible-path/picard-tools-2.24.1\+dfsg/debian/.debhelper/generated/_source/home sh -c "find . -wholename .*build/tmp | xargs echo | sed -e 's^build/tmp^build^g' | xargs rm -Rf" sh -c "find . -wholename .*build/debian | xargs echo | sed -e 's^build/tmp^build^g' | xargs rm -Rf" rm -Rf /build/reproducible-path/picard-tools-2.24.1\+dfsg/.gradle /build/reproducible-path/picard-tools-2.24.1\+dfsg/buildSrc/.gradle .m2 dh_autoreconf_clean -O--buildsystem=gradle jh_clean -O--buildsystem=gradle rm -fr debian/_jh_manifest* debian/_jh_build* rm -fr debian/.eclipse-build rm -f debian/orbitdeps.debhelper mh_clean -O--buildsystem=gradle debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/picard-tools-2.24.1+dfsg' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/picard-tools.substvars debian/libpicard-java.substvars debian/libpicard-java-doc.substvars debian/files rm -fr -- debian/picard-tools/ debian/tmp/ debian/libpicard-java/ debian/libpicard-java-doc/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) # also remove bai files that are left after tests # find testdata -iname "*.bai" -exec rm {} \; # This needs to be more fine grained since testdata/picard/indices/index_test_b.bam.bai needs to stay! rm -f debian/bd-temp-substvars rm -f debian/bd.substvars make[1]: Leaving directory '/build/reproducible-path/picard-tools-2.24.1+dfsg' debian/rules binary dh binary --buildsystem=gradle --with javahelper,jh_maven_repo_helper dh_update_autotools_config -O--buildsystem=gradle dh_autoreconf -O--buildsystem=gradle dh_auto_configure -O--buildsystem=gradle install -d /build/reproducible-path/picard-tools-2.24.1\+dfsg/debian/.debhelper/generated/_source/home jh_linkjars -O--buildsystem=gradle debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/picard-tools-2.24.1+dfsg' blhc: ignore-line-regexp: .*gradle.*ScriptTransformer.* dh_auto_build -- jar javadoc mkdir -p .gradle/init.d cp /usr/share/gradle-debian-helper/init.gradle .gradle/init.d/ gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=picard-tools -Dfile.encoding=UTF-8 --parallel --max-workers=20 jar javadoc Initialized native services in: /build/reproducible-path/picard-tools-2.24.1+dfsg/.gradle/native To honour the JVM settings for this build a new JVM will be forked. Please consider using the daemon: https://docs.gradle.org/4.4.1/userguide/gradle_daemon.html. Starting process 'Gradle build daemon'. Working directory: /build/reproducible-path/picard-tools-2.24.1+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-11-openjdk-amd64/bin/java -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Duser.variant -cp /usr/share/gradle/lib/gradle-launcher-4.4.1.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 Successfully started process 'Gradle build daemon' An attempt to start the daemon took 1.418 secs. The client will now receive all logging from the daemon (pid: 3246486). The daemon log file: /build/reproducible-path/picard-tools-2.24.1+dfsg/.gradle/daemon/4.4.1/daemon-3246486.out.log Daemon will be stopped at the end of the build stopping after processing Closing daemon's stdin at end of input. The daemon will no longer process any standard input. Using 20 worker leases. Creating new cache for fileHashes, path /build/reproducible-path/picard-tools-2.24.1+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@2d417fa8 Creating new cache for resourceHashesCache, path /build/reproducible-path/picard-tools-2.24.1+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@2d417fa8 Creating new cache for fileHashes, path /build/reproducible-path/picard-tools-2.24.1+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@791d43c5 Starting Build Compiling initialization script '/build/reproducible-path/picard-tools-2.24.1+dfsg/.gradle/init.d/init.gradle' using SubsetScriptTransformer. Creating new cache for metadata-1.1/results, path /build/reproducible-path/picard-tools-2.24.1+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@52b49eec Compiling initialization script '/build/reproducible-path/picard-tools-2.24.1+dfsg/.gradle/init.d/init.gradle' using BuildScriptTransformer. Compiling settings file '/build/reproducible-path/picard-tools-2.24.1+dfsg/settings.gradle' using SubsetScriptTransformer. Compiling settings file '/build/reproducible-path/picard-tools-2.24.1+dfsg/settings.gradle' using BuildScriptTransformer. Settings evaluated using settings file '/build/reproducible-path/picard-tools-2.24.1+dfsg/settings.gradle'. Projects loaded. Root project using build file '/build/reproducible-path/picard-tools-2.24.1+dfsg/build.gradle'. Included projects: [root project 'picard'] Keep-alive timer started Adding Debian repository to project 'picard' Parallel execution is an incubating feature. Evaluating root project 'picard' using build file '/build/reproducible-path/picard-tools-2.24.1+dfsg/build.gradle'. Compiling build file '/build/reproducible-path/picard-tools-2.24.1+dfsg/build.gradle' using SubsetScriptTransformer. Compiling build file '/build/reproducible-path/picard-tools-2.24.1+dfsg/build.gradle' using BuildScriptTransformer. Starting process 'command 'dpkg-parsechangelog''. Working directory: /build/reproducible-path/picard-tools-2.24.1+dfsg Command: dpkg-parsechangelog -S Version Successfully started process 'command 'dpkg-parsechangelog'' build for version:2.24.1 Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/picard-tools-2.24.1+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@5d0b0479 Loading the Maven rules... Replacing com.intel.gkl:gkl:jar:0.8.5 -> com.intel.gkl:gkl:jar:debian Replacing com.google.guava:guava:jar:15.0 -> com.google.guava:guava:jar:debian Passing through com.google.guava:guava-parent:jar:debian Passing through commons-io:commons-io:jar:debian Passing through org.apache.commons:commons-parent:jar:debian Passing through org.apache:apache:jar:debian Replacing org.apache.commons:commons-math3:jar:3.5 -> org.apache.commons:commons-math3:jar:debian Replacing org.apache.commons:commons-collections4:jar:4.3 -> org.apache.commons:commons-collections4:jar:debian Replacing commons-lang:commons-lang:jar:2.6 -> commons-lang:commons-lang:jar:debian Replacing com.github.samtools:htsjdk:jar:2.23.0 -> com.github.samtools:htsjdk:jar:debian Replacing org.broadinstitute:barclay:jar:3.0.0 -> org.broadinstitute:barclay:jar:debian Passing through org.apache.commons:commons-lang3:jar:debian Passing through org.broadinstitute:gatk-native-bindings:jar:debian Passing through org.apache.logging.log4j:log4j-api:jar:debian Passing through org.apache.logging.log4j:log4j:jar:debian Passing through org.apache.logging.log4j:log4j-core:jar:debian Passing through org.jsr-305:jsr305:jar:0.x Passing through org.apache.commons:commons-jexl:jar:debian Passing through commons-logging:commons-logging:jar:debian Passing through org.xerial.snappy:snappy-java:jar:debian Passing through org.apache.commons:commons-compress:jar:debian Passing through org.tukaani:xz:jar:debian Passing through gov.nih.nlm.ncbi:ngs-java:jar:debian Passing through net.sf.jopt-simple:jopt-simple:jar:debian Passing through com.google.code.gson:gson:jar:debian Passing through com.google.code.gson:gson-parent:jar:debian Passing through org.freemarker:freemarker:jar:debian Adding Maven pom generation to project 'picard' Linking the generated javadoc to the system JDK API documentation All projects evaluated. Selected primary task 'jar' from project : Creating new cache for annotation-processors, path /build/reproducible-path/picard-tools-2.24.1+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@62998577 Selected primary task 'javadoc' from project : Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':debianMavenPom', task ':jar', task ':javadoc'] Creating new cache for resourceHashesCache, path /build/reproducible-path/picard-tools-2.24.1+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@791d43c5 Creating new cache for taskHistory, path /build/reproducible-path/picard-tools-2.24.1+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@705ab71 Creating new cache for outputFiles, path /build/reproducible-path/picard-tools-2.24.1+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@7f86561c :compileJava (Thread[Task worker for ':',5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.01 secs. Up-to-date check for task ':compileJava' took 3.345 secs. It is not up-to-date because: No history is available. All input files are considered out-of-date for incremental task ':compileJava'. Compiling with JDK Java compiler API. /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/util/help/PicardHelpDoclet.java:3: warning: [removal] ClassDoc in com.sun.javadoc has been deprecated and marked for removal import com.sun.javadoc.ClassDoc; ^ /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/util/help/PicardHelpDoclet.java:4: warning: [removal] RootDoc in com.sun.javadoc has been deprecated and marked for removal import com.sun.javadoc.RootDoc; ^ /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/util/help/PicardHelpDoclet.java:3: warning: [removal] ClassDoc in com.sun.javadoc has been deprecated and marked for removal import com.sun.javadoc.ClassDoc; ^ /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/util/help/PicardHelpDoclet.java:4: warning: [removal] RootDoc in com.sun.javadoc has been deprecated and marked for removal import com.sun.javadoc.RootDoc; ^ /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/util/help/PicardHelpDoclet.java:3: warning: [removal] ClassDoc in com.sun.javadoc has been deprecated and marked for removal import com.sun.javadoc.ClassDoc; ^ /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/util/help/PicardHelpDoclet.java:4: warning: [removal] RootDoc in com.sun.javadoc has been deprecated and marked for removal import com.sun.javadoc.RootDoc; ^ /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/util/help/PicardHelpDoclet.java:32: warning: [removal] RootDoc in com.sun.javadoc has been deprecated and marked for removal public static boolean start(final RootDoc rootDoc) throws IOException { ^ /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/util/help/PicardHelpDoclet.java:32: warning: [removal] RootDoc in com.sun.javadoc has been deprecated and marked for removal public static boolean start(final RootDoc rootDoc) throws IOException { ^ /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/util/help/PicardHelpDoclet.java:32: warning: [removal] RootDoc in com.sun.javadoc has been deprecated and marked for removal public static boolean start(final RootDoc rootDoc) throws IOException { ^ /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/util/help/PicardHelpDoclet.java:58: warning: [removal] ClassDoc in com.sun.javadoc has been deprecated and marked for removal final ClassDoc classDoc, ^ /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/util/help/PicardHelpDoclet.java:58: warning: [removal] ClassDoc in com.sun.javadoc has been deprecated and marked for removal final ClassDoc classDoc, ^ /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/util/help/PicardHelpDoclet.java:58: warning: [removal] ClassDoc in com.sun.javadoc has been deprecated and marked for removal final ClassDoc classDoc, ^ Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. 12 warnings :compileJava (Thread[Task worker for ':',5,main]) completed. Took 16.144 secs. :processResources (Thread[Task worker for ':',5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. Up-to-date check for task ':processResources' took 0.027 secs. It is not up-to-date because: No history is available. :processResources (Thread[Task worker for ':',5,main]) completed. Took 0.09 secs. :classes (Thread[Task worker for ':',5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes (Thread[Task worker for ':',5,main]) completed. Took 0.001 secs. :debianMavenPom (Thread[Task worker for ':',5,main]) started. :debianMavenPom Putting task artifact state for task ':debianMavenPom' into context took 0.0 secs. Up-to-date check for task ':debianMavenPom' took 0.001 secs. It is not up-to-date because: No history is available. Generating pom file /build/reproducible-path/picard-tools-2.24.1+dfsg/build/debian/picard.pom :debianMavenPom (Thread[Task worker for ':',5,main]) completed. Took 0.065 secs. :jar (Thread[Task worker for ':',5,main]) started. :jar Putting task artifact state for task ':jar' into context took 0.0 secs. Up-to-date check for task ':jar' took 0.042 secs. It is not up-to-date because: No history is available. :jar (Thread[Task worker for ':',5,main]) completed. Took 0.512 secs. :javadoc (Thread[Task worker for ':',5,main]) started. :javadoc Putting task artifact state for task ':javadoc' into context took 0.0 secs. Up-to-date check for task ':javadoc' took 0.065 secs. It is not up-to-date because: No history is available. Starting process 'command '/usr/lib/jvm/java-11-openjdk-amd64/bin/javadoc''. Working directory: /build/reproducible-path/picard-tools-2.24.1+dfsg Command: /usr/lib/jvm/java-11-openjdk-amd64/bin/javadoc @/build/reproducible-path/picard-tools-2.24.1+dfsg/build/tmp/javadoc/javadoc.options Successfully started process 'command '/usr/lib/jvm/java-11-openjdk-amd64/bin/javadoc'' /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/CollectAlignmentSummaryMetrics.java:62: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/CollectAlignmentSummaryMetrics.java:64: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/CollectAlignmentSummaryMetrics.java:68: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/CollectOxoGMetrics.java:55: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/CollectOxoGMetrics.java:187: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/CollectOxoGMetrics.java:187: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/CollectOxoGMetrics.java:194: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/CollectOxoGMetrics.java:194: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/CollectOxoGMetrics.java:187: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/CollectOxoGMetrics.java:187: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/CollectOxoGMetrics.java:194: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/CollectOxoGMetrics.java:194: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/FingerprintingSummaryMetrics.java:71: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/FingerprintingSummaryMetrics.java:74: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/FingerprintingSummaryMetrics.java:77: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/FingerprintingSummaryMetrics.java:71: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/FingerprintingSummaryMetrics.java:74: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/FingerprintingSummaryMetrics.java:77: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/RrbsSummaryMetrics.java:39: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/RrbsSummaryMetrics.java:39: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/RrbsSummaryMetrics.java:39: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/RrbsSummaryMetrics.java:39: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/artifacts/ErrorSummaryMetrics.java:10: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/artifacts/ErrorSummaryMetrics.java:10: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/artifacts/ErrorSummaryMetrics.java:10: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/artifacts/SequencingArtifactMetrics.java:87: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/artifacts/SequencingArtifactMetrics.java:88: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/artifacts/SequencingArtifactMetrics.java:88: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/artifacts/SequencingArtifactMetrics.java:23: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/artifacts/SequencingArtifactMetrics.java:23: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/artifacts/SequencingArtifactMetrics.java:24: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/artifacts/SequencingArtifactMetrics.java:24: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/directed/PanelMetricsBase.java:152: warning - invalid usage of tag < /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/directed/PanelMetricsBase.java:160: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/directed/PanelMetricsBase.java:55: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/directed/PanelMetricsBase.java:58: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/directed/PanelMetricsBase.java:52: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/directed/PanelMetricsBase.java:52: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/directed/PanelMetricsBase.java:55: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/directed/PanelMetricsBase.java:58: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/directed/PanelMetricsBase.java:152: warning - invalid usage of tag < /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/directed/PanelMetricsBase.java:154: warning - invalid usage of tag < /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/directed/PanelMetricsBase.java:155: warning - invalid usage of tag < /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/directed/PanelMetricsBase.java:160: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/directed/PanelMetricsBase.java:162: warning - invalid usage of tag < /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/directed/PanelMetricsBase.java:163: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/directed/TargetMetricsCollector.java:192: warning - invalid usage of tag < /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/directed/TargetMetricsCollector.java:192: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/directed/TargetMetricsCollector.java:192: warning - invalid usage of tag < /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/directed/TargetMetricsCollector.java:192: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/directed/TargetMetricsCollector.java:982: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/analysis/directed/TargetMetricsCollector.java:982: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/fingerprint/FingerprintChecker.java:181: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/fingerprint/FingerprintChecker.java:291: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/fingerprint/FingerprintChecker.java:230: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/fingerprint/FingerprintChecker.java:305: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/fingerprint/FingerprintChecker.java:246: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/fingerprint/FingerprintChecker.java:181: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/fingerprint/FingerprintChecker.java:230: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/fingerprint/FingerprintChecker.java:246: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/fingerprint/FingerprintChecker.java:291: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/fingerprint/FingerprintChecker.java:305: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/fingerprint/FingerprintMetrics.java:62: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/fingerprint/FingerprintMetrics.java:62: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/illumina/ExtractIlluminaBarcodes.java:90: warning - invalid usage of tag & /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/illumina/ExtractIlluminaBarcodes.java:451: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/illumina/ExtractIlluminaBarcodes.java:451: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/illumina/IlluminaBasecallsConverter.java:109: warning - invalid usage of tag < /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/illumina/IlluminaBasecallsConverter.java:154: warning - invalid usage of tag < /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/illumina/IlluminaPhasingMetrics.java:52: warning - invalid usage of tag & /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/illumina/IlluminaPhasingMetrics.java:52: warning - invalid usage of tag & /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/illumina/NewIlluminaBasecallsConverter.java:52: warning - invalid usage of tag < /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/sam/markduplicates/EstimateLibraryComplexity.java:76: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/sam/markduplicates/MarkDuplicates.java:127: warning - invalid usage of tag & /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/sam/markduplicates/MarkDuplicates.java:127: warning - invalid usage of tag & /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/illumina/parser/IlluminaDataProviderFactory.java:322: warning - invalid usage of tag < /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/illumina/parser/IlluminaDataProviderFactory.java:322: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/illumina/parser/BclParser.java:112: warning - invalid usage of tag < /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/illumina/parser/BclParser.java:113: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/illumina/parser/BclParser.java:113: warning - invalid usage of tag < /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/illumina/parser/BclParser.java:114: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/illumina/parser/BclParser.java:118: warning - invalid usage of tag < /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/illumina/parser/BclParser.java:127: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/illumina/parser/Tile.java:38: warning - invalid usage of tag & /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/illumina/parser/TileMetricsUtil.java:178: warning - invalid usage of tag & /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/illumina/parser/TileMetricsUtil.java:179: warning - invalid usage of tag & /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/pedigree/PedFile.java:19: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/illumina/quality/CollectHiSeqXPfFailMetrics.java:391: warning - invalid usage of tag < /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/illumina/quality/CollectHiSeqXPfFailMetrics.java:394: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/illumina/parser/readers/CbclReader.java:37: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/illumina/parser/readers/ClocsFileReader.java:57: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/illumina/parser/readers/ClocsFileReader.java:57: warning - invalid usage of tag & /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/illumina/parser/readers/ClocsFileReader.java:57: warning - invalid usage of tag & /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/illumina/parser/readers/TileMetricsOutReader.java:145: warning - invalid usage of tag & /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/illumina/parser/readers/TileMetricsOutReader.java:145: warning - invalid usage of tag & /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/sam/AbstractAlignmentMerger.java:775: warning - invalid usage of tag < /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/sam/AbstractAlignmentMerger.java:776: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/sam/AbstractAlignmentMerger.java:778: warning - invalid usage of tag < /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/sam/AbstractAlignmentMerger.java:779: warning - invalid usage of tag > /build/reproducible-path/picard-tools-2.24.1+dfsg/src/main/java/picard/sam/AbstractAlignmentMerger.java:781: warning - invalid usage of tag < 100 warnings :javadoc (Thread[Task worker for ':',5,main]) completed. Took 13.786 secs. BUILD SUCCESSFUL in 41s 5 actionable tasks: 5 executed make[1]: Leaving directory '/build/reproducible-path/picard-tools-2.24.1+dfsg' jh_build -O--buildsystem=gradle rm -f debian/libpicard-java-doc.debhelper.log debian/libpicard-java.debhelper.log debian/picard-tools.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/picard-tools-2.24.1+dfsg' # ensure the .jar can be executed /usr/bin/java -XX:ParallelGCThreads=1 -Xmx4G -Xss16M -Djava.io.tmpdir=/tmp -jar `find . -name "picard*.jar" BamIndexStats|head -n 1` -h > /dev/null find: paths must precede expression: `BamIndexStats' Usage: java [options] [args...] (to execute a class) or java [options] -jar [args...] (to execute a jar file) or java [options] -m [/] [args...] java [options] --module [/] [args...] (to execute the main class in a module) or java [options] [args] (to execute a single source-file program) Arguments following the main class, source file, -jar , -m or --module / are passed as the arguments to main class. where options include: -zero to select the "zero" VM -dcevm to select the "dcevm" VM -cp -classpath --class-path A : separated list of directories, JAR archives, and ZIP archives to search for class files. -p --module-path ... A : separated list of directories, each directory is a directory of modules. --upgrade-module-path ... A : separated list of directories, each directory is a directory of modules that replace upgradeable modules in the runtime image --add-modules [,...] root modules to resolve in addition to the initial module. can also be ALL-DEFAULT, ALL-SYSTEM, ALL-MODULE-PATH. --list-modules list observable modules and exit -d --describe-module describe a module and exit --dry-run create VM and load main class but do not execute main method. The --dry-run option may be useful for validating the command-line options such as the module system configuration. --validate-modules validate all modules and exit The --validate-modules option may be useful for finding conflicts and other errors with modules on the module path. -D= set a system property -verbose:[class|module|gc|jni] enable verbose output -version print product version to the error stream and exit --version print product version to the output stream and exit -showversion print product version to the error stream and continue --show-version print product version to the output stream and continue --show-module-resolution show module resolution output during startup -? -h -help print this help message to the error stream --help print this help message to the output stream -X print help on extra options to the error stream --help-extra print help on extra options to the output stream -ea[:...|:] -enableassertions[:...|:] enable assertions with specified granularity -da[:...|:] -disableassertions[:...|:] disable assertions with specified granularity -esa | -enablesystemassertions enable system assertions -dsa | -disablesystemassertions disable system assertions -agentlib:[=] load native agent library , e.g. -agentlib:jdwp see also -agentlib:jdwp=help -agentpath:[=] load native agent library by full pathname -javaagent:[=] load Java programming language agent, see java.lang.instrument -splash: show splash screen with specified image HiDPI scaled images are automatically supported and used if available. The unscaled image filename, e.g. image.ext, should always be passed as the argument to the -splash option. The most appropriate scaled image provided will be picked up automatically. See the SplashScreen API documentation for more information @argument files one or more argument files containing options -disable-@files prevent further argument file expansion --enable-preview allow classes to depend on preview features of this release To specify an argument for a long option, you can use --= or -- . # Tests do not work with locales with a different decimal separator # (for example ',') env LC_ALL=C \ dh_auto_build -- test mkdir -p .gradle/init.d cp /usr/share/gradle-debian-helper/init.gradle .gradle/init.d/ gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=picard-tools -Dfile.encoding=UTF-8 --parallel --max-workers=20 test Initialized native services in: /build/reproducible-path/picard-tools-2.24.1+dfsg/.gradle/native To honour the JVM settings for this build a new JVM will be forked. Please consider using the daemon: https://docs.gradle.org/4.4.1/userguide/gradle_daemon.html. Starting process 'Gradle build daemon'. Working directory: /build/reproducible-path/picard-tools-2.24.1+dfsg/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-11-openjdk-amd64/bin/java -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Duser.variant -cp /usr/share/gradle/lib/gradle-launcher-4.4.1.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 Successfully started process 'Gradle build daemon' An attempt to start the daemon took 1.506 secs. The client will now receive all logging from the daemon (pid: 3257394). The daemon log file: /build/reproducible-path/picard-tools-2.24.1+dfsg/.gradle/daemon/4.4.1/daemon-3257394.out.log Daemon will be stopped at the end of the build stopping after processing Closing daemon's stdin at end of input. The daemon will no longer process any standard input. Using 20 worker leases. Creating new cache for fileHashes, path /build/reproducible-path/picard-tools-2.24.1+dfsg/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@69961851 Creating new cache for resourceHashesCache, path /build/reproducible-path/picard-tools-2.24.1+dfsg/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@69961851 Creating new cache for fileHashes, path /build/reproducible-path/picard-tools-2.24.1+dfsg/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@52637a84 Starting Build Creating new cache for metadata-1.1/results, path /build/reproducible-path/picard-tools-2.24.1+dfsg/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@1eff2b22 Settings evaluated using settings file '/build/reproducible-path/picard-tools-2.24.1+dfsg/settings.gradle'. Projects loaded. Root project using build file '/build/reproducible-path/picard-tools-2.24.1+dfsg/build.gradle'. Included projects: [root project 'picard'] Keep-alive timer started Adding Debian repository to project 'picard' Parallel execution is an incubating feature. Evaluating root project 'picard' using build file '/build/reproducible-path/picard-tools-2.24.1+dfsg/build.gradle'. Starting process 'command 'dpkg-parsechangelog''. Working directory: /build/reproducible-path/picard-tools-2.24.1+dfsg Command: dpkg-parsechangelog -S Version Successfully started process 'command 'dpkg-parsechangelog'' build for version:2.24.1 Creating new cache for metadata-2.36/module-metadata, path /build/reproducible-path/picard-tools-2.24.1+dfsg/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@59ee21b6 Loading the Maven rules... Replacing com.intel.gkl:gkl:jar:0.8.5 -> com.intel.gkl:gkl:jar:debian Replacing com.google.guava:guava:jar:15.0 -> com.google.guava:guava:jar:debian Passing through com.google.guava:guava-parent:jar:debian Passing through commons-io:commons-io:jar:debian Passing through org.apache.commons:commons-parent:jar:debian Passing through org.apache:apache:jar:debian Replacing org.apache.commons:commons-math3:jar:3.5 -> org.apache.commons:commons-math3:jar:debian Replacing org.apache.commons:commons-collections4:jar:4.3 -> org.apache.commons:commons-collections4:jar:debian Replacing commons-lang:commons-lang:jar:2.6 -> commons-lang:commons-lang:jar:debian Replacing com.github.samtools:htsjdk:jar:2.23.0 -> com.github.samtools:htsjdk:jar:debian Replacing org.broadinstitute:barclay:jar:3.0.0 -> org.broadinstitute:barclay:jar:debian Passing through org.apache.commons:commons-lang3:jar:debian Passing through org.broadinstitute:gatk-native-bindings:jar:debian Passing through org.apache.logging.log4j:log4j-api:jar:debian Passing through org.apache.logging.log4j:log4j:jar:debian Passing through org.apache.logging.log4j:log4j-core:jar:debian Passing through org.jsr-305:jsr305:jar:0.x Passing through org.apache.commons:commons-jexl:jar:debian Passing through commons-logging:commons-logging:jar:debian Passing through org.xerial.snappy:snappy-java:jar:debian Passing through org.apache.commons:commons-compress:jar:debian Passing through org.tukaani:xz:jar:debian Passing through gov.nih.nlm.ncbi:ngs-java:jar:debian Passing through net.sf.jopt-simple:jopt-simple:jar:debian Passing through com.google.code.gson:gson:jar:debian Passing through com.google.code.gson:gson-parent:jar:debian Passing through org.freemarker:freemarker:jar:debian Adding Maven pom generation to project 'picard' Linking the generated javadoc to the system JDK API documentation All projects evaluated. Selected primary task 'test' from project : Creating new cache for annotation-processors, path /build/reproducible-path/picard-tools-2.24.1+dfsg/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@233c0f5c Tasks to be executed: [task ':compileJava', task ':processResources', task ':classes', task ':compileTestJava', task ':processTestResources', task ':testClasses', task ':test'] Creating new cache for resourceHashesCache, path /build/reproducible-path/picard-tools-2.24.1+dfsg/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@52637a84 Creating new cache for taskHistory, path /build/reproducible-path/picard-tools-2.24.1+dfsg/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@70a5fbba Creating new cache for outputFiles, path /build/reproducible-path/picard-tools-2.24.1+dfsg/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@fe28201 :compileJava (Thread[Task worker for ':',5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.009 secs. Skipping task ':compileJava' as it is up-to-date (took 0.601 secs). :compileJava UP-TO-DATE :compileJava (Thread[Task worker for ':',5,main]) completed. Took 0.661 secs. :processResources (Thread[Task worker for ':',5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. Skipping task ':processResources' as it is up-to-date (took 0.018 secs). :processResources UP-TO-DATE :processResources (Thread[Task worker for ':',5,main]) completed. Took 0.023 secs. :classes (Thread[Task worker for ':',5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes UP-TO-DATE :classes (Thread[Task worker for ':',5,main]) completed. Took 0.0 secs. :compileTestJava (Thread[Task worker for ':',5,main]) started. :compileTestJava Putting task artifact state for task ':compileTestJava' into context took 0.0 secs. Passing through org.testng:testng:jar:debian Passing through org.beanshell:bsh:jar:debian Passing through com.beust:jcommander:jar:debian Up-to-date check for task ':compileTestJava' took 1.581 secs. It is not up-to-date because: No history is available. All input files are considered out-of-date for incremental task ':compileTestJava'. Compiling with JDK Java compiler API. Note: Some input files use or override a deprecated API. Note: Recompile with -Xlint:deprecation for details. Note: Some input files use unchecked or unsafe operations. Note: Recompile with -Xlint:unchecked for details. :compileTestJava (Thread[Task worker for ':',5,main]) completed. Took 13.186 secs. :processTestResources (Thread[Task worker for ':',5,main]) started. :processTestResources Putting task artifact state for task ':processTestResources' into context took 0.0 secs. Up-to-date check for task ':processTestResources' took 0.041 secs. It is not up-to-date because: No history is available. :processTestResources (Thread[Task worker for ':',5,main]) completed. Took 0.072 secs. :testClasses (Thread[Task worker for ':',5,main]) started. :testClasses Skipping task ':testClasses' as it has no actions. :testClasses (Thread[Task worker for ':',5,main]) completed. Took 0.0 secs. :test (Thread[Task worker for ':',5,main]) started. :test Putting task artifact state for task ':test' into context took 0.004 secs. Up-to-date check for task ':test' took 0.164 secs. It is not up-to-date because: Task.upToDateWhen is false. Starting process 'Gradle Test Executor 1'. Working directory: /build/reproducible-path/picard-tools-2.24.1+dfsg Command: /usr/lib/jvm/java-11-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath7919233342577552188txt -Xms1G -Xmx2G -Dfile.encoding=UTF-8 -Duser.country=US -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 1' Successfully started process 'Gradle Test Executor 1' Gradle Test Executor 1 started executing tests. Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:19 SortSam Gradle suite > Gradle test STANDARD_ERROR INFO 2024-07-02 11:19:19 SortSam Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test suite 'Gradle test' produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** SortSam -INPUT /tmp/CollectGcBias17519527883114087587.bam -OUTPUT /tmp/CollectGcBias18028020853166826936.bam -SORT_ORDER coordinate ********** SortSam -INPUT /tmp/CollectGcBias17519527883114087587.bam -OUTPUT /tmp/CollectGcBias18028020853166826936.bam -SORT_ORDER coordinate Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.159 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:20.159 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.163 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:20.163 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.167 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:20.167 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.167 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:20.167 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] SortSam INPUT=/tmp/CollectGcBias17519527883114087587.bam OUTPUT=/tmp/CollectGcBias18028020853166826936.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:20 GMT+14:00 2024] SortSam INPUT=/tmp/CollectGcBias17519527883114087587.bam OUTPUT=/tmp/CollectGcBias18028020853166826936.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 SortSam Finished reading inputs, merging and writing to output now. INFO 2024-07-02 11:19:20 SortSam Finished reading inputs, merging and writing to output now. Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:19:20 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.00 minutes. Test: Test suite 'Gradle test' produced standard out/err: Runtime.totalMemory()=1075838976 Runtime.totalMemory()=1075838976 Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 SortSam INFO 2024-07-02 11:19:20 SortSam Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test suite 'Gradle test' produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** SortSam -INPUT /tmp/CollectGcBias17519527883114087587.bam -OUTPUT /tmp/CollectGcBias13823779816851466163.bam -SORT_ORDER coordinate ********** SortSam -INPUT /tmp/CollectGcBias17519527883114087587.bam -OUTPUT /tmp/CollectGcBias13823779816851466163.bam -SORT_ORDER coordinate Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.311 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:20.311 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.311 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:20.311 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.312 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:20.312 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.312 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:20.312 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] SortSam INPUT=/tmp/CollectGcBias17519527883114087587.bam OUTPUT=/tmp/CollectGcBias13823779816851466163.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:20 GMT+14:00 2024] SortSam INPUT=/tmp/CollectGcBias17519527883114087587.bam OUTPUT=/tmp/CollectGcBias13823779816851466163.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 SortSam Finished reading inputs, merging and writing to output now. INFO 2024-07-02 11:19:20 SortSam Finished reading inputs, merging and writing to output now. Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:19:20 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.00 minutes. Test: Test suite 'Gradle test' produced standard out/err: Runtime.totalMemory()=1075838976 Runtime.totalMemory()=1075838976 Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 MergeSamFiles INFO 2024-07-02 11:19:20 MergeSamFiles Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test suite 'Gradle test' produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** MergeSamFiles -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/independent_replicates/twopairs.sam -CREATE_INDEX true -OUTPUT /tmp/convertSamToBam10192042766333982448dir/twopairs.bam ********** MergeSamFiles -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/independent_replicates/twopairs.sam -CREATE_INDEX true -OUTPUT /tmp/convertSamToBam10192042766333982448dir/twopairs.bam Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.493 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:20.493 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.493 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:20.493 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.494 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:20.494 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.494 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:20.494 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] MergeSamFiles INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/independent_replicates/twopairs.sam] OUTPUT=/tmp/convertSamToBam10192042766333982448dir/twopairs.bam CREATE_INDEX=true SORT_ORDER=coordinate ASSUME_SORTED=false MERGE_SEQUENCE_DICTIONARIES=false USE_THREADING=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:20 GMT+14:00 2024] MergeSamFiles INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/independent_replicates/twopairs.sam] OUTPUT=/tmp/convertSamToBam10192042766333982448dir/twopairs.bam CREATE_INDEX=true SORT_ORDER=coordinate ASSUME_SORTED=false MERGE_SEQUENCE_DICTIONARIES=false USE_THREADING=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 MergeSamFiles Input files are in same order as output so sorting to temp directory is not needed. INFO 2024-07-02 11:19:20 MergeSamFiles Input files are in same order as output so sorting to temp directory is not needed. Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 MergeSamFiles Finished reading inputs. INFO 2024-07-02 11:19:20 MergeSamFiles Finished reading inputs. Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] picard.sam.MergeSamFiles done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:19:20 GMT+14:00 2024] picard.sam.MergeSamFiles done. Elapsed time: 0.00 minutes. Test: Test suite 'Gradle test' produced standard out/err: Runtime.totalMemory()=1075838976 Runtime.totalMemory()=1075838976 Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 MergeSamFiles INFO 2024-07-02 11:19:20 MergeSamFiles Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test suite 'Gradle test' produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** MergeSamFiles -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/independent_replicates/twopairsWithUMIs.sam -CREATE_INDEX true -OUTPUT /tmp/convertSamToBam10192042766333982448dir/twopairsWithUMIs.bam ********** MergeSamFiles -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/independent_replicates/twopairsWithUMIs.sam -CREATE_INDEX true -OUTPUT /tmp/convertSamToBam10192042766333982448dir/twopairsWithUMIs.bam Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.542 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:20.542 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.542 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:20.542 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.543 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:20.543 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.543 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:20.543 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] MergeSamFiles INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/independent_replicates/twopairsWithUMIs.sam] OUTPUT=/tmp/convertSamToBam10192042766333982448dir/twopairsWithUMIs.bam CREATE_INDEX=true SORT_ORDER=coordinate ASSUME_SORTED=false MERGE_SEQUENCE_DICTIONARIES=false USE_THREADING=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:20 GMT+14:00 2024] MergeSamFiles INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/independent_replicates/twopairsWithUMIs.sam] OUTPUT=/tmp/convertSamToBam10192042766333982448dir/twopairsWithUMIs.bam CREATE_INDEX=true SORT_ORDER=coordinate ASSUME_SORTED=false MERGE_SEQUENCE_DICTIONARIES=false USE_THREADING=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 MergeSamFiles Input files are in same order as output so sorting to temp directory is not needed. INFO 2024-07-02 11:19:20 MergeSamFiles Input files are in same order as output so sorting to temp directory is not needed. Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 MergeSamFiles Finished reading inputs. INFO 2024-07-02 11:19:20 MergeSamFiles Finished reading inputs. Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] picard.sam.MergeSamFiles done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:19:20 GMT+14:00 2024] picard.sam.MergeSamFiles done. Elapsed time: 0.00 minutes. Test: Test suite 'Gradle test' produced standard out/err: Runtime.totalMemory()=1075838976 Runtime.totalMemory()=1075838976 Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 MergeSamFiles INFO 2024-07-02 11:19:20 MergeSamFiles Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test suite 'Gradle test' produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** MergeSamFiles -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/independent_replicates/twopairsWithBadUMIs.sam -CREATE_INDEX true -OUTPUT /tmp/convertSamToBam10192042766333982448dir/twopairsWithBadUMIs.bam ********** MergeSamFiles -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/independent_replicates/twopairsWithBadUMIs.sam -CREATE_INDEX true -OUTPUT /tmp/convertSamToBam10192042766333982448dir/twopairsWithBadUMIs.bam Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.562 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:20.562 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.562 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:20.562 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.563 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:20.563 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.563 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:20.563 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] MergeSamFiles INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/independent_replicates/twopairsWithBadUMIs.sam] OUTPUT=/tmp/convertSamToBam10192042766333982448dir/twopairsWithBadUMIs.bam CREATE_INDEX=true SORT_ORDER=coordinate ASSUME_SORTED=false MERGE_SEQUENCE_DICTIONARIES=false USE_THREADING=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:20 GMT+14:00 2024] MergeSamFiles INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/independent_replicates/twopairsWithBadUMIs.sam] OUTPUT=/tmp/convertSamToBam10192042766333982448dir/twopairsWithBadUMIs.bam CREATE_INDEX=true SORT_ORDER=coordinate ASSUME_SORTED=false MERGE_SEQUENCE_DICTIONARIES=false USE_THREADING=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 MergeSamFiles Input files are in same order as output so sorting to temp directory is not needed. INFO 2024-07-02 11:19:20 MergeSamFiles Input files are in same order as output so sorting to temp directory is not needed. Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 MergeSamFiles Finished reading inputs. INFO 2024-07-02 11:19:20 MergeSamFiles Finished reading inputs. Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] picard.sam.MergeSamFiles done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:19:20 GMT+14:00 2024] picard.sam.MergeSamFiles done. Elapsed time: 0.00 minutes. Test: Test suite 'Gradle test' produced standard out/err: Runtime.totalMemory()=1075838976 Runtime.totalMemory()=1075838976 Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 MergeSamFiles INFO 2024-07-02 11:19:20 MergeSamFiles Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test suite 'Gradle test' produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** MergeSamFiles -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/independent_replicates/aTriple.sam -CREATE_INDEX true -OUTPUT /tmp/convertSamToBam10192042766333982448dir/aTriple.bam ********** MergeSamFiles -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/independent_replicates/aTriple.sam -CREATE_INDEX true -OUTPUT /tmp/convertSamToBam10192042766333982448dir/aTriple.bam Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.578 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:20.578 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.579 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:20.579 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.579 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:20.579 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.579 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:20.579 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] MergeSamFiles INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/independent_replicates/aTriple.sam] OUTPUT=/tmp/convertSamToBam10192042766333982448dir/aTriple.bam CREATE_INDEX=true SORT_ORDER=coordinate ASSUME_SORTED=false MERGE_SEQUENCE_DICTIONARIES=false USE_THREADING=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:20 GMT+14:00 2024] MergeSamFiles INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/independent_replicates/aTriple.sam] OUTPUT=/tmp/convertSamToBam10192042766333982448dir/aTriple.bam CREATE_INDEX=true SORT_ORDER=coordinate ASSUME_SORTED=false MERGE_SEQUENCE_DICTIONARIES=false USE_THREADING=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 MergeSamFiles Input files are in same order as output so sorting to temp directory is not needed. INFO 2024-07-02 11:19:20 MergeSamFiles Input files are in same order as output so sorting to temp directory is not needed. Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 MergeSamFiles Finished reading inputs. INFO 2024-07-02 11:19:20 MergeSamFiles Finished reading inputs. Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] picard.sam.MergeSamFiles done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:19:20 GMT+14:00 2024] picard.sam.MergeSamFiles done. Elapsed time: 0.00 minutes. Test: Test suite 'Gradle test' produced standard out/err: Runtime.totalMemory()=1075838976 Runtime.totalMemory()=1075838976 Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 MergeSamFiles INFO 2024-07-02 11:19:20 MergeSamFiles Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test suite 'Gradle test' produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** MergeSamFiles -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/independent_replicates/aTripleWithUMIs.sam -CREATE_INDEX true -OUTPUT /tmp/convertSamToBam10192042766333982448dir/aTripleWithUMIs.bam ********** MergeSamFiles -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/independent_replicates/aTripleWithUMIs.sam -CREATE_INDEX true -OUTPUT /tmp/convertSamToBam10192042766333982448dir/aTripleWithUMIs.bam Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.598 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:20.598 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.599 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:20.599 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.600 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:20.600 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.600 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:20.600 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] MergeSamFiles INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/independent_replicates/aTripleWithUMIs.sam] OUTPUT=/tmp/convertSamToBam10192042766333982448dir/aTripleWithUMIs.bam CREATE_INDEX=true SORT_ORDER=coordinate ASSUME_SORTED=false MERGE_SEQUENCE_DICTIONARIES=false USE_THREADING=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:20 GMT+14:00 2024] MergeSamFiles INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/independent_replicates/aTripleWithUMIs.sam] OUTPUT=/tmp/convertSamToBam10192042766333982448dir/aTripleWithUMIs.bam CREATE_INDEX=true SORT_ORDER=coordinate ASSUME_SORTED=false MERGE_SEQUENCE_DICTIONARIES=false USE_THREADING=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 MergeSamFiles Input files are in same order as output so sorting to temp directory is not needed. INFO 2024-07-02 11:19:20 MergeSamFiles Input files are in same order as output so sorting to temp directory is not needed. Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 MergeSamFiles Finished reading inputs. INFO 2024-07-02 11:19:20 MergeSamFiles Finished reading inputs. Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] picard.sam.MergeSamFiles done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:19:20 GMT+14:00 2024] picard.sam.MergeSamFiles done. Elapsed time: 0.00 minutes. Test: Test suite 'Gradle test' produced standard out/err: Runtime.totalMemory()=1075838976 Runtime.totalMemory()=1075838976 Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 MergeSamFiles INFO 2024-07-02 11:19:20 MergeSamFiles Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test suite 'Gradle test' produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** MergeSamFiles -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/independent_replicates/multipleContigs.sam -CREATE_INDEX true -OUTPUT /tmp/convertSamToBam10192042766333982448dir/multipleContigs.bam ********** MergeSamFiles -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/independent_replicates/multipleContigs.sam -CREATE_INDEX true -OUTPUT /tmp/convertSamToBam10192042766333982448dir/multipleContigs.bam Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.616 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:20.616 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.617 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:20.617 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.617 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:20.617 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.618 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:20.618 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] MergeSamFiles INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/independent_replicates/multipleContigs.sam] OUTPUT=/tmp/convertSamToBam10192042766333982448dir/multipleContigs.bam CREATE_INDEX=true SORT_ORDER=coordinate ASSUME_SORTED=false MERGE_SEQUENCE_DICTIONARIES=false USE_THREADING=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:20 GMT+14:00 2024] MergeSamFiles INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/independent_replicates/multipleContigs.sam] OUTPUT=/tmp/convertSamToBam10192042766333982448dir/multipleContigs.bam CREATE_INDEX=true SORT_ORDER=coordinate ASSUME_SORTED=false MERGE_SEQUENCE_DICTIONARIES=false USE_THREADING=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 MergeSamFiles Input files are in same order as output so sorting to temp directory is not needed. INFO 2024-07-02 11:19:20 MergeSamFiles Input files are in same order as output so sorting to temp directory is not needed. Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 MergeSamFiles Finished reading inputs. INFO 2024-07-02 11:19:20 MergeSamFiles Finished reading inputs. Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] picard.sam.MergeSamFiles done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:19:20 GMT+14:00 2024] picard.sam.MergeSamFiles done. Elapsed time: 0.00 minutes. Test: Test suite 'Gradle test' produced standard out/err: Runtime.totalMemory()=1075838976 Runtime.totalMemory()=1075838976 Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 MergeSamFiles INFO 2024-07-02 11:19:20 MergeSamFiles Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test suite 'Gradle test' produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** MergeSamFiles -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/independent_replicates/twopairsWithUMIsMultipleOrientations.sam -CREATE_INDEX true -OUTPUT /tmp/convertSamToBam10192042766333982448dir/twopairsWithUMIsMultipleOrientations.bam ********** MergeSamFiles -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/independent_replicates/twopairsWithUMIsMultipleOrientations.sam -CREATE_INDEX true -OUTPUT /tmp/convertSamToBam10192042766333982448dir/twopairsWithUMIsMultipleOrientations.bam Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.639 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:20.639 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.639 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:20.639 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.640 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:20.640 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.640 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:20.640 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] MergeSamFiles INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/independent_replicates/twopairsWithUMIsMultipleOrientations.sam] OUTPUT=/tmp/convertSamToBam10192042766333982448dir/twopairsWithUMIsMultipleOrientations.bam CREATE_INDEX=true SORT_ORDER=coordinate ASSUME_SORTED=false MERGE_SEQUENCE_DICTIONARIES=false USE_THREADING=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:20 GMT+14:00 2024] MergeSamFiles INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/independent_replicates/twopairsWithUMIsMultipleOrientations.sam] OUTPUT=/tmp/convertSamToBam10192042766333982448dir/twopairsWithUMIsMultipleOrientations.bam CREATE_INDEX=true SORT_ORDER=coordinate ASSUME_SORTED=false MERGE_SEQUENCE_DICTIONARIES=false USE_THREADING=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 MergeSamFiles Input files are in same order as output so sorting to temp directory is not needed. INFO 2024-07-02 11:19:20 MergeSamFiles Input files are in same order as output so sorting to temp directory is not needed. Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 MergeSamFiles Finished reading inputs. INFO 2024-07-02 11:19:20 MergeSamFiles Finished reading inputs. Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] picard.sam.MergeSamFiles done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:19:20 GMT+14:00 2024] picard.sam.MergeSamFiles done. Elapsed time: 0.00 minutes. Test: Test suite 'Gradle test' produced standard out/err: Runtime.totalMemory()=1075838976 Runtime.totalMemory()=1075838976 Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 SortSam INFO 2024-07-02 11:19:20 SortSam Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test suite 'Gradle test' produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** SortSam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias8336485591475586296.bam -OUTPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias16671323870963296687.bam -SORT_ORDER coordinate ********** SortSam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias8336485591475586296.bam -OUTPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias16671323870963296687.bam -SORT_ORDER coordinate Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.682 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:20.682 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.683 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:20.683 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.683 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:20.683 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.684 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:20.684 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] SortSam INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias8336485591475586296.bam OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias16671323870963296687.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:20 GMT+14:00 2024] SortSam INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias8336485591475586296.bam OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias16671323870963296687.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 SortSam Finished reading inputs, merging and writing to output now. INFO 2024-07-02 11:19:20 SortSam Finished reading inputs, merging and writing to output now. Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:19:20 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.00 minutes. Test: Test suite 'Gradle test' produced standard out/err: Runtime.totalMemory()=1075838976 Runtime.totalMemory()=1075838976 Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 CollectSamErrorMetrics INFO 2024-07-02 11:19:20 CollectSamErrorMetrics Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test suite 'Gradle test' produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** CollectSamErrorMetrics -INPUT testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/simpleSamWithBaseErrors1.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS ERROR:TWO_BASE_PADDED_CONTEXT -ERROR_METRICS ERROR:CONSENSUS -ERROR_METRICS ERROR:NS_IN_READ -ERROR_METRICS ERROR:BINNED_CYCLE -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/simpleSamWithBaseErrors1.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS ERROR:TWO_BASE_PADDED_CONTEXT -ERROR_METRICS ERROR:CONSENSUS -ERROR_METRICS ERROR:NS_IN_READ -ERROR_METRICS ERROR:BINNED_CYCLE -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.839 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:20.839 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.839 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:20.839 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.840 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:20.840 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:20.840 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:20.840 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] CollectSamErrorMetrics INPUT=testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/simpleSamWithBaseErrors1.sam ERROR_METRICS=[ERROR, ERROR:BASE_QUALITY, ERROR:INSERT_LENGTH, ERROR:GC_CONTENT, ERROR:READ_DIRECTION, ERROR:PAIR_ORIENTATION, ERROR:HOMOPOLYMER, ERROR:BINNED_HOMOPOLYMER, ERROR:CYCLE, ERROR:READ_ORDINALITY, ERROR:READ_ORDINALITY:CYCLE, ERROR:READ_ORDINALITY:HOMOPOLYMER, ERROR:READ_ORDINALITY:GC_CONTENT, ERROR:READ_ORDINALITY:PRE_DINUC, ERROR:MAPPING_QUALITY, ERROR:READ_GROUP, ERROR:MISMATCHES_IN_READ, ERROR:ONE_BASE_PADDED_CONTEXT, OVERLAPPING_ERROR, OVERLAPPING_ERROR:BASE_QUALITY, OVERLAPPING_ERROR:INSERT_LENGTH, OVERLAPPING_ERROR:READ_ORDINALITY, OVERLAPPING_ERROR:READ_ORDINALITY:CYCLE, OVERLAPPING_ERROR:READ_ORDINALITY:HOMOPOLYMER, OVERLAPPING_ERROR:READ_ORDINALITY:GC_CONTENT, INDEL_ERROR, ERROR:TWO_BASE_PADDED_CONTEXT, ERROR:CONSENSUS, ERROR:NS_IN_READ, ERROR:BINNED_CYCLE] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:20 GMT+14:00 2024] CollectSamErrorMetrics INPUT=testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/simpleSamWithBaseErrors1.sam ERROR_METRICS=[ERROR, ERROR:BASE_QUALITY, ERROR:INSERT_LENGTH, ERROR:GC_CONTENT, ERROR:READ_DIRECTION, ERROR:PAIR_ORIENTATION, ERROR:HOMOPOLYMER, ERROR:BINNED_HOMOPOLYMER, ERROR:CYCLE, ERROR:READ_ORDINALITY, ERROR:READ_ORDINALITY:CYCLE, ERROR:READ_ORDINALITY:HOMOPOLYMER, ERROR:READ_ORDINALITY:GC_CONTENT, ERROR:READ_ORDINALITY:PRE_DINUC, ERROR:MAPPING_QUALITY, ERROR:READ_GROUP, ERROR:MISMATCHES_IN_READ, ERROR:ONE_BASE_PADDED_CONTEXT, OVERLAPPING_ERROR, OVERLAPPING_ERROR:BASE_QUALITY, OVERLAPPING_ERROR:INSERT_LENGTH, OVERLAPPING_ERROR:READ_ORDINALITY, OVERLAPPING_ERROR:READ_ORDINALITY:CYCLE, OVERLAPPING_ERROR:READ_ORDINALITY:HOMOPOLYMER, OVERLAPPING_ERROR:READ_ORDINALITY:GC_CONTENT, INDEL_ERROR, ERROR:TWO_BASE_PADDED_CONTEXT, ERROR:CONSENSUS, ERROR:NS_IN_READ, ERROR:BINNED_CYCLE] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:19:20 CollectSamErrorMetrics Getting SamLocusIterator Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 CollectSamErrorMetrics Using 30 aggregators. INFO 2024-07-02 11:19:20 CollectSamErrorMetrics Using 30 aggregators. Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:19:20 CollectSamErrorMetrics Starting iteration over loci Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:19:20 CollectSamErrorMetrics Really starting iteration now. Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:20 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:19:20 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Examined 37 loci, Processed 37 loci, Skipped 0 loci. INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Examined 37 loci, Processed 37 loci, Skipped 0 loci. Test: Test suite 'Gradle test' produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:21 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:19:21 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test suite 'Gradle test' produced standard out/err: Runtime.totalMemory()=1075838976 Runtime.totalMemory()=1075838976 Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test suite 'Gradle test' produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** CollectSamErrorMetrics -INPUT testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/simpleSamWithBaseErrors2.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS ERROR:TWO_BASE_PADDED_CONTEXT -ERROR_METRICS ERROR:CONSENSUS -ERROR_METRICS ERROR:NS_IN_READ -ERROR_METRICS ERROR:BINNED_CYCLE -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/simpleSamWithBaseErrors2.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS ERROR:TWO_BASE_PADDED_CONTEXT -ERROR_METRICS ERROR:CONSENSUS -ERROR_METRICS ERROR:NS_IN_READ -ERROR_METRICS ERROR:BINNED_CYCLE -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: 11:19:21.056 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:21.056 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:21.056 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:21.056 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: 11:19:21.057 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:21.057 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:21.057 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:21.057 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:21 GMT+14:00 2024] CollectSamErrorMetrics INPUT=testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/simpleSamWithBaseErrors2.sam ERROR_METRICS=[ERROR, ERROR:BASE_QUALITY, ERROR:INSERT_LENGTH, ERROR:GC_CONTENT, ERROR:READ_DIRECTION, ERROR:PAIR_ORIENTATION, ERROR:HOMOPOLYMER, ERROR:BINNED_HOMOPOLYMER, ERROR:CYCLE, ERROR:READ_ORDINALITY, ERROR:READ_ORDINALITY:CYCLE, ERROR:READ_ORDINALITY:HOMOPOLYMER, ERROR:READ_ORDINALITY:GC_CONTENT, ERROR:READ_ORDINALITY:PRE_DINUC, ERROR:MAPPING_QUALITY, ERROR:READ_GROUP, ERROR:MISMATCHES_IN_READ, ERROR:ONE_BASE_PADDED_CONTEXT, OVERLAPPING_ERROR, OVERLAPPING_ERROR:BASE_QUALITY, OVERLAPPING_ERROR:INSERT_LENGTH, OVERLAPPING_ERROR:READ_ORDINALITY, OVERLAPPING_ERROR:READ_ORDINALITY:CYCLE, OVERLAPPING_ERROR:READ_ORDINALITY:HOMOPOLYMER, OVERLAPPING_ERROR:READ_ORDINALITY:GC_CONTENT, INDEL_ERROR, ERROR:TWO_BASE_PADDED_CONTEXT, ERROR:CONSENSUS, ERROR:NS_IN_READ, ERROR:BINNED_CYCLE] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:21 GMT+14:00 2024] CollectSamErrorMetrics INPUT=testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/simpleSamWithBaseErrors2.sam ERROR_METRICS=[ERROR, ERROR:BASE_QUALITY, ERROR:INSERT_LENGTH, ERROR:GC_CONTENT, ERROR:READ_DIRECTION, ERROR:PAIR_ORIENTATION, ERROR:HOMOPOLYMER, ERROR:BINNED_HOMOPOLYMER, ERROR:CYCLE, ERROR:READ_ORDINALITY, ERROR:READ_ORDINALITY:CYCLE, ERROR:READ_ORDINALITY:HOMOPOLYMER, ERROR:READ_ORDINALITY:GC_CONTENT, ERROR:READ_ORDINALITY:PRE_DINUC, ERROR:MAPPING_QUALITY, ERROR:READ_GROUP, ERROR:MISMATCHES_IN_READ, ERROR:ONE_BASE_PADDED_CONTEXT, OVERLAPPING_ERROR, OVERLAPPING_ERROR:BASE_QUALITY, OVERLAPPING_ERROR:INSERT_LENGTH, OVERLAPPING_ERROR:READ_ORDINALITY, OVERLAPPING_ERROR:READ_ORDINALITY:CYCLE, OVERLAPPING_ERROR:READ_ORDINALITY:HOMOPOLYMER, OVERLAPPING_ERROR:READ_ORDINALITY:GC_CONTENT, INDEL_ERROR, ERROR:TWO_BASE_PADDED_CONTEXT, ERROR:CONSENSUS, ERROR:NS_IN_READ, ERROR:BINNED_CYCLE] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Getting SamLocusIterator Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Using 30 aggregators. INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Using 30 aggregators. Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Starting iteration over loci Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Really starting iteration now. Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Examined 37 loci, Processed 37 loci, Skipped 0 loci. INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Examined 37 loci, Processed 37 loci, Skipped 0 loci. Test: Test suite 'Gradle test' produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:21 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:19:21 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test suite 'Gradle test' produced standard out/err: Runtime.totalMemory()=1075838976 Runtime.totalMemory()=1075838976 Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test suite 'Gradle test' produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** CollectSamErrorMetrics -INPUT testdata/picard/sam/BamErrorMetrics/simpleSingleStrandConsensusSamWithBaseErrors.sam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/simpleSingleStrandConsensusSamWithBaseErrors.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS ERROR:TWO_BASE_PADDED_CONTEXT -ERROR_METRICS ERROR:CONSENSUS -ERROR_METRICS ERROR:NS_IN_READ -ERROR_METRICS ERROR:BINNED_CYCLE -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT testdata/picard/sam/BamErrorMetrics/simpleSingleStrandConsensusSamWithBaseErrors.sam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/simpleSingleStrandConsensusSamWithBaseErrors.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS ERROR:TWO_BASE_PADDED_CONTEXT -ERROR_METRICS ERROR:CONSENSUS -ERROR_METRICS ERROR:NS_IN_READ -ERROR_METRICS ERROR:BINNED_CYCLE -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: 11:19:21.162 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:21.162 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:21.162 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:21.162 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: 11:19:21.163 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:21.163 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:21.163 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:21.163 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:21 GMT+14:00 2024] CollectSamErrorMetrics INPUT=testdata/picard/sam/BamErrorMetrics/simpleSingleStrandConsensusSamWithBaseErrors.sam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/simpleSingleStrandConsensusSamWithBaseErrors.sam ERROR_METRICS=[ERROR, ERROR:BASE_QUALITY, ERROR:INSERT_LENGTH, ERROR:GC_CONTENT, ERROR:READ_DIRECTION, ERROR:PAIR_ORIENTATION, ERROR:HOMOPOLYMER, ERROR:BINNED_HOMOPOLYMER, ERROR:CYCLE, ERROR:READ_ORDINALITY, ERROR:READ_ORDINALITY:CYCLE, ERROR:READ_ORDINALITY:HOMOPOLYMER, ERROR:READ_ORDINALITY:GC_CONTENT, ERROR:READ_ORDINALITY:PRE_DINUC, ERROR:MAPPING_QUALITY, ERROR:READ_GROUP, ERROR:MISMATCHES_IN_READ, ERROR:ONE_BASE_PADDED_CONTEXT, OVERLAPPING_ERROR, OVERLAPPING_ERROR:BASE_QUALITY, OVERLAPPING_ERROR:INSERT_LENGTH, OVERLAPPING_ERROR:READ_ORDINALITY, OVERLAPPING_ERROR:READ_ORDINALITY:CYCLE, OVERLAPPING_ERROR:READ_ORDINALITY:HOMOPOLYMER, OVERLAPPING_ERROR:READ_ORDINALITY:GC_CONTENT, INDEL_ERROR, ERROR:TWO_BASE_PADDED_CONTEXT, ERROR:CONSENSUS, ERROR:NS_IN_READ, ERROR:BINNED_CYCLE] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:21 GMT+14:00 2024] CollectSamErrorMetrics INPUT=testdata/picard/sam/BamErrorMetrics/simpleSingleStrandConsensusSamWithBaseErrors.sam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/simpleSingleStrandConsensusSamWithBaseErrors.sam ERROR_METRICS=[ERROR, ERROR:BASE_QUALITY, ERROR:INSERT_LENGTH, ERROR:GC_CONTENT, ERROR:READ_DIRECTION, ERROR:PAIR_ORIENTATION, ERROR:HOMOPOLYMER, ERROR:BINNED_HOMOPOLYMER, ERROR:CYCLE, ERROR:READ_ORDINALITY, ERROR:READ_ORDINALITY:CYCLE, ERROR:READ_ORDINALITY:HOMOPOLYMER, ERROR:READ_ORDINALITY:GC_CONTENT, ERROR:READ_ORDINALITY:PRE_DINUC, ERROR:MAPPING_QUALITY, ERROR:READ_GROUP, ERROR:MISMATCHES_IN_READ, ERROR:ONE_BASE_PADDED_CONTEXT, OVERLAPPING_ERROR, OVERLAPPING_ERROR:BASE_QUALITY, OVERLAPPING_ERROR:INSERT_LENGTH, OVERLAPPING_ERROR:READ_ORDINALITY, OVERLAPPING_ERROR:READ_ORDINALITY:CYCLE, OVERLAPPING_ERROR:READ_ORDINALITY:HOMOPOLYMER, OVERLAPPING_ERROR:READ_ORDINALITY:GC_CONTENT, INDEL_ERROR, ERROR:TWO_BASE_PADDED_CONTEXT, ERROR:CONSENSUS, ERROR:NS_IN_READ, ERROR:BINNED_CYCLE] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Getting SamLocusIterator Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Using 30 aggregators. INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Using 30 aggregators. Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Starting iteration over loci Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Really starting iteration now. Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Examined 37 loci, Processed 37 loci, Skipped 0 loci. INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Examined 37 loci, Processed 37 loci, Skipped 0 loci. Test: Test suite 'Gradle test' produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:21 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:19:21 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test suite 'Gradle test' produced standard out/err: Runtime.totalMemory()=1075838976 Runtime.totalMemory()=1075838976 Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test suite 'Gradle test' produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** CollectSamErrorMetrics -INPUT testdata/picard/sam/BamErrorMetrics/simpleDuplexConsensusSamWithBaseErrors.sam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/simpleDuplexConsensusSamWithBaseErrors.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS ERROR:TWO_BASE_PADDED_CONTEXT -ERROR_METRICS ERROR:CONSENSUS -ERROR_METRICS ERROR:NS_IN_READ -ERROR_METRICS ERROR:BINNED_CYCLE -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT testdata/picard/sam/BamErrorMetrics/simpleDuplexConsensusSamWithBaseErrors.sam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/simpleDuplexConsensusSamWithBaseErrors.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS ERROR:TWO_BASE_PADDED_CONTEXT -ERROR_METRICS ERROR:CONSENSUS -ERROR_METRICS ERROR:NS_IN_READ -ERROR_METRICS ERROR:BINNED_CYCLE -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: 11:19:21.227 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:21.227 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:21.228 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:21.228 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: 11:19:21.228 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:21.228 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:21.228 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:21.228 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:21 GMT+14:00 2024] CollectSamErrorMetrics INPUT=testdata/picard/sam/BamErrorMetrics/simpleDuplexConsensusSamWithBaseErrors.sam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/simpleDuplexConsensusSamWithBaseErrors.sam ERROR_METRICS=[ERROR, ERROR:BASE_QUALITY, ERROR:INSERT_LENGTH, ERROR:GC_CONTENT, ERROR:READ_DIRECTION, ERROR:PAIR_ORIENTATION, ERROR:HOMOPOLYMER, ERROR:BINNED_HOMOPOLYMER, ERROR:CYCLE, ERROR:READ_ORDINALITY, ERROR:READ_ORDINALITY:CYCLE, ERROR:READ_ORDINALITY:HOMOPOLYMER, ERROR:READ_ORDINALITY:GC_CONTENT, ERROR:READ_ORDINALITY:PRE_DINUC, ERROR:MAPPING_QUALITY, ERROR:READ_GROUP, ERROR:MISMATCHES_IN_READ, ERROR:ONE_BASE_PADDED_CONTEXT, OVERLAPPING_ERROR, OVERLAPPING_ERROR:BASE_QUALITY, OVERLAPPING_ERROR:INSERT_LENGTH, OVERLAPPING_ERROR:READ_ORDINALITY, OVERLAPPING_ERROR:READ_ORDINALITY:CYCLE, OVERLAPPING_ERROR:READ_ORDINALITY:HOMOPOLYMER, OVERLAPPING_ERROR:READ_ORDINALITY:GC_CONTENT, INDEL_ERROR, ERROR:TWO_BASE_PADDED_CONTEXT, ERROR:CONSENSUS, ERROR:NS_IN_READ, ERROR:BINNED_CYCLE] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:21 GMT+14:00 2024] CollectSamErrorMetrics INPUT=testdata/picard/sam/BamErrorMetrics/simpleDuplexConsensusSamWithBaseErrors.sam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/simpleDuplexConsensusSamWithBaseErrors.sam ERROR_METRICS=[ERROR, ERROR:BASE_QUALITY, ERROR:INSERT_LENGTH, ERROR:GC_CONTENT, ERROR:READ_DIRECTION, ERROR:PAIR_ORIENTATION, ERROR:HOMOPOLYMER, ERROR:BINNED_HOMOPOLYMER, ERROR:CYCLE, ERROR:READ_ORDINALITY, ERROR:READ_ORDINALITY:CYCLE, ERROR:READ_ORDINALITY:HOMOPOLYMER, ERROR:READ_ORDINALITY:GC_CONTENT, ERROR:READ_ORDINALITY:PRE_DINUC, ERROR:MAPPING_QUALITY, ERROR:READ_GROUP, ERROR:MISMATCHES_IN_READ, ERROR:ONE_BASE_PADDED_CONTEXT, OVERLAPPING_ERROR, OVERLAPPING_ERROR:BASE_QUALITY, OVERLAPPING_ERROR:INSERT_LENGTH, OVERLAPPING_ERROR:READ_ORDINALITY, OVERLAPPING_ERROR:READ_ORDINALITY:CYCLE, OVERLAPPING_ERROR:READ_ORDINALITY:HOMOPOLYMER, OVERLAPPING_ERROR:READ_ORDINALITY:GC_CONTENT, INDEL_ERROR, ERROR:TWO_BASE_PADDED_CONTEXT, ERROR:CONSENSUS, ERROR:NS_IN_READ, ERROR:BINNED_CYCLE] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Getting SamLocusIterator Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Using 30 aggregators. INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Using 30 aggregators. Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Starting iteration over loci Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Really starting iteration now. Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Examined 37 loci, Processed 37 loci, Skipped 0 loci. INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Examined 37 loci, Processed 37 loci, Skipped 0 loci. Test: Test suite 'Gradle test' produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:21 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:19:21 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test suite 'Gradle test' produced standard out/err: Runtime.totalMemory()=1075838976 Runtime.totalMemory()=1075838976 Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test suite 'Gradle test' produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** CollectSamErrorMetrics -INPUT testdata/picard/sam/BamErrorMetrics/chrMReadsWithClips.sam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/chrMReadsWithClips.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS ERROR:TWO_BASE_PADDED_CONTEXT -ERROR_METRICS ERROR:CONSENSUS -ERROR_METRICS ERROR:NS_IN_READ -ERROR_METRICS ERROR:BINNED_CYCLE -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT testdata/picard/sam/BamErrorMetrics/chrMReadsWithClips.sam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/chrMReadsWithClips.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS ERROR:TWO_BASE_PADDED_CONTEXT -ERROR_METRICS ERROR:CONSENSUS -ERROR_METRICS ERROR:NS_IN_READ -ERROR_METRICS ERROR:BINNED_CYCLE -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: 11:19:21.290 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:21.290 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:21.290 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:21.290 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: 11:19:21.291 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:21.291 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:21.291 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:21.291 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:21 GMT+14:00 2024] CollectSamErrorMetrics INPUT=testdata/picard/sam/BamErrorMetrics/chrMReadsWithClips.sam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/chrMReadsWithClips.sam ERROR_METRICS=[ERROR, ERROR:BASE_QUALITY, ERROR:INSERT_LENGTH, ERROR:GC_CONTENT, ERROR:READ_DIRECTION, ERROR:PAIR_ORIENTATION, ERROR:HOMOPOLYMER, ERROR:BINNED_HOMOPOLYMER, ERROR:CYCLE, ERROR:READ_ORDINALITY, ERROR:READ_ORDINALITY:CYCLE, ERROR:READ_ORDINALITY:HOMOPOLYMER, ERROR:READ_ORDINALITY:GC_CONTENT, ERROR:READ_ORDINALITY:PRE_DINUC, ERROR:MAPPING_QUALITY, ERROR:READ_GROUP, ERROR:MISMATCHES_IN_READ, ERROR:ONE_BASE_PADDED_CONTEXT, OVERLAPPING_ERROR, OVERLAPPING_ERROR:BASE_QUALITY, OVERLAPPING_ERROR:INSERT_LENGTH, OVERLAPPING_ERROR:READ_ORDINALITY, OVERLAPPING_ERROR:READ_ORDINALITY:CYCLE, OVERLAPPING_ERROR:READ_ORDINALITY:HOMOPOLYMER, OVERLAPPING_ERROR:READ_ORDINALITY:GC_CONTENT, INDEL_ERROR, ERROR:TWO_BASE_PADDED_CONTEXT, ERROR:CONSENSUS, ERROR:NS_IN_READ, ERROR:BINNED_CYCLE] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:21 GMT+14:00 2024] CollectSamErrorMetrics INPUT=testdata/picard/sam/BamErrorMetrics/chrMReadsWithClips.sam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/chrMReadsWithClips.sam ERROR_METRICS=[ERROR, ERROR:BASE_QUALITY, ERROR:INSERT_LENGTH, ERROR:GC_CONTENT, ERROR:READ_DIRECTION, ERROR:PAIR_ORIENTATION, ERROR:HOMOPOLYMER, ERROR:BINNED_HOMOPOLYMER, ERROR:CYCLE, ERROR:READ_ORDINALITY, ERROR:READ_ORDINALITY:CYCLE, ERROR:READ_ORDINALITY:HOMOPOLYMER, ERROR:READ_ORDINALITY:GC_CONTENT, ERROR:READ_ORDINALITY:PRE_DINUC, ERROR:MAPPING_QUALITY, ERROR:READ_GROUP, ERROR:MISMATCHES_IN_READ, ERROR:ONE_BASE_PADDED_CONTEXT, OVERLAPPING_ERROR, OVERLAPPING_ERROR:BASE_QUALITY, OVERLAPPING_ERROR:INSERT_LENGTH, OVERLAPPING_ERROR:READ_ORDINALITY, OVERLAPPING_ERROR:READ_ORDINALITY:CYCLE, OVERLAPPING_ERROR:READ_ORDINALITY:HOMOPOLYMER, OVERLAPPING_ERROR:READ_ORDINALITY:GC_CONTENT, INDEL_ERROR, ERROR:TWO_BASE_PADDED_CONTEXT, ERROR:CONSENSUS, ERROR:NS_IN_READ, ERROR:BINNED_CYCLE] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Getting SamLocusIterator Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Using 30 aggregators. INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Using 30 aggregators. Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Starting iteration over loci Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Really starting iteration now. Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Examined 56 loci, Processed 56 loci, Skipped 0 loci. INFO 2024-07-02 11:19:21 CollectSamErrorMetrics Examined 56 loci, Processed 56 loci, Skipped 0 loci. Test: Test suite 'Gradle test' produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:21 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:19:21 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test suite 'Gradle test' produced standard out/err: Runtime.totalMemory()=1075838976 Runtime.totalMemory()=1075838976 Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:22 SortSam INFO 2024-07-02 11:19:22 SortSam Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test suite 'Gradle test' produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** SortSam -INPUT /tmp/CollectTargetedMetrics8608586384488273019.bam -OUTPUT /tmp/CollectTargetedMetrics11358391683139703357.bam -SORT_ORDER coordinate ********** SortSam -INPUT /tmp/CollectTargetedMetrics8608586384488273019.bam -OUTPUT /tmp/CollectTargetedMetrics11358391683139703357.bam -SORT_ORDER coordinate Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: 11:19:22.794 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:22.794 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:22.794 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:22.794 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: 11:19:22.795 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:22.795 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:22.795 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:22.795 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:22 GMT+14:00 2024] SortSam INPUT=/tmp/CollectTargetedMetrics8608586384488273019.bam OUTPUT=/tmp/CollectTargetedMetrics11358391683139703357.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:22 GMT+14:00 2024] SortSam INPUT=/tmp/CollectTargetedMetrics8608586384488273019.bam OUTPUT=/tmp/CollectTargetedMetrics11358391683139703357.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:23 SortSam Finished reading inputs, merging and writing to output now. INFO 2024-07-02 11:19:23 SortSam Finished reading inputs, merging and writing to output now. Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:24 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:19:24 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.02 minutes. Test: Test suite 'Gradle test' produced standard out/err: Runtime.totalMemory()=1075838976 Runtime.totalMemory()=1075838976 Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:25 SortSam INFO 2024-07-02 11:19:25 SortSam Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test suite 'Gradle test' produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: ********** SortSam -INPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder6431134366308026252.bam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam -SORT_ORDER coordinate ********** SortSam -INPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder6431134366308026252.bam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam -SORT_ORDER coordinate Test: Test suite 'Gradle test' produced standard out/err: ********** ********** Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: Test: Test suite 'Gradle test' produced standard out/err: 11:19:25.235 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:25.235 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:25.236 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:25.236 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: 11:19:25.236 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:25.236 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test suite 'Gradle test' produced standard out/err: 11:19:25.236 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:25.236 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:25 GMT+14:00 2024] SortSam INPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder6431134366308026252.bam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:25 GMT+14:00 2024] SortSam INPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder6431134366308026252.bam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test suite 'Gradle test' produced standard out/err: INFO 2024-07-02 11:19:25 SortSam Finished reading inputs, merging and writing to output now. INFO 2024-07-02 11:19:25 SortSam Finished reading inputs, merging and writing to output now. Test: Test suite 'Gradle test' produced standard out/err: [Tue Jul 02 11:19:25 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:19:25 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.01 minutes. Test: Test suite 'Gradle test' produced standard out/err: Runtime.totalMemory()=1075838976 Runtime.totalMemory()=1075838976 Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[0](1, 0, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[1](1, 0, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[2](2, 0, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[3](2, 0, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[4](3, 0, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[5](3, 0, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[6](4, 1, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[7](4, 1, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[8](5, 2, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[9](5, 2, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[10](6, 3, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[11](6, 3, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[12](7, 4, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[13](7, 4, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[14](8, 5, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[15](8, 5, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[16](9, 6, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[17](9, 6, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[18](10, 7, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[19](10, 7, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[20](11, 8, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[21](11, 8, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[22](12, 8, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[23](12, 8, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[24](13, 8, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[25](13, 8, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[26](14, 8, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[27](14, 8, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[28](15, 8, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[29](15, 8, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[30](16, 9, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[31](16, 9, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[32](17, 10, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[33](17, 10, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[34](18, 11, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[35](18, 11, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[36](19, 12, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[37](19, 12, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[38](20, 17, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[39](20, 17, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[40](21, 18, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[41](21, 18, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[42](22, 19, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[43](22, 19, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[44](23, 20, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[45](23, 20, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[46](24, 20, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[47](24, 20, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[48](25, 20, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[49](25, 20, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[50](26, 20, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[51](26, 20, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[52](27, 20, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[53](27, 20, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[54](28, 21, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[55](28, 21, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[56](29, 22, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[57](29, 22, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[58](30, 23, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[59](30, 23, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[60](31, 24, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[61](31, 24, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[62](32, 0, false)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionAtReferencePositionIgnoreSoftClips[63](32, 0, true)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionIgnoringSoftClips[0](26S58M62S, 3688, 3827, 0)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionIgnoringSoftClips[1](26S58M62S, 3688, 3665, 4)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionIgnoringSoftClips[2](26S58M62S, 3688, 3660, 0)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionIgnoringSoftClips[3](10S100M2S, 5, 10, 16)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionIgnoringSoftClips[4](10S100M2S, 5, 3, 9)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionIgnoringSoftClips[5](10S100M2S, 10, 12, 13)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testGetReadPositionIgnoringSoftClips[6](10S100M2S, 5, 107, 0)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[0](110, false, 100, 200, 110M, 110M, false, true, 100, 200, 110M, 110M, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, null, null, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[1](110, false, 200, 100, 110M, 110M, true, false, 200, 100, 110M, 110M, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, null, null, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[2](110, false, 100, 200, 110M, 110M, false, true, 100, 200, 110M, 110M, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, null, null, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[3](110, false, 200, 100, 110M, 110M, true, false, 200, 100, 110M, 110M, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, null, null, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[4](110, false, 100, 300, 110M, 110M, false, true, 100, 300, 110M, 110M, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, null, null, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[5](110, false, 300, 100, 110M, 110M, true, false, 300, 100, 110M, 110M, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, null, null, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[6](110, false, 100, 300, 110M, 110M, false, true, 100, 300, 110M, 110M, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, null, null, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[7](110, false, 300, 100, 110M, 110M, true, false, 300, 100, 110M, 110M, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, null, null, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[8](110, false, 100, 210, 110M, 110M, true, false, 100, 210, 110M, 110M, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, null, null, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[9](110, false, 210, 100, 110M, 110M, false, true, 210, 100, 110M, 110M, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, null, null, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[10](110, false, 100, 210, 110M, 110M, true, false, 100, 210, 110M, 110M, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, null, null, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[11](110, false, 210, 100, 110M, 110M, false, true, 210, 100, 110M, 110M, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, null, null, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[12](110, false, 100, 210, 110M, 110M, false, true, 100, 210, 110M, 110M, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, null, null, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[13](110, false, 210, 100, 110M, 110M, true, false, 210, 100, 110M, 110M, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, null, null, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[14](110, false, 100, 210, 110M, 110M, false, true, 100, 210, 110M, 110M, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, null, null, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[15](110, false, 210, 100, 110M, 110M, true, false, 210, 100, 110M, 110M, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, null, null, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[16](110, false, 100, 209, 110M, 110M, true, false, 209, 209, 109S1M, 1M109S, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, null, null, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[17](110, false, 209, 100, 110M, 110M, false, true, 209, 209, 1M109S, 109S1M, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, null, null, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[18](110, true, 100, 209, 110M, 110M, true, false, 209, 209, 109H1M, 1M109H, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, T, G, GGAGAATCTGGTCAGCCACTGCAGCCTCCTGAGATATTTTTAGAGACTGGACCTGAGGCCTCTGGAGGCTACTGATGATGCCTGCTGTGAACGCAGACACTGGTGTGAT, CCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, F, F, FF.FFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[19](110, true, 209, 100, 110M, 110M, false, true, 209, 209, 1M109H, 109H1M, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, G, T, CCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, GGAGAATCTGGTCAGCCACTGCAGCCTCCTGAGATATTTTTAGAGACTGGACCTGAGGCCTCTGGAGGCTACTGATGATGCCTGCTGTGAACGCAGACACTGGTGTGAT, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, F, F, FFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FF.FFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[20](110, true, 100, 200, 110M, 110M, false, true, 100, 200, 110M, 110M, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, null, null, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[21](110, true, 200, 100, 110M, 110M, true, false, 200, 100, 110M, 110M, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, null, null, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[22](110, false, 100, 200, 110M, 110M, false, false, 100, 200, 110M, 110M, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, null, null, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[23](110, false, 200, 100, 110M, 110M, false, false, 200, 100, 110M, 110M, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, null, null, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[24](110, true, 100, 200, 110M, 110M, false, false, 100, 200, 110M, 110M, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, null, null, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[25](110, true, 200, 100, 110M, 110M, false, false, 200, 100, 110M, 110M, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, null, null, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[26](110, false, 100, 200, 110M, 110M, true, true, 100, 200, 110M, 110M, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, null, null, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[27](110, false, 200, 100, 110M, 110M, true, true, 200, 100, 110M, 110M, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, null, null, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[28](110, true, 100, 200, 110M, 110M, true, true, 100, 200, 110M, 110M, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, null, null, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[29](110, true, 200, 100, 110M, 110M, true, true, 200, 100, 110M, 110M, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, null, null, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[30](110, false, 100, 300, 110M, 110M, true, false, 100, 300, 110M, 110M, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, null, null, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[31](110, false, 300, 100, 110M, 110M, false, true, 300, 100, 110M, 110M, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, null, null, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[32](110, true, 100, 300, 110M, 110M, true, false, 100, 300, 110M, 110M, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, null, null, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[33](110, true, 300, 100, 110M, 110M, false, true, 300, 100, 110M, 110M, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, null, null, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[34](110, false, 100, 90, 110M, 110M, false, true, 100, 100, 100M10S, 10S100M, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, null, null, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[35](110, false, 90, 100, 110M, 110M, true, false, 100, 100, 10S100M, 100M10S, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, null, null, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[36](110, true, 100, 90, 110M, 110M, false, true, 100, 100, 100M10H, 10H100M, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, AGATTCTCCT, TGTGCCCGGC, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FF.FFF.FFF, FFF.FFFFFF)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[37](110, true, 90, 100, 110M, 110M, true, false, 100, 100, 10H100M, 100M10H, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, TGTGCCCGGC, AGATTCTCCT, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFF.FFFFFF, FF.FFF.FFF)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[38](120, false, 100, 95, 110M10S5H, 5H15S105M, false, true, 100, 100, 100M20S5H, 5H20S100M, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCTGTCAGTTTGC, CGTTGGCAATGCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCTGTCAGTTTGC, CGTTGGCAATGCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, null, null, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF.FFF, FFFFFF.FFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF.FFF, FFFFFF.FFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[39](120, false, 95, 100, 5H15S105M, 110M10S5H, true, false, 100, 100, 5H20S100M, 100M20S5H, CGTTGGCAATGCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCTGTCAGTTTGC, CGTTGGCAATGCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCTGTCAGTTTGC, null, null, FFFFFF.FFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF.FFF, FFFFFF.FFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF.FFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[40](120, true, 100, 95, 110M10S5H, 5H15S105M, false, true, 100, 100, 100M25H, 25H100M, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCTGTCAGTTTGC, CGTTGGCAATGCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, AGATTCTCCTGTCAGTTTGC, TGTGCCCGGCATTGCCAACG, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF.FFF, FFFFFF.FFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFF.FFF.FFF.FFF, FFFFFFF.FFFFF.FFFFFF)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[41](120, true, 95, 100, 5H15S105M, 110M10S5H, true, false, 100, 100, 25H100M, 100M25H, CGTTGGCAATGCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCTGTCAGTTTGC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, TGTGCCCGGCATTGCCAACG, AGATTCTCCTGTCAGTTTGC, FFFFFF.FFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF.FFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFF.FFFFF.FFFFFF, FFFFFFFF.FFF.FFF.FFF)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[42](120, false, 100, 95, 110M10S, 15S105M, false, true, 100, 100, 100M20S, 20S100M, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCTGTCAGTTTGC, CGTTGGCAATGCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCTGTCAGTTTGC, CGTTGGCAATGCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, null, null, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF.FFF, FFFFFF.FFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF.FFF, FFFFFF.FFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[43](120, false, 95, 100, 15S105M, 110M10S, true, false, 100, 100, 20S100M, 100M20S, CGTTGGCAATGCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCTGTCAGTTTGC, CGTTGGCAATGCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCTGTCAGTTTGC, null, null, FFFFFF.FFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF.FFF, FFFFFF.FFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF.FFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[44](120, true, 100, 95, 110M10S, 15S105M, false, true, 100, 100, 100M20H, 20H100M, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCTGTCAGTTTGC, CGTTGGCAATGCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, AGATTCTCCTGTCAGTTTGC, TGTGCCCGGCATTGCCAACG, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF.FFF, FFFFFF.FFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFF.FFF.FFF.FFF, FFFFFFF.FFFFF.FFFFFF)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[45](120, true, 95, 100, 15S105M, 110M10S, true, false, 100, 100, 20H100M, 100M20H, CGTTGGCAATGCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCTGTCAGTTTGC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, TGTGCCCGGCATTGCCAACG, AGATTCTCCTGTCAGTTTGC, FFFFFF.FFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF.FFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFF.FFFFF.FFFFFF, FFFFFFFF.FFF.FFF.FFF)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[46](120, true, 100, 95, 95M25S, 15S105M, false, true, 100, 100, 95M5S20H, 20H100M, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCTGTCAGTTTGC, CGTTGGCAATGCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, AGATTCTCCTGTCAGTTTGC, TGTGCCCGGCATTGCCAACG, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF.FFF, FFFFFF.FFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFF.FFF.FFF.FFF, FFFFFFF.FFFFF.FFFFFF)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[47](120, true, 95, 100, 15S105M, 95M25S, true, false, 100, 100, 20H100M, 95M5S20H, CGTTGGCAATGCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCTGTCAGTTTGC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, TGTGCCCGGCATTGCCAACG, AGATTCTCCTGTCAGTTTGC, FFFFFF.FFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF.FFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFF.FFFFF.FFFFFF, FFFFFFFF.FFF.FFF.FFF)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[48](110, false, 105, 90, 5S105M, 103M7S, false, true, 105, 105, 5S88M17S, 15S88M7S, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, null, null, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[49](110, false, 90, 105, 103M7S, 5S105M, true, false, 105, 105, 15S88M7S, 5S88M17S, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, null, null, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[50](110, true, 105, 90, 5S105M, 103M7S, false, true, 105, 105, 5S88M7S10H, 10H5S88M7S, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, AGATTCTCCT, TGTGCCCGGC, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FF.FFF.FFF, FFF.FFFFFF)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[51](110, true, 90, 105, 103M7S, 5S105M, true, false, 105, 105, 10H5S88M7S, 5S88M7S10H, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, TGTGCCCGGC, AGATTCTCCT, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFF.FFFFFF, FF.FFF.FFF)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[52](110, false, 105, 100, 10S100M, 10S95M5S, false, true, 105, 105, 10S90M10S, 15S90M5S, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, null, null, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[53](110, false, 100, 105, 10S95M5S, 10S100M, true, false, 105, 105, 15S90M5S, 10S90M10S, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, null, null, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[54](110, true, 105, 100, 10S100M, 10S95M5S, false, true, 105, 105, 10S90M5S5H, 5H10S90M5S, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATT, GCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, CTCCT, CCGGC, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FF, F.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, F.FFF, FFFFF)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[55](110, true, 100, 105, 10S95M5S, 10S100M, true, false, 105, 105, 5H10S90M5S, 10S90M5S5H, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATT, CCGGC, CTCCT, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, F.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FF, FFFFF, F.FFF)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[56](110, false, 105, 100, 10S100M, 103M7S, false, true, 105, 105, 10S98M2S, 5S98M7S, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, null, null, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[57](110, false, 100, 105, 103M7S, 10S100M, true, false, 105, 105, 5S98M7S, 10S98M2S, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, null, null, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[58](110, false, 105, 100, 10S100M, 103M7S, false, true, 105, 105, 10S98M2S, 5S98M7S, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, null, null, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[59](110, false, 100, 105, 103M7S, 10S100M, true, false, 105, 105, 5S98M7S, 10S98M2S, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, null, null, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[60](110, false, 105, 100, 10S97M3S, 99M11S, false, true, 105, 105, 10S94M6S, 5S94M11S, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, null, null, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[61](110, false, 100, 105, 99M11S, 10S97M3S, true, false, 105, 105, 5S94M11S, 10S94M6S, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, null, null, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[62](110, false, 105, 100, 10S97M3S, 99M11S, false, true, 105, 105, 10S94M6S, 5S94M11S, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, null, null, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[63](110, false, 100, 105, 99M11S, 10S97M3S, true, false, 105, 105, 5S94M11S, 10S94M6S, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, null, null, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[64](110, false, 105, 96, 12S80M18S, 13S97M, false, true, 105, 105, 12S80M18S, 22S88M, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, null, null, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[65](110, false, 96, 105, 13S97M, 12S80M18S, true, false, 105, 105, 22S88M, 12S80M18S, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, null, null, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[66](110, true, 105, 96, 12S80M18S, 13S97M, false, true, 105, 105, 12S80M8S10H, 10H12S88M, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, AGATTCTCCT, TGTGCCCGGC, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FF.FFF.FFF, FFF.FFFFFF)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[67](110, true, 96, 105, 13S97M, 12S80M18S, true, false, 105, 105, 10H12S88M, 12S80M8S10H, GCCGGGCACAATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACCAGATTCTCCT, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, ATCACACCAGTGTCTGCGTTCACAGCAGGCATCATCAGTAGCCTCCAGAGGCCTCAGGTCCAGTCTCTAAAAATATCTCAGGAGGCTGCAGTGGCTGACC, TGTGCCCGGC, AGATTCTCCT, FFFFFF.FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.FFF.FFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF, FFF.FFFFFF, FF.FFF.FFF)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[68](27, false, 18, 14, 18M9S, 8S3M1D16M, false, true, 18, 18, 16M11S, 11S16M, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, null, null, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[69](27, false, 14, 18, 8S3M1D16M, 18M9S, true, false, 18, 18, 11S16M, 16M11S, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, null, null, abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[70](27, false, 18, 12, 18M9S, 8S3M3D16M, false, true, 18, 18, 16M11S, 11S16M, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, null, null, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[71](27, false, 12, 18, 8S3M3D16M, 18M9S, true, false, 18, 18, 11S16M, 16M11S, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, null, null, abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[72](27, false, 14, 18, 8S19M, 15M1D3M9S, true, false, 18, 18, 12S15M, 15M12S, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, null, null, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[73](27, false, 18, 14, 15M1D3M9S, 8S19M, false, true, 18, 18, 15M12S, 12S15M, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, null, null, abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[74](27, false, 14, 18, 8S19M, 15M3D3M9S, true, false, 18, 18, 12S15M, 15M12S, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, null, null, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[75](27, false, 18, 14, 15M3D3M9S, 8S19M, false, true, 18, 18, 15M12S, 12S15M, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, null, null, abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[76](27, false, 14, 18, 8S19M, 14M3D4M9S, true, false, 18, 18, 12S15M, 14M13S, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, null, null, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[77](27, false, 18, 14, 14M3D4M9S, 8S19M, false, true, 18, 18, 14M13S, 12S15M, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, null, null, abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[78](27, false, 14, 6, 8S19M, 27M1D, true, false, 14, 6, 8S19M, 27M1D, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, null, null, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[79](27, false, 6, 14, 27M1D, 8S19M, false, true, 6, 14, 27M1D, 8S19M, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, null, null, abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[80](27, false, 18, 15, 18M9S, 5S2M2I18M, false, true, 18, 18, 17M10S, 10S17M, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, null, null, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[81](27, false, 15, 18, 5S2M2I18M, 18M9S, true, false, 18, 18, 10S17M, 17M10S, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, null, null, abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[82](27, false, 14, 18, 7S20M, 17M2I1M7S, true, false, 18, 18, 11S16M, 16M11S, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, null, null, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[83](27, false, 18, 14, 17M2I1M7S, 7S20M, false, true, 18, 18, 16M11S, 11S16M, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, null, null, abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[84](27, false, 14, 18, 7S20M, 16M2I2M7S, true, false, 18, 18, 11S16M, 16M11S, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, null, null, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[85](27, false, 18, 14, 16M2I2M7S, 7S20M, false, true, 18, 18, 16M11S, 11S16M, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, null, null, abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[86](27, false, 14, 18, 7S20M, 16M1I3M7S, true, false, 18, 18, 11S16M, 16M11S, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, null, null, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[87](27, false, 18, 14, 16M1I3M7S, 7S20M, false, true, 18, 18, 16M11S, 11S16M, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, null, null, abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[88](27, false, 14, 18, 7S20M, 17M2I2M6S, true, false, 18, 18, 11S16M, 16M11S, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, null, null, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[89](27, false, 18, 14, 17M2I2M6S, 7S20M, false, true, 18, 18, 16M11S, 11S16M, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, null, null, abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[90](27, true, 18, 14, 18M9S, 8S3M1D16M, false, true, 18, 18, 16M11H, 11H16M, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCC, GATTCTCCTCTTGTGC, CGGCAGATTCT, TGCCGGGCACA, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOP, lmnopqrstuvwxyz,, QRSTUVWXYZ., kjihgfedcba)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[91](27, true, 14, 18, 8S3M1D16M, 18M9S, true, false, 18, 18, 11H16M, 16M11H, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, GATTCTCCTCTTGTGC, AGATTCTCCTTGTGCC, TGCCGGGCACA, CGGCAGATTCT, abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., lmnopqrstuvwxyz,, ABCDEFGHIJKLMNOP, kjihgfedcba, QRSTUVWXYZ.)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[92](27, true, 18, 12, 18M9S, 8S3M3D16M, false, true, 18, 18, 16M11H, 11H16M, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCC, GATTCTCCTCTTGTGC, CGGCAGATTCT, TGCCGGGCACA, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOP, lmnopqrstuvwxyz,, QRSTUVWXYZ., kjihgfedcba)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[93](27, true, 12, 18, 8S3M3D16M, 18M9S, true, false, 18, 18, 11H16M, 16M11H, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, GATTCTCCTCTTGTGC, AGATTCTCCTTGTGCC, TGCCGGGCACA, CGGCAGATTCT, abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., lmnopqrstuvwxyz,, ABCDEFGHIJKLMNOP, kjihgfedcba, QRSTUVWXYZ.)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[94](27, true, 14, 18, 8S19M, 15M1D3M9S, true, false, 18, 18, 12H15M, 15M12H, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, TGCCCGGCAGATTCT, TGTGCCCGGCAGATT, CAAGGAGAATCT, CTCCTCTTGTGC, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, MNOPQRSTUVWXYZ., abcdefghijklmno, LKJIHGFEDCBA, pqrstuvwxyz,)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[95](27, true, 18, 14, 15M1D3M9S, 8S19M, false, true, 18, 18, 15M12H, 12H15M, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATT, TGCCCGGCAGATTCT, CTCCTCTTGTGC, CAAGGAGAATCT, abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmno, MNOPQRSTUVWXYZ., pqrstuvwxyz,, LKJIHGFEDCBA)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[96](27, true, 14, 18, 8S19M, 15M3D3M9S, true, false, 18, 18, 12H15M, 15M12H, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, TGCCCGGCAGATTCT, TGTGCCCGGCAGATT, CAAGGAGAATCT, CTCCTCTTGTGC, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, MNOPQRSTUVWXYZ., abcdefghijklmno, LKJIHGFEDCBA, pqrstuvwxyz,)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[97](27, true, 18, 14, 15M3D3M9S, 8S19M, false, true, 18, 18, 15M12H, 12H15M, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATT, TGCCCGGCAGATTCT, CTCCTCTTGTGC, CAAGGAGAATCT, abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmno, MNOPQRSTUVWXYZ., pqrstuvwxyz,, LKJIHGFEDCBA)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[98](27, true, 14, 18, 8S19M, 14M3D4M9S, true, false, 18, 18, 12H15M, 14M1S12H, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, TGCCCGGCAGATTCT, TGTGCCCGGCAGATT, CAAGGAGAATCT, CTCCTCTTGTGC, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, MNOPQRSTUVWXYZ., abcdefghijklmno, LKJIHGFEDCBA, pqrstuvwxyz,)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[99](27, true, 18, 14, 14M3D4M9S, 8S19M, false, true, 18, 18, 14M1S12H, 12H15M, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATT, TGCCCGGCAGATTCT, CTCCTCTTGTGC, CAAGGAGAATCT, abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmno, MNOPQRSTUVWXYZ., pqrstuvwxyz,, LKJIHGFEDCBA)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[100](27, true, 14, 6, 8S19M, 27M1D, true, false, 14, 6, 8S19M, 27M1D, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, null, null, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[101](27, true, 6, 14, 27M1D, 8S19M, false, true, 6, 14, 27M1D, 8S19M, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, null, null, abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., null, null)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[102](27, true, 18, 15, 18M9S, 5S2M2I18M, false, true, 18, 18, 17M10H, 10H17M, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCC, AGATTCTCCTCTTGTGC, GGCAGATTCT, GCCGGGCACA, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQ, klmnopqrstuvwxyz,, RSTUVWXYZ., jihgfedcba)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[103](27, true, 15, 18, 5S2M2I18M, 18M9S, true, false, 18, 18, 10H17M, 17M10H, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, AGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCC, GCCGGGCACA, GGCAGATTCT, abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., klmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQ, jihgfedcba, RSTUVWXYZ.)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[104](27, true, 14, 18, 7S20M, 17M2I1M7S, true, false, 18, 18, 11H16M, 16M11H, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, GTGCCCGGCAGATTCT, TGTGCCCGGCAGATTC, AAGGAGAATCT, TCCTCTTGTGC, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, LMNOPQRSTUVWXYZ., abcdefghijklmnop, KJIHGFEDCBA, qrstuvwxyz,)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[105](27, true, 18, 14, 17M2I1M7S, 7S20M, false, true, 18, 18, 16M11H, 11H16M, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTC, GTGCCCGGCAGATTCT, TCCTCTTGTGC, AAGGAGAATCT, abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnop, LMNOPQRSTUVWXYZ., qrstuvwxyz,, KJIHGFEDCBA)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[106](27, true, 14, 18, 7S20M, 16M2I2M7S, true, false, 18, 18, 11H16M, 16M11H, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, GTGCCCGGCAGATTCT, TGTGCCCGGCAGATTC, AAGGAGAATCT, TCCTCTTGTGC, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, LMNOPQRSTUVWXYZ., abcdefghijklmnop, KJIHGFEDCBA, qrstuvwxyz,)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[107](27, true, 18, 14, 16M2I2M7S, 7S20M, false, true, 18, 18, 16M11H, 11H16M, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTC, GTGCCCGGCAGATTCT, TCCTCTTGTGC, AAGGAGAATCT, abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnop, LMNOPQRSTUVWXYZ., qrstuvwxyz,, KJIHGFEDCBA)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[108](27, true, 14, 18, 7S20M, 16M1I3M7S, true, false, 18, 18, 11H16M, 16M11H, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, GTGCCCGGCAGATTCT, TGTGCCCGGCAGATTC, AAGGAGAATCT, TCCTCTTGTGC, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, LMNOPQRSTUVWXYZ., abcdefghijklmnop, KJIHGFEDCBA, qrstuvwxyz,)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[109](27, true, 18, 14, 16M1I3M7S, 7S20M, false, true, 18, 18, 16M11H, 11H16M, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTC, GTGCCCGGCAGATTCT, TCCTCTTGTGC, AAGGAGAATCT, abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnop, LMNOPQRSTUVWXYZ., qrstuvwxyz,, KJIHGFEDCBA)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[110](27, true, 14, 18, 7S20M, 17M2I2M6S, true, false, 18, 18, 11H16M, 16M11H, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTCTCCTCTTGTGC, GTGCCCGGCAGATTCT, TGTGCCCGGCAGATTC, AAGGAGAATCT, TCCTCTTGTGC, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnopqrstuvwxyz,, LMNOPQRSTUVWXYZ., abcdefghijklmnop, KJIHGFEDCBA, qrstuvwxyz,)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testOverlappedReadClipping[111](27, true, 18, 14, 17M2I2M6S, 7S20M, false, true, 18, 18, 16M11H, 11H16M, TGTGCCCGGCAGATTCTCCTCTTGTGC, AGATTCTCCTTGTGCCCGGCAGATTCT, TGTGCCCGGCAGATTC, GTGCCCGGCAGATTCT, TCCTCTTGTGC, AAGGAGAATCT, abcdefghijklmnopqrstuvwxyz,, ABCDEFGHIJKLMNOPQRSTUVWXYZ., abcdefghijklmnop, LMNOPQRSTUVWXYZ., qrstuvwxyz,, KJIHGFEDCBA)(picard.sam.AbstractAlignmentMergerTest) Running Test: Test method testUnmapBacterialContamination(picard.sam.AbstractAlignmentMergerTest) Test: Test method testUnmapBacterialContamination(picard.sam.AbstractAlignmentMergerTest) produced standard out/err: INFO 2024-07-02 11:19:27 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned1267043563093013879.sam] Gradle suite > Gradle test > picard.sam.AbstractAlignmentMergerTest.testUnmapBacterialContamination STANDARD_ERROR INFO 2024-07-02 11:19:27 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned1267043563093013879.sam] Test: Test method testUnmapBacterialContamination(picard.sam.AbstractAlignmentMergerTest) produced standard out/err: INFO 2024-07-02 11:19:27 AbstractAlignmentMerger Wrote 0 alignment records and 10 unmapped reads. INFO 2024-07-02 11:19:27 AbstractAlignmentMerger Wrote 0 alignment records and 10 unmapped reads. Running Test: Test method invalidFileNamesTest[0](whatever.locs)(picard.illumina.parser.readers.AbstractIlluminaPositionFileReaderTest) Running Test: Test method invalidFileNamesTest[1](whatever.clocs)(picard.illumina.parser.readers.AbstractIlluminaPositionFileReaderTest) Running Test: Test method invalidFileNamesTest[2](whatever.pos)(picard.illumina.parser.readers.AbstractIlluminaPositionFileReaderTest) Running Test: Test method invalidFileNamesTest[3](s_1.clocs)(picard.illumina.parser.readers.AbstractIlluminaPositionFileReaderTest) Running Test: Test method invalidFileNamesTest[4](s__2.clocs)(picard.illumina.parser.readers.AbstractIlluminaPositionFileReaderTest) Running Test: Test method invalidFileNamesTest[5](s_1_4.Notclocs)(picard.illumina.parser.readers.AbstractIlluminaPositionFileReaderTest) Running Test: Test method invalidFileNamesTest[6](a_1_4.pos)(picard.illumina.parser.readers.AbstractIlluminaPositionFileReaderTest) Running Test: Test method invalidFileNamesTest[7](a_1_4.pos.txt)(picard.illumina.parser.readers.AbstractIlluminaPositionFileReaderTest) Running Test: Test method invalidReaderTest[0]([F@7708875d, [F@cc68af3)(picard.illumina.parser.readers.AbstractIlluminaPositionFileReaderTest) Running Test: Test method invalidReaderTest[1]([F@6b22cdee, [F@4589d97b)(picard.illumina.parser.readers.AbstractIlluminaPositionFileReaderTest) Running Test: Test method invalidReaderTest[2]([F@74e82f2f, [F@9d8d1e1)(picard.illumina.parser.readers.AbstractIlluminaPositionFileReaderTest) Running Test: Test method invalidReaderTest[3]([F@5747ef5b, [F@62e323cb)(picard.illumina.parser.readers.AbstractIlluminaPositionFileReaderTest) Running Test: Test method invalidReaderTest[4]([F@23f92b33, [F@4bac2520)(picard.illumina.parser.readers.AbstractIlluminaPositionFileReaderTest) Running Test: Test method iteratorRemoveTest(picard.illumina.parser.readers.AbstractIlluminaPositionFileReaderTest) Running Test: Test method validReaderTest(picard.illumina.parser.readers.AbstractIlluminaPositionFileReaderTest) Running Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:27 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testBulkFragmentsNoDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:19:27 MarkDuplicates Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.14371216183989848508.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14371216183989848508.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14371216183989848508.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.14371216183989848508.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14371216183989848508.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14371216183989848508.tmp/output.sam Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:27.737 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:27.737 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:27.737 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:27.737 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:27.738 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:27.738 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:27.738 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:27.738 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:27 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.14371216183989848508.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.14371216183989848508.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.14371216183989848508.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:27 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.14371216183989848508.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.14371216183989848508.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.14371216183989848508.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:27 MarkDuplicates Start of doWork freeMemory: 1020720856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:27 MarkDuplicates Start of doWork freeMemory: 1020720856; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:27 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:19:27 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:27 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:19:27 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:19:27 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:19:27 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:28 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2024-07-02 11:19:28 MarkDuplicates Read 10000 records. 0 pairs never matched. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 957648376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 957648376; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:19:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:28 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:19:28 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:28 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:19:28 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:28 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:19:28 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 751798184; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:19:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 751798184; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:28 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:19:28 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:28 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:19:28 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:28 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:19:28 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:28 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:19:28 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:28 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:19:28 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:28 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:19:28 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:29 MarkDuplicates Before output close freeMemory: 768385648; totalMemory: 1090519040; maxMemory: 2147483648 INFO 2024-07-02 11:19:29 MarkDuplicates Before output close freeMemory: 768385648; totalMemory: 1090519040; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:29 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:19:29 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:29 MarkDuplicates After output close freeMemory: 762093696; totalMemory: 1084227584; maxMemory: 2147483648 INFO 2024-07-02 11:19:29 MarkDuplicates After output close freeMemory: 762093696; totalMemory: 1084227584; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:19:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:29 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testBulkFragmentsNoDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:19:29 MarkDuplicates Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11688854920182838274.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11688854920182838274.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11688854920182838274.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11688854920182838274.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11688854920182838274.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11688854920182838274.tmp/output.sam Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:29.517 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:29.517 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:29.517 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:29.517 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:29.518 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:29.518 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:29.518 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:29.518 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:29 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11688854920182838274.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11688854920182838274.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11688854920182838274.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:29 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11688854920182838274.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11688854920182838274.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11688854920182838274.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:29 MarkDuplicates Start of doWork freeMemory: 1021208936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:29 MarkDuplicates Start of doWork freeMemory: 1021208936; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:29 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:19:29 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:29 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:19:29 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:19:29 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:19:29 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:29 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2024-07-02 11:19:29 MarkDuplicates Read 10000 records. 0 pairs never matched. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 957502648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 957502648; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:19:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:30 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:19:30 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:30 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:19:30 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:30 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:19:30 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 482300920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 482300920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:30 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:19:30 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:30 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:19:30 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:30 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:19:30 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:30 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:19:30 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:30 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:19:30 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:30 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:19:30 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:30 MarkDuplicates Before output close freeMemory: 751505104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:30 MarkDuplicates Before output close freeMemory: 751505104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:30 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:19:30 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:30 MarkDuplicates After output close freeMemory: 751570816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:30 MarkDuplicates After output close freeMemory: 751570816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:30 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:19:30 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:32 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testBulkFragmentsNoDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:19:32 MarkDuplicates Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6705896081807019397.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6705896081807019397.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6705896081807019397.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester7700576201601875683/input.fasta ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6705896081807019397.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6705896081807019397.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6705896081807019397.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester7700576201601875683/input.fasta Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:32.039 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:32.039 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:32.040 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:32.040 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:32.040 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:32.040 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:32.041 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:32.041 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:32 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6705896081807019397.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6705896081807019397.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6705896081807019397.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester7700576201601875683/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:32 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6705896081807019397.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6705896081807019397.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6705896081807019397.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester7700576201601875683/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:32 MarkDuplicates Start of doWork freeMemory: 1021093528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:32 MarkDuplicates Start of doWork freeMemory: 1021093528; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:32 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:19:32 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:32 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:19:32 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:19:32 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:19:32 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:32 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2024-07-02 11:19:32 MarkDuplicates Read 10000 records. 0 pairs never matched. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 957505088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 957505088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:19:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:19:33 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:19:33 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:33 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:19:33 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 482172600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 482172600; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:33 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:19:33 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:33 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:19:33 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:33 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:19:33 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:33 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:19:33 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:33 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:19:33 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:33 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:19:33 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:33 MarkDuplicates Before output close freeMemory: 743835720; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:33 MarkDuplicates Before output close freeMemory: 743835720; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:33 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:19:33 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:34 MarkDuplicates After output close freeMemory: 743311464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:34 MarkDuplicates After output close freeMemory: 743311464; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:19:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:34 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testBulkFragmentsWithDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:19:34 MarkDuplicates Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17600613596982418252.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17600613596982418252.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17600613596982418252.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17600613596982418252.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17600613596982418252.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17600613596982418252.tmp/output.sam Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:34.378 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:34.378 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:34.379 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:34.379 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:34.382 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:34.382 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:34.382 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:34.382 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:34 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17600613596982418252.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17600613596982418252.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17600613596982418252.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:34 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17600613596982418252.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17600613596982418252.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17600613596982418252.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:34 MarkDuplicates Start of doWork freeMemory: 1012950296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:34 MarkDuplicates Start of doWork freeMemory: 1012950296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:34 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:19:34 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:34 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:19:34 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:19:34 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:19:34 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:35 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2024-07-02 11:19:35 MarkDuplicates Read 21000 records. 0 pairs never matched. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 948520440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 948520440; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:19:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:35 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:19:35 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:35 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:19:35 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:35 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:19:35 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 743463112; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:19:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 743463112; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:35 MarkDuplicates Marking 20000 records as duplicates. INFO 2024-07-02 11:19:35 MarkDuplicates Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:35 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:19:35 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:35 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:19:35 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:35 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:19:35 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:35 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:19:35 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:35 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:19:35 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:35 MarkDuplicates Before output close freeMemory: 781023568; totalMemory: 1111490560; maxMemory: 2147483648 INFO 2024-07-02 11:19:35 MarkDuplicates Before output close freeMemory: 781023568; totalMemory: 1111490560; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:35 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:19:35 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:36 MarkDuplicates After output close freeMemory: 777877416; totalMemory: 1108344832; maxMemory: 2147483648 INFO 2024-07-02 11:19:36 MarkDuplicates After output close freeMemory: 777877416; totalMemory: 1108344832; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:36 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:19:36 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1108344832 Runtime.totalMemory()=1108344832 Running Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:36 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testBulkFragmentsWithDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:19:36 MarkDuplicates Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6387967451509304332.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6387967451509304332.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6387967451509304332.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6387967451509304332.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6387967451509304332.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6387967451509304332.tmp/output.sam Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:36.844 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:36.844 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:36.844 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:36.844 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:36.845 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:36.845 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:36.845 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:36.845 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:36 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6387967451509304332.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6387967451509304332.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6387967451509304332.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:36 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6387967451509304332.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6387967451509304332.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6387967451509304332.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:36 MarkDuplicates Start of doWork freeMemory: 1012885928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:36 MarkDuplicates Start of doWork freeMemory: 1012885928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:36 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:19:36 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:36 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:19:36 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:19:37 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:19:37 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:37 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2024-07-02 11:19:37 MarkDuplicates Read 21000 records. 0 pairs never matched. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 947863104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 947863104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:19:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:19:37 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:19:37 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:37 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:19:37 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 743461696; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:19:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 743461696; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:38 MarkDuplicates Marking 20000 records as duplicates. INFO 2024-07-02 11:19:38 MarkDuplicates Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:38 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:19:38 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:38 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:19:38 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:38 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:19:38 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:38 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:19:38 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:38 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:19:38 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:38 MarkDuplicates Before output close freeMemory: 788277528; totalMemory: 1118830592; maxMemory: 2147483648 INFO 2024-07-02 11:19:38 MarkDuplicates Before output close freeMemory: 788277528; totalMemory: 1118830592; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:38 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:19:38 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:38 MarkDuplicates After output close freeMemory: 788417376; totalMemory: 1118830592; maxMemory: 2147483648 INFO 2024-07-02 11:19:38 MarkDuplicates After output close freeMemory: 788417376; totalMemory: 1118830592; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:38 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:19:38 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1118830592 Runtime.totalMemory()=1118830592 Running Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:40 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testBulkFragmentsWithDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:19:40 MarkDuplicates Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3718513565390957036.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3718513565390957036.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3718513565390957036.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester12350746203134884452/input.fasta ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3718513565390957036.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3718513565390957036.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3718513565390957036.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester12350746203134884452/input.fasta Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:40.056 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:40.056 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:40.057 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:40.057 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:40.057 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:40.057 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:40.057 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:40.057 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:40 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3718513565390957036.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3718513565390957036.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3718513565390957036.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester12350746203134884452/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:40 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3718513565390957036.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3718513565390957036.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3718513565390957036.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester12350746203134884452/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:40 MarkDuplicates Start of doWork freeMemory: 1012948048; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:40 MarkDuplicates Start of doWork freeMemory: 1012948048; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:40 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:19:40 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:40 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:19:40 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:19:40 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:19:40 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:41 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2024-07-02 11:19:41 MarkDuplicates Read 21000 records. 0 pairs never matched. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 947990984; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 947990984; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:19:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:19:41 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:19:41 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:41 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:19:41 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 743458384; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:19:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 743458384; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:41 MarkDuplicates Marking 20000 records as duplicates. INFO 2024-07-02 11:19:41 MarkDuplicates Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:41 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:19:41 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:19:41 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:42 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:19:42 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:42 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:19:42 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:42 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:19:42 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:42 MarkDuplicates Before output close freeMemory: 788405680; totalMemory: 1118830592; maxMemory: 2147483648 INFO 2024-07-02 11:19:42 MarkDuplicates Before output close freeMemory: 788405680; totalMemory: 1118830592; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:42 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:19:42 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:42 MarkDuplicates After output close freeMemory: 784930944; totalMemory: 1115684864; maxMemory: 2147483648 INFO 2024-07-02 11:19:42 MarkDuplicates After output close freeMemory: 784930944; totalMemory: 1115684864; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:19:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1115684864 Runtime.totalMemory()=1115684864 Running Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:43 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testBulkPairsNoDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:19:43 MarkDuplicates Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6319223351080813417.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6319223351080813417.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6319223351080813417.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6319223351080813417.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6319223351080813417.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6319223351080813417.tmp/output.sam Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:43.346 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:43.346 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:43.346 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:43.346 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:43.346 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:43.346 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:43.347 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:43.347 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:43 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6319223351080813417.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6319223351080813417.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6319223351080813417.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:43 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6319223351080813417.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6319223351080813417.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6319223351080813417.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:43 MarkDuplicates Start of doWork freeMemory: 1011904616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:43 MarkDuplicates Start of doWork freeMemory: 1011904616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:43 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:19:43 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:43 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:19:43 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:19:43 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:19:43 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:44 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2024-07-02 11:19:44 MarkDuplicates Read 20200 records. 0 pairs never matched. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 947328712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 947328712; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:19:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:19:44 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:44 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:19:44 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:44 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:19:44 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 473456136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 473456136; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:44 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:19:44 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:44 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:19:44 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:44 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:19:44 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:44 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:19:44 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:44 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:19:44 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:44 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:19:44 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:44 MarkDuplicates Before output close freeMemory: 742799288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:44 MarkDuplicates Before output close freeMemory: 742799288; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:44 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:19:44 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:45 MarkDuplicates After output close freeMemory: 742474584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:45 MarkDuplicates After output close freeMemory: 742474584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:19:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:45 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testBulkPairsNoDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:19:45 MarkDuplicates Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.18112769707495474192.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.18112769707495474192.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.18112769707495474192.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.18112769707495474192.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.18112769707495474192.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.18112769707495474192.tmp/output.sam Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:45.631 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:45.631 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:45.631 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:45.631 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:45.631 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:45.631 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:45.632 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:45.632 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:45 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.18112769707495474192.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.18112769707495474192.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.18112769707495474192.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:45 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.18112769707495474192.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.18112769707495474192.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.18112769707495474192.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:45 MarkDuplicates Start of doWork freeMemory: 1012360448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:45 MarkDuplicates Start of doWork freeMemory: 1012360448; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:45 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:19:45 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:45 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:19:45 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:19:45 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:19:45 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:46 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2024-07-02 11:19:46 MarkDuplicates Read 20200 records. 0 pairs never matched. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 947195480; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 947195480; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:19:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:46 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:19:46 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:46 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:19:46 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:46 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:19:46 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 473454848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 473454848; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:46 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:19:46 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:46 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:19:46 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:46 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:19:46 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:46 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:19:46 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:46 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:19:46 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:46 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:19:46 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:46 MarkDuplicates Before output close freeMemory: 742658928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:46 MarkDuplicates Before output close freeMemory: 742658928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:46 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:19:46 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:46 MarkDuplicates After output close freeMemory: 742724640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:46 MarkDuplicates After output close freeMemory: 742724640; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:19:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:48 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testBulkPairsNoDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:19:48 MarkDuplicates Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.8199905061712811534.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8199905061712811534.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8199905061712811534.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester2051697433342744028/input.fasta ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.8199905061712811534.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8199905061712811534.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8199905061712811534.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester2051697433342744028/input.fasta Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:48.618 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:48.618 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:48.618 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:48.618 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:48.619 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:48.619 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:48.619 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:48.619 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:48 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8199905061712811534.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8199905061712811534.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8199905061712811534.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester2051697433342744028/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:48 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8199905061712811534.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8199905061712811534.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8199905061712811534.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester2051697433342744028/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:48 MarkDuplicates Start of doWork freeMemory: 1012345344; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:48 MarkDuplicates Start of doWork freeMemory: 1012345344; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:48 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:19:48 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:48 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:19:48 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:19:49 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:19:49 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:49 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2024-07-02 11:19:49 MarkDuplicates Read 20200 records. 0 pairs never matched. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 947308296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 947308296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:49 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:19:49 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:50 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:19:50 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:50 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:19:50 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:50 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:19:50 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 742920800; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:19:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 742920800; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:50 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:19:50 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:50 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:19:50 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:50 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:19:50 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:51 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:19:51 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:51 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:19:51 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:51 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:19:51 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:51 MarkDuplicates Before output close freeMemory: 787868240; totalMemory: 1118830592; maxMemory: 2147483648 INFO 2024-07-02 11:19:51 MarkDuplicates Before output close freeMemory: 787868240; totalMemory: 1118830592; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:51 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:19:51 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:51 MarkDuplicates After output close freeMemory: 788008536; totalMemory: 1118830592; maxMemory: 2147483648 INFO 2024-07-02 11:19:51 MarkDuplicates After output close freeMemory: 788008536; totalMemory: 1118830592; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:19:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1118830592 Runtime.totalMemory()=1118830592 Running Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:51 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testBulkPairsWithDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:19:51 MarkDuplicates Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.146581527826533876.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.146581527826533876.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.146581527826533876.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.146581527826533876.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.146581527826533876.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.146581527826533876.tmp/output.sam Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:51.791 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:51.791 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:51.791 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:51.791 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:51.791 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:51.791 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:51.791 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:51.791 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:51 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.146581527826533876.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.146581527826533876.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.146581527826533876.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:51 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.146581527826533876.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.146581527826533876.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.146581527826533876.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:51 MarkDuplicates Start of doWork freeMemory: 1022560872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:51 MarkDuplicates Start of doWork freeMemory: 1022560872; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:51 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:19:51 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:51 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:19:51 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:19:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:19:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:52 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2024-07-02 11:19:52 MarkDuplicates Read 6820 records. 0 pairs never matched. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 958906776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 958906776; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:19:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:52 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:19:52 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:52 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:19:52 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:52 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:19:52 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:52 MarkDuplicates After generateDuplicateIndexes freeMemory: 483950648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:52 MarkDuplicates After generateDuplicateIndexes freeMemory: 483950648; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:52 MarkDuplicates Marking 6200 records as duplicates. INFO 2024-07-02 11:19:52 MarkDuplicates Marking 6200 records as duplicates. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:52 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:19:52 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:52 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:19:52 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:52 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:19:52 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:52 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:19:52 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:52 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:19:52 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:52 MarkDuplicates Before output close freeMemory: 752976640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:52 MarkDuplicates Before output close freeMemory: 752976640; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:52 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:19:52 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:53 MarkDuplicates After output close freeMemory: 753434840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:53 MarkDuplicates After output close freeMemory: 753434840; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:19:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:53 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testBulkPairsWithDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:19:53 MarkDuplicates Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13605484884713884283.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13605484884713884283.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13605484884713884283.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13605484884713884283.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13605484884713884283.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13605484884713884283.tmp/output.sam Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:53.389 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:53.389 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:53.390 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:53.390 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:53.390 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:53.390 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:53.390 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:53.390 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:53 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13605484884713884283.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13605484884713884283.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13605484884713884283.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:53 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13605484884713884283.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13605484884713884283.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13605484884713884283.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:53 MarkDuplicates Start of doWork freeMemory: 1022857920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:53 MarkDuplicates Start of doWork freeMemory: 1022857920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:53 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:19:53 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:53 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:19:53 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:19:53 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:19:53 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:53 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2024-07-02 11:19:53 MarkDuplicates Read 6820 records. 0 pairs never matched. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 958768280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 958768280; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:19:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:54 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:19:54 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:54 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:19:54 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:54 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:19:54 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 753432896; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:19:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 753432896; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:54 MarkDuplicates Marking 6200 records as duplicates. INFO 2024-07-02 11:19:54 MarkDuplicates Marking 6200 records as duplicates. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:54 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:19:54 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:54 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:19:54 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:54 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:19:54 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:54 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:19:54 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:54 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:19:54 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:54 MarkDuplicates Before output close freeMemory: 769937696; totalMemory: 1090519040; maxMemory: 2147483648 INFO 2024-07-02 11:19:54 MarkDuplicates Before output close freeMemory: 769937696; totalMemory: 1090519040; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:54 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:19:54 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:54 MarkDuplicates After output close freeMemory: 767063624; totalMemory: 1087373312; maxMemory: 2147483648 INFO 2024-07-02 11:19:54 MarkDuplicates After output close freeMemory: 767063624; totalMemory: 1087373312; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:54 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:19:54 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1087373312 Runtime.totalMemory()=1087373312 Running Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:54 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testBulkPairsWithDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:19:54 MarkDuplicates Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6339946057877817100.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6339946057877817100.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6339946057877817100.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester815668262519239007/input.fasta ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6339946057877817100.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6339946057877817100.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6339946057877817100.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester815668262519239007/input.fasta Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:54.948 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:54.948 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:54.948 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:54.948 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:54.949 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:54.949 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:54.949 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:54.949 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:54 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6339946057877817100.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6339946057877817100.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6339946057877817100.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester815668262519239007/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:54 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6339946057877817100.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6339946057877817100.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6339946057877817100.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester815668262519239007/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:55 MarkDuplicates Start of doWork freeMemory: 1022918952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:55 MarkDuplicates Start of doWork freeMemory: 1022918952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:55 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:19:55 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:55 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:19:55 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:19:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:19:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:55 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2024-07-02 11:19:55 MarkDuplicates Read 6820 records. 0 pairs never matched. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 959261712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 959261712; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:19:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:19:55 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:55 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:19:55 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:55 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:19:55 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 483945104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 483945104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:55 MarkDuplicates Marking 6200 records as duplicates. INFO 2024-07-02 11:19:55 MarkDuplicates Marking 6200 records as duplicates. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:55 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:19:55 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:55 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:19:55 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:56 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:19:56 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:56 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:19:56 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:56 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:19:56 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:56 MarkDuplicates Before output close freeMemory: 753288776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:56 MarkDuplicates Before output close freeMemory: 753288776; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:56 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:19:56 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:56 MarkDuplicates After output close freeMemory: 753428960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:56 MarkDuplicates After output close freeMemory: 753428960; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:56 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:19:56 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:56 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testDifferentChromosomesInOppositeOrder STANDARD_ERROR INFO 2024-07-02 11:19:56 MarkDuplicates Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15459476617743289158.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15459476617743289158.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15459476617743289158.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15459476617743289158.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15459476617743289158.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15459476617743289158.tmp/output.sam Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:56.350 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:56.350 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:56.350 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:56.350 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:56.351 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:56.351 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:56.351 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:56.351 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:56 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15459476617743289158.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15459476617743289158.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15459476617743289158.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:56 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15459476617743289158.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15459476617743289158.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15459476617743289158.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:56 MarkDuplicates Start of doWork freeMemory: 1028040328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:56 MarkDuplicates Start of doWork freeMemory: 1028040328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:56 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:19:56 MarkDuplicates Reading input file and constructing read end information. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:56 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:19:56 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:56 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:19:56 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 973507208; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 973507208; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:19:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:56 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:19:56 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:56 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:19:56 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:56 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:19:56 MarkDuplicates Sorting list of duplicate records. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 489065496; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 489065496; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:56 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:19:56 MarkDuplicates Marking 2 records as duplicates. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:56 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:19:56 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:56 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:19:56 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:56 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:19:56 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:56 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:19:56 MarkDuplicates Duplicate Index cleanup. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:56 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:19:56 MarkDuplicates Getting Memory Stats. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:56 MarkDuplicates Before output close freeMemory: 758408120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:56 MarkDuplicates Before output close freeMemory: 758408120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:56 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:19:56 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:57 MarkDuplicates After output close freeMemory: 758548872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:57 MarkDuplicates After output close freeMemory: 758548872; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:57 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:19:57 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:57 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:19:57 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.18382262920284709856.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.18382262920284709856.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.18382262920284709856.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.18382262920284709856.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.18382262920284709856.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.18382262920284709856.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:57.083 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:57.083 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:57.084 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:57.084 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:57.084 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:57.084 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:57.084 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:57.084 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:57 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.18382262920284709856.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.18382262920284709856.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.18382262920284709856.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:57 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.18382262920284709856.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.18382262920284709856.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.18382262920284709856.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:57 MarkDuplicates Start of doWork freeMemory: 1028031856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:57 MarkDuplicates Start of doWork freeMemory: 1028031856; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:57 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:19:57 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:57 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:19:57 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:57 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:19:57 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 973498656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 973498656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:19:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:57 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:19:57 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:57 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:19:57 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:57 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:19:57 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 489057736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 489057736; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:57 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:19:57 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:57 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:19:57 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:57 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:19:57 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:57 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:19:57 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:57 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:19:57 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:57 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:19:57 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:57 MarkDuplicates Before output close freeMemory: 758401536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:57 MarkDuplicates Before output close freeMemory: 758401536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:57 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:19:57 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:57 MarkDuplicates After output close freeMemory: 758191416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:57 MarkDuplicates After output close freeMemory: 758191416; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:57 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:19:57 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:57 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:19:57 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10746111114873677687.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10746111114873677687.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10746111114873677687.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10746111114873677687.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10746111114873677687.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10746111114873677687.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:57.870 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:57.870 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:57.871 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:57.871 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:57.871 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:57.871 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:57.871 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:57.871 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:57 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10746111114873677687.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10746111114873677687.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10746111114873677687.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:57 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10746111114873677687.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10746111114873677687.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10746111114873677687.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:57 MarkDuplicates Start of doWork freeMemory: 1028031176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:57 MarkDuplicates Start of doWork freeMemory: 1028031176; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:57 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:19:57 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:57 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:19:57 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:58 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:19:58 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 973498192; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 973498192; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:19:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:58 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:19:58 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:58 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:19:58 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:58 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:19:58 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 489057272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 489057272; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:58 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:19:58 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:58 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:19:58 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:58 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:19:58 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:58 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:19:58 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:58 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:19:58 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:58 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:19:58 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:58 MarkDuplicates Before output close freeMemory: 758400856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:58 MarkDuplicates Before output close freeMemory: 758400856; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:58 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:19:58 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:58 MarkDuplicates After output close freeMemory: 758541176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:58 MarkDuplicates After output close freeMemory: 758541176; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:19:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:58 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:19:58 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17298490382464523429.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17298490382464523429.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17298490382464523429.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17298490382464523429.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17298490382464523429.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17298490382464523429.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:58.649 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:58.649 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:58.650 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:58.650 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:58.650 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:58.650 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:58.650 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:58.650 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:58 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17298490382464523429.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17298490382464523429.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17298490382464523429.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:58 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17298490382464523429.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17298490382464523429.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17298490382464523429.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:58 MarkDuplicates Start of doWork freeMemory: 1028029400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:58 MarkDuplicates Start of doWork freeMemory: 1028029400; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:58 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:19:58 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:58 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:19:58 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:58 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:19:58 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 973496200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 973496200; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:19:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:19:59 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:19:59 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:19:59 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 489055496; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 489055496; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:19:59 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:19:59 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:19:59 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:19:59 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:19:59 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:19:59 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates Before output close freeMemory: 758399080; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:59 MarkDuplicates Before output close freeMemory: 758399080; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:19:59 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates After output close freeMemory: 758182584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:59 MarkDuplicates After output close freeMemory: 758182584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:59 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:19:59 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:19:59 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5943958848989417110.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5943958848989417110.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5943958848989417110.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5943958848989417110.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5943958848989417110.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5943958848989417110.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:59.378 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:59.378 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:59.378 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:59.378 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:59.378 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:19:59.378 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:19:59.378 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:19:59.378 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:59 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5943958848989417110.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5943958848989417110.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5943958848989417110.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:19:59 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5943958848989417110.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5943958848989417110.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5943958848989417110.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:19:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:19:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates Start of doWork freeMemory: 1027659280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:59 MarkDuplicates Start of doWork freeMemory: 1027659280; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:19:59 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:19:59 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:19:59 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 973127792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 973127792; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:19:59 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:19:59 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:19:59 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:19:59 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 489053688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 489053688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:19:59 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:19:59 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:19:59 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:19:59 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:19:59 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:19:59 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates Before output close freeMemory: 758037400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:19:59 MarkDuplicates Before output close freeMemory: 758037400; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:19:59 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:19:59 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:00 MarkDuplicates After output close freeMemory: 758179592; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:00 MarkDuplicates After output close freeMemory: 758179592; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:00 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:20:00 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.1942488248794891091.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1942488248794891091.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1942488248794891091.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.1942488248794891091.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1942488248794891091.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1942488248794891091.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:00.092 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:00.092 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:00.092 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:00.092 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:00.092 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:00.092 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:00.093 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:00.093 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:00 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1942488248794891091.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1942488248794891091.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1942488248794891091.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:00 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1942488248794891091.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1942488248794891091.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1942488248794891091.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:00 MarkDuplicates Start of doWork freeMemory: 1028024128; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:00 MarkDuplicates Start of doWork freeMemory: 1028024128; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:00 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:00 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:00 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:00 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:00 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:20:00 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 973127096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 973127096; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:00 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:00 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:00 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:00 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:00 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:00 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 489053056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 489053056; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:00 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:20:00 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:00 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:20:00 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:00 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:00 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:00 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:00 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:00 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:00 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:00 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:00 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:00 MarkDuplicates Before output close freeMemory: 758035320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:00 MarkDuplicates Before output close freeMemory: 758035320; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:00 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:00 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:00 MarkDuplicates After output close freeMemory: 758536664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:00 MarkDuplicates After output close freeMemory: 758536664; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:00 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:20:00 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12116881353974370359.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12116881353974370359.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12116881353974370359.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12116881353974370359.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12116881353974370359.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12116881353974370359.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:00.928 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:00.928 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:00.929 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:00.929 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:00.929 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:00.929 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:00.929 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:00.929 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:00 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12116881353974370359.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12116881353974370359.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12116881353974370359.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:00 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12116881353974370359.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12116881353974370359.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12116881353974370359.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:01 MarkDuplicates Start of doWork freeMemory: 1028026304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:01 MarkDuplicates Start of doWork freeMemory: 1028026304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:01 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:01 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:01 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:01 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:01 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:20:01 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 973126440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 973126440; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:01 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:01 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:01 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:01 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:01 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:01 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 489052400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 489052400; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:01 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:20:01 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:01 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:20:01 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:01 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:01 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:01 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:01 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:01 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:01 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:01 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:01 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:01 MarkDuplicates Before output close freeMemory: 758395784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:01 MarkDuplicates Before output close freeMemory: 758395784; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:01 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:01 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:01 MarkDuplicates After output close freeMemory: 758535736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:01 MarkDuplicates After output close freeMemory: 758535736; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:01 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:01 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:01 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testMappedFragmentAndMappedPairFirstOfPairNonPrimary STANDARD_ERROR INFO 2024-07-02 11:20:01 MarkDuplicates Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7059339518181781135.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7059339518181781135.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7059339518181781135.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7059339518181781135.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7059339518181781135.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7059339518181781135.tmp/output.sam Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:01.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:01.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:01.744 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:01.744 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:01.744 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:01.744 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:01.744 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:01.744 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:01 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7059339518181781135.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7059339518181781135.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7059339518181781135.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:01 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7059339518181781135.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7059339518181781135.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7059339518181781135.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:01 MarkDuplicates Start of doWork freeMemory: 1028029784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:01 MarkDuplicates Start of doWork freeMemory: 1028029784; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:01 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:01 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:01 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:01 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:01 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:20:01 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 973133424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 973133424; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:02 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:02 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:02 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:02 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:02 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:02 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:02 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:02 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 489058864; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 489058864; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:02 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:20:02 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:02 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:02 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:02 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:02 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:02 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:02 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:02 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:02 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:02 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:02 MarkDuplicates Getting Memory Stats. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:02 MarkDuplicates Before output close freeMemory: 758402216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:02 MarkDuplicates Before output close freeMemory: 758402216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:02 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:02 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:02 MarkDuplicates After output close freeMemory: 758179464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:02 MarkDuplicates After output close freeMemory: 758179464; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:02 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:02 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:02 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testMappedFragmentAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:20:02 MarkDuplicates Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16930133617890978799.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16930133617890978799.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16930133617890978799.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16930133617890978799.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16930133617890978799.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16930133617890978799.tmp/output.sam Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:02.592 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:02.592 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:02.593 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:02.593 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:02.593 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:02.593 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:02.594 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:02.594 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:02 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16930133617890978799.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16930133617890978799.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16930133617890978799.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:02 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16930133617890978799.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16930133617890978799.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16930133617890978799.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:02 MarkDuplicates Start of doWork freeMemory: 1028031232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:02 MarkDuplicates Start of doWork freeMemory: 1028031232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:02 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:02 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:02 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:02 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:02 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:02 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:02 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2024-07-02 11:20:02 MarkDuplicates Read 3 records. 0 pairs never matched. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 973499576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 973499576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:02 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:02 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:03 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:03 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:03 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 489057840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 489057840; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:20:03 MarkDuplicates Marking 1 records as duplicates. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:03 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:03 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:03 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:03 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:03 MarkDuplicates Getting Memory Stats. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates Before output close freeMemory: 758401704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:03 MarkDuplicates Before output close freeMemory: 758401704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:03 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates After output close freeMemory: 758541248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:03 MarkDuplicates After output close freeMemory: 758541248; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:03 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:03 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testMappedFragmentAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:20:03 MarkDuplicates Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7474036703987206325.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7474036703987206325.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7474036703987206325.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7474036703987206325.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7474036703987206325.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7474036703987206325.tmp/output.sam Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:03.315 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:03.315 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:03.316 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:03.316 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:03.316 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:03.316 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:03.316 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:03.316 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:03 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7474036703987206325.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7474036703987206325.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7474036703987206325.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:03 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7474036703987206325.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7474036703987206325.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7474036703987206325.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates Start of doWork freeMemory: 1028025224; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:03 MarkDuplicates Start of doWork freeMemory: 1028025224; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:03 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:03 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2024-07-02 11:20:03 MarkDuplicates Read 3 records. 0 pairs never matched. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 973498512; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 973498512; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:03 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:03 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:03 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:03 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 489056776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 489056776; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:20:03 MarkDuplicates Marking 1 records as duplicates. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:03 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:03 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:03 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:03 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:03 MarkDuplicates Getting Memory Stats. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates Before output close freeMemory: 758400008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:03 MarkDuplicates Before output close freeMemory: 758400008; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:03 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:03 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:04 MarkDuplicates After output close freeMemory: 758174680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:04 MarkDuplicates After output close freeMemory: 758174680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:04 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:04 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:04 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testMappedPairAndMappedFragmentAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:20:04 MarkDuplicates Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7291619420447252094.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7291619420447252094.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7291619420447252094.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7291619420447252094.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7291619420447252094.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7291619420447252094.tmp/output.sam Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:04.090 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:04.090 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:04.091 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:04.091 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:04.091 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:04.091 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:04.091 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:04.091 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:04 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7291619420447252094.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7291619420447252094.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7291619420447252094.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:04 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7291619420447252094.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7291619420447252094.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7291619420447252094.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:04 MarkDuplicates Start of doWork freeMemory: 1028026232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:04 MarkDuplicates Start of doWork freeMemory: 1028026232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:04 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:04 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:04 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:04 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:04 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:04 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:04 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:20:04 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 973495904; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 973495904; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:04 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:04 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:04 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:04 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:04 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:04 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:04 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:04 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 489054256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 489054256; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:04 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:04 MarkDuplicates Marking 2 records as duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:04 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:04 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:04 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:04 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:04 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:04 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:04 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:04 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:04 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:04 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:04 MarkDuplicates Before output close freeMemory: 758397904; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:04 MarkDuplicates Before output close freeMemory: 758397904; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:04 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:04 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:04 MarkDuplicates After output close freeMemory: 758538088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:04 MarkDuplicates After output close freeMemory: 758538088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:04 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:04 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:04 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testMappedPairAndMappedFragmentAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:20:04 MarkDuplicates Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11857256946733854986.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11857256946733854986.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11857256946733854986.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11857256946733854986.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11857256946733854986.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11857256946733854986.tmp/output.sam Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:04.773 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:04.773 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:04.773 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:04.773 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:04.774 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:04.774 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:04.774 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:04.774 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:04 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11857256946733854986.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11857256946733854986.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11857256946733854986.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:04 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11857256946733854986.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11857256946733854986.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11857256946733854986.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:04 MarkDuplicates Start of doWork freeMemory: 1028027048; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:04 MarkDuplicates Start of doWork freeMemory: 1028027048; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:04 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:04 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:04 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:04 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:04 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:04 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:04 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:20:04 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 973495008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 973495008; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:05 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:05 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:05 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:05 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:05 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:05 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 560356528; totalMemory: 1145044992; maxMemory: 2147483648 INFO 2024-07-02 11:20:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 560356528; totalMemory: 1145044992; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:05 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:05 MarkDuplicates Marking 2 records as duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:05 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:05 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:05 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:05 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:05 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:05 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:05 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:05 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:05 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:05 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:05 MarkDuplicates Before output close freeMemory: 758397008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:05 MarkDuplicates Before output close freeMemory: 758397008; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:05 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:05 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:05 MarkDuplicates After output close freeMemory: 758537264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:05 MarkDuplicates After output close freeMemory: 758537264; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:05 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:05 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:05 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:20:05 MarkDuplicates Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15005978940979704896.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15005978940979704896.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15005978940979704896.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15005978940979704896.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15005978940979704896.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15005978940979704896.tmp/output.sam Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:05.520 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:05.520 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:05.520 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:05.520 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:05.521 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:05.521 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:05.521 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:05.521 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:05 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15005978940979704896.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15005978940979704896.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15005978940979704896.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:05 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15005978940979704896.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15005978940979704896.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15005978940979704896.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:05 MarkDuplicates Start of doWork freeMemory: 1028026640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:05 MarkDuplicates Start of doWork freeMemory: 1028026640; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:05 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:05 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:05 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:05 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:05 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:05 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:05 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:05 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 973494688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 973494688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:05 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:05 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:05 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:05 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:05 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:05 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 489052952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 489052952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:20:06 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:06 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:06 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:06 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:06 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:06 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates Before output close freeMemory: 758030456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:06 MarkDuplicates Before output close freeMemory: 758030456; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:06 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates After output close freeMemory: 758536360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:06 MarkDuplicates After output close freeMemory: 758536360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:06 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:06 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testMappedPairAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:20:06 MarkDuplicates Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.14858439787997691564.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14858439787997691564.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14858439787997691564.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.14858439787997691564.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14858439787997691564.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14858439787997691564.tmp/output.sam Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:06.286 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:06.286 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:06.286 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:06.286 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:06.287 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:06.287 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:06.287 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:06.287 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:06 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.14858439787997691564.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.14858439787997691564.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.14858439787997691564.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:06 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.14858439787997691564.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.14858439787997691564.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.14858439787997691564.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates Start of doWork freeMemory: 1028023200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:06 MarkDuplicates Start of doWork freeMemory: 1028023200; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:06 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:06 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:06 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 973493480; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 973493480; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:06 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:06 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:06 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:06 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 489052344; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 489052344; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:20:06 MarkDuplicates Marking 1 records as duplicates. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:06 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:06 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:06 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:06 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:06 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates Before output close freeMemory: 758395992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:06 MarkDuplicates Before output close freeMemory: 758395992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:06 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:06 MarkDuplicates After output close freeMemory: 758169688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:06 MarkDuplicates After output close freeMemory: 758169688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:06 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:06 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:07 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testMappedPairAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:20:07 MarkDuplicates Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12421711439580513008.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12421711439580513008.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12421711439580513008.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12421711439580513008.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12421711439580513008.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12421711439580513008.tmp/output.sam Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:07.012 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:07.012 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:07.012 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:07.012 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:07.012 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:07.012 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:07.012 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:07.012 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:07 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12421711439580513008.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12421711439580513008.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12421711439580513008.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:07 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12421711439580513008.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12421711439580513008.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12421711439580513008.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:07 MarkDuplicates Start of doWork freeMemory: 1028024328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:07 MarkDuplicates Start of doWork freeMemory: 1028024328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:07 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:07 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:07 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:07 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:07 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:07 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 973492384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 973492384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:07 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:07 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:07 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:07 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:07 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:07 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:07 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:07 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 489050648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 489050648; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:07 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:20:07 MarkDuplicates Marking 1 records as duplicates. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:07 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:07 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:07 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:07 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:07 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:07 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:07 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:07 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:07 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:07 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:07 MarkDuplicates Before output close freeMemory: 758026664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:07 MarkDuplicates Before output close freeMemory: 758026664; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:07 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:07 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:07 MarkDuplicates After output close freeMemory: 758167664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:07 MarkDuplicates After output close freeMemory: 758167664; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:07 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:07 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:07 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testMappedPairWithFirstEndSamePositionAndOther STANDARD_ERROR INFO 2024-07-02 11:20:07 MarkDuplicates Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7580590043625644147.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7580590043625644147.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7580590043625644147.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7580590043625644147.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7580590043625644147.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7580590043625644147.tmp/output.sam Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:07.759 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:07.759 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:07.759 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:07.759 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:07.760 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:07.760 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:07.760 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:07.760 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:07 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7580590043625644147.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7580590043625644147.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7580590043625644147.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:07 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7580590043625644147.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7580590043625644147.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7580590043625644147.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:07 MarkDuplicates Start of doWork freeMemory: 1028022824; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:07 MarkDuplicates Start of doWork freeMemory: 1028022824; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:07 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:07 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:07 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:07 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:07 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:07 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 973490696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 973490696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:08 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:08 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:08 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:08 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:08 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:08 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 489049136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 489049136; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:08 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:20:08 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:08 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:08 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:08 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:08 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:08 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:08 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:08 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:08 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:08 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:08 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:08 MarkDuplicates Before output close freeMemory: 758392784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:08 MarkDuplicates Before output close freeMemory: 758392784; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:08 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:08 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:08 MarkDuplicates After output close freeMemory: 758532744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:08 MarkDuplicates After output close freeMemory: 758532744; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:08 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:08 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:08 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testMappedPairWithSamePosition STANDARD_ERROR INFO 2024-07-02 11:20:08 MarkDuplicates Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2169751009615886646.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2169751009615886646.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2169751009615886646.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2169751009615886646.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2169751009615886646.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2169751009615886646.tmp/output.sam Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:08.480 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:08.480 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:08.480 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:08.480 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:08.481 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:08.481 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:08.481 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:08.481 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:08 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2169751009615886646.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2169751009615886646.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2169751009615886646.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:08 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2169751009615886646.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2169751009615886646.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2169751009615886646.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:08 MarkDuplicates Start of doWork freeMemory: 1028023432; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:08 MarkDuplicates Start of doWork freeMemory: 1028023432; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:08 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:08 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:08 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:08 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:08 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:20:08 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 973491568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 973491568; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:08 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:08 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:08 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:08 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:08 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:08 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 489049744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 489049744; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:20:09 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:09 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:09 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:09 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:09 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:09 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Before output close freeMemory: 758393392; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:09 MarkDuplicates Before output close freeMemory: 758393392; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:09 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates After output close freeMemory: 758166416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:09 MarkDuplicates After output close freeMemory: 758166416; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:09 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:09 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testMappedPairWithSamePositionSameCigar STANDARD_ERROR INFO 2024-07-02 11:20:09 MarkDuplicates Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.1482717388383251689.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1482717388383251689.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1482717388383251689.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.1482717388383251689.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1482717388383251689.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1482717388383251689.tmp/output.sam Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:09.207 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:09.207 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:09.208 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:09.208 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:09.208 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:09.208 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:09.208 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:09.208 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:09 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1482717388383251689.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1482717388383251689.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1482717388383251689.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:09 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1482717388383251689.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1482717388383251689.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1482717388383251689.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Start of doWork freeMemory: 1028022600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:09 MarkDuplicates Start of doWork freeMemory: 1028022600; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:09 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:09 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:09 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:09 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:20:09 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 973490736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 973490736; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:09 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:09 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:09 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 489048912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 489048912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:20:09 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:09 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:09 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:09 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:09 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:09 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Before output close freeMemory: 758026928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:09 MarkDuplicates Before output close freeMemory: 758026928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:09 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates After output close freeMemory: 758165584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:09 MarkDuplicates After output close freeMemory: 758165584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:09 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:09 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:20:09 MarkDuplicates Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2561210765697855513.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2561210765697855513.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2561210765697855513.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2561210765697855513.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2561210765697855513.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2561210765697855513.tmp/output.sam Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:09.892 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:09.892 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:09.893 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:09.893 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:09.893 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:09.893 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:09.893 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:09.893 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:09 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2561210765697855513.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2561210765697855513.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2561210765697855513.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:09 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2561210765697855513.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2561210765697855513.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2561210765697855513.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Start of doWork freeMemory: 1028021992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:09 MarkDuplicates Start of doWork freeMemory: 1028021992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:09 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:09 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:09 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:09 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:09 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:20:09 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 973489824; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 973489824; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:10 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:10 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:10 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:10 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:10 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:10 MarkDuplicates Sorting list of duplicate records. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 489048600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 489048600; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:10 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:20:10 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:10 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:10 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:10 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:10 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:10 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:10 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:10 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:10 MarkDuplicates Duplicate Index cleanup. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:10 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:10 MarkDuplicates Getting Memory Stats. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:10 MarkDuplicates Before output close freeMemory: 758391952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:10 MarkDuplicates Before output close freeMemory: 758391952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:10 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:10 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:10 MarkDuplicates After output close freeMemory: 758532280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:10 MarkDuplicates After output close freeMemory: 758532280; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:10 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:10 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:10 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:20:10 MarkDuplicates Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13320278411633319192.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13320278411633319192.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13320278411633319192.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13320278411633319192.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13320278411633319192.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13320278411633319192.tmp/output.sam Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:10.572 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:10.572 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:10.572 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:10.572 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:10.572 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:10.572 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:10.572 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:10.572 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:10 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13320278411633319192.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13320278411633319192.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13320278411633319192.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:10 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13320278411633319192.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13320278411633319192.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13320278411633319192.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:10 MarkDuplicates Start of doWork freeMemory: 1028020736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:10 MarkDuplicates Start of doWork freeMemory: 1028020736; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:10 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:10 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:10 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:10 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:10 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:10 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:10 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:20:10 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 973488000; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 973488000; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:11 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:11 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:11 MarkDuplicates Sorting list of duplicate records. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 489046776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 489046776; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:20:11 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:11 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:11 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:11 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:11 MarkDuplicates Duplicate Index cleanup. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:11 MarkDuplicates Getting Memory Stats. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates Before output close freeMemory: 758390656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:11 MarkDuplicates Before output close freeMemory: 758390656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:11 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates After output close freeMemory: 758530184; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:11 MarkDuplicates After output close freeMemory: 758530184; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:11 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:11 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testOpticalDuplicateBehaviorNullRegex STANDARD_ERROR INFO 2024-07-02 11:20:11 MarkDuplicates Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10214976834681903008.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_NAME_REGEX null -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10214976834681903008.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10214976834681903008.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10214976834681903008.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_NAME_REGEX null -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10214976834681903008.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10214976834681903008.tmp/output.sam Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:11.286 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:11.286 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:11.286 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:11.286 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:11.286 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:11.286 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:11.286 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:11.286 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:11 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10214976834681903008.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10214976834681903008.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10214976834681903008.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH READ_NAME_REGEX=null MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:11 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10214976834681903008.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10214976834681903008.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10214976834681903008.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH READ_NAME_REGEX=null MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates Start of doWork freeMemory: 1028017744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:11 MarkDuplicates Start of doWork freeMemory: 1028017744; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:11 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:11 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:11 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 973485400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 973485400; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:11 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:11 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:11 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 489044232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 489044232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:11 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:11 MarkDuplicates Skipped optical duplicate cluster discovery; library size estimation may be inaccurate! WARNING 2024-07-02 11:20:11 MarkDuplicates Skipped optical duplicate cluster discovery; library size estimation may be inaccurate! Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:11 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:11 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:11 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:11 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates Before output close freeMemory: 758387896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:11 MarkDuplicates Before output close freeMemory: 758387896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:11 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates After output close freeMemory: 758160992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:11 MarkDuplicates After output close freeMemory: 758160992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:11 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:11 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:11 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testOpticalDuplicateClusterOneEndSamePositionOneCluster STANDARD_ERROR INFO 2024-07-02 11:20:11 MarkDuplicates Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2990572377737895805.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2990572377737895805.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2990572377737895805.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2990572377737895805.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2990572377737895805.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2990572377737895805.tmp/output.sam Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:11.951 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:11.951 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:11.951 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:11.951 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:11.951 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:11.951 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:11.951 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:11.951 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:11 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2990572377737895805.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2990572377737895805.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2990572377737895805.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:11 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2990572377737895805.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2990572377737895805.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2990572377737895805.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:12 MarkDuplicates Start of doWork freeMemory: 1028016656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:12 MarkDuplicates Start of doWork freeMemory: 1028016656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:12 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:12 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:12 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:12 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:12 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:12 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 973117576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 973117576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:12 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:12 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:12 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:12 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:12 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:12 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:12 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:12 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 489042752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 489042752; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:12 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:12 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:12 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:20:12 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:12 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:12 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:12 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:12 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:12 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:12 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:12 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:12 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:12 MarkDuplicates Before output close freeMemory: 758386112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:12 MarkDuplicates Before output close freeMemory: 758386112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:12 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:12 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:12 MarkDuplicates After output close freeMemory: 758159768; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:12 MarkDuplicates After output close freeMemory: 758159768; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:12 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:12 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:12 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:20:12 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.18168765801662683597.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.18168765801662683597.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.18168765801662683597.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.18168765801662683597.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.18168765801662683597.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.18168765801662683597.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:12.623 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:12.623 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:12.624 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:12.624 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:12.624 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:12.624 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:12.624 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:12.624 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:12 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.18168765801662683597.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.18168765801662683597.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.18168765801662683597.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:12 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.18168765801662683597.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.18168765801662683597.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.18168765801662683597.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:12 MarkDuplicates Start of doWork freeMemory: 1028013688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:12 MarkDuplicates Start of doWork freeMemory: 1028013688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:12 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:12 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:12 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:12 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:12 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:12 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 973114608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 973114608; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:12 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:12 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:13 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:13 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:13 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 489039936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 489039936; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:13 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:13 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:13 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:13 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:13 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:13 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Before output close freeMemory: 758383520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:13 MarkDuplicates Before output close freeMemory: 758383520; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:13 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates After output close freeMemory: 758156680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:13 MarkDuplicates After output close freeMemory: 758156680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:13 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:13 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:20:13 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2040763299166133713.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2040763299166133713.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2040763299166133713.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2040763299166133713.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2040763299166133713.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2040763299166133713.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:13.279 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:13.279 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:13.279 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:13.279 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:13.279 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:13.279 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:13.279 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:13.279 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:13 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2040763299166133713.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2040763299166133713.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2040763299166133713.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:13 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2040763299166133713.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2040763299166133713.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2040763299166133713.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Start of doWork freeMemory: 1028013032; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:13 MarkDuplicates Start of doWork freeMemory: 1028013032; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:13 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:13 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:13 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 973113960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 973113960; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:13 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:13 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:13 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:13 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 489039280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 489039280; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:13 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:13 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:13 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:13 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:13 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:13 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Before output close freeMemory: 758382192; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:13 MarkDuplicates Before output close freeMemory: 758382192; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:13 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates After output close freeMemory: 758522016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:13 MarkDuplicates After output close freeMemory: 758522016; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:13 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:13 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:13 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:20:13 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12770909770807600594.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12770909770807600594.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12770909770807600594.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12770909770807600594.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12770909770807600594.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12770909770807600594.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:13.992 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:13.992 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:13.992 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:13.992 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:13.992 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:13.992 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:13.993 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:13.993 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:13 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12770909770807600594.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12770909770807600594.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12770909770807600594.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:13 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12770909770807600594.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12770909770807600594.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12770909770807600594.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:14 MarkDuplicates Start of doWork freeMemory: 1028011328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:14 MarkDuplicates Start of doWork freeMemory: 1028011328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:14 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:14 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:14 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:14 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:14 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:14 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 973112656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 973112656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:14 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:14 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:14 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:14 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:14 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:14 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:14 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 489037976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 489037976; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:14 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:14 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:14 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:14 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:14 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:14 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:14 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:14 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:14 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:14 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:14 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:14 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:14 MarkDuplicates Before output close freeMemory: 758381560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:14 MarkDuplicates Before output close freeMemory: 758381560; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:14 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:14 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:14 MarkDuplicates After output close freeMemory: 758521384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:14 MarkDuplicates After output close freeMemory: 758521384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:14 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:14 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:14 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:20:14 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.14103608535739475421.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14103608535739475421.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14103608535739475421.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.14103608535739475421.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14103608535739475421.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14103608535739475421.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:14.650 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:14.650 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:14.650 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:14.650 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:14.650 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:14.650 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:14.650 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:14.650 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:14 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.14103608535739475421.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.14103608535739475421.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.14103608535739475421.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:14 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.14103608535739475421.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.14103608535739475421.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.14103608535739475421.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:14 MarkDuplicates Start of doWork freeMemory: 1028010784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:14 MarkDuplicates Start of doWork freeMemory: 1028010784; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:14 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:14 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:14 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:14 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:14 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:14 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 973478376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 973478376; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:14 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:14 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:15 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:15 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:15 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 758521064; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:20:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 758521064; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:15 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:15 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:15 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:15 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:15 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:15 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates Before output close freeMemory: 758013320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:15 MarkDuplicates Before output close freeMemory: 758013320; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:15 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates After output close freeMemory: 758520936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:15 MarkDuplicates After output close freeMemory: 758520936; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:20:15 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2128934778717320300.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2128934778717320300.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2128934778717320300.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2128934778717320300.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2128934778717320300.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2128934778717320300.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:15.448 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:15.448 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:15.448 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:15.448 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:15.448 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:15.448 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:15.448 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:15.448 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:15 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2128934778717320300.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2128934778717320300.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2128934778717320300.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:15 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2128934778717320300.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2128934778717320300.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2128934778717320300.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates Start of doWork freeMemory: 1028010176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:15 MarkDuplicates Start of doWork freeMemory: 1028010176; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:15 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:15 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:15 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates After buildSortedReadEndLists freeMemory: 973111096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:15 MarkDuplicates After buildSortedReadEndLists freeMemory: 973111096; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:15 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:15 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:15 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:15 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 489036424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 489036424; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:15 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:15 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:15 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:15 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:15 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:15 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:15 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:16 MarkDuplicates Before output close freeMemory: 758379808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:16 MarkDuplicates Before output close freeMemory: 758379808; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:16 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:16 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:16 MarkDuplicates After output close freeMemory: 758519632; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:16 MarkDuplicates After output close freeMemory: 758519632; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:16 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:16 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:16 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:20:16 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13853969284067570045.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13853969284067570045.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13853969284067570045.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13853969284067570045.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13853969284067570045.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13853969284067570045.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:16.119 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:16.119 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:16.119 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:16.119 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:16.120 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:16.120 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:16.120 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:16.120 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:16 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13853969284067570045.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13853969284067570045.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13853969284067570045.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:16 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13853969284067570045.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13853969284067570045.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13853969284067570045.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:16 MarkDuplicates Start of doWork freeMemory: 1028009200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:16 MarkDuplicates Start of doWork freeMemory: 1028009200; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:16 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:16 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:16 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:16 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:16 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:16 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 973110120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 973110120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:16 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:16 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:16 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:16 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:16 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:16 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 918951608; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2024-07-02 11:20:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 918951608; totalMemory: 1503657984; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:16 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:16 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:16 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:16 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:16 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:16 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:16 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:16 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:16 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:16 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:16 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:16 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:16 MarkDuplicates Before output close freeMemory: 758378624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:16 MarkDuplicates Before output close freeMemory: 758378624; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:16 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:16 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:16 MarkDuplicates After output close freeMemory: 758518448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:16 MarkDuplicates After output close freeMemory: 758518448; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:16 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:16 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:16 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:20:16 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12227372469369429902.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12227372469369429902.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12227372469369429902.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12227372469369429902.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12227372469369429902.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12227372469369429902.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:16.867 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:16.867 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:16.867 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:16.867 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:16.867 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:16.867 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:16.868 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:16.868 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:16 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12227372469369429902.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12227372469369429902.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12227372469369429902.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:16 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12227372469369429902.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12227372469369429902.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12227372469369429902.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:16 MarkDuplicates Start of doWork freeMemory: 1028008576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:16 MarkDuplicates Start of doWork freeMemory: 1028008576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:16 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:16 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:16 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:16 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:17 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:17 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 973476384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 973476384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:17 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:17 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:17 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:17 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:17 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:17 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:17 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:17 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 489034824; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 489034824; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:17 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:17 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:17 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:17 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:17 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:17 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:17 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:17 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:17 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:17 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:17 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:17 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:17 MarkDuplicates Before output close freeMemory: 758377816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:17 MarkDuplicates Before output close freeMemory: 758377816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:17 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:17 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:17 MarkDuplicates After output close freeMemory: 758518136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:17 MarkDuplicates After output close freeMemory: 758518136; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:17 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:17 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:17 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:20:17 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.18285673473282107752.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.18285673473282107752.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.18285673473282107752.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.18285673473282107752.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.18285673473282107752.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.18285673473282107752.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:17.739 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:17.739 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:17.739 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:17.739 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:17.740 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:17.740 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:17.740 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:17.740 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:17 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.18285673473282107752.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.18285673473282107752.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.18285673473282107752.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:17 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.18285673473282107752.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.18285673473282107752.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.18285673473282107752.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:17 MarkDuplicates Start of doWork freeMemory: 1028007360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:17 MarkDuplicates Start of doWork freeMemory: 1028007360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:17 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:17 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:17 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:17 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:17 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:17 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 973475168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 973475168; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:18 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:18 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:18 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:18 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:18 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:18 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 489033608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 489033608; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:18 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:18 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:18 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:18 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:18 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:18 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:18 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:18 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:18 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:18 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:18 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:18 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:18 MarkDuplicates Before output close freeMemory: 758377192; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:18 MarkDuplicates Before output close freeMemory: 758377192; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:18 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:18 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:18 MarkDuplicates After output close freeMemory: 758517440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:18 MarkDuplicates After output close freeMemory: 758517440; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:18 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:18 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:18 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:20:18 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9669524568654145617.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9669524568654145617.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9669524568654145617.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9669524568654145617.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9669524568654145617.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9669524568654145617.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:18.546 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:18.546 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:18.547 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:18.547 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:18.547 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:18.547 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:18.547 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:18.547 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:18 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9669524568654145617.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9669524568654145617.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9669524568654145617.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:18 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9669524568654145617.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9669524568654145617.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9669524568654145617.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:18 MarkDuplicates Start of doWork freeMemory: 1028006752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:18 MarkDuplicates Start of doWork freeMemory: 1028006752; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:18 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:18 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:18 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:18 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:18 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:18 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 973474560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 973474560; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:19 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:19 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:19 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:19 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:19 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 489033000; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 489033000; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:19 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:19 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:19 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:19 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:19 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:19 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:19 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:19 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:19 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:19 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:19 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:19 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:19 MarkDuplicates Before output close freeMemory: 758375880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:19 MarkDuplicates Before output close freeMemory: 758375880; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:19 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:19 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:19 MarkDuplicates After output close freeMemory: 758515704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:19 MarkDuplicates After output close freeMemory: 758515704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:19 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:19 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:19 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:20:19 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5869762750002802065.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5869762750002802065.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5869762750002802065.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5869762750002802065.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5869762750002802065.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5869762750002802065.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:19.404 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:19.404 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:19.404 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:19.404 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:19.407 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:19.407 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:19.407 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:19.407 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:19 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5869762750002802065.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5869762750002802065.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5869762750002802065.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:19 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5869762750002802065.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5869762750002802065.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5869762750002802065.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:19 MarkDuplicates Start of doWork freeMemory: 1028006056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:19 MarkDuplicates Start of doWork freeMemory: 1028006056; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:19 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:19 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:19 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:19 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:19 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:19 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 973473648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 973473648; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:19 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:19 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:19 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:19 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:19 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:19 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:19 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 489032304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 489032304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:20 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:20 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:20 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:20 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:20 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:20 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates Before output close freeMemory: 758375688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:20 MarkDuplicates Before output close freeMemory: 758375688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:20 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates After output close freeMemory: 758515984; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:20 MarkDuplicates After output close freeMemory: 758515984; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:20 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:20 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756) STANDARD_ERROR INFO 2024-07-02 11:20:20 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15583755567337582458.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15583755567337582458.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15583755567337582458.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15583755567337582458.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15583755567337582458.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15583755567337582458.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:20.230 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:20.230 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:20.230 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:20.230 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:20.230 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:20.230 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:20.230 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:20.230 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:20 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15583755567337582458.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15583755567337582458.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15583755567337582458.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:20 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15583755567337582458.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15583755567337582458.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15583755567337582458.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates Start of doWork freeMemory: 1028005416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:20 MarkDuplicates Start of doWork freeMemory: 1028005416; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:20 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:20 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:20 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 973473136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 973473136; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:20 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:20 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:20 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 489031792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 489031792; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:20 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:20 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:20 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:20 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:20 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:20 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates Before output close freeMemory: 758008304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:20 MarkDuplicates Before output close freeMemory: 758008304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:20 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:20 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:21 MarkDuplicates After output close freeMemory: 758515128; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:21 MarkDuplicates After output close freeMemory: 758515128; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:21 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:21 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:21 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756) STANDARD_ERROR INFO 2024-07-02 11:20:21 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15582443302199816346.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15582443302199816346.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15582443302199816346.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15582443302199816346.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15582443302199816346.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15582443302199816346.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:21.050 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:21.050 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:21.051 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:21.051 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:21.051 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:21.051 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:21.051 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:21.051 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:21 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15582443302199816346.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15582443302199816346.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15582443302199816346.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:21 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15582443302199816346.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15582443302199816346.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15582443302199816346.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:21 MarkDuplicates Start of doWork freeMemory: 1028004896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:21 MarkDuplicates Start of doWork freeMemory: 1028004896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:21 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:21 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:21 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:21 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:21 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:21 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 973472464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 973472464; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:21 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:21 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:21 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:21 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:21 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:21 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:21 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:21 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 601228776; totalMemory: 1185939456; maxMemory: 2147483648 INFO 2024-07-02 11:20:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 601228776; totalMemory: 1185939456; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:21 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:21 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:21 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:21 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:21 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:21 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:21 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:21 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:21 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:21 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:21 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:21 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:21 MarkDuplicates Before output close freeMemory: 758374728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:21 MarkDuplicates Before output close freeMemory: 758374728; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:21 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:21 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:21 MarkDuplicates After output close freeMemory: 758515048; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:21 MarkDuplicates After output close freeMemory: 758515048; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:21 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:21 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:21 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756) STANDARD_ERROR INFO 2024-07-02 11:20:21 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.730308915983947906.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.730308915983947906.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.730308915983947906.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.730308915983947906.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.730308915983947906.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.730308915983947906.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:21.959 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:21.959 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:21.959 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:21.959 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:21.960 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:21.960 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:21.960 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:21.960 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:21 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.730308915983947906.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.730308915983947906.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.730308915983947906.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:21 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.730308915983947906.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.730308915983947906.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.730308915983947906.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:22 MarkDuplicates Start of doWork freeMemory: 1028000496; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:22 MarkDuplicates Start of doWork freeMemory: 1028000496; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:22 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:22 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:22 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:22 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:22 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:22 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 973470912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 973470912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:22 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:22 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:22 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:22 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:22 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:22 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 489029568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 489029568; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:22 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:22 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:22 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:22 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:22 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:22 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:22 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:22 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:22 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:22 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:22 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:22 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:22 MarkDuplicates Before output close freeMemory: 758372584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:22 MarkDuplicates Before output close freeMemory: 758372584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:22 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:22 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:22 MarkDuplicates After output close freeMemory: 758146448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:22 MarkDuplicates After output close freeMemory: 758146448; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:22 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:22 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:22 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756) STANDARD_ERROR INFO 2024-07-02 11:20:22 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11219053042137579083.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11219053042137579083.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11219053042137579083.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11219053042137579083.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11219053042137579083.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11219053042137579083.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:22.784 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:22.784 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:22.785 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:22.785 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:22.785 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:22.785 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:22.785 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:22.785 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:22 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11219053042137579083.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11219053042137579083.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11219053042137579083.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:22 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11219053042137579083.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11219053042137579083.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11219053042137579083.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:22 MarkDuplicates Start of doWork freeMemory: 1027998880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:22 MarkDuplicates Start of doWork freeMemory: 1027998880; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:22 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:22 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:22 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:22 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:22 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:22 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 973468744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 973468744; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:23 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:23 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:23 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:23 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:23 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:23 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 489027400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 489027400; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:23 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:23 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:23 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:23 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:23 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:23 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:23 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:23 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:23 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:23 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:23 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:23 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:23 MarkDuplicates Before output close freeMemory: 758370984; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:23 MarkDuplicates Before output close freeMemory: 758370984; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:23 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:23 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:23 MarkDuplicates After output close freeMemory: 758144144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:23 MarkDuplicates After output close freeMemory: 758144144; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:23 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:23 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:23 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance STANDARD_ERROR INFO 2024-07-02 11:20:23 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7639944476859748992.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7639944476859748992.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7639944476859748992.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7639944476859748992.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7639944476859748992.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7639944476859748992.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:23.585 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:23.585 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:23.585 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:23.585 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:23.586 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:23.586 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:23.586 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:23.586 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:23 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7639944476859748992.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7639944476859748992.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7639944476859748992.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:23 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7639944476859748992.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7639944476859748992.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7639944476859748992.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:23 MarkDuplicates Start of doWork freeMemory: 1028000672; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:23 MarkDuplicates Start of doWork freeMemory: 1028000672; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:23 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:23 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:23 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:23 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:23 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:23 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 973468480; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 973468480; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:24 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:24 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:24 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:24 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:24 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:24 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 489026920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 489026920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:24 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:24 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:24 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:24 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:24 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:24 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:24 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:24 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:24 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:24 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:24 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:24 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:24 MarkDuplicates Before output close freeMemory: 758370504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:24 MarkDuplicates Before output close freeMemory: 758370504; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:24 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:24 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:24 MarkDuplicates After output close freeMemory: 758510824; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:24 MarkDuplicates After output close freeMemory: 758510824; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:24 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:20:24 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:24 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance STANDARD_ERROR INFO 2024-07-02 11:20:24 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17260583743226881086.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17260583743226881086.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17260583743226881086.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17260583743226881086.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17260583743226881086.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17260583743226881086.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:24.526 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:24.526 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:24.526 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:24.526 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:24.527 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:24.527 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:24.527 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:24.527 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:24 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17260583743226881086.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17260583743226881086.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17260583743226881086.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:24 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17260583743226881086.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17260583743226881086.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17260583743226881086.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:24 MarkDuplicates Start of doWork freeMemory: 1028000376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:24 MarkDuplicates Start of doWork freeMemory: 1028000376; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:24 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:24 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:24 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:24 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:24 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:24 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 973467968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 973467968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:24 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:24 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:25 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:25 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:25 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:25 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:25 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:25 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 489026472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 489026472; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:25 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:25 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:25 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:20:25 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:25 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:25 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:25 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:25 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:25 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:25 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:25 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:25 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:25 MarkDuplicates Before output close freeMemory: 758370168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:25 MarkDuplicates Before output close freeMemory: 758370168; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:25 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:25 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:25 MarkDuplicates After output close freeMemory: 758510376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:25 MarkDuplicates After output close freeMemory: 758510376; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:25 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:20:25 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:25 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate STANDARD_ERROR INFO 2024-07-02 11:20:25 MarkDuplicates Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15640484626756795974.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15640484626756795974.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15640484626756795974.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15640484626756795974.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15640484626756795974.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15640484626756795974.tmp/output.sam Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:25.492 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:25.492 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:25.492 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:25.492 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:25.492 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:25.492 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:25.492 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:25.492 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:25 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15640484626756795974.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15640484626756795974.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15640484626756795974.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:25 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15640484626756795974.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15640484626756795974.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15640484626756795974.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:25 MarkDuplicates Start of doWork freeMemory: 1027999424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:25 MarkDuplicates Start of doWork freeMemory: 1027999424; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:25 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:25 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:25 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:25 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:25 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:25 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 973467016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 973467016; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:25 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:25 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:25 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:25 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:25 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:25 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:25 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:25 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 489025520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 489025520; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:26 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:20:26 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:26 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:26 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:26 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:26 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates Before output close freeMemory: 758369144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:26 MarkDuplicates Before output close freeMemory: 758369144; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:26 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates After output close freeMemory: 758142192; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:26 MarkDuplicates After output close freeMemory: 758142192; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:26 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:26 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testOpticalDuplicateFinding STANDARD_ERROR INFO 2024-07-02 11:20:26 MarkDuplicates Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.1276763132371587280.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1276763132371587280.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1276763132371587280.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.1276763132371587280.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1276763132371587280.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1276763132371587280.tmp/output.sam Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:26.292 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:26.292 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:26.292 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:26.292 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:26.292 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:26.292 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:26.293 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:26.293 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:26 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1276763132371587280.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1276763132371587280.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1276763132371587280.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:26 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1276763132371587280.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1276763132371587280.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1276763132371587280.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates Start of doWork freeMemory: 1027994544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:26 MarkDuplicates Start of doWork freeMemory: 1027994544; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:26 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:26 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:20:26 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 973464928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 973464928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:26 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:26 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:26 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 489023480; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 489023480; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:20:26 MarkDuplicates Marking 4 records as duplicates. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:20:26 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:26 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:26 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:26 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:26 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates Before output close freeMemory: 757999872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:26 MarkDuplicates Before output close freeMemory: 757999872; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:26 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates After output close freeMemory: 758140152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:26 MarkDuplicates After output close freeMemory: 758140152; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:26 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:26 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:26 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testPathologicalOrderingAtTheSamePosition STANDARD_ERROR INFO 2024-07-02 11:20:26 MarkDuplicates Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17656441836480627214.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17656441836480627214.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17656441836480627214.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17656441836480627214.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17656441836480627214.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17656441836480627214.tmp/output.sam Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:26.938 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:26.938 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:26.938 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:26.938 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:26.938 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:26.938 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:26.938 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:26.938 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:26 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17656441836480627214.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17656441836480627214.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17656441836480627214.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:26 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17656441836480627214.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17656441836480627214.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17656441836480627214.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates Start of doWork freeMemory: 1027997400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:27 MarkDuplicates Start of doWork freeMemory: 1027997400; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:27 MarkDuplicates Reading input file and constructing read end information. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:27 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:27 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 973464992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 973464992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:27 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:27 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:27 MarkDuplicates Sorting list of duplicate records. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 489023496; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 489023496; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:27 MarkDuplicates Marking 2 records as duplicates. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:20:27 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:27 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:27 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:27 MarkDuplicates Duplicate Index cleanup. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:27 MarkDuplicates Getting Memory Stats. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates Before output close freeMemory: 758366512; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:27 MarkDuplicates Before output close freeMemory: 758366512; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:27 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates After output close freeMemory: 758139536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:27 MarkDuplicates After output close freeMemory: 758139536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:27 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:27 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testSecondEndIsBeforeFirstInCoordinate STANDARD_ERROR INFO 2024-07-02 11:20:27 MarkDuplicates Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11542813401739242061.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11542813401739242061.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11542813401739242061.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11542813401739242061.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11542813401739242061.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11542813401739242061.tmp/output.sam Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:27.569 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:27.569 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:27.569 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:27.569 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:27.569 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:27.569 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:27.569 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:27.569 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:27 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11542813401739242061.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11542813401739242061.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11542813401739242061.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:27 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11542813401739242061.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11542813401739242061.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11542813401739242061.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates Start of doWork freeMemory: 1027995024; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:27 MarkDuplicates Start of doWork freeMemory: 1027995024; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:27 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:27 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:27 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:27 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:20:27 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 973465992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 973465992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:27 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:27 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:27 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:27 MarkDuplicates Sorting list of duplicate records. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 488810272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 488810272; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:20:28 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:28 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:28 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:28 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:28 MarkDuplicates Duplicate Index cleanup. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:28 MarkDuplicates Getting Memory Stats. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Before output close freeMemory: 758367632; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:28 MarkDuplicates Before output close freeMemory: 758367632; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:28 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates After output close freeMemory: 758507848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:28 MarkDuplicates After output close freeMemory: 758507848; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:28 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:28 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testSingleMappedFragment STANDARD_ERROR INFO 2024-07-02 11:20:28 MarkDuplicates Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.652590532004453834.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.652590532004453834.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.652590532004453834.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.652590532004453834.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.652590532004453834.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.652590532004453834.tmp/output.sam Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:28.218 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:28.218 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:28.218 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:28.218 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:28.218 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:28.218 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:28.219 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:28.219 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:28 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.652590532004453834.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.652590532004453834.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.652590532004453834.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:28 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.652590532004453834.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.652590532004453834.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.652590532004453834.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Start of doWork freeMemory: 1027995048; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:28 MarkDuplicates Start of doWork freeMemory: 1027995048; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:28 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:28 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:28 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:28 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Read 1 records. 0 pairs never matched. INFO 2024-07-02 11:20:28 MarkDuplicates Read 1 records. 0 pairs never matched. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 973464680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 973464680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:28 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:28 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:28 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 489023456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 489023456; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:20:28 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:28 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:28 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:28 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:28 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:28 MarkDuplicates Getting Memory Stats. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Before output close freeMemory: 758367288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:28 MarkDuplicates Before output close freeMemory: 758367288; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:28 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates After output close freeMemory: 758140200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:28 MarkDuplicates After output close freeMemory: 758140200; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:28 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:28 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testSingleMappedFragmentAndSingleMappedPair STANDARD_ERROR INFO 2024-07-02 11:20:28 MarkDuplicates Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5070851299398150710.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5070851299398150710.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5070851299398150710.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5070851299398150710.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5070851299398150710.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5070851299398150710.tmp/output.sam Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:28.893 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:28.893 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:28.893 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:28.893 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:28.893 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:28.893 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:28.894 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:28.894 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:28 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5070851299398150710.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5070851299398150710.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5070851299398150710.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:28 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5070851299398150710.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5070851299398150710.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5070851299398150710.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Start of doWork freeMemory: 1027994920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:28 MarkDuplicates Start of doWork freeMemory: 1027994920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:28 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:28 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:28 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:28 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:28 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2024-07-02 11:20:28 MarkDuplicates Read 3 records. 0 pairs never matched. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 973462968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 973462968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:29 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:29 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:29 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:29 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:29 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:29 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 489021232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 489021232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:29 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:20:29 MarkDuplicates Marking 1 records as duplicates. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:29 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:29 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:29 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:29 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:29 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:29 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:29 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:29 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:29 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:29 MarkDuplicates Getting Memory Stats. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:29 MarkDuplicates Before output close freeMemory: 758364952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:29 MarkDuplicates Before output close freeMemory: 758364952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:29 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:29 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:29 MarkDuplicates After output close freeMemory: 758504640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:29 MarkDuplicates After output close freeMemory: 758504640; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:29 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testSingleMappedFragmentAndTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:20:29 MarkDuplicates Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6698744637300266225.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6698744637300266225.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6698744637300266225.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6698744637300266225.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6698744637300266225.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6698744637300266225.tmp/output.sam Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:29.544 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:29.544 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:29.544 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:29.544 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:29.544 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:29.544 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:29.544 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:29.544 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:29 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6698744637300266225.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6698744637300266225.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6698744637300266225.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:29 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6698744637300266225.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6698744637300266225.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6698744637300266225.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:29 MarkDuplicates Start of doWork freeMemory: 1027992696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:29 MarkDuplicates Start of doWork freeMemory: 1027992696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:29 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:29 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:29 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:29 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:29 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:29 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:29 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:20:29 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 973460480; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 973460480; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:29 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:29 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:29 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:29 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:29 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:29 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 918935168; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2024-07-02 11:20:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 918935168; totalMemory: 1503657984; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:30 MarkDuplicates Marking 3 records as duplicates. INFO 2024-07-02 11:20:30 MarkDuplicates Marking 3 records as duplicates. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:30 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:30 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:30 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:30 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:30 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:30 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:30 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:30 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:30 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:30 MarkDuplicates Getting Memory Stats. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:30 MarkDuplicates Before output close freeMemory: 758362728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:30 MarkDuplicates Before output close freeMemory: 758362728; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:30 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:30 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:30 MarkDuplicates After output close freeMemory: 758136016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:30 MarkDuplicates After output close freeMemory: 758136016; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:30 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:30 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:30 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testSingleMappedPair STANDARD_ERROR INFO 2024-07-02 11:20:30 MarkDuplicates Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.91528850952246940.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.91528850952246940.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.91528850952246940.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.91528850952246940.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.91528850952246940.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.91528850952246940.tmp/output.sam Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:30.417 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:30.417 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:30.418 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:30.418 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:30.418 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:30.418 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:30.418 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:30.418 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:30 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.91528850952246940.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.91528850952246940.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.91528850952246940.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:30 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.91528850952246940.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.91528850952246940.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.91528850952246940.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:30 MarkDuplicates Start of doWork freeMemory: 1027993904; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:30 MarkDuplicates Start of doWork freeMemory: 1027993904; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:30 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:30 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:30 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:30 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:30 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:20:30 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 973095160; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 973095160; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:30 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:30 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:30 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:30 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:30 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:30 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 489020216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 489020216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:30 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:20:30 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:30 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:30 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:30 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:30 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:30 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:30 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:30 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:30 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:30 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:30 MarkDuplicates Getting Memory Stats. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:31 MarkDuplicates Before output close freeMemory: 758362368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:31 MarkDuplicates Before output close freeMemory: 758362368; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:31 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:31 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:31 MarkDuplicates After output close freeMemory: 758504120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:31 MarkDuplicates After output close freeMemory: 758504120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:31 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:31 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:31 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testSingleUnmappedFragment STANDARD_ERROR INFO 2024-07-02 11:20:31 MarkDuplicates Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.913204961067306736.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.913204961067306736.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.913204961067306736.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.913204961067306736.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.913204961067306736.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.913204961067306736.tmp/output.sam Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:31.121 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:31.121 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:31.121 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:31.121 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:31.122 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:31.122 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:31.122 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:31.122 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:31 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.913204961067306736.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.913204961067306736.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.913204961067306736.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:31 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.913204961067306736.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.913204961067306736.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.913204961067306736.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:31 MarkDuplicates Start of doWork freeMemory: 1027991144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:31 MarkDuplicates Start of doWork freeMemory: 1027991144; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:31 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:31 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:31 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:31 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:31 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2024-07-02 11:20:31 MarkDuplicates Read 0 records. 0 pairs never matched. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 973462384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 973462384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:31 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:31 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:31 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:31 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:31 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:31 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 489020688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 489020688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:31 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:20:31 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:31 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:31 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:31 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:31 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:31 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:31 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:31 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:31 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:31 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:31 MarkDuplicates Getting Memory Stats. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:31 MarkDuplicates Before output close freeMemory: 758364728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:31 MarkDuplicates Before output close freeMemory: 758364728; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:31 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:31 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:31 MarkDuplicates After output close freeMemory: 758137432; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:31 MarkDuplicates After output close freeMemory: 758137432; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:31 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:31 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:31 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testSingleUnmappedPair STANDARD_ERROR INFO 2024-07-02 11:20:31 MarkDuplicates Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4811700220766000879.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4811700220766000879.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4811700220766000879.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4811700220766000879.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4811700220766000879.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4811700220766000879.tmp/output.sam Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:31.947 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:31.947 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:31.947 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:31.947 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:31.947 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:31.947 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:31.948 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:31.948 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:31 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4811700220766000879.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4811700220766000879.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4811700220766000879.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:31 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4811700220766000879.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4811700220766000879.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4811700220766000879.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:32 MarkDuplicates Start of doWork freeMemory: 1027992488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:32 MarkDuplicates Start of doWork freeMemory: 1027992488; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:32 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:32 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:32 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:32 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:32 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2024-07-02 11:20:32 MarkDuplicates Read 0 records. 0 pairs never matched. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 973461512; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 973461512; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:32 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:32 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:32 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:32 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:32 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:32 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 489019600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 489019600; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:32 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:20:32 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:32 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:32 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:32 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:32 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:32 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:32 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:32 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:32 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:32 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:32 MarkDuplicates Getting Memory Stats. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:32 MarkDuplicates Before output close freeMemory: 758363640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:32 MarkDuplicates Before output close freeMemory: 758363640; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:32 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:32 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:32 MarkDuplicates After output close freeMemory: 758503008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:32 MarkDuplicates After output close freeMemory: 758503008; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:32 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testStackOverFlowPairSetSwap STANDARD_ERROR INFO 2024-07-02 11:20:32 MarkDuplicates Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4219480143115864941.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4219480143115864941.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4219480143115864941.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4219480143115864941.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4219480143115864941.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4219480143115864941.tmp/output.sam Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:32.760 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:32.760 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:32.760 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:32.760 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:32.760 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:32.760 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:32.760 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:32.760 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:32 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4219480143115864941.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4219480143115864941.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4219480143115864941.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:32 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4219480143115864941.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4219480143115864941.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4219480143115864941.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:32 MarkDuplicates Start of doWork freeMemory: 1027882896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:32 MarkDuplicates Start of doWork freeMemory: 1027882896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:32 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:32 MarkDuplicates Reading input file and constructing read end information. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:32 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:32 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:32 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:32 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 973322176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 973322176; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:33 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:33 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:33 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:33 MarkDuplicates Sorting list of duplicate records. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 594786856; totalMemory: 1179648000; maxMemory: 2147483648 INFO 2024-07-02 11:20:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 594786856; totalMemory: 1179648000; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:33 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:33 MarkDuplicates Marking 2 records as duplicates. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:33 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:20:33 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:33 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:33 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:33 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:33 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:33 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:33 MarkDuplicates Duplicate Index cleanup. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:33 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:33 MarkDuplicates Getting Memory Stats. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:33 MarkDuplicates Before output close freeMemory: 758195832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:33 MarkDuplicates Before output close freeMemory: 758195832; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:33 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:33 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:33 MarkDuplicates After output close freeMemory: 758364512; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:33 MarkDuplicates After output close freeMemory: 758364512; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:33 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:33 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:33 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:20:33 MarkDuplicates Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4257159615387144701.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4257159615387144701.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4257159615387144701.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4257159615387144701.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4257159615387144701.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4257159615387144701.tmp/output.sam Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:33.631 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:33.631 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:33.632 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:33.632 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:33.632 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:33.632 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:33.632 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:33.632 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:33 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4257159615387144701.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4257159615387144701.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4257159615387144701.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:33 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4257159615387144701.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4257159615387144701.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4257159615387144701.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:33 MarkDuplicates Start of doWork freeMemory: 1027974336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:33 MarkDuplicates Start of doWork freeMemory: 1027974336; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:33 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:33 MarkDuplicates Reading input file and constructing read end information. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:33 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:33 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:33 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:33 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:33 MarkDuplicates Read 18 records. 0 pairs never matched. INFO 2024-07-02 11:20:33 MarkDuplicates Read 18 records. 0 pairs never matched. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 973444968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 973444968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:34 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:34 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:34 MarkDuplicates Sorting list of duplicate records. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 488791960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 488791960; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates Marking 12 records as duplicates. INFO 2024-07-02 11:20:34 MarkDuplicates Marking 12 records as duplicates. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:34 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:34 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:34 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:34 MarkDuplicates Duplicate Index cleanup. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:34 MarkDuplicates Getting Memory Stats. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates Before output close freeMemory: 758349576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:34 MarkDuplicates Before output close freeMemory: 758349576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:34 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates After output close freeMemory: 758489464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:34 MarkDuplicates After output close freeMemory: 758489464; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:20:34 MarkDuplicates Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16626164068267598697.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16626164068267598697.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16626164068267598697.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16626164068267598697.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16626164068267598697.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16626164068267598697.tmp/output.sam Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:34.376 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:34.376 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:34.376 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:34.376 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:34.376 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:34.376 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:34.376 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:34.376 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:34 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16626164068267598697.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16626164068267598697.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16626164068267598697.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:34 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16626164068267598697.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16626164068267598697.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16626164068267598697.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates Start of doWork freeMemory: 1027986416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:34 MarkDuplicates Start of doWork freeMemory: 1027986416; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:34 MarkDuplicates Reading input file and constructing read end information. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:34 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:34 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:34 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:20:34 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates After buildSortedReadEndLists freeMemory: 973453896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:34 MarkDuplicates After buildSortedReadEndLists freeMemory: 973453896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:34 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:34 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:34 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:34 MarkDuplicates Sorting list of duplicate records. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 489012600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 489012600; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:20:34 MarkDuplicates Marking 4 records as duplicates. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:34 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:34 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:34 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:34 MarkDuplicates Duplicate Index cleanup. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:34 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:34 MarkDuplicates Getting Memory Stats. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:35 MarkDuplicates Before output close freeMemory: 758355912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:35 MarkDuplicates Before output close freeMemory: 758355912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:35 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:35 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:35 MarkDuplicates After output close freeMemory: 758495936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:35 MarkDuplicates After output close freeMemory: 758495936; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:35 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:35 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:35 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testThreeMappedPairsWithMatchingSecondMate STANDARD_ERROR INFO 2024-07-02 11:20:35 MarkDuplicates Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4495087344121569307.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4495087344121569307.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4495087344121569307.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4495087344121569307.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4495087344121569307.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4495087344121569307.tmp/output.sam Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:35.172 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:35.172 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:35.172 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:35.172 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:35.172 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:35.172 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:35.173 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:35.173 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:35 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4495087344121569307.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4495087344121569307.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4495087344121569307.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:35 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4495087344121569307.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4495087344121569307.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4495087344121569307.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:35 MarkDuplicates Start of doWork freeMemory: 1027983232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:35 MarkDuplicates Start of doWork freeMemory: 1027983232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:35 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:35 MarkDuplicates Reading input file and constructing read end information. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:35 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:35 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:35 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:35 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:35 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:20:35 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 973452152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 973452152; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:35 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:35 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:35 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:35 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:35 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:35 MarkDuplicates Sorting list of duplicate records. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 489011000; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 489011000; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:35 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:35 MarkDuplicates Marking 2 records as duplicates. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:35 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:35 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:35 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:35 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:35 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:35 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:35 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:35 MarkDuplicates Duplicate Index cleanup. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:35 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:35 MarkDuplicates Getting Memory Stats. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:35 MarkDuplicates Before output close freeMemory: 758354648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:35 MarkDuplicates Before output close freeMemory: 758354648; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:35 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:35 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:35 MarkDuplicates After output close freeMemory: 758494336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:35 MarkDuplicates After output close freeMemory: 758494336; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:35 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:35 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:35 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:20:35 MarkDuplicates Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.1889728576056506270.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1889728576056506270.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1889728576056506270.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.1889728576056506270.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1889728576056506270.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1889728576056506270.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:35.882 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:35.882 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:35.882 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:35.882 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:35.882 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:35.882 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:35.882 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:35.882 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:35 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1889728576056506270.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1889728576056506270.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1889728576056506270.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:35 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1889728576056506270.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1889728576056506270.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1889728576056506270.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:35 MarkDuplicates Start of doWork freeMemory: 1027979744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:35 MarkDuplicates Start of doWork freeMemory: 1027979744; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:35 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:35 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:35 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:35 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:35 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:35 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:35 MarkDuplicates Read 12 records. 0 pairs never matched. INFO 2024-07-02 11:20:35 MarkDuplicates Read 12 records. 0 pairs never matched. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 973446832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 973446832; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:36 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:36 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:36 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:36 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:36 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:36 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 489006328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 489006328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:36 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:20:36 MarkDuplicates Marking 8 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:36 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:36 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:36 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:36 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:36 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:36 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:36 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:36 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:36 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:36 MarkDuplicates Getting Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:36 MarkDuplicates Before output close freeMemory: 757982528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:36 MarkDuplicates Before output close freeMemory: 757982528; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:36 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:36 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:36 MarkDuplicates After output close freeMemory: 758490008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:36 MarkDuplicates After output close freeMemory: 758490008; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:36 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:36 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:36 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoGroupsOnDifferentChromosomesOfTwoFragments STANDARD_ERROR INFO 2024-07-02 11:20:36 MarkDuplicates Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7353312347591984589.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7353312347591984589.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7353312347591984589.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7353312347591984589.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7353312347591984589.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7353312347591984589.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:36.570 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:36.570 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:36.571 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:36.571 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:36.571 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:36.571 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:36.571 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:36.571 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:36 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7353312347591984589.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7353312347591984589.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7353312347591984589.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:36 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7353312347591984589.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7353312347591984589.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7353312347591984589.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:36 MarkDuplicates Start of doWork freeMemory: 1027984840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:36 MarkDuplicates Start of doWork freeMemory: 1027984840; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:36 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:36 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:36 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:36 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:36 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:36 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:36 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:36 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 973453008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 973453008; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:36 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:36 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:36 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:36 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:36 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:36 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 489011448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 489011448; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:37 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:37 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:37 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:37 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:37 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:37 MarkDuplicates Getting Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates Before output close freeMemory: 758354872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:37 MarkDuplicates Before output close freeMemory: 758354872; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:37 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates After output close freeMemory: 758495352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:37 MarkDuplicates After output close freeMemory: 758495352; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:20:37 MarkDuplicates Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13614120729546321155.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13614120729546321155.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13614120729546321155.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13614120729546321155.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13614120729546321155.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13614120729546321155.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:37.304 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:37.304 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:37.305 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:37.305 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:37.305 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:37.305 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:37.305 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:37.305 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:37 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13614120729546321155.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13614120729546321155.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13614120729546321155.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:37 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13614120729546321155.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13614120729546321155.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13614120729546321155.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates Start of doWork freeMemory: 1027981336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:37 MarkDuplicates Start of doWork freeMemory: 1027981336; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:37 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:37 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:37 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:37 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates Read 8 records. 0 pairs never matched. INFO 2024-07-02 11:20:37 MarkDuplicates Read 8 records. 0 pairs never matched. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 973448560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 973448560; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:37 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:37 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:37 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 489007528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 489007528; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:20:37 MarkDuplicates Marking 4 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:37 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:37 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:37 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:37 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:37 MarkDuplicates Getting Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates Before output close freeMemory: 757983952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:37 MarkDuplicates Before output close freeMemory: 757983952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:37 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:37 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:38 MarkDuplicates After output close freeMemory: 758491360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:38 MarkDuplicates After output close freeMemory: 758491360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:38 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:38 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:38 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoMappedFragments STANDARD_ERROR INFO 2024-07-02 11:20:38 MarkDuplicates Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2661501793037820934.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2661501793037820934.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2661501793037820934.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2661501793037820934.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2661501793037820934.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2661501793037820934.tmp/output.sam Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:38.042 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:38.042 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:38.043 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:38.043 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:38.043 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:38.043 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:38.043 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:38.043 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:38 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2661501793037820934.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2661501793037820934.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2661501793037820934.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:38 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2661501793037820934.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2661501793037820934.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2661501793037820934.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:38 MarkDuplicates Start of doWork freeMemory: 1027984552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:38 MarkDuplicates Start of doWork freeMemory: 1027984552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:38 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:38 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:38 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:38 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:38 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:38 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:38 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:20:38 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 973452896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 973452896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:38 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:38 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:38 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:38 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:38 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:38 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 489011160; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 489011160; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:38 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:20:38 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:38 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:38 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:38 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:38 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:38 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:38 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:38 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:38 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:38 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:38 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:38 MarkDuplicates Before output close freeMemory: 758354992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:38 MarkDuplicates Before output close freeMemory: 758354992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:38 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:38 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:38 MarkDuplicates After output close freeMemory: 758127832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:38 MarkDuplicates After output close freeMemory: 758127832; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:38 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:38 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:38 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoMappedPairWithSamePosition STANDARD_ERROR INFO 2024-07-02 11:20:38 MarkDuplicates Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2676163273702817980.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2676163273702817980.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2676163273702817980.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2676163273702817980.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2676163273702817980.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2676163273702817980.tmp/output.sam Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:38.771 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:38.771 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:38.771 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:38.771 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:38.771 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:38.771 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:38.772 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:38.772 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:38 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2676163273702817980.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2676163273702817980.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2676163273702817980.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:38 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2676163273702817980.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2676163273702817980.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2676163273702817980.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:38 MarkDuplicates Start of doWork freeMemory: 1027982392; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:38 MarkDuplicates Start of doWork freeMemory: 1027982392; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:38 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:38 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:38 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:38 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:38 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:38 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:38 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:38 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 973450264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 973450264; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:39 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:39 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:39 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:39 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:39 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:39 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 489008704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 489008704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:39 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:39 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:39 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:39 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:39 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:39 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:39 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:39 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:39 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:39 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:39 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:39 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:39 MarkDuplicates Before output close freeMemory: 758352152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:39 MarkDuplicates Before output close freeMemory: 758352152; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:39 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:39 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:39 MarkDuplicates After output close freeMemory: 758125176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:39 MarkDuplicates After output close freeMemory: 758125176; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:39 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoMappedPairWithSamePositionDifferentStrands STANDARD_ERROR INFO 2024-07-02 11:20:39 MarkDuplicates Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4102636535954939812.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4102636535954939812.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4102636535954939812.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4102636535954939812.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4102636535954939812.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4102636535954939812.tmp/output.sam Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:39.576 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:39.576 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:39.576 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:39.576 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:39.579 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:39.579 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:39.579 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:39.579 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:39 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4102636535954939812.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4102636535954939812.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4102636535954939812.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:39 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4102636535954939812.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4102636535954939812.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4102636535954939812.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:39 MarkDuplicates Start of doWork freeMemory: 1027981816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:39 MarkDuplicates Start of doWork freeMemory: 1027981816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:39 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:39 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:39 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:39 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:39 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:39 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:39 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:39 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 973449688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 973449688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:40 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:40 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:40 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:40 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:40 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 489008128; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 489008128; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:40 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:40 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:40 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:40 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:40 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:40 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:40 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:40 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:40 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:40 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:40 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:40 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:40 MarkDuplicates Before output close freeMemory: 758351216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:40 MarkDuplicates Before output close freeMemory: 758351216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:40 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:40 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:40 MarkDuplicates After output close freeMemory: 758492032; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:40 MarkDuplicates After output close freeMemory: 758492032; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:40 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:40 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:40 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoMappedPairWithSamePositionDifferentStrands2 STANDARD_ERROR INFO 2024-07-02 11:20:40 MarkDuplicates Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16057084097058115792.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16057084097058115792.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16057084097058115792.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16057084097058115792.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16057084097058115792.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16057084097058115792.tmp/output.sam Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:40.395 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:40.395 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:40.395 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:40.395 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:40.396 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:40.396 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:40.396 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:40.396 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:40 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16057084097058115792.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16057084097058115792.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16057084097058115792.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:40 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16057084097058115792.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16057084097058115792.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16057084097058115792.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:40 MarkDuplicates Start of doWork freeMemory: 1027981080; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:40 MarkDuplicates Start of doWork freeMemory: 1027981080; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:40 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:40 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:40 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:40 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:40 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:40 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:40 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:40 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 973082072; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 973082072; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:40 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:40 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:40 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:40 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:40 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 614836512; totalMemory: 1199570944; maxMemory: 2147483648 INFO 2024-07-02 11:20:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 614836512; totalMemory: 1199570944; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:40 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:40 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:40 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:40 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:40 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:40 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:41 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:41 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:41 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:41 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:41 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:41 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:41 MarkDuplicates Before output close freeMemory: 757983816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:41 MarkDuplicates Before output close freeMemory: 757983816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:41 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:41 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:41 MarkDuplicates After output close freeMemory: 758490728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:41 MarkDuplicates After output close freeMemory: 758490728; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:41 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:20:41 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:41 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:20:41 MarkDuplicates Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.900821633796046648.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.900821633796046648.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.900821633796046648.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.900821633796046648.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.900821633796046648.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.900821633796046648.tmp/output.sam Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:41.339 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:41.339 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:41.340 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:41.340 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:41.340 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:41.340 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:41.340 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:41.340 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:41 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.900821633796046648.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.900821633796046648.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.900821633796046648.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:41 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.900821633796046648.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.900821633796046648.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.900821633796046648.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:41 MarkDuplicates Start of doWork freeMemory: 1027980144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:41 MarkDuplicates Start of doWork freeMemory: 1027980144; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:41 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:41 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:41 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:41 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:41 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:41 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:41 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:41 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 973448016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 973448016; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:41 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:41 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:41 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:41 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 489006456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 489006456; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:42 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:42 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:42 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:42 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:42 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:42 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:42 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:42 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:42 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:42 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:42 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:42 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:42 MarkDuplicates Before output close freeMemory: 757983104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:42 MarkDuplicates Before output close freeMemory: 757983104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:42 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:42 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:42 MarkDuplicates After output close freeMemory: 758123472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:42 MarkDuplicates After output close freeMemory: 758123472; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:20:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:42 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoMappedPairsAndMappedSecondaryFragment STANDARD_ERROR INFO 2024-07-02 11:20:42 MarkDuplicates Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12585028813714701937.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12585028813714701937.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12585028813714701937.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12585028813714701937.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12585028813714701937.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12585028813714701937.tmp/output.sam Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:42.396 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:42.396 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:42.396 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:42.396 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:42.396 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:42.396 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:42.396 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:42.396 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:42 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12585028813714701937.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12585028813714701937.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12585028813714701937.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:42 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12585028813714701937.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12585028813714701937.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12585028813714701937.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:42 MarkDuplicates Start of doWork freeMemory: 1027978328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:42 MarkDuplicates Start of doWork freeMemory: 1027978328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:42 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:42 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:42 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:42 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:42 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:42 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:42 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:20:42 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 973445992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 973445992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:42 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:42 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:42 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:42 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:42 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:42 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 489005032; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 489005032; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:42 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:42 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:42 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:42 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:42 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:42 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:42 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:42 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:42 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:42 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:42 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:42 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:43 MarkDuplicates Before output close freeMemory: 758348232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:43 MarkDuplicates Before output close freeMemory: 758348232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:43 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:43 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:43 MarkDuplicates After output close freeMemory: 758488936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:43 MarkDuplicates After output close freeMemory: 758488936; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:43 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:43 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:43 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoMappedPairsAndTerminalUnmappedFragment STANDARD_ERROR INFO 2024-07-02 11:20:43 MarkDuplicates Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.14828108461419860291.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14828108461419860291.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14828108461419860291.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.14828108461419860291.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14828108461419860291.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14828108461419860291.tmp/output.sam Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:43.146 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:43.146 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:43.146 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:43.146 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:43.146 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:43.146 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:43.147 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:43.147 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:43 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.14828108461419860291.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.14828108461419860291.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.14828108461419860291.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:43 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.14828108461419860291.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.14828108461419860291.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.14828108461419860291.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:43 MarkDuplicates Start of doWork freeMemory: 1027976088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:43 MarkDuplicates Start of doWork freeMemory: 1027976088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:43 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:43 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:43 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:43 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:43 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:43 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:43 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:43 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 973445872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 973445872; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:43 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:43 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:43 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:43 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:43 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:43 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 489004312; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 489004312; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:43 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:43 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:43 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:43 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:43 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:43 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:43 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:43 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:43 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:43 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:43 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:43 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:44 MarkDuplicates Before output close freeMemory: 758348352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:44 MarkDuplicates Before output close freeMemory: 758348352; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:44 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:44 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:44 MarkDuplicates After output close freeMemory: 758487648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:44 MarkDuplicates After output close freeMemory: 758487648; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:44 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:20:44 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:44 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoMappedPairsAndTerminalUnmappedPair STANDARD_ERROR INFO 2024-07-02 11:20:44 MarkDuplicates Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.8263180468259611584.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8263180468259611584.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8263180468259611584.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.8263180468259611584.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8263180468259611584.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8263180468259611584.tmp/output.sam Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:44.302 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:44.302 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:44.302 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:44.302 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:44.302 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:44.302 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:44.302 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:44.302 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:44 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8263180468259611584.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8263180468259611584.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8263180468259611584.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:44 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8263180468259611584.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8263180468259611584.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8263180468259611584.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:44 MarkDuplicates Start of doWork freeMemory: 1027976800; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:44 MarkDuplicates Start of doWork freeMemory: 1027976800; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:44 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:44 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:44 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:44 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:44 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:44 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:44 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:44 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 973444672; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 973444672; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:44 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:44 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:44 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:44 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:44 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 489003112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 489003112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:45 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:45 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:45 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:45 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:45 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:45 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:45 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:45 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:45 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:45 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:45 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:45 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:45 MarkDuplicates Before output close freeMemory: 758347152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:45 MarkDuplicates Before output close freeMemory: 758347152; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:45 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:45 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:45 MarkDuplicates After output close freeMemory: 758487016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:45 MarkDuplicates After output close freeMemory: 758487016; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:20:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:45 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoMappedPairsMatesSoftClipped STANDARD_ERROR INFO 2024-07-02 11:20:45 MarkDuplicates Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5532474096246407832.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5532474096246407832.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5532474096246407832.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5532474096246407832.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5532474096246407832.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5532474096246407832.tmp/output.sam Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:45.295 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:45.295 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:45.295 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:45.295 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:45.296 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:45.296 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:45.296 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:45.296 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:45 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5532474096246407832.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5532474096246407832.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5532474096246407832.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:45 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5532474096246407832.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5532474096246407832.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5532474096246407832.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:45 MarkDuplicates Start of doWork freeMemory: 1027976808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:45 MarkDuplicates Start of doWork freeMemory: 1027976808; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:45 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:45 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:45 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:45 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:45 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:45 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:45 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:45 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 973444680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 973444680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:45 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:45 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:45 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:45 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:45 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:45 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 489003120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 489003120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:45 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:20:45 MarkDuplicates Marking 0 records as duplicates. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:45 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:45 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:45 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:45 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:45 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:45 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:45 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:45 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:45 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:45 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:46 MarkDuplicates Before output close freeMemory: 758346768; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:46 MarkDuplicates Before output close freeMemory: 758346768; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:46 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:46 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:46 MarkDuplicates After output close freeMemory: 758487024; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:46 MarkDuplicates After output close freeMemory: 758487024; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:20:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:46 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoMappedPairsWithOppositeOrientations STANDARD_ERROR INFO 2024-07-02 11:20:46 MarkDuplicates Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2644478338023273647.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2644478338023273647.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2644478338023273647.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2644478338023273647.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2644478338023273647.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2644478338023273647.tmp/output.sam Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:46.233 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:46.233 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:46.234 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:46.234 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:46.234 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:46.234 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:46.234 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:46.234 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:46 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2644478338023273647.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2644478338023273647.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2644478338023273647.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:46 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2644478338023273647.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2644478338023273647.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2644478338023273647.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:46 MarkDuplicates Start of doWork freeMemory: 1027975752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:46 MarkDuplicates Start of doWork freeMemory: 1027975752; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:46 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:46 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:46 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:46 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:46 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:46 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:46 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:46 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 973443624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 973443624; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:46 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:46 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:46 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:46 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:46 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:46 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 489002064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 489002064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:46 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:46 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:46 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:46 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:46 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:46 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:46 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:46 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:46 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:46 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:46 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:46 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:46 MarkDuplicates Before output close freeMemory: 758345712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:46 MarkDuplicates Before output close freeMemory: 758345712; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:47 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:47 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:47 MarkDuplicates After output close freeMemory: 758485968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:47 MarkDuplicates After output close freeMemory: 758485968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:47 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:47 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:47 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoMappedPairsWithOppositeOrientationsNumberTwo STANDARD_ERROR INFO 2024-07-02 11:20:47 MarkDuplicates Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7608578256988919618.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7608578256988919618.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7608578256988919618.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7608578256988919618.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7608578256988919618.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7608578256988919618.tmp/output.sam Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:47.158 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:47.158 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:47.158 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:47.158 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:47.159 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:47.159 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:47.159 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:47.159 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:47 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7608578256988919618.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7608578256988919618.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7608578256988919618.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:47 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7608578256988919618.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7608578256988919618.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7608578256988919618.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:47 MarkDuplicates Start of doWork freeMemory: 1027974976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:47 MarkDuplicates Start of doWork freeMemory: 1027974976; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:47 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:47 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:47 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:47 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:47 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:47 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:47 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:47 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 973442848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 973442848; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:47 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:47 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:47 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:47 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:47 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:47 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 489001288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 489001288; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:47 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:47 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:47 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:47 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:47 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:47 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:47 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:47 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:47 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:47 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:47 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:47 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:47 MarkDuplicates Before output close freeMemory: 757977640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:47 MarkDuplicates Before output close freeMemory: 757977640; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:47 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:47 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:48 MarkDuplicates After output close freeMemory: 758118304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:48 MarkDuplicates After output close freeMemory: 758118304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:48 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:20:48 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:48 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoMappedPairsWithSoftClipping STANDARD_ERROR INFO 2024-07-02 11:20:48 MarkDuplicates Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6403217101246492074.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6403217101246492074.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6403217101246492074.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6403217101246492074.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6403217101246492074.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6403217101246492074.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:48.099 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:48.099 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:48.100 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:48.100 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:48.100 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:48.100 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:48.100 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:48.100 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:48 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6403217101246492074.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6403217101246492074.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6403217101246492074.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:48 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6403217101246492074.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6403217101246492074.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6403217101246492074.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:48 MarkDuplicates Start of doWork freeMemory: 1027974056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:48 MarkDuplicates Start of doWork freeMemory: 1027974056; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:48 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:48 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:48 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:48 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:48 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:48 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:48 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:48 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 973074984; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 973074984; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:48 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:48 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:48 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:48 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:48 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:48 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:48 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:48 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 489000304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 489000304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:48 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:48 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:48 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:48 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:48 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:48 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:48 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:48 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:48 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:48 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:48 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:48 MarkDuplicates Before output close freeMemory: 757976880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:48 MarkDuplicates Before output close freeMemory: 757976880; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:48 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:48 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:48 MarkDuplicates After output close freeMemory: 758483640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:48 MarkDuplicates After output close freeMemory: 758483640; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:48 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:48 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:48 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoMappedPairsWithSoftClippingBoth STANDARD_ERROR INFO 2024-07-02 11:20:48 MarkDuplicates Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16701977073856392778.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16701977073856392778.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16701977073856392778.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16701977073856392778.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16701977073856392778.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16701977073856392778.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:48.859 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:48.859 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:48.859 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:48.859 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:48.859 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:48.859 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:48.859 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:48.859 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:48 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16701977073856392778.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16701977073856392778.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16701977073856392778.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:48 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16701977073856392778.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16701977073856392778.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16701977073856392778.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:48 MarkDuplicates Start of doWork freeMemory: 1027970320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:48 MarkDuplicates Start of doWork freeMemory: 1027970320; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:48 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:48 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:48 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:48 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:48 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:48 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:48 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:20:48 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 973440424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 973440424; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:49 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:49 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:49 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:49 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:49 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:49 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:49 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:49 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 488999464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 488999464; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:49 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:49 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:49 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:49 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:49 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:49 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:49 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:49 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:49 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:49 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:49 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:49 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:49 MarkDuplicates Before output close freeMemory: 758343112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:49 MarkDuplicates Before output close freeMemory: 758343112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:49 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:49 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:49 MarkDuplicates After output close freeMemory: 758483144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:49 MarkDuplicates After output close freeMemory: 758483144; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:49 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar STANDARD_ERROR INFO 2024-07-02 11:20:49 MarkDuplicates Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5032590196225031971.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5032590196225031971.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5032590196225031971.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5032590196225031971.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5032590196225031971.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5032590196225031971.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:49.625 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:49.625 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:49.625 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:49.625 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:49.626 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:49.626 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:49.626 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:49.626 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:49 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5032590196225031971.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5032590196225031971.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5032590196225031971.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:49 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5032590196225031971.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5032590196225031971.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5032590196225031971.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:49 MarkDuplicates Start of doWork freeMemory: 1027970728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:49 MarkDuplicates Start of doWork freeMemory: 1027970728; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:49 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:49 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:49 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:49 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:49 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:20:49 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:49 MarkDuplicates Read 2 records. 2 pairs never matched. INFO 2024-07-02 11:20:49 MarkDuplicates Read 2 records. 2 pairs never matched. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 973441576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 973441576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:49 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:49 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:50 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:50 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:50 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 489033752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 489033752; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:20:50 MarkDuplicates Marking 0 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:50 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:50 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:50 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:50 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:50 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates Before output close freeMemory: 758377040; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:50 MarkDuplicates Before output close freeMemory: 758377040; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:50 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates After output close freeMemory: 758517360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:50 MarkDuplicates After output close freeMemory: 758517360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoMappedPairsWithSupplementaryReads[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:20:50 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7307512312722905112.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7307512312722905112.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7307512312722905112.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7307512312722905112.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7307512312722905112.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7307512312722905112.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:50.371 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:50.371 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:50.372 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:50.372 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:50.372 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:50.372 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:50.372 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:50.372 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:50 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7307512312722905112.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7307512312722905112.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7307512312722905112.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:50 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7307512312722905112.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7307512312722905112.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7307512312722905112.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates Start of doWork freeMemory: 1028004128; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:50 MarkDuplicates Start of doWork freeMemory: 1028004128; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:50 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:50 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:20:50 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 973471752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 973471752; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:50 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:50 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:50 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 918946384; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2024-07-02 11:20:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 918946384; totalMemory: 1503657984; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:50 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:20:50 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:50 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:50 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:50 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:50 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:50 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:51 MarkDuplicates Before output close freeMemory: 758373848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:51 MarkDuplicates Before output close freeMemory: 758373848; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:51 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:51 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:51 MarkDuplicates After output close freeMemory: 758513560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:51 MarkDuplicates After output close freeMemory: 758513560; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:51 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoMappedPairsWithSupplementaryReads[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:20:51 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15194874327710203084.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15194874327710203084.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15194874327710203084.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15194874327710203084.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15194874327710203084.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15194874327710203084.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:51.155 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:51.155 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:51.156 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:51.156 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:51.156 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:51.156 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:51.156 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:51.156 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:51 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15194874327710203084.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15194874327710203084.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15194874327710203084.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:51 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15194874327710203084.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15194874327710203084.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15194874327710203084.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:51 MarkDuplicates Start of doWork freeMemory: 1027633896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:51 MarkDuplicates Start of doWork freeMemory: 1027633896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:51 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:51 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:51 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:51 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:51 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:20:51 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 973104112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 973104112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:51 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:51 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:51 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:51 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:51 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:51 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:51 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:51 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 488815992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 488815992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:51 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:51 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:51 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:20:51 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:51 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:51 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:51 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:51 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:51 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:51 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:51 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:51 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:51 MarkDuplicates Before output close freeMemory: 758372712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:51 MarkDuplicates Before output close freeMemory: 758372712; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:51 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:51 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:52 MarkDuplicates After output close freeMemory: 758146304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:52 MarkDuplicates After output close freeMemory: 758146304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:52 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoMappedPairsWithSupplementaryReads[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:20:52 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7074433179768307265.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7074433179768307265.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7074433179768307265.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7074433179768307265.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7074433179768307265.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7074433179768307265.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:52.041 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:52.041 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:52.041 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:52.041 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:52.042 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:52.042 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:52.042 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:52.042 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:52 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7074433179768307265.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7074433179768307265.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7074433179768307265.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:52 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7074433179768307265.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7074433179768307265.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7074433179768307265.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:52 MarkDuplicates Start of doWork freeMemory: 1028002576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:52 MarkDuplicates Start of doWork freeMemory: 1028002576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:52 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:52 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:52 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:52 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:52 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:20:52 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 972736800; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 972736800; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:52 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:52 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:52 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:52 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:52 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:52 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:52 MarkDuplicates After generateDuplicateIndexes freeMemory: 489027912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:52 MarkDuplicates After generateDuplicateIndexes freeMemory: 489027912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:52 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:52 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:52 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:20:52 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:52 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:52 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:52 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:52 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:52 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:52 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:52 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:52 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:52 MarkDuplicates Before output close freeMemory: 758004672; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:52 MarkDuplicates Before output close freeMemory: 758004672; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:52 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:52 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:52 MarkDuplicates After output close freeMemory: 758511816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:52 MarkDuplicates After output close freeMemory: 758511816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:52 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoMappedPairsWithSupplementaryReads[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:20:52 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11613996268363229284.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11613996268363229284.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11613996268363229284.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11613996268363229284.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11613996268363229284.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11613996268363229284.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:52.745 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:52.745 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:52.745 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:52.745 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:52.745 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:52.745 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:52.746 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:52.746 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:52 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11613996268363229284.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11613996268363229284.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11613996268363229284.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:52 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11613996268363229284.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11613996268363229284.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11613996268363229284.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:52 MarkDuplicates Start of doWork freeMemory: 1028001168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:52 MarkDuplicates Start of doWork freeMemory: 1028001168; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:52 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:52 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:52 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:52 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:52 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:20:52 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 973468760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 973468760; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:53 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:53 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:53 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 489027264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 489027264; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:53 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:20:53 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:53 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:53 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:53 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:53 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates Before output close freeMemory: 758370888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:53 MarkDuplicates Before output close freeMemory: 758370888; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:53 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates After output close freeMemory: 758511168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:53 MarkDuplicates After output close freeMemory: 758511168; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoMappedPairsWithSupplementaryReads[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:20:53 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9741947402736315798.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9741947402736315798.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9741947402736315798.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9741947402736315798.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9741947402736315798.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9741947402736315798.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:53.437 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:53.437 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:53.437 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:53.437 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:53.438 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:53.438 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:53.438 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:53.438 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:53 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9741947402736315798.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9741947402736315798.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9741947402736315798.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:53 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9741947402736315798.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9741947402736315798.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9741947402736315798.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates Start of doWork freeMemory: 1028000112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:53 MarkDuplicates Start of doWork freeMemory: 1028000112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:53 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:53 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:20:53 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 973468072; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 973468072; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:53 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:53 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:53 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 488813304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 488813304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:53 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:20:53 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:53 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:53 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:53 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:53 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:53 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates Before output close freeMemory: 758370224; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:54 MarkDuplicates Before output close freeMemory: 758370224; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:54 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates After output close freeMemory: 758143344; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:54 MarkDuplicates After output close freeMemory: 758143344; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:54 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:54 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoMappedPairsWithSupplementaryReads[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:20:54 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.434838924202646117.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.434838924202646117.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.434838924202646117.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.434838924202646117.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.434838924202646117.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.434838924202646117.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:54.128 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:54.128 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:54.129 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:54.129 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:54.129 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:54.129 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:54.129 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:54.129 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:54 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.434838924202646117.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.434838924202646117.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.434838924202646117.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:54 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.434838924202646117.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.434838924202646117.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.434838924202646117.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates Start of doWork freeMemory: 1027999880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:54 MarkDuplicates Start of doWork freeMemory: 1027999880; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:54 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:54 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:20:54 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 973467472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 973467472; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:54 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:54 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:54 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:54 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 489025976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 489025976; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:54 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:20:54 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:54 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:54 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:54 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:54 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates Before output close freeMemory: 758369400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:54 MarkDuplicates Before output close freeMemory: 758369400; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:54 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates After output close freeMemory: 758142984; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:54 MarkDuplicates After output close freeMemory: 758142984; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:54 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:54 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:20:54 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6105825992878412471.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6105825992878412471.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6105825992878412471.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6105825992878412471.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6105825992878412471.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6105825992878412471.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:54.798 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:54.798 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:54.798 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:54.798 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:54.798 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:54.798 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:54.799 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:54.799 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:54 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6105825992878412471.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6105825992878412471.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6105825992878412471.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:54 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6105825992878412471.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6105825992878412471.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6105825992878412471.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates Start of doWork freeMemory: 1027998696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:54 MarkDuplicates Start of doWork freeMemory: 1027998696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:54 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:54 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:20:54 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 973466232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 973466232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:55 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:55 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:55 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 585493728; totalMemory: 1170210816; maxMemory: 2147483648 INFO 2024-07-02 11:20:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 585493728; totalMemory: 1170210816; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:55 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:20:55 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:55 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:55 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:55 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:55 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates Before output close freeMemory: 758368520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:55 MarkDuplicates Before output close freeMemory: 758368520; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:55 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates After output close freeMemory: 758141480; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:55 MarkDuplicates After output close freeMemory: 758141480; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:55 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:55 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:20:55 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13633580718396079901.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13633580718396079901.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13633580718396079901.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13633580718396079901.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13633580718396079901.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13633580718396079901.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:55.460 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:55.460 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:55.460 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:55.460 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:55.460 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:55.460 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:55.460 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:55.460 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:55 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13633580718396079901.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13633580718396079901.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13633580718396079901.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:55 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13633580718396079901.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13633580718396079901.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13633580718396079901.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates Start of doWork freeMemory: 1027630928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:55 MarkDuplicates Start of doWork freeMemory: 1027630928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:55 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:55 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:20:55 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 973465576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 973465576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:55 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:55 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:55 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 489024080; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 489024080; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:55 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:20:55 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:55 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:55 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:55 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:55 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:55 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:56 MarkDuplicates Before output close freeMemory: 758367864; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:56 MarkDuplicates Before output close freeMemory: 758367864; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:56 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:56 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:56 MarkDuplicates After output close freeMemory: 758140824; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:56 MarkDuplicates After output close freeMemory: 758140824; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:56 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:56 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:56 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:20:56 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.1516177344517171687.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1516177344517171687.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1516177344517171687.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.1516177344517171687.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1516177344517171687.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1516177344517171687.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:56.136 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:56.136 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:56.136 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:56.136 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:56.136 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:56.136 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:56.136 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:56.136 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:56 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1516177344517171687.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1516177344517171687.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1516177344517171687.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:56 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1516177344517171687.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1516177344517171687.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1516177344517171687.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:56 MarkDuplicates Start of doWork freeMemory: 1027997368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:56 MarkDuplicates Start of doWork freeMemory: 1027997368; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:56 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:56 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:56 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:56 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:56 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:20:56 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 973464960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 973464960; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:56 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:56 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:56 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:56 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:56 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:56 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 489023464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 489023464; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:56 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:56 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:56 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:20:56 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:56 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:56 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:56 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:56 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:56 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:56 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:56 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:56 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:56 MarkDuplicates Before output close freeMemory: 758367248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:56 MarkDuplicates Before output close freeMemory: 758367248; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:56 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:56 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:56 MarkDuplicates After output close freeMemory: 758507368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:56 MarkDuplicates After output close freeMemory: 758507368; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:56 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:56 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:56 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:20:56 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.400085325838519025.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.400085325838519025.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.400085325838519025.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.400085325838519025.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.400085325838519025.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.400085325838519025.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:56.801 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:56.801 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:56.801 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:56.801 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:56.801 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:56.801 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:56.801 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:56.801 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:56 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.400085325838519025.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.400085325838519025.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.400085325838519025.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:56 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.400085325838519025.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.400085325838519025.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.400085325838519025.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:56 MarkDuplicates Start of doWork freeMemory: 1027996744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:56 MarkDuplicates Start of doWork freeMemory: 1027996744; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:56 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:56 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:56 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:56 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:56 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:20:56 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 973097664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 973097664; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:57 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:57 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:57 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 489022840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 489022840; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:57 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:20:57 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:57 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:57 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:57 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:57 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates Before output close freeMemory: 758366624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:57 MarkDuplicates Before output close freeMemory: 758366624; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:57 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates After output close freeMemory: 758139888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:57 MarkDuplicates After output close freeMemory: 758139888; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:57 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:57 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:20:57 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12940695708723020587.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12940695708723020587.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12940695708723020587.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12940695708723020587.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12940695708723020587.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12940695708723020587.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:57.500 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:57.500 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:57.500 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:57.500 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:57.500 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:57.500 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:57.501 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:57.501 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:57 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12940695708723020587.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12940695708723020587.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12940695708723020587.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:57 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12940695708723020587.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12940695708723020587.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12940695708723020587.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates Start of doWork freeMemory: 1027996088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:57 MarkDuplicates Start of doWork freeMemory: 1027996088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:57 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:57 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:20:57 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 973097008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 973097008; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:57 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:57 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:57 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 489022184; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 489022184; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:57 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:20:57 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:57 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:57 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:57 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:57 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:57 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:58 MarkDuplicates Before output close freeMemory: 758365968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:58 MarkDuplicates Before output close freeMemory: 758365968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:58 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:58 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:58 MarkDuplicates After output close freeMemory: 758138928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:58 MarkDuplicates After output close freeMemory: 758138928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:58 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:20:58 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12158357514054861839.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12158357514054861839.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12158357514054861839.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12158357514054861839.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12158357514054861839.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12158357514054861839.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:58.150 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:58.150 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:58.150 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:58.150 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:58.150 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:58.150 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:58.150 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:58.150 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:58 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12158357514054861839.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12158357514054861839.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12158357514054861839.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:58 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12158357514054861839.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12158357514054861839.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12158357514054861839.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:58 MarkDuplicates Start of doWork freeMemory: 1027628400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:58 MarkDuplicates Start of doWork freeMemory: 1027628400; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:58 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:58 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:58 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:58 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:58 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:20:58 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 973463264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 973463264; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:58 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:58 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:58 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:58 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:58 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:58 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 489021552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 489021552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:58 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:20:58 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:58 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:20:58 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:58 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:58 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:58 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:58 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:58 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:58 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:58 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:58 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:58 MarkDuplicates Before output close freeMemory: 758365336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:58 MarkDuplicates Before output close freeMemory: 758365336; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:58 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:58 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:58 MarkDuplicates After output close freeMemory: 758138296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:58 MarkDuplicates After output close freeMemory: 758138296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:58 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoUnmappedFragments STANDARD_ERROR INFO 2024-07-02 11:20:58 MarkDuplicates Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5108465060474601617.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5108465060474601617.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5108465060474601617.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5108465060474601617.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5108465060474601617.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5108465060474601617.tmp/output.sam Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:58.818 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:58.818 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:58.818 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:58.818 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:58.819 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:58.819 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:58.819 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:58.819 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:58 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5108465060474601617.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5108465060474601617.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5108465060474601617.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:58 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5108465060474601617.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5108465060474601617.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5108465060474601617.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:58 MarkDuplicates Start of doWork freeMemory: 1027994520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:58 MarkDuplicates Start of doWork freeMemory: 1027994520; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:58 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:58 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:58 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:20:58 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:58 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2024-07-02 11:20:58 MarkDuplicates Read 0 records. 0 pairs never matched. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 973465768; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 973465768; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:59 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:59 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:59 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:59 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 489024072; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 489024072; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:20:59 MarkDuplicates Marking 0 records as duplicates. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:59 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:59 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:59 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:59 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:59 MarkDuplicates Getting Memory Stats. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Before output close freeMemory: 758368112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:59 MarkDuplicates Before output close freeMemory: 758368112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:59 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates After output close freeMemory: 758140816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:59 MarkDuplicates After output close freeMemory: 758140816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:59 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:20:59 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]}) STANDARD_ERROR INFO 2024-07-02 11:20:59 MarkDuplicates Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam -OUTPUT /tmp/MarkDuplicates.6969589279046050888.tmp/MarkDuplicates.sam -METRICS_FILE /tmp/MarkDuplicates.6969589279046050888.tmp/MarkDuplicates.duplicate_metrics -ADD_PG_TAG_TO_READS true ********** MarkDuplicates -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam -OUTPUT /tmp/MarkDuplicates.6969589279046050888.tmp/MarkDuplicates.sam -METRICS_FILE /tmp/MarkDuplicates.6969589279046050888.tmp/MarkDuplicates.duplicate_metrics -ADD_PG_TAG_TO_READS true Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:59.444 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:59.444 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:59.444 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:59.444 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:59.445 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:20:59.445 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:20:59.445 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:20:59.445 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:59 GMT+14:00 2024] MarkDuplicates ADD_PG_TAG_TO_READS=true INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.6969589279046050888.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.6969589279046050888.tmp/MarkDuplicates.duplicate_metrics MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:20:59 GMT+14:00 2024] MarkDuplicates ADD_PG_TAG_TO_READS=true INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.6969589279046050888.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.6969589279046050888.tmp/MarkDuplicates.duplicate_metrics MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:20:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:20:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Start of doWork freeMemory: 1028001392; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:59 MarkDuplicates Start of doWork freeMemory: 1028001392; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:20:59 MarkDuplicates Reading input file and constructing read end information. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:20:59 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:20:59 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name '1AAXX.1.1'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. WARNING 2024-07-02 11:20:59 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name '1AAXX.1.1'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:20:59 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 965078360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 965078360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2024-07-02 11:20:59 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:20:59 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:20:59 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:20:59 MarkDuplicates Sorting list of duplicate records. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 490074344; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 490074344; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:20:59 MarkDuplicates Marking 4 records as duplicates. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:20:59 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:20:59 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:20:59 MarkDuplicates Writing complete. Closing input iterator. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:20:59 MarkDuplicates Duplicate Index cleanup. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:20:59 MarkDuplicates Getting Memory Stats. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Before output close freeMemory: 1027850176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:20:59 MarkDuplicates Before output close freeMemory: 1027850176; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:20:59 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:20:59 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:00 MarkDuplicates After output close freeMemory: 1027992432; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:00 MarkDuplicates After output close freeMemory: 1027992432; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4945815b, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1bc5856e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@ae5d2f3], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4bd9fdd9, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2e73e2a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@192aecf5]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:00 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]}) STANDARD_ERROR INFO 2024-07-02 11:21:00 MarkDuplicates Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam -OUTPUT /tmp/MarkDuplicates.5743900398088327782.tmp/MarkDuplicates.sam -METRICS_FILE /tmp/MarkDuplicates.5743900398088327782.tmp/MarkDuplicates.duplicate_metrics -ADD_PG_TAG_TO_READS true -PROGRAM_RECORD_ID null ********** MarkDuplicates -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam -OUTPUT /tmp/MarkDuplicates.5743900398088327782.tmp/MarkDuplicates.sam -METRICS_FILE /tmp/MarkDuplicates.5743900398088327782.tmp/MarkDuplicates.duplicate_metrics -ADD_PG_TAG_TO_READS true -PROGRAM_RECORD_ID null Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:00.077 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:00.077 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:00.077 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:00.077 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:00.078 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:00.078 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:00.078 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:00.078 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:00 GMT+14:00 2024] MarkDuplicates ADD_PG_TAG_TO_READS=true INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.5743900398088327782.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.5743900398088327782.tmp/MarkDuplicates.duplicate_metrics PROGRAM_RECORD_ID=null MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:00 GMT+14:00 2024] MarkDuplicates ADD_PG_TAG_TO_READS=true INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.5743900398088327782.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.5743900398088327782.tmp/MarkDuplicates.duplicate_metrics PROGRAM_RECORD_ID=null MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:00 MarkDuplicates Start of doWork freeMemory: 1027997136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:00 MarkDuplicates Start of doWork freeMemory: 1027997136; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:00 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:00 MarkDuplicates Reading input file and constructing read end information. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:00 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:21:00 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:00 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name '1AAXX.1.1'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. WARNING 2024-07-02 11:21:00 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name '1AAXX.1.1'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:00 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:21:00 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 965076496; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 965076496; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:00 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:00 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:00 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:00 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:00 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:00 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:00 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:00 MarkDuplicates Sorting list of duplicate records. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 1027992728; totalMemory: 1611661312; maxMemory: 2147483648 INFO 2024-07-02 11:21:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 1027992728; totalMemory: 1611661312; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:00 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:21:00 MarkDuplicates Marking 4 records as duplicates. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:00 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:00 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:00 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:00 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:00 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:00 MarkDuplicates Writing complete. Closing input iterator. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:00 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:00 MarkDuplicates Duplicate Index cleanup. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:00 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:00 MarkDuplicates Getting Memory Stats. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:00 MarkDuplicates Before output close freeMemory: 1027849976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:00 MarkDuplicates Before output close freeMemory: 1027849976; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:00 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:00 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:00 MarkDuplicates After output close freeMemory: 1027991096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:00 MarkDuplicates After output close freeMemory: 1027991096; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@71311a44, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@569259d9], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b19cb27], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:00 MarkDuplicates Start of doWork freeMemory: 1028014680; totalMemory: 1073741824; maxMemory: 2147483648 Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1) STANDARD_ERROR INFO 2024-07-02 11:21:00 MarkDuplicates Start of doWork freeMemory: 1028014680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:00 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:00 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:00 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:21:00 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:00 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:21:00 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 965093936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 965093936; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:01 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:01 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:01 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:01 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 490089624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 490089624; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:21:01 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:21:01 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:01 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:01 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:01 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:01 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates Before output close freeMemory: 1027503184; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:01 MarkDuplicates Before output close freeMemory: 1027503184; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:01 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates After output close freeMemory: 1028008968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:01 MarkDuplicates After output close freeMemory: 1028008968; totalMemory: 1073741824; maxMemory: 2147483648 Running Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates Start of doWork freeMemory: 1028013664; totalMemory: 1073741824; maxMemory: 2147483648 Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1) STANDARD_ERROR INFO 2024-07-02 11:21:01 MarkDuplicates Start of doWork freeMemory: 1028013664; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:01 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:21:01 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:21:01 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 965093120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 965093120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:01 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:01 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:01 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:01 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 490088592; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 490088592; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:21:01 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:21:01 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:01 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:01 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:01 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:01 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:01 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:02 MarkDuplicates Before output close freeMemory: 1027869048; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:02 MarkDuplicates Before output close freeMemory: 1027869048; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:02 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:02 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:02 MarkDuplicates After output close freeMemory: 1028008056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:02 MarkDuplicates After output close freeMemory: 1028008056; totalMemory: 1073741824; maxMemory: 2147483648 Running Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:02 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testTwoMappedPairsWithSoftClippingFirstOfPairOnly STANDARD_ERROR INFO 2024-07-02 11:21:02 MarkDuplicates Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2729948382211793050.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2729948382211793050.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2729948382211793050.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2729948382211793050.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2729948382211793050.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2729948382211793050.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:02.149 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:02.149 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:02.149 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:02.149 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:02.150 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:02.150 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:02.150 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:02.150 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:02 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2729948382211793050.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2729948382211793050.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2729948382211793050.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:02 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2729948382211793050.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2729948382211793050.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2729948382211793050.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:02 MarkDuplicates Start of doWork freeMemory: 1027989248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:02 MarkDuplicates Start of doWork freeMemory: 1027989248; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:02 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:02 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:02 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:02 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:02 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:21:02 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:02 MarkDuplicates Read 2 records. 2 pairs never matched. INFO 2024-07-02 11:21:02 MarkDuplicates Read 2 records. 2 pairs never matched. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 973457400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 973457400; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:02 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:02 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:02 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:02 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:02 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:02 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:02 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:02 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 918931824; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2024-07-02 11:21:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 918931824; totalMemory: 1503657984; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:02 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:21:02 MarkDuplicates Marking 0 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:02 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:02 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:02 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:02 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:02 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:02 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:02 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:02 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:02 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:02 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:02 MarkDuplicates Before output close freeMemory: 758359288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:02 MarkDuplicates Before output close freeMemory: 758359288; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:02 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:02 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:02 MarkDuplicates After output close freeMemory: 758132336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:02 MarkDuplicates After output close freeMemory: 758132336; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:02 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:02 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:02 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testWithBarcodeComplex STANDARD_ERROR INFO 2024-07-02 11:21:02 MarkDuplicates Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3604526617094078774.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3604526617094078774.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3604526617094078774.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3604526617094078774.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3604526617094078774.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3604526617094078774.tmp/output.sam Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:02.892 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:02.892 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:02.892 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:02.892 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:02.893 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:02.893 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:02.893 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:02.893 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:02 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3604526617094078774.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3604526617094078774.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3604526617094078774.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:02 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3604526617094078774.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3604526617094078774.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3604526617094078774.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:02 MarkDuplicates Start of doWork freeMemory: 1027984992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:02 MarkDuplicates Start of doWork freeMemory: 1027984992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:02 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:02 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:02 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:02 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:03 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:21:03 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 973452296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 973452296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:03 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:03 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:03 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:03 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:03 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:03 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:03 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:03 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 489011064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 489011064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:03 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:21:03 MarkDuplicates Marking 2 records as duplicates. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:03 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:03 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:03 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:03 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:03 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:03 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:03 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:03 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:03 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:03 MarkDuplicates Getting Memory Stats. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:03 MarkDuplicates Before output close freeMemory: 758354640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:03 MarkDuplicates Before output close freeMemory: 758354640; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:03 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:03 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:03 MarkDuplicates After output close freeMemory: 758494968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:03 MarkDuplicates After output close freeMemory: 758494968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:03 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:03 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:03 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testWithBarcodeDuplicate STANDARD_ERROR INFO 2024-07-02 11:21:03 MarkDuplicates Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12965003150625589742.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12965003150625589742.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12965003150625589742.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12965003150625589742.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12965003150625589742.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12965003150625589742.tmp/output.sam Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:03.596 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:03.596 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:03.596 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:03.596 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:03.597 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:03.597 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:03.597 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:03.597 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:03 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12965003150625589742.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12965003150625589742.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12965003150625589742.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:03 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12965003150625589742.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12965003150625589742.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12965003150625589742.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:03 MarkDuplicates Start of doWork freeMemory: 1027985536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:03 MarkDuplicates Start of doWork freeMemory: 1027985536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:03 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:03 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:03 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:03 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:03 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:21:03 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 973453344; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 973453344; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:03 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:03 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:04 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:04 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:04 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 489011784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 489011784; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:21:04 MarkDuplicates Marking 2 records as duplicates. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:04 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:04 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:04 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:04 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:04 MarkDuplicates Getting Memory Stats. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Before output close freeMemory: 758355360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:04 MarkDuplicates Before output close freeMemory: 758355360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:04 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates After output close freeMemory: 758495616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:04 MarkDuplicates After output close freeMemory: 758495616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:04 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:04 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testWithBarcodeFragmentDuplicate STANDARD_ERROR INFO 2024-07-02 11:21:04 MarkDuplicates Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9961097706139992817.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9961097706139992817.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9961097706139992817.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9961097706139992817.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9961097706139992817.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9961097706139992817.tmp/output.sam Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:04.305 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:04.305 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:04.305 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:04.305 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:04.305 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:04.305 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:04.305 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:04.305 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:04 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9961097706139992817.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9961097706139992817.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9961097706139992817.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:04 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9961097706139992817.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9961097706139992817.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9961097706139992817.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Start of doWork freeMemory: 1027986312; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:04 MarkDuplicates Start of doWork freeMemory: 1027986312; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:04 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:04 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:04 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:21:04 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:21:04 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 973454656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 973454656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:04 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:04 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:04 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:04 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 489012920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 489012920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:21:04 MarkDuplicates Marking 1 records as duplicates. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:04 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:04 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:04 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:04 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:04 MarkDuplicates Getting Memory Stats. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Before output close freeMemory: 758356680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:04 MarkDuplicates Before output close freeMemory: 758356680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:04 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates After output close freeMemory: 758129664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:04 MarkDuplicates After output close freeMemory: 758129664; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:04 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:04 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:04 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testWithIndividualReadBarcodes STANDARD_ERROR INFO 2024-07-02 11:21:04 MarkDuplicates Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9798139964245536170.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -READ_ONE_BARCODE_TAG BX -READ_TWO_BARCODE_TAG BX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9798139964245536170.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9798139964245536170.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9798139964245536170.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -READ_ONE_BARCODE_TAG BX -READ_TWO_BARCODE_TAG BX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9798139964245536170.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9798139964245536170.tmp/output.sam Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:04.995 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:04.995 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:04.995 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:04.995 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:04.996 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:04.996 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:04.996 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:04.996 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:04 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC READ_ONE_BARCODE_TAG=BX READ_TWO_BARCODE_TAG=BX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9798139964245536170.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9798139964245536170.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9798139964245536170.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:04 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC READ_ONE_BARCODE_TAG=BX READ_TWO_BARCODE_TAG=BX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9798139964245536170.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9798139964245536170.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9798139964245536170.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:05 MarkDuplicates Start of doWork freeMemory: 1027979304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:05 MarkDuplicates Start of doWork freeMemory: 1027979304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:05 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:05 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:05 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:05 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:05 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:21:05 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 973449712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 973449712; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:05 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:05 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:05 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:05 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:05 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:05 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 489008240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 489008240; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:05 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:21:05 MarkDuplicates Marking 2 records as duplicates. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:05 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:05 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:05 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:05 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:05 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:05 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:05 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:05 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:05 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:05 MarkDuplicates Getting Memory Stats. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:05 MarkDuplicates Before output close freeMemory: 757983512; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:05 MarkDuplicates Before output close freeMemory: 757983512; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:05 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:05 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:05 MarkDuplicates After output close freeMemory: 758491920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:05 MarkDuplicates After output close freeMemory: 758491920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:05 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:05 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:05 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true]) STANDARD_ERROR INFO 2024-07-02 11:21:05 MarkDuplicates Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11387696027543335782.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI false -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11387696027543335782.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11387696027543335782.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11387696027543335782.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI false -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11387696027543335782.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11387696027543335782.tmp/output.sam Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:05.685 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:05.685 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:05.685 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:05.685 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:05.685 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:05.685 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:05.685 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:05.685 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:05 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=false INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11387696027543335782.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11387696027543335782.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11387696027543335782.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:05 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=false INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11387696027543335782.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11387696027543335782.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11387696027543335782.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:05 MarkDuplicates Start of doWork freeMemory: 1027978104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:05 MarkDuplicates Start of doWork freeMemory: 1027978104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:05 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:05 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:05 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:05 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:05 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. WARNING 2024-07-02 11:21:05 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:05 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:21:05 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 973448800; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 973448800; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:06 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:06 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:06 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 489007240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 489007240; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:21:06 MarkDuplicates Marking 2 records as duplicates. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:06 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:06 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:06 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:06 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:06 MarkDuplicates Getting Memory Stats. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates Before output close freeMemory: 758350112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:06 MarkDuplicates Before output close freeMemory: 758350112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:06 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates After output close freeMemory: 758491144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:06 MarkDuplicates After output close freeMemory: 758491144; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:06 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:06 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true]) STANDARD_ERROR INFO 2024-07-02 11:21:06 MarkDuplicates Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17707245327298786058.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI false -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17707245327298786058.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17707245327298786058.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17707245327298786058.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI false -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17707245327298786058.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17707245327298786058.tmp/output.sam Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:06.379 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:06.379 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:06.380 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:06.380 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:06.380 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:06.380 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:06.380 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:06.380 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:06 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=false INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17707245327298786058.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17707245327298786058.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17707245327298786058.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:06 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=false INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17707245327298786058.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17707245327298786058.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17707245327298786058.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates Start of doWork freeMemory: 1027980384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:06 MarkDuplicates Start of doWork freeMemory: 1027980384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:06 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:06 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. WARNING 2024-07-02 11:21:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:21:06 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 973448256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 973448256; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:06 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:06 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:06 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:06 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 489006696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 489006696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:21:06 MarkDuplicates Marking 0 records as duplicates. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:06 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:06 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:06 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:06 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:06 MarkDuplicates Getting Memory Stats. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates Before output close freeMemory: 758350224; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:06 MarkDuplicates Before output close freeMemory: 758350224; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:06 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:06 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:07 MarkDuplicates After output close freeMemory: 758490600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:07 MarkDuplicates After output close freeMemory: 758490600; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:07 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:07 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:07 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false]) STANDARD_ERROR INFO 2024-07-02 11:21:07 MarkDuplicates Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11751096453355291068.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI true -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11751096453355291068.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11751096453355291068.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11751096453355291068.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI true -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11751096453355291068.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11751096453355291068.tmp/output.sam Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:07.067 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:07.067 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:07.067 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:07.067 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:07.068 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:07.068 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:07.068 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:07.068 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:07 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=true INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11751096453355291068.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11751096453355291068.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11751096453355291068.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:07 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=true INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11751096453355291068.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11751096453355291068.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11751096453355291068.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:07 MarkDuplicates Start of doWork freeMemory: 1027979736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:07 MarkDuplicates Start of doWork freeMemory: 1027979736; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:07 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:07 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:07 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:07 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. WARNING 2024-07-02 11:21:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:07 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:21:07 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 973447264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 973447264; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:07 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:07 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:07 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:07 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:07 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:07 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:07 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:07 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 489005704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 489005704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:07 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:21:07 MarkDuplicates Marking 2 records as duplicates. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:07 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:07 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:07 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:07 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:07 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:07 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:07 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:07 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:07 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:07 MarkDuplicates Getting Memory Stats. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:07 MarkDuplicates Before output close freeMemory: 757982568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:07 MarkDuplicates Before output close freeMemory: 757982568; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:07 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:07 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:07 MarkDuplicates After output close freeMemory: 758489112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:07 MarkDuplicates After output close freeMemory: 758489112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:07 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:07 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:07 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest.testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false]) STANDARD_ERROR INFO 2024-07-02 11:21:07 MarkDuplicates Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.1050910641866138286.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI true -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1050910641866138286.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1050910641866138286.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.1050910641866138286.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI true -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1050910641866138286.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1050910641866138286.tmp/output.sam Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:07.759 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:07.759 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:07.759 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:07.759 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:07.760 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:07.760 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: 11:21:07.760 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:07.760 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:07 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=true INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1050910641866138286.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1050910641866138286.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1050910641866138286.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:07 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=true INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1050910641866138286.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1050910641866138286.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1050910641866138286.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:07 MarkDuplicates Start of doWork freeMemory: 1027978680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:07 MarkDuplicates Start of doWork freeMemory: 1027978680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:07 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:07 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:07 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:07 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. WARNING 2024-07-02 11:21:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:07 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:21:07 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 973446552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 973446552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:08 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:08 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:08 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:08 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:08 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:08 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 678797248; totalMemory: 1263534080; maxMemory: 2147483648 INFO 2024-07-02 11:21:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 678797248; totalMemory: 1263534080; maxMemory: 2147483648 Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:08 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:21:08 MarkDuplicates Marking 0 records as duplicates. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:08 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:08 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:08 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:08 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:08 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:08 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:08 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:08 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:08 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:08 MarkDuplicates Getting Memory Stats. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:08 MarkDuplicates Before output close freeMemory: 758348088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:08 MarkDuplicates Before output close freeMemory: 758348088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:08 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:08 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:08 MarkDuplicates After output close freeMemory: 758488672; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:08 MarkDuplicates After output close freeMemory: 758488672; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:08 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:08 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:08 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testBulkFragmentsNoDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:21:08 MarkDuplicates Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15533878722317567732.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15533878722317567732.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15533878722317567732.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15533878722317567732.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15533878722317567732.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15533878722317567732.tmp/output.sam Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:08.567 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:08.567 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:08.567 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:08.567 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:08.567 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:08.567 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:08.567 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:08.567 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:08 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15533878722317567732.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15533878722317567732.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15533878722317567732.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:08 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15533878722317567732.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15533878722317567732.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15533878722317567732.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:08 MarkDuplicates Start of doWork freeMemory: 1021041840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:08 MarkDuplicates Start of doWork freeMemory: 1021041840; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:08 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:08 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:08 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:21:08 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:21:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:08 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2024-07-02 11:21:08 MarkDuplicates Read 10000 records. 0 pairs never matched. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 957401672; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 957401672; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:09 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:09 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:09 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:09 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:09 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:09 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 482068368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 482068368; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:09 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:21:09 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:09 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:09 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:09 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:09 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:09 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:09 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:09 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:09 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:09 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:09 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:09 MarkDuplicates Before output close freeMemory: 751411696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:09 MarkDuplicates Before output close freeMemory: 751411696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:09 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:09 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:09 MarkDuplicates After output close freeMemory: 751552048; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:09 MarkDuplicates After output close freeMemory: 751552048; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:09 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:21:09 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:10 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testBulkFragmentsNoDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:21:10 MarkDuplicates Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13068433293905622991.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13068433293905622991.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13068433293905622991.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13068433293905622991.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13068433293905622991.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13068433293905622991.tmp/output.sam Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:10.025 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:10.025 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:10.025 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:10.025 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:10.025 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:10.025 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:10.025 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:10.025 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:10 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13068433293905622991.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13068433293905622991.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13068433293905622991.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:10 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13068433293905622991.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13068433293905622991.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13068433293905622991.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:10 MarkDuplicates Start of doWork freeMemory: 1020974792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:10 MarkDuplicates Start of doWork freeMemory: 1020974792; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:10 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:10 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:10 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:21:10 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:10 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:21:10 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:10 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2024-07-02 11:21:10 MarkDuplicates Read 10000 records. 0 pairs never matched. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 957268504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 957268504; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:10 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:10 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:10 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:10 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:10 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:10 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 1021034840; totalMemory: 1612709888; maxMemory: 2147483648 INFO 2024-07-02 11:21:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 1021034840; totalMemory: 1612709888; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:10 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:21:10 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:10 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:10 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:10 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:10 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:10 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:10 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:10 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:10 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:10 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:10 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:11 MarkDuplicates Before output close freeMemory: 775395696; totalMemory: 1097859072; maxMemory: 2147483648 INFO 2024-07-02 11:21:11 MarkDuplicates Before output close freeMemory: 775395696; totalMemory: 1097859072; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:11 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:11 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:11 MarkDuplicates After output close freeMemory: 765181440; totalMemory: 1087373312; maxMemory: 2147483648 INFO 2024-07-02 11:21:11 MarkDuplicates After output close freeMemory: 765181440; totalMemory: 1087373312; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:11 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:21:11 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1087373312 Runtime.totalMemory()=1087373312 Running Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:11 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testBulkFragmentsNoDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:21:11 MarkDuplicates Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17801665966704418608.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17801665966704418608.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17801665966704418608.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester10980414948767810841/input.fasta ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17801665966704418608.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17801665966704418608.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17801665966704418608.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester10980414948767810841/input.fasta Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:11.770 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:11.770 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:11.770 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:11.770 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:11.771 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:11.771 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:11.771 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:11.771 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:11 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17801665966704418608.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17801665966704418608.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17801665966704418608.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester10980414948767810841/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:11 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17801665966704418608.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17801665966704418608.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17801665966704418608.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester10980414948767810841/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:11 MarkDuplicates Start of doWork freeMemory: 1021037344; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:11 MarkDuplicates Start of doWork freeMemory: 1021037344; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:11 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:11 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:11 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:21:11 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:21:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:12 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2024-07-02 11:21:12 MarkDuplicates Read 10000 records. 0 pairs never matched. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 957396936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 957396936; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:12 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:12 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:12 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:12 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:12 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:12 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:12 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:12 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 1021032080; totalMemory: 1612709888; maxMemory: 2147483648 INFO 2024-07-02 11:21:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 1021032080; totalMemory: 1612709888; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:12 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:21:12 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:12 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:12 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:12 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:12 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:13 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:13 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:13 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:13 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:13 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:13 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:13 MarkDuplicates Before output close freeMemory: 782487440; totalMemory: 1105199104; maxMemory: 2147483648 INFO 2024-07-02 11:21:13 MarkDuplicates Before output close freeMemory: 782487440; totalMemory: 1105199104; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:13 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:13 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:13 MarkDuplicates After output close freeMemory: 765178544; totalMemory: 1087373312; maxMemory: 2147483648 INFO 2024-07-02 11:21:13 MarkDuplicates After output close freeMemory: 765178544; totalMemory: 1087373312; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:13 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:21:13 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1087373312 Runtime.totalMemory()=1087373312 Running Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:13 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testBulkFragmentsWithDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:21:13 MarkDuplicates Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4339705166721842281.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4339705166721842281.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4339705166721842281.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4339705166721842281.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4339705166721842281.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4339705166721842281.tmp/output.sam Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:13.639 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:13.639 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:13.640 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:13.640 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:13.640 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:13.640 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:13.640 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:13.640 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:13 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4339705166721842281.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4339705166721842281.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4339705166721842281.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:13 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4339705166721842281.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4339705166721842281.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4339705166721842281.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:13 MarkDuplicates Start of doWork freeMemory: 1012839152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:13 MarkDuplicates Start of doWork freeMemory: 1012839152; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:13 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:13 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:13 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:21:13 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:21:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:14 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2024-07-02 11:21:14 MarkDuplicates Read 21000 records. 0 pairs never matched. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 948407168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 948407168; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:14 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:14 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:14 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:14 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:14 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:14 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:14 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 743349896; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:21:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 743349896; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:14 MarkDuplicates Marking 20000 records as duplicates. INFO 2024-07-02 11:21:14 MarkDuplicates Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:14 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:14 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:14 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:14 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:15 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:15 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:15 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:15 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:15 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:15 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:15 MarkDuplicates Before output close freeMemory: 785151976; totalMemory: 1115684864; maxMemory: 2147483648 INFO 2024-07-02 11:21:15 MarkDuplicates Before output close freeMemory: 785151976; totalMemory: 1115684864; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:15 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:15 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:15 MarkDuplicates After output close freeMemory: 784912192; totalMemory: 1115684864; maxMemory: 2147483648 INFO 2024-07-02 11:21:15 MarkDuplicates After output close freeMemory: 784912192; totalMemory: 1115684864; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:21:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1115684864 Runtime.totalMemory()=1115684864 Running Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:15 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testBulkFragmentsWithDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:21:15 MarkDuplicates Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.1423202262335076956.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1423202262335076956.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1423202262335076956.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.1423202262335076956.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1423202262335076956.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1423202262335076956.tmp/output.sam Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:15.800 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:15.800 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:15.800 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:15.800 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:15.800 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:15.800 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:15.801 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:15.801 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:15 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1423202262335076956.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1423202262335076956.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1423202262335076956.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:15 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1423202262335076956.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1423202262335076956.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1423202262335076956.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:15 MarkDuplicates Start of doWork freeMemory: 1012772872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:15 MarkDuplicates Start of doWork freeMemory: 1012772872; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:15 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:15 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:15 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:21:15 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:15 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:21:15 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:16 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2024-07-02 11:21:16 MarkDuplicates Read 21000 records. 0 pairs never matched. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 948274584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 948274584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:16 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:16 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:16 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:16 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:16 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:16 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 743348888; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:21:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 743348888; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:16 MarkDuplicates Marking 20000 records as duplicates. INFO 2024-07-02 11:21:16 MarkDuplicates Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:16 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:16 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:16 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:16 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:17 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:17 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:17 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:17 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:17 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:17 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:17 MarkDuplicates Before output close freeMemory: 795505384; totalMemory: 1126170624; maxMemory: 2147483648 INFO 2024-07-02 11:21:17 MarkDuplicates Before output close freeMemory: 795505384; totalMemory: 1126170624; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:17 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:17 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:17 MarkDuplicates After output close freeMemory: 788437120; totalMemory: 1118830592; maxMemory: 2147483648 INFO 2024-07-02 11:21:17 MarkDuplicates After output close freeMemory: 788437120; totalMemory: 1118830592; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:17 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:21:17 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1118830592 Runtime.totalMemory()=1118830592 Running Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:18 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testBulkFragmentsWithDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:21:18 MarkDuplicates Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10941910221754591855.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10941910221754591855.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10941910221754591855.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester14692447646157064007/input.fasta ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10941910221754591855.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10941910221754591855.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10941910221754591855.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester14692447646157064007/input.fasta Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:18.357 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:18.357 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:18.357 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:18.357 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:18.357 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:18.357 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:18.358 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:18.358 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:18 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10941910221754591855.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10941910221754591855.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10941910221754591855.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester14692447646157064007/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:18 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10941910221754591855.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10941910221754591855.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10941910221754591855.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester14692447646157064007/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:18 MarkDuplicates Start of doWork freeMemory: 1012835912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:18 MarkDuplicates Start of doWork freeMemory: 1012835912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:18 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:18 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:18 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:21:18 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:18 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:21:18 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:19 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2024-07-02 11:21:19 MarkDuplicates Read 21000 records. 0 pairs never matched. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 948402688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 948402688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:19 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:19 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:19 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:19 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:19 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:19 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:19 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 743345800; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:21:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 743345800; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:19 MarkDuplicates Marking 20000 records as duplicates. INFO 2024-07-02 11:21:19 MarkDuplicates Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:19 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:19 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:19 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:19 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:20 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:20 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:20 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:20 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:20 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:20 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:20 MarkDuplicates Before output close freeMemory: 798779448; totalMemory: 1129316352; maxMemory: 2147483648 INFO 2024-07-02 11:21:20 MarkDuplicates Before output close freeMemory: 798779448; totalMemory: 1129316352; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:20 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:20 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:20 MarkDuplicates After output close freeMemory: 785288440; totalMemory: 1115684864; maxMemory: 2147483648 INFO 2024-07-02 11:21:20 MarkDuplicates After output close freeMemory: 785288440; totalMemory: 1115684864; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:20 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:21:20 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1115684864 Runtime.totalMemory()=1115684864 Running Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:20 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testBulkPairsNoDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:21:20 MarkDuplicates Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13415155487025249031.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13415155487025249031.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13415155487025249031.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13415155487025249031.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13415155487025249031.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13415155487025249031.tmp/output.sam Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:20.815 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:20.815 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:20.815 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:20.815 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:20.816 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:20.816 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:20.816 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:20.816 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:20 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13415155487025249031.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13415155487025249031.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13415155487025249031.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:20 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13415155487025249031.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13415155487025249031.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13415155487025249031.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:20 MarkDuplicates Start of doWork freeMemory: 1012319744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:20 MarkDuplicates Start of doWork freeMemory: 1012319744; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:20 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:20 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:20 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:21:20 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:20 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:21:20 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:21 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2024-07-02 11:21:21 MarkDuplicates Read 20200 records. 0 pairs never matched. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 946851144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 946851144; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:21 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:21 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:21 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:21 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:21 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:21 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:21 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:21 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 742830192; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:21:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 742830192; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:21 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:21:21 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:21 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:21 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:21 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:21 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:22 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:22 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:22 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:22 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:22 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:22 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:22 MarkDuplicates Before output close freeMemory: 795118584; totalMemory: 1126170624; maxMemory: 2147483648 INFO 2024-07-02 11:21:22 MarkDuplicates Before output close freeMemory: 795118584; totalMemory: 1126170624; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:22 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:22 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:22 MarkDuplicates After output close freeMemory: 787582400; totalMemory: 1118830592; maxMemory: 2147483648 INFO 2024-07-02 11:21:22 MarkDuplicates After output close freeMemory: 787582400; totalMemory: 1118830592; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:22 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:21:22 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1118830592 Runtime.totalMemory()=1118830592 Running Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:22 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testBulkPairsNoDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:21:22 MarkDuplicates Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12391040527066039645.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12391040527066039645.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12391040527066039645.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12391040527066039645.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12391040527066039645.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12391040527066039645.tmp/output.sam Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:22.968 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:22.968 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:22.968 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:22.968 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:22.968 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:22.968 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:22.969 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:22.969 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:22 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12391040527066039645.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12391040527066039645.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12391040527066039645.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:22 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12391040527066039645.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12391040527066039645.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12391040527066039645.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:23 MarkDuplicates Start of doWork freeMemory: 1012253392; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:23 MarkDuplicates Start of doWork freeMemory: 1012253392; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:23 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:23 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:23 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:21:23 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:21:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:23 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2024-07-02 11:21:23 MarkDuplicates Read 20200 records. 0 pairs never matched. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 947085384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 947085384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:23 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:23 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:23 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:23 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:23 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:23 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 742829112; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:21:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 742829112; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:23 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:21:23 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:23 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:23 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:23 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:23 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:24 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:24 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:24 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:24 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:24 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:24 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:24 MarkDuplicates Before output close freeMemory: 790791216; totalMemory: 1121976320; maxMemory: 2147483648 INFO 2024-07-02 11:21:24 MarkDuplicates Before output close freeMemory: 790791216; totalMemory: 1121976320; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:24 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:24 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:24 MarkDuplicates After output close freeMemory: 787917344; totalMemory: 1118830592; maxMemory: 2147483648 INFO 2024-07-02 11:21:24 MarkDuplicates After output close freeMemory: 787917344; totalMemory: 1118830592; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:24 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:21:24 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1118830592 Runtime.totalMemory()=1118830592 Running Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:25 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testBulkPairsNoDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:21:25 MarkDuplicates Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10297054717963896221.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10297054717963896221.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10297054717963896221.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester2561073562813955488/input.fasta ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10297054717963896221.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10297054717963896221.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10297054717963896221.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester2561073562813955488/input.fasta Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:25.782 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:25.782 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:25.782 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:25.782 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:25.782 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:25.782 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:25.782 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:25.782 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:25 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10297054717963896221.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10297054717963896221.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10297054717963896221.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester2561073562813955488/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:25 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10297054717963896221.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10297054717963896221.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10297054717963896221.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester2561073562813955488/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:25 MarkDuplicates Start of doWork freeMemory: 1012316272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:25 MarkDuplicates Start of doWork freeMemory: 1012316272; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:25 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:25 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:25 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:21:25 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:21:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:26 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2024-07-02 11:21:26 MarkDuplicates Read 20200 records. 0 pairs never matched. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 947212104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 947212104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:26 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:26 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:26 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:26 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:26 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:26 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 742824416; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:21:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 742824416; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:27 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:21:27 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:27 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:27 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:27 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:27 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:27 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:27 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:27 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:27 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:27 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:27 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:27 MarkDuplicates Before output close freeMemory: 795112880; totalMemory: 1126170624; maxMemory: 2147483648 INFO 2024-07-02 11:21:27 MarkDuplicates Before output close freeMemory: 795112880; totalMemory: 1126170624; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:27 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:27 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:27 MarkDuplicates After output close freeMemory: 795252936; totalMemory: 1126170624; maxMemory: 2147483648 INFO 2024-07-02 11:21:27 MarkDuplicates After output close freeMemory: 795252936; totalMemory: 1126170624; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:27 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:21:27 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1126170624 Runtime.totalMemory()=1126170624 Running Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:28 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testBulkPairsWithDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:21:28 MarkDuplicates Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13968732686972451137.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13968732686972451137.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13968732686972451137.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13968732686972451137.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13968732686972451137.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13968732686972451137.tmp/output.sam Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:28.145 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:28.145 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:28.145 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:28.145 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:28.145 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:28.145 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:28.145 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:28.145 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:28 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13968732686972451137.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13968732686972451137.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13968732686972451137.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:28 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13968732686972451137.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13968732686972451137.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13968732686972451137.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:28 MarkDuplicates Start of doWork freeMemory: 1022834440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:28 MarkDuplicates Start of doWork freeMemory: 1022834440; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:28 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:28 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:28 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:21:28 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:28 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:21:28 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:28 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2024-07-02 11:21:28 MarkDuplicates Read 6820 records. 0 pairs never matched. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 959177552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 959177552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:28 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:28 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:28 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:28 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:28 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:28 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 753344888; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:21:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 753344888; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:28 MarkDuplicates Marking 6200 records as duplicates. INFO 2024-07-02 11:21:28 MarkDuplicates Marking 6200 records as duplicates. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:28 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:28 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:28 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:28 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:28 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:28 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:28 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:28 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:28 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:28 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:29 MarkDuplicates Before output close freeMemory: 763689584; totalMemory: 1084227584; maxMemory: 2147483648 INFO 2024-07-02 11:21:29 MarkDuplicates Before output close freeMemory: 763689584; totalMemory: 1084227584; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:29 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:29 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:29 MarkDuplicates After output close freeMemory: 759635088; totalMemory: 1080033280; maxMemory: 2147483648 INFO 2024-07-02 11:21:29 MarkDuplicates After output close freeMemory: 759635088; totalMemory: 1080033280; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:21:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1080033280 Runtime.totalMemory()=1080033280 Running Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:29 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testBulkPairsWithDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:21:29 MarkDuplicates Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11199257745604565830.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11199257745604565830.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11199257745604565830.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11199257745604565830.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11199257745604565830.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11199257745604565830.tmp/output.sam Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:29.357 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:29.357 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:29.358 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:29.358 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:29.358 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:29.358 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:29.358 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:29.358 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:29 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11199257745604565830.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11199257745604565830.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11199257745604565830.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:29 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11199257745604565830.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11199257745604565830.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11199257745604565830.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:29 MarkDuplicates Start of doWork freeMemory: 1022765304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:29 MarkDuplicates Start of doWork freeMemory: 1022765304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:29 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:29 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:29 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:21:29 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:29 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:21:29 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:29 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2024-07-02 11:21:29 MarkDuplicates Read 6820 records. 0 pairs never matched. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 959045144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 959045144; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:29 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:29 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:29 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:29 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:29 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:29 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 483859800; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 483859800; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:30 MarkDuplicates Marking 6200 records as duplicates. INFO 2024-07-02 11:21:30 MarkDuplicates Marking 6200 records as duplicates. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:30 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:30 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:30 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:30 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:30 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:30 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:30 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:30 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:30 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:30 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:30 MarkDuplicates Before output close freeMemory: 753070784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:30 MarkDuplicates Before output close freeMemory: 753070784; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:30 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:30 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:30 MarkDuplicates After output close freeMemory: 753343072; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:30 MarkDuplicates After output close freeMemory: 753343072; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:30 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:21:30 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:30 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testBulkPairsWithDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:21:30 MarkDuplicates Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.14137780114401880005.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14137780114401880005.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14137780114401880005.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester2550713307988196238/input.fasta ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.14137780114401880005.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14137780114401880005.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14137780114401880005.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester2550713307988196238/input.fasta Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:30.844 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:30.844 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:30.845 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:30.845 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:30.845 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:30.845 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:30.845 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:30.845 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:30 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.14137780114401880005.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.14137780114401880005.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.14137780114401880005.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester2550713307988196238/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:30 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.14137780114401880005.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.14137780114401880005.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.14137780114401880005.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester2550713307988196238/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:30 MarkDuplicates Start of doWork freeMemory: 1022830208; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:30 MarkDuplicates Start of doWork freeMemory: 1022830208; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:30 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:30 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:30 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:21:30 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:31 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:21:31 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:31 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2024-07-02 11:21:31 MarkDuplicates Read 6820 records. 0 pairs never matched. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 959173176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 959173176; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:31 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:31 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:31 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:31 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:31 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:31 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 1022824480; totalMemory: 1612709888; maxMemory: 2147483648 INFO 2024-07-02 11:21:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 1022824480; totalMemory: 1612709888; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:31 MarkDuplicates Marking 6200 records as duplicates. INFO 2024-07-02 11:21:31 MarkDuplicates Marking 6200 records as duplicates. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:31 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:31 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:31 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:31 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:31 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:31 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:31 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:31 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:31 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:31 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:32 MarkDuplicates Before output close freeMemory: 769977176; totalMemory: 1090519040; maxMemory: 2147483648 INFO 2024-07-02 11:21:32 MarkDuplicates Before output close freeMemory: 769977176; totalMemory: 1090519040; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:32 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:32 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:32 MarkDuplicates After output close freeMemory: 766971760; totalMemory: 1087373312; maxMemory: 2147483648 INFO 2024-07-02 11:21:32 MarkDuplicates After output close freeMemory: 766971760; totalMemory: 1087373312; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:21:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1087373312 Runtime.totalMemory()=1087373312 Running Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:32 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testDifferentChromosomesInOppositeOrder STANDARD_ERROR INFO 2024-07-02 11:21:32 MarkDuplicates Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7230497861825395910.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7230497861825395910.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7230497861825395910.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7230497861825395910.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7230497861825395910.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7230497861825395910.tmp/output.sam Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:32.242 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:32.242 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:32.242 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:32.242 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:32.243 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:32.243 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:32.243 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:32.243 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:32 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7230497861825395910.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7230497861825395910.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7230497861825395910.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:32 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7230497861825395910.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7230497861825395910.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7230497861825395910.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:32 MarkDuplicates Start of doWork freeMemory: 1027951968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:32 MarkDuplicates Start of doWork freeMemory: 1027951968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:32 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:32 MarkDuplicates Reading input file and constructing read end information. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:32 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:32 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:32 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:21:32 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 973417712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 973417712; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:32 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:32 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:32 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:32 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:32 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:32 MarkDuplicates Sorting list of duplicate records. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 488976000; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 488976000; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:32 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:21:32 MarkDuplicates Marking 2 records as duplicates. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:32 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:21:32 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:32 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:32 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:32 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:32 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:32 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:32 MarkDuplicates Duplicate Index cleanup. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:32 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:32 MarkDuplicates Getting Memory Stats. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:32 MarkDuplicates Before output close freeMemory: 758319560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:32 MarkDuplicates Before output close freeMemory: 758319560; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:32 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:32 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:32 MarkDuplicates After output close freeMemory: 758459904; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:32 MarkDuplicates After output close freeMemory: 758459904; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:32 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:21:32 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17628357645195302431.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17628357645195302431.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17628357645195302431.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17628357645195302431.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17628357645195302431.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17628357645195302431.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:32.975 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:32.975 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:32.975 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:32.975 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:32.975 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:32.975 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:32.975 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:32.975 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:32 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17628357645195302431.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17628357645195302431.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17628357645195302431.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:32 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17628357645195302431.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17628357645195302431.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17628357645195302431.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:33 MarkDuplicates Start of doWork freeMemory: 1027943216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:33 MarkDuplicates Start of doWork freeMemory: 1027943216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:33 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:33 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:33 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:33 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:33 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:21:33 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 973410264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 973410264; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:33 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:33 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:33 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:33 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 758453344; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:21:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 758453344; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:33 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:21:33 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:33 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:21:33 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:33 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:33 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:33 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:33 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:33 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:33 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:33 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:33 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:33 MarkDuplicates Before output close freeMemory: 758312896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:33 MarkDuplicates Before output close freeMemory: 758312896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:33 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:33 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:33 MarkDuplicates After output close freeMemory: 758452720; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:33 MarkDuplicates After output close freeMemory: 758452720; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:33 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:33 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:33 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:21:33 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6659940827435719939.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6659940827435719939.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6659940827435719939.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6659940827435719939.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6659940827435719939.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6659940827435719939.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:33.764 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:33.764 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:33.764 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:33.764 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:33.765 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:33.765 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:33.765 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:33.765 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:33 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6659940827435719939.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6659940827435719939.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6659940827435719939.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:33 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6659940827435719939.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6659940827435719939.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6659940827435719939.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:33 MarkDuplicates Start of doWork freeMemory: 1027942552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:33 MarkDuplicates Start of doWork freeMemory: 1027942552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:33 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:33 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:33 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:33 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:33 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:21:33 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 973409360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 973409360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:34 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:34 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:34 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:34 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:34 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:34 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:34 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 488968656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 488968656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:34 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:21:34 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:34 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:21:34 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:34 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:34 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:34 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:34 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:34 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:34 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:34 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:34 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:34 MarkDuplicates Before output close freeMemory: 758311384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:34 MarkDuplicates Before output close freeMemory: 758311384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:34 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:34 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:34 MarkDuplicates After output close freeMemory: 758100600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:34 MarkDuplicates After output close freeMemory: 758100600; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:34 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:21:34 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.14669479956328340752.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14669479956328340752.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14669479956328340752.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.14669479956328340752.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14669479956328340752.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14669479956328340752.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:34.549 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:34.549 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:34.549 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:34.549 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:34.550 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:34.550 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:34.550 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:34.550 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:34 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.14669479956328340752.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.14669479956328340752.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.14669479956328340752.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:34 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.14669479956328340752.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.14669479956328340752.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.14669479956328340752.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:34 MarkDuplicates Start of doWork freeMemory: 1027941904; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:34 MarkDuplicates Start of doWork freeMemory: 1027941904; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:34 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:34 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:34 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:34 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:34 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:21:34 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:34 MarkDuplicates After buildSortedReadEndLists freeMemory: 973408920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:34 MarkDuplicates After buildSortedReadEndLists freeMemory: 973408920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:34 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:34 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:34 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:34 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:34 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:34 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:34 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 488968000; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 488968000; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:21:35 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:21:35 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:35 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:35 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:35 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:35 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates Before output close freeMemory: 758311584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:35 MarkDuplicates Before output close freeMemory: 758311584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:35 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates After output close freeMemory: 758451336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:35 MarkDuplicates After output close freeMemory: 758451336; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:35 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:35 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:21:35 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16944877083298651398.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16944877083298651398.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16944877083298651398.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16944877083298651398.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16944877083298651398.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16944877083298651398.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:35.278 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:35.278 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:35.278 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:35.278 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:35.278 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:35.278 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:35.278 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:35.278 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:35 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16944877083298651398.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16944877083298651398.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16944877083298651398.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:35 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16944877083298651398.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16944877083298651398.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16944877083298651398.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates Start of doWork freeMemory: 1027569104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:35 MarkDuplicates Start of doWork freeMemory: 1027569104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:35 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:35 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:21:35 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 973408296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 973408296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:35 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:35 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:35 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 488967376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 488967376; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:21:35 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:21:35 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:35 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:35 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:35 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:35 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates Before output close freeMemory: 758310960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:35 MarkDuplicates Before output close freeMemory: 758310960; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:35 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:35 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:36 MarkDuplicates After output close freeMemory: 758093080; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:36 MarkDuplicates After output close freeMemory: 758093080; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:36 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:36 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:36 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:21:36 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12189907777346107406.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12189907777346107406.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12189907777346107406.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12189907777346107406.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12189907777346107406.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12189907777346107406.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:36.038 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:36.038 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:36.038 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:36.038 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:36.038 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:36.038 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:36.038 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:36.038 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:36 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12189907777346107406.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12189907777346107406.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12189907777346107406.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:36 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12189907777346107406.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12189907777346107406.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12189907777346107406.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:36 MarkDuplicates Start of doWork freeMemory: 1027940648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:36 MarkDuplicates Start of doWork freeMemory: 1027940648; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:36 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:36 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:36 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:36 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:36 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:21:36 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 973407448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 973407448; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:36 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:36 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:36 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:36 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:36 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:36 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 488966744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 488966744; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:36 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:21:36 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:36 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:21:36 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:36 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:36 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:36 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:36 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:36 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:36 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:36 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:36 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:36 MarkDuplicates Before output close freeMemory: 758309472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:36 MarkDuplicates Before output close freeMemory: 758309472; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:36 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:36 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:36 MarkDuplicates After output close freeMemory: 758449224; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:36 MarkDuplicates After output close freeMemory: 758449224; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:36 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:36 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:36 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:21:36 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.14489488929294740625.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14489488929294740625.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14489488929294740625.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.14489488929294740625.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14489488929294740625.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14489488929294740625.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:36.801 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:36.801 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:36.801 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:36.801 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:36.801 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:36.801 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:36.801 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:36.801 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:36 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.14489488929294740625.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.14489488929294740625.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.14489488929294740625.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:36 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.14489488929294740625.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.14489488929294740625.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.14489488929294740625.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:36 MarkDuplicates Start of doWork freeMemory: 1027939880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:36 MarkDuplicates Start of doWork freeMemory: 1027939880; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:36 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:36 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:36 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:36 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:36 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:21:36 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 973406680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 973406680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:37 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:37 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:37 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:37 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 578094936; totalMemory: 1162870784; maxMemory: 2147483648 INFO 2024-07-02 11:21:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 578094936; totalMemory: 1162870784; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:37 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:21:37 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:37 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:21:37 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:37 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:37 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:37 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:37 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:37 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:37 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:37 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:37 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:37 MarkDuplicates Before output close freeMemory: 758309360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:37 MarkDuplicates Before output close freeMemory: 758309360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:37 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:37 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:37 MarkDuplicates After output close freeMemory: 758449656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:37 MarkDuplicates After output close freeMemory: 758449656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:37 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testMappedFragmentAndMappedPairFirstOfPairNonPrimary STANDARD_ERROR INFO 2024-07-02 11:21:37 MarkDuplicates Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13541346323120920301.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13541346323120920301.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13541346323120920301.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13541346323120920301.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13541346323120920301.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13541346323120920301.tmp/output.sam Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:37.548 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:37.548 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:37.548 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:37.548 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:37.549 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:37.549 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:37.549 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:37.549 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:37 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13541346323120920301.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13541346323120920301.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13541346323120920301.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:37 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13541346323120920301.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13541346323120920301.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13541346323120920301.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:37 MarkDuplicates Start of doWork freeMemory: 1027946104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:37 MarkDuplicates Start of doWork freeMemory: 1027946104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:37 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:37 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:37 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:37 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:37 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:21:37 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:37 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:21:37 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 973414536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 973414536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:37 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:37 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:37 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:37 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 488972712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 488972712; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:21:38 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:38 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:38 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:38 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:38 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:38 MarkDuplicates Getting Memory Stats. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates Before output close freeMemory: 758315616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:38 MarkDuplicates Before output close freeMemory: 758315616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:38 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates After output close freeMemory: 758092712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:38 MarkDuplicates After output close freeMemory: 758092712; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:38 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:38 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testMappedFragmentAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:21:38 MarkDuplicates Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11403483265766996974.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11403483265766996974.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11403483265766996974.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11403483265766996974.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11403483265766996974.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11403483265766996974.tmp/output.sam Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:38.276 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:38.276 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:38.276 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:38.276 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:38.276 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:38.276 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:38.276 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:38.276 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:38 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11403483265766996974.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11403483265766996974.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11403483265766996974.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:38 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11403483265766996974.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11403483265766996974.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11403483265766996974.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates Start of doWork freeMemory: 1027945184; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:38 MarkDuplicates Start of doWork freeMemory: 1027945184; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:38 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:38 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:38 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:21:38 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2024-07-02 11:21:38 MarkDuplicates Read 3 records. 0 pairs never matched. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 973413528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 973413528; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:38 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:38 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:38 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 488971792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 488971792; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:21:38 MarkDuplicates Marking 1 records as duplicates. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:38 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:38 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:38 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:38 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:38 MarkDuplicates Getting Memory Stats. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates Before output close freeMemory: 758315656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:38 MarkDuplicates Before output close freeMemory: 758315656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:38 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:38 MarkDuplicates After output close freeMemory: 758455128; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:38 MarkDuplicates After output close freeMemory: 758455128; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:38 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:38 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:39 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testMappedFragmentAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:21:39 MarkDuplicates Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2762400148330908876.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2762400148330908876.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2762400148330908876.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2762400148330908876.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2762400148330908876.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2762400148330908876.tmp/output.sam Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:39.020 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:39.020 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:39.020 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:39.020 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:39.020 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:39.020 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:39.020 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:39.020 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:39 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2762400148330908876.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2762400148330908876.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2762400148330908876.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:39 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2762400148330908876.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2762400148330908876.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2762400148330908876.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:39 MarkDuplicates Start of doWork freeMemory: 1027944664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:39 MarkDuplicates Start of doWork freeMemory: 1027944664; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:39 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:39 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:39 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:39 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:39 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:21:39 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:39 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2024-07-02 11:21:39 MarkDuplicates Read 3 records. 0 pairs never matched. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 973413008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 973413008; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:39 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:39 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:39 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:39 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:39 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:39 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 488971272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 488971272; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:39 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:21:39 MarkDuplicates Marking 1 records as duplicates. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:39 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:39 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:39 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:39 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:39 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:39 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:39 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:39 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:39 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:39 MarkDuplicates Getting Memory Stats. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:39 MarkDuplicates Before output close freeMemory: 757952080; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:39 MarkDuplicates Before output close freeMemory: 757952080; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:39 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:39 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:39 MarkDuplicates After output close freeMemory: 758455104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:39 MarkDuplicates After output close freeMemory: 758455104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:39 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testMappedPairAndMappedFragmentAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:21:39 MarkDuplicates Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.8208463321901986461.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8208463321901986461.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8208463321901986461.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.8208463321901986461.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8208463321901986461.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8208463321901986461.tmp/output.sam Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:39.811 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:39.811 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:39.812 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:39.812 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:39.812 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:39.812 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:39.812 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:39.812 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:39 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8208463321901986461.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8208463321901986461.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8208463321901986461.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:39 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8208463321901986461.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8208463321901986461.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8208463321901986461.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:39 MarkDuplicates Start of doWork freeMemory: 1027942624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:39 MarkDuplicates Start of doWork freeMemory: 1027942624; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:39 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:39 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:39 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:39 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:39 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:21:39 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:39 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:21:39 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 973043704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 973043704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:40 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:40 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:40 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:40 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:40 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 488968712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 488968712; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:40 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:21:40 MarkDuplicates Marking 2 records as duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:40 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:40 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:40 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:40 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:40 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:40 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:40 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:40 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:40 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:40 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:40 MarkDuplicates Before output close freeMemory: 758311728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:40 MarkDuplicates Before output close freeMemory: 758311728; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:40 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:40 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:40 MarkDuplicates After output close freeMemory: 758451488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:40 MarkDuplicates After output close freeMemory: 758451488; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:40 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:40 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:40 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testMappedPairAndMappedFragmentAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:21:40 MarkDuplicates Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.948377600957548391.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.948377600957548391.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.948377600957548391.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.948377600957548391.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.948377600957548391.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.948377600957548391.tmp/output.sam Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:40.600 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:40.600 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:40.600 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:40.600 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:40.600 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:40.600 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:40.600 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:40.600 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:40 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.948377600957548391.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.948377600957548391.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.948377600957548391.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:40 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.948377600957548391.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.948377600957548391.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.948377600957548391.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:40 MarkDuplicates Start of doWork freeMemory: 1027936136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:40 MarkDuplicates Start of doWork freeMemory: 1027936136; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:40 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:40 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:40 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:40 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:40 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:21:40 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:40 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:21:40 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 973409528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 973409528; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:41 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:41 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:41 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 654642888; totalMemory: 1239416832; maxMemory: 2147483648 INFO 2024-07-02 11:21:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 654642888; totalMemory: 1239416832; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:21:41 MarkDuplicates Marking 2 records as duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:41 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:41 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:41 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:41 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:41 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates Before output close freeMemory: 758310896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:41 MarkDuplicates Before output close freeMemory: 758310896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:41 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates After output close freeMemory: 758450584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:41 MarkDuplicates After output close freeMemory: 758450584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:41 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:41 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:21:41 MarkDuplicates Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17240485655079198042.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17240485655079198042.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17240485655079198042.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17240485655079198042.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17240485655079198042.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17240485655079198042.tmp/output.sam Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:41.417 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:41.417 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:41.417 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:41.417 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:41.417 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:41.417 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:41.417 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:41.417 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:41 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17240485655079198042.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17240485655079198042.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17240485655079198042.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:41 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17240485655079198042.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17240485655079198042.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17240485655079198042.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates Start of doWork freeMemory: 1027941272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:41 MarkDuplicates Start of doWork freeMemory: 1027941272; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:41 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:41 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:41 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:21:41 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:21:41 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 973409320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 973409320; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:41 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:41 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:41 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 488967584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 488967584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:21:41 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:41 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:41 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:41 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:41 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:41 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:41 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:42 MarkDuplicates Before output close freeMemory: 758311184; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:42 MarkDuplicates Before output close freeMemory: 758311184; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:42 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:42 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:42 MarkDuplicates After output close freeMemory: 758450888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:42 MarkDuplicates After output close freeMemory: 758450888; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:42 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testMappedPairAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:21:42 MarkDuplicates Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10449811355319016038.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10449811355319016038.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10449811355319016038.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10449811355319016038.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10449811355319016038.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10449811355319016038.tmp/output.sam Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:42.199 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:42.199 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:42.200 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:42.200 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:42.200 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:42.200 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:42.200 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:42.200 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:42 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10449811355319016038.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10449811355319016038.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10449811355319016038.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:42 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10449811355319016038.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10449811355319016038.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10449811355319016038.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:42 MarkDuplicates Start of doWork freeMemory: 1027940600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:42 MarkDuplicates Start of doWork freeMemory: 1027940600; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:42 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:42 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:42 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:42 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:42 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:21:42 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:42 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:21:42 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 973408648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 973408648; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:42 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:42 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:42 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:42 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:42 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:42 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 488966912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 488966912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:42 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:21:42 MarkDuplicates Marking 1 records as duplicates. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:42 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:42 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:42 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:42 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:42 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:42 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:42 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:42 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:42 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:42 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:42 MarkDuplicates Before output close freeMemory: 757944296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:42 MarkDuplicates Before output close freeMemory: 757944296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:42 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:42 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:42 MarkDuplicates After output close freeMemory: 758450816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:42 MarkDuplicates After output close freeMemory: 758450816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:42 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testMappedPairAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:21:42 MarkDuplicates Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17862146711687582240.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17862146711687582240.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17862146711687582240.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17862146711687582240.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17862146711687582240.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17862146711687582240.tmp/output.sam Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:42.942 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:42.942 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:42.942 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:42.942 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:42.942 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:42.942 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:42.942 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:42.942 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:42 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17862146711687582240.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17862146711687582240.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17862146711687582240.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:42 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17862146711687582240.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17862146711687582240.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17862146711687582240.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:43 MarkDuplicates Start of doWork freeMemory: 1027939912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:43 MarkDuplicates Start of doWork freeMemory: 1027939912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:43 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:43 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:43 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:43 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:43 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:21:43 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:43 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:21:43 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 973407960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 973407960; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:43 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:43 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:43 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:43 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:43 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:43 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 488966224; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 488966224; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:43 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:21:43 MarkDuplicates Marking 1 records as duplicates. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:43 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:43 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:43 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:43 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:43 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:43 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:43 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:43 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:43 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:43 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:43 MarkDuplicates Before output close freeMemory: 758309872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:43 MarkDuplicates Before output close freeMemory: 758309872; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:43 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:43 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:43 MarkDuplicates After output close freeMemory: 758082968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:43 MarkDuplicates After output close freeMemory: 758082968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:43 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:43 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:43 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testMappedPairWithFirstEndSamePositionAndOther STANDARD_ERROR INFO 2024-07-02 11:21:43 MarkDuplicates Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6449380092999592167.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6449380092999592167.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6449380092999592167.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6449380092999592167.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6449380092999592167.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6449380092999592167.tmp/output.sam Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:43.803 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:43.803 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:43.803 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:43.803 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:43.803 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:43.803 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:43.804 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:43.804 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:43 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6449380092999592167.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6449380092999592167.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6449380092999592167.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:43 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6449380092999592167.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6449380092999592167.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6449380092999592167.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:43 MarkDuplicates Start of doWork freeMemory: 1027939000; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:43 MarkDuplicates Start of doWork freeMemory: 1027939000; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:43 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:43 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:43 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:43 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:43 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:21:43 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:43 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:21:43 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 973406872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 973406872; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:44 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:44 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:44 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:44 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:44 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 703923392; totalMemory: 1288699904; maxMemory: 2147483648 INFO 2024-07-02 11:21:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 703923392; totalMemory: 1288699904; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:44 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:21:44 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:44 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:44 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:44 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:44 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:44 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:44 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:44 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:44 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:44 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:44 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:44 MarkDuplicates Before output close freeMemory: 758308328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:44 MarkDuplicates Before output close freeMemory: 758308328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:44 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:44 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:44 MarkDuplicates After output close freeMemory: 758448992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:44 MarkDuplicates After output close freeMemory: 758448992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:44 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:44 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:44 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testMappedPairWithSamePosition STANDARD_ERROR INFO 2024-07-02 11:21:44 MarkDuplicates Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3417738817491075837.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3417738817491075837.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3417738817491075837.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3417738817491075837.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3417738817491075837.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3417738817491075837.tmp/output.sam Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:44.590 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:44.590 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:44.590 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:44.590 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:44.591 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:44.591 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:44.591 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:44.591 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:44 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3417738817491075837.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3417738817491075837.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3417738817491075837.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:44 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3417738817491075837.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3417738817491075837.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3417738817491075837.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:44 MarkDuplicates Start of doWork freeMemory: 1027939648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:44 MarkDuplicates Start of doWork freeMemory: 1027939648; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:44 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:44 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:44 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:44 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:44 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:21:44 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:44 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:21:44 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 973407184; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 973407184; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:45 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:45 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:45 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 488752064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 488752064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:21:45 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:45 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:45 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:45 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:45 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:45 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates Before output close freeMemory: 758309200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:45 MarkDuplicates Before output close freeMemory: 758309200; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:45 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates After output close freeMemory: 758082976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:45 MarkDuplicates After output close freeMemory: 758082976; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testMappedPairWithSamePositionSameCigar STANDARD_ERROR INFO 2024-07-02 11:21:45 MarkDuplicates Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16610707095279674928.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16610707095279674928.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16610707095279674928.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16610707095279674928.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16610707095279674928.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16610707095279674928.tmp/output.sam Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:45.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:45.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:45.477 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:45.477 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:45.477 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:45.477 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:45.477 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:45.477 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:45 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16610707095279674928.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16610707095279674928.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16610707095279674928.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:45 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16610707095279674928.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16610707095279674928.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16610707095279674928.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates Start of doWork freeMemory: 1027938904; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:45 MarkDuplicates Start of doWork freeMemory: 1027938904; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:45 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:45 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:45 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:21:45 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:21:45 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 973407040; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 973407040; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:45 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:45 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:45 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 488965216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 488965216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:21:45 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:45 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:45 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:45 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:45 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:45 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:45 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:46 MarkDuplicates Before output close freeMemory: 758307296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:46 MarkDuplicates Before output close freeMemory: 758307296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:46 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:46 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:46 MarkDuplicates After output close freeMemory: 758449120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:46 MarkDuplicates After output close freeMemory: 758449120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:46 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:21:46 MarkDuplicates Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16814511716670477097.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16814511716670477097.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16814511716670477097.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16814511716670477097.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16814511716670477097.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16814511716670477097.tmp/output.sam Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:46.196 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:46.196 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:46.196 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:46.196 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:46.197 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:46.197 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:46.197 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:46.197 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:46 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16814511716670477097.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16814511716670477097.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16814511716670477097.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:46 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16814511716670477097.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16814511716670477097.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16814511716670477097.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:46 MarkDuplicates Start of doWork freeMemory: 1027938336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:46 MarkDuplicates Start of doWork freeMemory: 1027938336; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:46 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:46 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:46 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:46 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:46 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:21:46 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:46 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:21:46 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 973406768; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 973406768; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:46 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:46 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:46 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:46 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:46 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:46 MarkDuplicates Sorting list of duplicate records. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 488964944; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 488964944; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:46 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:21:46 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:46 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:46 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:46 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:46 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:46 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:46 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:46 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:46 MarkDuplicates Duplicate Index cleanup. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:46 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:46 MarkDuplicates Getting Memory Stats. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:46 MarkDuplicates Before output close freeMemory: 758308704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:46 MarkDuplicates Before output close freeMemory: 758308704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:46 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:46 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:47 MarkDuplicates After output close freeMemory: 758448848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:47 MarkDuplicates After output close freeMemory: 758448848; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:47 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:47 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:47 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:21:47 MarkDuplicates Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11572799780711156881.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11572799780711156881.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11572799780711156881.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11572799780711156881.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11572799780711156881.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11572799780711156881.tmp/output.sam Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:47.051 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:47.051 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:47.051 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:47.051 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:47.052 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:47.052 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:47.052 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:47.052 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:47 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11572799780711156881.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11572799780711156881.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11572799780711156881.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:47 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11572799780711156881.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11572799780711156881.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11572799780711156881.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:47 MarkDuplicates Start of doWork freeMemory: 1027935448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:47 MarkDuplicates Start of doWork freeMemory: 1027935448; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:47 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:47 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:47 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:47 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:47 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:21:47 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:47 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:21:47 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 973405552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 973405552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:47 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:47 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:47 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:47 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:47 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:47 MarkDuplicates Sorting list of duplicate records. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 488964328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 488964328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:47 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:21:47 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:47 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:47 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:47 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:47 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:47 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:47 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:47 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:47 MarkDuplicates Duplicate Index cleanup. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:47 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:47 MarkDuplicates Getting Memory Stats. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:48 MarkDuplicates Before output close freeMemory: 758306672; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:48 MarkDuplicates Before output close freeMemory: 758306672; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:48 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:48 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:48 MarkDuplicates After output close freeMemory: 758446448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:48 MarkDuplicates After output close freeMemory: 758446448; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:48 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:21:48 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:48 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testOpticalDuplicateBehaviorNullRegex STANDARD_ERROR INFO 2024-07-02 11:21:48 MarkDuplicates Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5399160266423105660.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_NAME_REGEX null -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5399160266423105660.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5399160266423105660.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5399160266423105660.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_NAME_REGEX null -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5399160266423105660.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5399160266423105660.tmp/output.sam Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:48.243 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:48.243 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:48.244 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:48.244 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:48.244 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:48.244 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:48.244 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:48.244 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:48 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5399160266423105660.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5399160266423105660.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5399160266423105660.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH READ_NAME_REGEX=null MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:48 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5399160266423105660.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5399160266423105660.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5399160266423105660.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH READ_NAME_REGEX=null MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:48 MarkDuplicates Start of doWork freeMemory: 1027566832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:48 MarkDuplicates Start of doWork freeMemory: 1027566832; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:48 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:48 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:48 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:48 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:48 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:21:48 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 973403352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 973403352; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:48 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:48 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:48 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:48 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:48 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:48 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:48 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:48 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 488747696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 488747696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:48 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:21:48 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:21:48 MarkDuplicates Skipped optical duplicate cluster discovery; library size estimation may be inaccurate! WARNING 2024-07-02 11:21:48 MarkDuplicates Skipped optical duplicate cluster discovery; library size estimation may be inaccurate! Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:48 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:48 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:48 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:48 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:48 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:48 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:48 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:49 MarkDuplicates Before output close freeMemory: 758305216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:49 MarkDuplicates Before output close freeMemory: 758305216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:49 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:49 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:49 MarkDuplicates After output close freeMemory: 758078240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:49 MarkDuplicates After output close freeMemory: 758078240; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:21:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:49 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testOpticalDuplicateClusterOneEndSamePositionOneCluster STANDARD_ERROR INFO 2024-07-02 11:21:49 MarkDuplicates Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10992473500227060096.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10992473500227060096.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10992473500227060096.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10992473500227060096.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10992473500227060096.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10992473500227060096.tmp/output.sam Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:49.285 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:49.285 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:49.285 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:49.285 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:49.286 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:49.286 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:49.286 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:49.286 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:49 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10992473500227060096.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10992473500227060096.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10992473500227060096.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:49 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10992473500227060096.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10992473500227060096.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10992473500227060096.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:49 MarkDuplicates Start of doWork freeMemory: 1027934608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:49 MarkDuplicates Start of doWork freeMemory: 1027934608; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:49 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:49 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:49 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:49 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:49 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:21:49 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 973402416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 973402416; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:49 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:49 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:49 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:49 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:49 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:49 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:49 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:49 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 488960704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 488960704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:49 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:21:49 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:49 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:21:49 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:49 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:49 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:49 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:49 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:49 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:49 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:49 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:49 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:50 MarkDuplicates Before output close freeMemory: 758303632; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:50 MarkDuplicates Before output close freeMemory: 758303632; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:50 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:50 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:50 MarkDuplicates After output close freeMemory: 758077720; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:50 MarkDuplicates After output close freeMemory: 758077720; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:21:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:50 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:21:50 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12196474805545185857.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12196474805545185857.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12196474805545185857.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12196474805545185857.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12196474805545185857.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12196474805545185857.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:50.259 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:50.259 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:50.259 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:50.259 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:50.259 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:50.259 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:50.259 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:50.259 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:50 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12196474805545185857.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12196474805545185857.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12196474805545185857.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:50 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12196474805545185857.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12196474805545185857.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12196474805545185857.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:50 MarkDuplicates Start of doWork freeMemory: 1027932856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:50 MarkDuplicates Start of doWork freeMemory: 1027932856; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:50 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:50 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:50 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:50 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:50 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:21:50 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 973400448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 973400448; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:50 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:50 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:50 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:50 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:50 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:50 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 587525248; totalMemory: 1172307968; maxMemory: 2147483648 INFO 2024-07-02 11:21:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 587525248; totalMemory: 1172307968; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:51 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:21:51 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:51 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:51 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:51 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:51 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:51 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:51 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:51 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:51 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:51 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:51 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:51 MarkDuplicates Before output close freeMemory: 758302688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:51 MarkDuplicates Before output close freeMemory: 758302688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:51 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:51 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:51 MarkDuplicates After output close freeMemory: 758076120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:51 MarkDuplicates After output close freeMemory: 758076120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:21:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:51 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:21:51 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10583459579631776593.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10583459579631776593.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10583459579631776593.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10583459579631776593.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10583459579631776593.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10583459579631776593.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:51.444 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:51.444 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:51.444 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:51.444 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:51.444 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:51.444 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:51.444 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:51.444 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:51 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10583459579631776593.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10583459579631776593.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10583459579631776593.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:51 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10583459579631776593.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10583459579631776593.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10583459579631776593.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:51 MarkDuplicates Start of doWork freeMemory: 1027931032; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:51 MarkDuplicates Start of doWork freeMemory: 1027931032; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:51 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:51 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:51 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:51 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:51 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:21:51 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 973398624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 973398624; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:51 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:51 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:52 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:52 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:52 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:52 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:52 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:52 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:52 MarkDuplicates After generateDuplicateIndexes freeMemory: 488957280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:52 MarkDuplicates After generateDuplicateIndexes freeMemory: 488957280; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:52 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:21:52 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:52 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:52 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:52 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:52 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:52 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:52 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:52 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:52 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:52 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:52 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:52 MarkDuplicates Before output close freeMemory: 758300864; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:52 MarkDuplicates Before output close freeMemory: 758300864; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:52 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:52 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:52 MarkDuplicates After output close freeMemory: 758441112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:52 MarkDuplicates After output close freeMemory: 758441112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:21:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:52 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:21:52 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10026915474684322490.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10026915474684322490.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10026915474684322490.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10026915474684322490.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10026915474684322490.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10026915474684322490.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:52.448 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:52.448 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:52.448 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:52.448 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:52.448 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:52.448 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:52.448 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:52.448 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:52 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10026915474684322490.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10026915474684322490.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10026915474684322490.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:52 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10026915474684322490.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10026915474684322490.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10026915474684322490.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:52 MarkDuplicates Start of doWork freeMemory: 1027930408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:52 MarkDuplicates Start of doWork freeMemory: 1027930408; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:52 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:52 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:52 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:52 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:52 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:21:52 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 973398216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 973398216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:53 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:53 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:53 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:53 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:53 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:53 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 488956656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 488956656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:53 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:21:53 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:53 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:53 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:53 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:53 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:53 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:53 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:53 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:53 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:53 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:53 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:53 MarkDuplicates Before output close freeMemory: 758300240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:53 MarkDuplicates Before output close freeMemory: 758300240; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:53 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:53 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:53 MarkDuplicates After output close freeMemory: 758073400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:53 MarkDuplicates After output close freeMemory: 758073400; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:21:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:53 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:21:53 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15472344915514430309.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15472344915514430309.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15472344915514430309.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15472344915514430309.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15472344915514430309.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15472344915514430309.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:53.504 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:53.504 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:53.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:53.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:53.504 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:53.504 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:53.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:53.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:53 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15472344915514430309.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15472344915514430309.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15472344915514430309.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:53 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15472344915514430309.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15472344915514430309.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15472344915514430309.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:53 MarkDuplicates Start of doWork freeMemory: 1027927872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:53 MarkDuplicates Start of doWork freeMemory: 1027927872; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:53 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:53 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:53 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:53 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:53 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:21:53 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 973396992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 973396992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:54 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:54 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:54 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:54 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:54 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:54 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 488955648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 488955648; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:54 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:21:54 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:54 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:54 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:54 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:54 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:54 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:54 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:54 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:54 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:54 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:54 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:54 MarkDuplicates Before output close freeMemory: 758299232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:54 MarkDuplicates Before output close freeMemory: 758299232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:54 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:54 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:54 MarkDuplicates After output close freeMemory: 758439360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:54 MarkDuplicates After output close freeMemory: 758439360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:54 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:21:54 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:54 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:21:54 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16694535307430021023.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16694535307430021023.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16694535307430021023.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16694535307430021023.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16694535307430021023.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16694535307430021023.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:54.401 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:54.401 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:54.402 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:54.402 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:54.402 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:54.402 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:54.402 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:54.402 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:54 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16694535307430021023.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16694535307430021023.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16694535307430021023.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:54 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16694535307430021023.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16694535307430021023.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16694535307430021023.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:54 MarkDuplicates Start of doWork freeMemory: 1027559280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:54 MarkDuplicates Start of doWork freeMemory: 1027559280; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:54 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:54 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:54 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:54 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:54 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:21:54 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 973396616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 973396616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:54 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:54 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:55 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:55 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:55 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:55 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:55 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 488955056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 488955056; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:55 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:21:55 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:55 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:55 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:55 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:55 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:55 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:55 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:55 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:55 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:55 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:55 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:55 MarkDuplicates Before output close freeMemory: 758297072; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:55 MarkDuplicates Before output close freeMemory: 758297072; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:55 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:55 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:55 MarkDuplicates After output close freeMemory: 758436896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:55 MarkDuplicates After output close freeMemory: 758436896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:55 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:21:55 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:55 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:21:55 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11439685240275673513.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11439685240275673513.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11439685240275673513.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11439685240275673513.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11439685240275673513.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11439685240275673513.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:55.895 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:55.895 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:55.895 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:55.895 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:55.895 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:55.895 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:55.895 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:55.895 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:55 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11439685240275673513.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11439685240275673513.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11439685240275673513.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:55 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11439685240275673513.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11439685240275673513.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11439685240275673513.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:56 MarkDuplicates Start of doWork freeMemory: 1027558688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:56 MarkDuplicates Start of doWork freeMemory: 1027558688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:56 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:56 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:56 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:56 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:56 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:21:56 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 973029112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 973029112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:56 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:56 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:56 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:56 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:56 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:56 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 703586952; totalMemory: 1288699904; maxMemory: 2147483648 INFO 2024-07-02 11:21:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 703586952; totalMemory: 1288699904; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:56 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:21:56 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:56 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:56 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:56 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:56 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:56 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:56 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:56 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:56 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:56 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:56 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:56 MarkDuplicates Before output close freeMemory: 757930496; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:56 MarkDuplicates Before output close freeMemory: 757930496; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:56 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:56 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:56 MarkDuplicates After output close freeMemory: 758437768; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:56 MarkDuplicates After output close freeMemory: 758437768; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:56 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:21:56 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:56 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:21:56 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7473534519958462514.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7473534519958462514.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7473534519958462514.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7473534519958462514.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7473534519958462514.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7473534519958462514.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:56.825 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:56.825 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:56.825 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:56.825 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:56.825 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:56.825 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:56.825 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:56.825 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:56 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7473534519958462514.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7473534519958462514.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7473534519958462514.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:56 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7473534519958462514.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7473534519958462514.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7473534519958462514.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:56 MarkDuplicates Start of doWork freeMemory: 1027926104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:56 MarkDuplicates Start of doWork freeMemory: 1027926104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:56 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:56 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:56 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:56 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:56 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:21:56 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 973393696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 973393696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:57 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:57 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:57 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:57 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:57 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:57 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 488952352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 488952352; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:57 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:21:57 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:57 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:57 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:57 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:57 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:57 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:57 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:57 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:57 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:57 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:57 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:57 MarkDuplicates Before output close freeMemory: 758294368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:57 MarkDuplicates Before output close freeMemory: 758294368; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:57 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:57 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:57 MarkDuplicates After output close freeMemory: 758067432; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:57 MarkDuplicates After output close freeMemory: 758067432; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:57 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:21:57 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:57 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:21:57 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17588700174815782048.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17588700174815782048.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17588700174815782048.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17588700174815782048.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17588700174815782048.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17588700174815782048.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:57.950 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:57.950 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:57.950 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:57.950 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:57.951 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:57.951 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:57.951 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:57.951 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:57 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17588700174815782048.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17588700174815782048.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17588700174815782048.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:57 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17588700174815782048.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17588700174815782048.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17588700174815782048.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:58 MarkDuplicates Start of doWork freeMemory: 1027922632; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:58 MarkDuplicates Start of doWork freeMemory: 1027922632; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:58 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:58 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:58 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:58 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:58 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:21:58 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 973393056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 973393056; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:58 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:58 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:58 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:58 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:58 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:58 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 488951712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 488951712; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:58 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:21:58 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:58 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:58 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:58 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:58 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:58 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:58 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:58 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:58 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:58 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:58 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:58 MarkDuplicates Before output close freeMemory: 758294664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:58 MarkDuplicates Before output close freeMemory: 758294664; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:58 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:21:58 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:58 MarkDuplicates After output close freeMemory: 758434488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:58 MarkDuplicates After output close freeMemory: 758434488; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:21:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:59 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:21:59 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6355608515476023493.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6355608515476023493.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6355608515476023493.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6355608515476023493.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6355608515476023493.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6355608515476023493.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:59.022 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:59.022 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:59.022 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:59.022 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:59.023 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:21:59.023 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:21:59.023 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:21:59.023 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:59 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6355608515476023493.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6355608515476023493.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6355608515476023493.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:21:59 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6355608515476023493.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6355608515476023493.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6355608515476023493.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:21:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:21:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:59 MarkDuplicates Start of doWork freeMemory: 1027922584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:59 MarkDuplicates Start of doWork freeMemory: 1027922584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:59 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:21:59 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:59 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:21:59 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:59 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:21:59 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 973392448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 973392448; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:59 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:21:59 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:59 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:21:59 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:59 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:21:59 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:59 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:21:59 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 488950408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:21:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 488950408; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:59 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:21:59 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:59 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:21:59 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:59 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:21:59 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:59 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:21:59 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:59 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:21:59 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:21:59 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:21:59 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:00 MarkDuplicates Before output close freeMemory: 758292424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:00 MarkDuplicates Before output close freeMemory: 758292424; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:00 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:00 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:00 MarkDuplicates After output close freeMemory: 758432176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:00 MarkDuplicates After output close freeMemory: 758432176; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:00 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:22:00 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9596466470380372779.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9596466470380372779.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9596466470380372779.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9596466470380372779.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9596466470380372779.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9596466470380372779.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:00.252 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:00.252 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:00.253 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:00.253 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:00.253 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:00.253 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:00.253 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:00.253 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:00 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9596466470380372779.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9596466470380372779.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9596466470380372779.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:00 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9596466470380372779.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9596466470380372779.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9596466470380372779.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:00 MarkDuplicates Start of doWork freeMemory: 1027924232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:00 MarkDuplicates Start of doWork freeMemory: 1027924232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:00 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:00 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:00 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:00 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:00 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:22:00 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 973025160; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 973025160; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:00 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:00 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:00 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:00 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:00 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:00 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 488950480; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 488950480; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:01 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:01 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:01 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:01 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:01 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:01 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:01 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:01 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:01 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:01 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:01 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:01 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:01 MarkDuplicates Before output close freeMemory: 758293432; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:01 MarkDuplicates Before output close freeMemory: 758293432; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:01 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:01 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:01 MarkDuplicates After output close freeMemory: 758433256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:01 MarkDuplicates After output close freeMemory: 758433256; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:01 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:01 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:01 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756) STANDARD_ERROR INFO 2024-07-02 11:22:01 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5187564973169632503.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5187564973169632503.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5187564973169632503.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5187564973169632503.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5187564973169632503.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5187564973169632503.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:01.292 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:01.292 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:01.293 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:01.293 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:01.293 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:01.293 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:01.293 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:01.293 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:01 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5187564973169632503.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5187564973169632503.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5187564973169632503.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:01 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5187564973169632503.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5187564973169632503.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5187564973169632503.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:01 MarkDuplicates Start of doWork freeMemory: 1027923608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:01 MarkDuplicates Start of doWork freeMemory: 1027923608; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:01 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:01 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:01 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:01 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:01 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:22:01 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 973391200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 973391200; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:01 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:01 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:01 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:01 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:01 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:01 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 607438944; totalMemory: 1192230912; maxMemory: 2147483648 INFO 2024-07-02 11:22:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 607438944; totalMemory: 1192230912; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:02 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:02 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:02 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:02 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:02 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:02 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:02 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:02 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:02 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:02 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:02 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:02 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:02 MarkDuplicates Before output close freeMemory: 758292808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:02 MarkDuplicates Before output close freeMemory: 758292808; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:02 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:02 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:02 MarkDuplicates After output close freeMemory: 758433536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:02 MarkDuplicates After output close freeMemory: 758433536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:02 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:02 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:02 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756) STANDARD_ERROR INFO 2024-07-02 11:22:02 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7844463453959442107.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7844463453959442107.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7844463453959442107.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7844463453959442107.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7844463453959442107.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7844463453959442107.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:02.417 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:02.417 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:02.417 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:02.417 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:02.417 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:02.417 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:02.418 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:02.418 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:02 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7844463453959442107.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7844463453959442107.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7844463453959442107.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:02 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7844463453959442107.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7844463453959442107.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7844463453959442107.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:02 MarkDuplicates Start of doWork freeMemory: 1027922960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:02 MarkDuplicates Start of doWork freeMemory: 1027922960; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:02 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:02 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:02 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:02 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:02 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:22:02 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 973390552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 973390552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:02 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:02 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:03 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:03 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:03 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 488949208; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 488949208; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:03 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:03 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:03 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:03 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:03 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:03 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates Before output close freeMemory: 758291224; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:03 MarkDuplicates Before output close freeMemory: 758291224; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:03 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates After output close freeMemory: 758066224; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:03 MarkDuplicates After output close freeMemory: 758066224; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:03 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:03 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756) STANDARD_ERROR INFO 2024-07-02 11:22:03 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3585167267832685471.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3585167267832685471.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3585167267832685471.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3585167267832685471.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3585167267832685471.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3585167267832685471.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:03.372 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:03.372 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:03.372 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:03.372 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:03.373 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:03.373 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:03.373 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:03.373 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:03 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3585167267832685471.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3585167267832685471.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3585167267832685471.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:03 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3585167267832685471.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3585167267832685471.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3585167267832685471.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates Start of doWork freeMemory: 1027922336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:03 MarkDuplicates Start of doWork freeMemory: 1027922336; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:03 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:03 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:22:03 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 973389928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 973389928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:03 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:03 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:03 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:03 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 488948584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 488948584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:03 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:03 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:03 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:03 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:03 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:03 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:03 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:04 MarkDuplicates Before output close freeMemory: 758291536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:04 MarkDuplicates Before output close freeMemory: 758291536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:04 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:04 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:04 MarkDuplicates After output close freeMemory: 758432192; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:04 MarkDuplicates After output close freeMemory: 758432192; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:04 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:22:04 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:04 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756) STANDARD_ERROR INFO 2024-07-02 11:22:04 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10301925222688181468.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10301925222688181468.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10301925222688181468.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10301925222688181468.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10301925222688181468.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10301925222688181468.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:04.229 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:04.229 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:04.229 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:04.229 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:04.229 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:04.229 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:04.229 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:04.229 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:04 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10301925222688181468.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10301925222688181468.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10301925222688181468.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:04 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10301925222688181468.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10301925222688181468.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10301925222688181468.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:04 MarkDuplicates Start of doWork freeMemory: 1027921696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:04 MarkDuplicates Start of doWork freeMemory: 1027921696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:04 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:04 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:04 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:04 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:04 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:22:04 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 973389288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 973389288; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:04 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:04 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:04 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:04 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:04 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:04 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:04 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:04 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 488947944; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 488947944; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:04 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:04 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:04 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:04 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:04 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:04 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:04 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:04 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:04 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:04 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:04 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:04 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:05 MarkDuplicates Before output close freeMemory: 758291528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:05 MarkDuplicates Before output close freeMemory: 758291528; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:05 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:05 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:05 MarkDuplicates After output close freeMemory: 758064616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:05 MarkDuplicates After output close freeMemory: 758064616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:05 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:05 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:05 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance STANDARD_ERROR INFO 2024-07-02 11:22:05 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12588430462847875627.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12588430462847875627.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12588430462847875627.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12588430462847875627.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12588430462847875627.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12588430462847875627.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:05.275 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:05.275 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:05.275 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:05.275 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:05.275 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:05.275 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:05.275 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:05.275 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:05 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12588430462847875627.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12588430462847875627.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12588430462847875627.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:05 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12588430462847875627.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12588430462847875627.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12588430462847875627.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:05 MarkDuplicates Start of doWork freeMemory: 1027918512; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:05 MarkDuplicates Start of doWork freeMemory: 1027918512; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:05 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:05 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:05 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:05 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:05 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:22:05 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 973389152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 973389152; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:05 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:05 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:05 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:05 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:05 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:05 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 488947592; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 488947592; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:06 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:06 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:06 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:06 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:06 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:06 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:06 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:06 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:06 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:06 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:06 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:06 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:06 MarkDuplicates Before output close freeMemory: 758290976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:06 MarkDuplicates Before output close freeMemory: 758290976; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:06 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:06 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:06 MarkDuplicates After output close freeMemory: 758431496; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:06 MarkDuplicates After output close freeMemory: 758431496; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:06 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:06 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:06 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance STANDARD_ERROR INFO 2024-07-02 11:22:06 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9438357327437095294.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9438357327437095294.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9438357327437095294.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9438357327437095294.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9438357327437095294.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9438357327437095294.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:06.463 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:06.463 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:06.464 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:06.464 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:06.464 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:06.464 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:06.464 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:06.464 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:06 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9438357327437095294.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9438357327437095294.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9438357327437095294.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:06 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9438357327437095294.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9438357327437095294.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9438357327437095294.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:06 MarkDuplicates Start of doWork freeMemory: 1027921168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:06 MarkDuplicates Start of doWork freeMemory: 1027921168; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:06 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:06 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:06 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:06 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:06 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:22:06 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 973388760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 973388760; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:06 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:06 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:07 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:07 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:07 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:07 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:07 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:07 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 616873536; totalMemory: 1201668096; maxMemory: 2147483648 INFO 2024-07-02 11:22:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 616873536; totalMemory: 1201668096; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:07 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:07 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:07 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:22:07 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:07 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:07 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:07 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:07 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:07 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:07 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:07 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:07 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:07 MarkDuplicates Before output close freeMemory: 758290960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:07 MarkDuplicates Before output close freeMemory: 758290960; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:07 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:07 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:07 MarkDuplicates After output close freeMemory: 758431096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:07 MarkDuplicates After output close freeMemory: 758431096; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:07 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:07 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:07 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate STANDARD_ERROR INFO 2024-07-02 11:22:07 MarkDuplicates Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5353406515630124642.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5353406515630124642.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5353406515630124642.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5353406515630124642.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5353406515630124642.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5353406515630124642.tmp/output.sam Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:07.531 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:07.531 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:07.532 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:07.532 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:07.532 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:07.532 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:07.532 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:07.532 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:07 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5353406515630124642.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5353406515630124642.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5353406515630124642.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:07 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5353406515630124642.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5353406515630124642.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5353406515630124642.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:07 MarkDuplicates Start of doWork freeMemory: 1027920256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:07 MarkDuplicates Start of doWork freeMemory: 1027920256; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:07 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:07 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:07 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:07 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:07 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:22:07 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 973387880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 973387880; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:07 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:07 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:08 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:08 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:08 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:08 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:08 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:08 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 488946352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 488946352; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:08 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:08 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:08 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:22:08 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:08 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:08 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:08 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:08 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:08 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:08 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:08 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:08 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:08 MarkDuplicates Before output close freeMemory: 758289976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:08 MarkDuplicates Before output close freeMemory: 758289976; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:08 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:08 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:08 MarkDuplicates After output close freeMemory: 758430256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:08 MarkDuplicates After output close freeMemory: 758430256; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:08 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:08 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:08 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testOpticalDuplicateFinding STANDARD_ERROR INFO 2024-07-02 11:22:08 MarkDuplicates Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.8069421293693615129.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8069421293693615129.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8069421293693615129.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.8069421293693615129.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8069421293693615129.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8069421293693615129.tmp/output.sam Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:08.463 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:08.463 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:08.463 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:08.463 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:08.463 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:08.463 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:08.463 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:08.463 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:08 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8069421293693615129.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8069421293693615129.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8069421293693615129.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:08 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8069421293693615129.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8069421293693615129.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8069421293693615129.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:08 MarkDuplicates Start of doWork freeMemory: 1027916824; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:08 MarkDuplicates Start of doWork freeMemory: 1027916824; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:08 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:08 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:08 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:08 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:08 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:22:08 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 973385872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 973385872; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:09 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:09 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:09 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:09 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:09 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:09 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 488730744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 488730744; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:09 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:22:09 MarkDuplicates Marking 4 records as duplicates. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:09 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:22:09 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:09 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:09 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:09 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:09 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:09 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:09 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:09 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:09 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:09 MarkDuplicates Before output close freeMemory: 758288328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:09 MarkDuplicates Before output close freeMemory: 758288328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:09 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:09 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:09 MarkDuplicates After output close freeMemory: 758428008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:09 MarkDuplicates After output close freeMemory: 758428008; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:09 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:09 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:09 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testPathologicalOrderingAtTheSamePosition STANDARD_ERROR INFO 2024-07-02 11:22:09 MarkDuplicates Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9400789273194031584.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9400789273194031584.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9400789273194031584.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9400789273194031584.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9400789273194031584.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9400789273194031584.tmp/output.sam Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:09.415 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:09.415 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:09.415 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:09.415 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:09.416 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:09.416 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:09.416 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:09.416 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:09 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9400789273194031584.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9400789273194031584.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9400789273194031584.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:09 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9400789273194031584.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9400789273194031584.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9400789273194031584.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:09 MarkDuplicates Start of doWork freeMemory: 1027918792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:09 MarkDuplicates Start of doWork freeMemory: 1027918792; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:09 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:09 MarkDuplicates Reading input file and constructing read end information. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:09 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:09 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:09 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:22:09 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 973019712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 973019712; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:09 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:09 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:09 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:09 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:09 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:09 MarkDuplicates Sorting list of duplicate records. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 488944888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 488944888; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:10 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:10 MarkDuplicates Marking 2 records as duplicates. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:10 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:22:10 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:10 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:10 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:10 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:10 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:10 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:10 MarkDuplicates Duplicate Index cleanup. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:10 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:10 MarkDuplicates Getting Memory Stats. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:10 MarkDuplicates Before output close freeMemory: 758286968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:10 MarkDuplicates Before output close freeMemory: 758286968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:10 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:10 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:10 MarkDuplicates After output close freeMemory: 758428792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:10 MarkDuplicates After output close freeMemory: 758428792; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:10 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:10 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:10 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testSecondEndIsBeforeFirstInCoordinate STANDARD_ERROR INFO 2024-07-02 11:22:10 MarkDuplicates Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15927659571866306282.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15927659571866306282.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15927659571866306282.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15927659571866306282.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15927659571866306282.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15927659571866306282.tmp/output.sam Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:10.488 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:10.488 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:10.488 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:10.488 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:10.488 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:10.488 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:10.488 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:10.488 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:10 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15927659571866306282.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15927659571866306282.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15927659571866306282.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:10 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15927659571866306282.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15927659571866306282.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15927659571866306282.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:10 MarkDuplicates Start of doWork freeMemory: 1027919320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:10 MarkDuplicates Start of doWork freeMemory: 1027919320; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:10 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:10 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:10 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:10 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:22:10 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:22:10 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:10 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:22:10 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 973387464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 973387464; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:11 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:11 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:11 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:11 MarkDuplicates Sorting list of duplicate records. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 488945640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 488945640; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:11 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:22:11 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:11 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:11 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:11 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:11 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:11 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:11 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:11 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:11 MarkDuplicates Duplicate Index cleanup. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:11 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:11 MarkDuplicates Getting Memory Stats. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:11 MarkDuplicates Before output close freeMemory: 758288896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:11 MarkDuplicates Before output close freeMemory: 758288896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:11 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:11 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:11 MarkDuplicates After output close freeMemory: 758429472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:11 MarkDuplicates After output close freeMemory: 758429472; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:11 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:11 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:11 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testSingleMappedFragment STANDARD_ERROR INFO 2024-07-02 11:22:11 MarkDuplicates Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11951907209739979159.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11951907209739979159.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11951907209739979159.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11951907209739979159.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11951907209739979159.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11951907209739979159.tmp/output.sam Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:11.607 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:11.607 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:11.608 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:11.608 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:11.608 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:11.608 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:11.608 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:11.608 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:11 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11951907209739979159.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11951907209739979159.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11951907209739979159.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:11 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11951907209739979159.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11951907209739979159.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11951907209739979159.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:11 MarkDuplicates Start of doWork freeMemory: 1027919360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:11 MarkDuplicates Start of doWork freeMemory: 1027919360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:11 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:11 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:11 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:11 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:22:11 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:22:11 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:11 MarkDuplicates Read 1 records. 0 pairs never matched. INFO 2024-07-02 11:22:11 MarkDuplicates Read 1 records. 0 pairs never matched. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 973387800; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 973387800; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:12 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:12 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:12 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:12 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:12 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:12 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 488945280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 488945280; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:12 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:22:12 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:12 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:12 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:12 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:12 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:12 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:12 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:12 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:12 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:12 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:12 MarkDuplicates Getting Memory Stats. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:12 MarkDuplicates Before output close freeMemory: 758288952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:12 MarkDuplicates Before output close freeMemory: 758288952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:12 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:12 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:12 MarkDuplicates After output close freeMemory: 758429584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:12 MarkDuplicates After output close freeMemory: 758429584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:12 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:22:12 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:12 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testSingleMappedFragmentAndSingleMappedPair STANDARD_ERROR INFO 2024-07-02 11:22:12 MarkDuplicates Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13426082780672423445.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13426082780672423445.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13426082780672423445.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13426082780672423445.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13426082780672423445.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13426082780672423445.tmp/output.sam Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:12.517 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:12.517 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:12.518 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:12.518 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:12.518 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:12.518 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:12.518 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:12.518 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:12 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13426082780672423445.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13426082780672423445.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13426082780672423445.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:12 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13426082780672423445.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13426082780672423445.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13426082780672423445.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:12 MarkDuplicates Start of doWork freeMemory: 1027917488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:12 MarkDuplicates Start of doWork freeMemory: 1027917488; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:12 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:12 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:12 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:12 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:22:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:22:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:12 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2024-07-02 11:22:12 MarkDuplicates Read 3 records. 0 pairs never matched. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 973385536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 973385536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:12 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:12 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:13 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:13 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:13 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:13 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:13 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:13 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 699707576; totalMemory: 1284505600; maxMemory: 2147483648 INFO 2024-07-02 11:22:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 699707576; totalMemory: 1284505600; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:13 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:22:13 MarkDuplicates Marking 1 records as duplicates. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:13 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:13 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:13 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:13 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:13 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:13 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:13 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:13 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:13 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:13 MarkDuplicates Getting Memory Stats. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:13 MarkDuplicates Before output close freeMemory: 758287320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:13 MarkDuplicates Before output close freeMemory: 758287320; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:13 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:13 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:13 MarkDuplicates After output close freeMemory: 758427704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:13 MarkDuplicates After output close freeMemory: 758427704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:13 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:13 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:13 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testSingleMappedFragmentAndTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:22:13 MarkDuplicates Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11415698114073858654.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11415698114073858654.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11415698114073858654.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11415698114073858654.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11415698114073858654.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11415698114073858654.tmp/output.sam Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:13.530 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:13.530 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:13.530 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:13.530 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:13.531 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:13.531 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:13.531 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:13.531 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:13 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11415698114073858654.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11415698114073858654.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11415698114073858654.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:13 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11415698114073858654.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11415698114073858654.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11415698114073858654.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:13 MarkDuplicates Start of doWork freeMemory: 1027915384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:13 MarkDuplicates Start of doWork freeMemory: 1027915384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:13 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:13 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:13 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:13 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:22:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:22:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:13 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:22:13 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 973383168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 973383168; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:13 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:13 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:14 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:14 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:14 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 488941696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 488941696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates Marking 3 records as duplicates. INFO 2024-07-02 11:22:14 MarkDuplicates Marking 3 records as duplicates. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:14 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:14 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:14 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:14 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:14 MarkDuplicates Getting Memory Stats. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates Before output close freeMemory: 758285416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:14 MarkDuplicates Before output close freeMemory: 758285416; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:14 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates After output close freeMemory: 758425032; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:14 MarkDuplicates After output close freeMemory: 758425032; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:14 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:22:14 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testSingleMappedPair STANDARD_ERROR INFO 2024-07-02 11:22:14 MarkDuplicates Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4133400454344868809.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4133400454344868809.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4133400454344868809.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4133400454344868809.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4133400454344868809.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4133400454344868809.tmp/output.sam Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:14.380 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:14.380 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:14.380 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:14.380 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:14.380 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:14.380 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:14.380 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:14.380 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:14 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4133400454344868809.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4133400454344868809.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4133400454344868809.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:14 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4133400454344868809.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4133400454344868809.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4133400454344868809.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates Start of doWork freeMemory: 1027916248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:14 MarkDuplicates Start of doWork freeMemory: 1027916248; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:14 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:14 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:22:14 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:22:14 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:22:14 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 973017512; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 973017512; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:14 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:14 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:14 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:14 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 488942952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 488942952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:22:14 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:14 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:14 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:14 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:14 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:14 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:14 MarkDuplicates Getting Memory Stats. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:15 MarkDuplicates Before output close freeMemory: 758286672; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:15 MarkDuplicates Before output close freeMemory: 758286672; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:15 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:15 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:15 MarkDuplicates After output close freeMemory: 758426288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:15 MarkDuplicates After output close freeMemory: 758426288; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:22:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:15 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testSingleUnmappedFragment STANDARD_ERROR INFO 2024-07-02 11:22:15 MarkDuplicates Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12605197599637321491.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12605197599637321491.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12605197599637321491.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12605197599637321491.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12605197599637321491.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12605197599637321491.tmp/output.sam Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:15.211 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:15.211 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:15.211 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:15.211 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:15.211 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:15.211 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:15.211 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:15.211 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:15 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12605197599637321491.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12605197599637321491.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12605197599637321491.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:15 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12605197599637321491.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12605197599637321491.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12605197599637321491.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:15 MarkDuplicates Start of doWork freeMemory: 1027911280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:15 MarkDuplicates Start of doWork freeMemory: 1027911280; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:15 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:15 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:15 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:15 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:15 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2024-07-02 11:22:15 MarkDuplicates Read 0 records. 0 pairs never matched. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:15 MarkDuplicates After buildSortedReadEndLists freeMemory: 973385144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:15 MarkDuplicates After buildSortedReadEndLists freeMemory: 973385144; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:15 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:15 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:15 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:15 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:15 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:15 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:15 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:15 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 488943448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 488943448; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:15 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:22:15 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:15 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:15 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:15 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:15 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:15 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:15 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:15 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:15 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:15 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:15 MarkDuplicates Getting Memory Stats. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:16 MarkDuplicates Before output close freeMemory: 758287488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:16 MarkDuplicates Before output close freeMemory: 758287488; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:16 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:16 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:16 MarkDuplicates After output close freeMemory: 758427352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:16 MarkDuplicates After output close freeMemory: 758427352; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:16 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:16 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:16 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testSingleUnmappedPair STANDARD_ERROR INFO 2024-07-02 11:22:16 MarkDuplicates Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.18040959403999544988.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.18040959403999544988.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.18040959403999544988.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.18040959403999544988.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.18040959403999544988.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.18040959403999544988.tmp/output.sam Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:16.223 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:16.223 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:16.224 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:16.224 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:16.224 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:16.224 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:16.224 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:16.224 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:16 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.18040959403999544988.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.18040959403999544988.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.18040959403999544988.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:16 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.18040959403999544988.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.18040959403999544988.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.18040959403999544988.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:16 MarkDuplicates Start of doWork freeMemory: 1027915688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:16 MarkDuplicates Start of doWork freeMemory: 1027915688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:16 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:16 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:16 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:16 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:16 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2024-07-02 11:22:16 MarkDuplicates Read 0 records. 0 pairs never matched. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 973384320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 973384320; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:17 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:17 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:17 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:17 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:17 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:17 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 488941744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 488941744; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:17 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:22:17 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:17 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:17 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:17 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:17 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:17 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:17 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:17 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:17 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:17 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:17 MarkDuplicates Getting Memory Stats. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:17 MarkDuplicates Before output close freeMemory: 758286448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:17 MarkDuplicates Before output close freeMemory: 758286448; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:17 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:17 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:17 MarkDuplicates After output close freeMemory: 758426312; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:17 MarkDuplicates After output close freeMemory: 758426312; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:17 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:17 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:17 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testStackOverFlowPairSetSwap STANDARD_ERROR INFO 2024-07-02 11:22:17 MarkDuplicates Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17358118007849478596.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17358118007849478596.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17358118007849478596.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17358118007849478596.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17358118007849478596.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17358118007849478596.tmp/output.sam Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:17.536 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:17.536 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:17.536 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:17.536 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:17.536 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:17.536 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:17.536 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:17.536 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:17 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17358118007849478596.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17358118007849478596.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17358118007849478596.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:17 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17358118007849478596.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17358118007849478596.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17358118007849478596.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:17 MarkDuplicates Start of doWork freeMemory: 1027805960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:17 MarkDuplicates Start of doWork freeMemory: 1027805960; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:17 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:17 MarkDuplicates Reading input file and constructing read end information. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:17 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:17 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:17 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:22:17 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 972878584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 972878584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:18 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:18 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:18 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:18 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:18 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:18 MarkDuplicates Sorting list of duplicate records. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 616730024; totalMemory: 1201668096; maxMemory: 2147483648 INFO 2024-07-02 11:22:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 616730024; totalMemory: 1201668096; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:18 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:18 MarkDuplicates Marking 2 records as duplicates. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:18 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:22:18 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:18 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:18 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:18 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:18 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:18 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:18 MarkDuplicates Duplicate Index cleanup. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:18 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:18 MarkDuplicates Getting Memory Stats. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:18 MarkDuplicates Before output close freeMemory: 758118048; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:18 MarkDuplicates Before output close freeMemory: 758118048; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:18 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:18 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:18 MarkDuplicates After output close freeMemory: 758286232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:18 MarkDuplicates After output close freeMemory: 758286232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:18 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:18 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:18 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:22:18 MarkDuplicates Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3931192333165396197.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3931192333165396197.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3931192333165396197.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3931192333165396197.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3931192333165396197.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3931192333165396197.tmp/output.sam Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:19.031 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:19.031 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:19.031 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:19.031 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:19.031 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:19.031 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:19.031 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:19.031 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:19 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3931192333165396197.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3931192333165396197.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3931192333165396197.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:19 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3931192333165396197.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3931192333165396197.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3931192333165396197.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:19 MarkDuplicates Start of doWork freeMemory: 1027899056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:19 MarkDuplicates Start of doWork freeMemory: 1027899056; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:19 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:19 MarkDuplicates Reading input file and constructing read end information. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:19 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:19 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:22:19 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:22:19 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:19 MarkDuplicates Read 18 records. 0 pairs never matched. INFO 2024-07-02 11:22:19 MarkDuplicates Read 18 records. 0 pairs never matched. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 973367064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 973367064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:19 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:19 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:19 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:19 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:19 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:19 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:19 MarkDuplicates Sorting list of duplicate records. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 488927568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 488927568; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:19 MarkDuplicates Marking 12 records as duplicates. INFO 2024-07-02 11:22:19 MarkDuplicates Marking 12 records as duplicates. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:19 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:19 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:19 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:19 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:19 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:19 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:19 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:19 MarkDuplicates Duplicate Index cleanup. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:19 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:19 MarkDuplicates Getting Memory Stats. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:19 MarkDuplicates Before output close freeMemory: 758271288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:19 MarkDuplicates Before output close freeMemory: 758271288; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:19 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:19 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:19 MarkDuplicates After output close freeMemory: 758044584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:19 MarkDuplicates After output close freeMemory: 758044584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:19 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:19 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:19 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:22:19 MarkDuplicates Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10913264257206632037.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10913264257206632037.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10913264257206632037.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10913264257206632037.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10913264257206632037.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10913264257206632037.tmp/output.sam Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:19.981 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:19.981 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:19.981 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:19.981 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:19.981 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:19.981 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:19.982 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:19.982 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:19 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10913264257206632037.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10913264257206632037.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10913264257206632037.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:19 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10913264257206632037.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10913264257206632037.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10913264257206632037.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:20 MarkDuplicates Start of doWork freeMemory: 1027905912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:20 MarkDuplicates Start of doWork freeMemory: 1027905912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:20 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:20 MarkDuplicates Reading input file and constructing read end information. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:20 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:20 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:22:20 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:22:20 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:20 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:22:20 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 973009088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 973009088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:20 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:20 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:20 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:20 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:20 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:20 MarkDuplicates Sorting list of duplicate records. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 488935056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 488935056; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:20 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:22:20 MarkDuplicates Marking 4 records as duplicates. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:20 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:20 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:20 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:20 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:20 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:20 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:20 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:20 MarkDuplicates Duplicate Index cleanup. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:20 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:20 MarkDuplicates Getting Memory Stats. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:20 MarkDuplicates Before output close freeMemory: 758278776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:20 MarkDuplicates Before output close freeMemory: 758278776; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:20 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:20 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:21 MarkDuplicates After output close freeMemory: 758418392; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:21 MarkDuplicates After output close freeMemory: 758418392; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:21 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:21 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:21 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testThreeMappedPairsWithMatchingSecondMate STANDARD_ERROR INFO 2024-07-02 11:22:21 MarkDuplicates Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13773720613033002659.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13773720613033002659.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13773720613033002659.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13773720613033002659.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13773720613033002659.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13773720613033002659.tmp/output.sam Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:21.170 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:21.170 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:21.170 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:21.170 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:21.170 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:21.170 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:21.171 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:21.171 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:21 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13773720613033002659.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13773720613033002659.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13773720613033002659.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:21 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13773720613033002659.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13773720613033002659.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13773720613033002659.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:21 MarkDuplicates Start of doWork freeMemory: 1027907864; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:21 MarkDuplicates Start of doWork freeMemory: 1027907864; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:21 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:21 MarkDuplicates Reading input file and constructing read end information. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:21 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:21 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:22:21 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:22:21 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:21 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:22:21 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 973374880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 973374880; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:21 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:21 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:21 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:21 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:21 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:21 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:21 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:21 MarkDuplicates Sorting list of duplicate records. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 488934008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 488934008; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:22 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:22 MarkDuplicates Marking 2 records as duplicates. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:22 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:22 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:22 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:22 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:22 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:22 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:22 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:22 MarkDuplicates Duplicate Index cleanup. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:22 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:22 MarkDuplicates Getting Memory Stats. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:22 MarkDuplicates Before output close freeMemory: 757909424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:22 MarkDuplicates Before output close freeMemory: 757909424; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:22 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:22 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:22 MarkDuplicates After output close freeMemory: 758417616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:22 MarkDuplicates After output close freeMemory: 758417616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:22 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:22 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:22 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:22:22 MarkDuplicates Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16858730049852820006.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16858730049852820006.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16858730049852820006.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16858730049852820006.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16858730049852820006.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16858730049852820006.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:22.602 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:22.602 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:22.602 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:22.602 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:22.602 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:22.602 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:22.602 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:22.602 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:22 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16858730049852820006.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16858730049852820006.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16858730049852820006.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:22 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16858730049852820006.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16858730049852820006.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16858730049852820006.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:22 MarkDuplicates Start of doWork freeMemory: 1027903232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:22 MarkDuplicates Start of doWork freeMemory: 1027903232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:22 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:22 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:22 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:22 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:22:22 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:22:22 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:22 MarkDuplicates Read 12 records. 0 pairs never matched. INFO 2024-07-02 11:22:22 MarkDuplicates Read 12 records. 0 pairs never matched. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 973369928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 973369928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:23 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:23 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:23 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:23 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:23 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:23 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 488929424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 488929424; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:23 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:22:23 MarkDuplicates Marking 8 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:23 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:23 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:23 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:23 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:23 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:23 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:23 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:23 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:23 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:23 MarkDuplicates Getting Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:24 MarkDuplicates Before output close freeMemory: 758271576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:24 MarkDuplicates Before output close freeMemory: 758271576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:24 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:24 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:24 MarkDuplicates After output close freeMemory: 758413104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:24 MarkDuplicates After output close freeMemory: 758413104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:24 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:22:24 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:24 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoGroupsOnDifferentChromosomesOfTwoFragments STANDARD_ERROR INFO 2024-07-02 11:22:24 MarkDuplicates Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.14488643099494445960.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14488643099494445960.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14488643099494445960.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.14488643099494445960.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14488643099494445960.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14488643099494445960.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:24.461 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:24.461 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:24.461 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:24.461 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:24.462 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:24.462 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:24.462 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:24.462 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:24 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.14488643099494445960.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.14488643099494445960.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.14488643099494445960.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:24 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.14488643099494445960.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.14488643099494445960.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.14488643099494445960.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:24 MarkDuplicates Start of doWork freeMemory: 1027907976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:24 MarkDuplicates Start of doWork freeMemory: 1027907976; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:24 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:24 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:24 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:24 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:22:24 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:22:24 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:24 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:22:24 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 973375544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 973375544; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:25 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:25 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:25 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:25 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:25 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:25 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:25 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:25 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 488934584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 488934584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:25 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:25 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:25 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:25 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:25 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:25 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:25 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:25 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:25 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:25 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:25 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:25 MarkDuplicates Getting Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:25 MarkDuplicates Before output close freeMemory: 758278416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:25 MarkDuplicates Before output close freeMemory: 758278416; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:25 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:25 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:26 MarkDuplicates After output close freeMemory: 758418416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:26 MarkDuplicates After output close freeMemory: 758418416; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:26 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:22:26 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:26 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:22:26 MarkDuplicates Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12520723572145953400.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12520723572145953400.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12520723572145953400.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12520723572145953400.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12520723572145953400.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12520723572145953400.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:26.212 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:26.212 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:26.212 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:26.212 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:26.212 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:26.212 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:26.212 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:26.212 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:26 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12520723572145953400.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12520723572145953400.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12520723572145953400.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:26 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12520723572145953400.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12520723572145953400.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12520723572145953400.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:26 MarkDuplicates Start of doWork freeMemory: 1027904528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:26 MarkDuplicates Start of doWork freeMemory: 1027904528; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:26 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:26 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:26 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:26 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:22:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:22:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:26 MarkDuplicates Read 8 records. 0 pairs never matched. INFO 2024-07-02 11:22:26 MarkDuplicates Read 8 records. 0 pairs never matched. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 973004488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 973004488; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:27 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:27 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:27 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:27 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 488964424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 488964424; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:27 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:22:27 MarkDuplicates Marking 4 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:27 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:27 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:27 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:27 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:27 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:27 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:27 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:27 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:27 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:27 MarkDuplicates Getting Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:27 MarkDuplicates Before output close freeMemory: 758306576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:27 MarkDuplicates Before output close freeMemory: 758306576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:27 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:27 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:28 MarkDuplicates After output close freeMemory: 758448328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:28 MarkDuplicates After output close freeMemory: 758448328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:28 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:22:28 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:28 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoMappedFragments STANDARD_ERROR INFO 2024-07-02 11:22:28 MarkDuplicates Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12885490169187693456.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12885490169187693456.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12885490169187693456.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12885490169187693456.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12885490169187693456.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12885490169187693456.tmp/output.sam Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:28.153 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:28.153 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:28.153 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:28.153 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:28.154 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:28.154 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:28.154 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:28.154 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:28 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12885490169187693456.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12885490169187693456.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12885490169187693456.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:28 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12885490169187693456.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12885490169187693456.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12885490169187693456.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:28 MarkDuplicates Start of doWork freeMemory: 1027938640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:28 MarkDuplicates Start of doWork freeMemory: 1027938640; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:28 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:28 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:28 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:28 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:22:28 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:22:28 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:28 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:22:28 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 973042552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 973042552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:29 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:29 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:29 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:29 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:29 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:29 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 488968080; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 488968080; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:29 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:22:29 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:29 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:29 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:29 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:29 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:29 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:29 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:29 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:29 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:29 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:29 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:29 MarkDuplicates Before output close freeMemory: 758311912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:29 MarkDuplicates Before output close freeMemory: 758311912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:29 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:29 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:29 MarkDuplicates After output close freeMemory: 758451416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:29 MarkDuplicates After output close freeMemory: 758451416; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:22:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:29 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoMappedPairWithSamePosition STANDARD_ERROR INFO 2024-07-02 11:22:29 MarkDuplicates Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7596524340504563287.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7596524340504563287.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7596524340504563287.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7596524340504563287.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7596524340504563287.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7596524340504563287.tmp/output.sam Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:29.987 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:29.987 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:29.988 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:29.988 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:29.988 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:29.988 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:29.988 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:29.988 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:29 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7596524340504563287.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7596524340504563287.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7596524340504563287.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:29 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7596524340504563287.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7596524340504563287.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7596524340504563287.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:30 MarkDuplicates Start of doWork freeMemory: 1027937656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:30 MarkDuplicates Start of doWork freeMemory: 1027937656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:30 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:30 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:30 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:30 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:22:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:22:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:30 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:22:30 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 973406640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 973406640; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:30 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:30 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:30 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:30 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:30 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:30 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 703923760; totalMemory: 1288699904; maxMemory: 2147483648 INFO 2024-07-02 11:22:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 703923760; totalMemory: 1288699904; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:31 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:31 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:31 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:31 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:31 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:31 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:31 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:31 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:31 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:31 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:31 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:31 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:31 MarkDuplicates Before output close freeMemory: 758308696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:31 MarkDuplicates Before output close freeMemory: 758308696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:31 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:31 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:31 MarkDuplicates After output close freeMemory: 758449360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:31 MarkDuplicates After output close freeMemory: 758449360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:31 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:22:31 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:31 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoMappedPairWithSamePositionDifferentStrands STANDARD_ERROR INFO 2024-07-02 11:22:31 MarkDuplicates Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17038549011651206940.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17038549011651206940.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17038549011651206940.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17038549011651206940.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17038549011651206940.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17038549011651206940.tmp/output.sam Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:31.586 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:31.586 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:31.587 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:31.587 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:31.587 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:31.587 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:31.587 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:31.587 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:31 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17038549011651206940.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17038549011651206940.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17038549011651206940.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:31 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17038549011651206940.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17038549011651206940.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17038549011651206940.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:31 MarkDuplicates Start of doWork freeMemory: 1027935984; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:31 MarkDuplicates Start of doWork freeMemory: 1027935984; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:31 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:31 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:31 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:31 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:22:31 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:22:31 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:31 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:22:31 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 973405944; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 973405944; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:32 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:32 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:32 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:32 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:32 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:32 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 488964288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 488964288; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:32 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:32 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:32 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:32 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:32 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:32 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:32 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:32 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:32 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:32 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:32 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:32 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:32 MarkDuplicates Before output close freeMemory: 758306440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:32 MarkDuplicates Before output close freeMemory: 758306440; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:32 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:32 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:33 MarkDuplicates After output close freeMemory: 758082328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:33 MarkDuplicates After output close freeMemory: 758082328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:33 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:22:33 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:33 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoMappedPairWithSamePositionDifferentStrands2 STANDARD_ERROR INFO 2024-07-02 11:22:33 MarkDuplicates Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10460015099163699974.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10460015099163699974.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10460015099163699974.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10460015099163699974.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10460015099163699974.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10460015099163699974.tmp/output.sam Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:33.139 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:33.139 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:33.140 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:33.140 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:33.140 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:33.140 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:33.140 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:33.140 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:33 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10460015099163699974.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10460015099163699974.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10460015099163699974.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:33 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10460015099163699974.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10460015099163699974.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10460015099163699974.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:33 MarkDuplicates Start of doWork freeMemory: 1027932544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:33 MarkDuplicates Start of doWork freeMemory: 1027932544; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:33 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:33 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:33 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:33 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:22:33 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:22:33 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:33 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:22:33 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 973405864; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 973405864; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:34 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:34 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:34 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:34 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:34 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 488964304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 488964304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:34 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:34 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:34 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:34 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:34 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:34 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:34 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:34 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:34 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:34 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:34 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:34 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:34 MarkDuplicates Before output close freeMemory: 758308024; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:34 MarkDuplicates Before output close freeMemory: 758308024; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:34 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:34 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:34 MarkDuplicates After output close freeMemory: 758448136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:34 MarkDuplicates After output close freeMemory: 758448136; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:22:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:34 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:22:34 MarkDuplicates Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6488462603993518509.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6488462603993518509.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6488462603993518509.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6488462603993518509.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6488462603993518509.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6488462603993518509.tmp/output.sam Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:34.752 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:34.752 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:34.752 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:34.752 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:34.752 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:34.752 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:34.752 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:34.752 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:34 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6488462603993518509.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6488462603993518509.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6488462603993518509.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:34 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6488462603993518509.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6488462603993518509.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6488462603993518509.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:35 MarkDuplicates Start of doWork freeMemory: 1027937088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:35 MarkDuplicates Start of doWork freeMemory: 1027937088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:35 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:35 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:35 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:35 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:22:35 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:22:35 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:35 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:22:35 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 973037696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 973037696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:35 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:35 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:35 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:35 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:35 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:35 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 488963400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 488963400; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:36 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:36 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:36 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:36 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:36 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:36 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:36 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:36 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:36 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:36 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:36 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:36 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:36 MarkDuplicates Before output close freeMemory: 758307120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:36 MarkDuplicates Before output close freeMemory: 758307120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:36 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:36 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:36 MarkDuplicates After output close freeMemory: 758447232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:36 MarkDuplicates After output close freeMemory: 758447232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:36 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:22:36 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:36 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoMappedPairsAndMappedSecondaryFragment STANDARD_ERROR INFO 2024-07-02 11:22:36 MarkDuplicates Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7145076005291050721.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7145076005291050721.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7145076005291050721.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7145076005291050721.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7145076005291050721.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7145076005291050721.tmp/output.sam Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:36.509 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:36.509 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:36.509 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:36.509 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:36.509 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:36.509 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:36.509 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:36.509 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:36 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7145076005291050721.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7145076005291050721.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7145076005291050721.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:36 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7145076005291050721.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7145076005291050721.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7145076005291050721.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:36 MarkDuplicates Start of doWork freeMemory: 1027932896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:36 MarkDuplicates Start of doWork freeMemory: 1027932896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:36 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:36 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:36 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:36 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:22:36 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:22:36 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:36 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:22:36 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 973036336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 973036336; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:37 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:37 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:37 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:37 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 488962040; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 488962040; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:37 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:37 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:37 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:37 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:37 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:37 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:37 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:37 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:37 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:37 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:37 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:37 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:37 MarkDuplicates Before output close freeMemory: 758304304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:37 MarkDuplicates Before output close freeMemory: 758304304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:37 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:37 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:37 MarkDuplicates After output close freeMemory: 758445872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:37 MarkDuplicates After output close freeMemory: 758445872; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:38 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoMappedPairsAndTerminalUnmappedFragment STANDARD_ERROR INFO 2024-07-02 11:22:38 MarkDuplicates Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5440549700104236824.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5440549700104236824.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5440549700104236824.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5440549700104236824.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5440549700104236824.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5440549700104236824.tmp/output.sam Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:38.023 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:38.023 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:38.023 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:38.023 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:38.023 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:38.023 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:38.023 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:38.023 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:38 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5440549700104236824.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5440549700104236824.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5440549700104236824.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:38 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5440549700104236824.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5440549700104236824.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5440549700104236824.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:38 MarkDuplicates Start of doWork freeMemory: 1027935136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:38 MarkDuplicates Start of doWork freeMemory: 1027935136; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:38 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:38 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:38 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:38 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:22:38 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:22:38 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:38 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:22:38 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 973402408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 973402408; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:38 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:38 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:38 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:38 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:38 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:38 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 703919528; totalMemory: 1288699904; maxMemory: 2147483648 INFO 2024-07-02 11:22:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 703919528; totalMemory: 1288699904; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:39 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:39 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:39 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:39 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:39 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:39 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:39 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:39 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:39 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:39 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:39 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:39 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:39 MarkDuplicates Before output close freeMemory: 758304632; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:39 MarkDuplicates Before output close freeMemory: 758304632; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:39 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:39 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:39 MarkDuplicates After output close freeMemory: 758444856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:39 MarkDuplicates After output close freeMemory: 758444856; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:39 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoMappedPairsAndTerminalUnmappedPair STANDARD_ERROR INFO 2024-07-02 11:22:39 MarkDuplicates Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16285667922471210152.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16285667922471210152.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16285667922471210152.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16285667922471210152.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16285667922471210152.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16285667922471210152.tmp/output.sam Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:39.458 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:39.458 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:39.458 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:39.458 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:39.458 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:39.458 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:39.458 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:39.458 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:39 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16285667922471210152.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16285667922471210152.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16285667922471210152.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:39 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16285667922471210152.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16285667922471210152.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16285667922471210152.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:39 MarkDuplicates Start of doWork freeMemory: 1027933944; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:39 MarkDuplicates Start of doWork freeMemory: 1027933944; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:39 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:39 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:39 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:39 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:22:39 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:22:39 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:39 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:22:39 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 973401816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 973401816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:40 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:40 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:40 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:40 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:40 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 488960256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 488960256; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:40 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:40 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:40 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:40 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:40 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:40 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:40 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:40 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:40 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:40 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:40 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:40 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:40 MarkDuplicates Before output close freeMemory: 758304296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:40 MarkDuplicates Before output close freeMemory: 758304296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:40 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:40 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:40 MarkDuplicates After output close freeMemory: 758444088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:40 MarkDuplicates After output close freeMemory: 758444088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:40 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:40 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:40 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoMappedPairsMatesSoftClipped STANDARD_ERROR INFO 2024-07-02 11:22:40 MarkDuplicates Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3212154054717928579.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3212154054717928579.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3212154054717928579.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3212154054717928579.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3212154054717928579.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3212154054717928579.tmp/output.sam Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:40.603 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:40.603 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:40.603 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:40.603 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:40.603 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:40.603 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:40.603 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:40.603 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:40 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3212154054717928579.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3212154054717928579.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3212154054717928579.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:40 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3212154054717928579.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3212154054717928579.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3212154054717928579.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:40 MarkDuplicates Start of doWork freeMemory: 1027928680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:40 MarkDuplicates Start of doWork freeMemory: 1027928680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:40 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:40 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:40 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:40 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:22:40 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:22:40 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:40 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:22:40 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 973402000; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 973402000; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:41 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:41 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:41 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:41 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 488960440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 488960440; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:41 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:22:41 MarkDuplicates Marking 0 records as duplicates. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:41 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:41 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:41 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:41 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:41 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:41 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:41 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:41 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:41 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:41 MarkDuplicates Before output close freeMemory: 758304088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:41 MarkDuplicates Before output close freeMemory: 758304088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:41 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:41 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:41 MarkDuplicates After output close freeMemory: 758443848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:41 MarkDuplicates After output close freeMemory: 758443848; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:41 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:41 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:41 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoMappedPairsWithOppositeOrientations STANDARD_ERROR INFO 2024-07-02 11:22:41 MarkDuplicates Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4199364056651305871.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4199364056651305871.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4199364056651305871.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4199364056651305871.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4199364056651305871.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4199364056651305871.tmp/output.sam Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:41.696 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:41.696 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:41.696 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:41.696 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:41.697 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:41.697 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:41.697 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:41.697 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:41 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4199364056651305871.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4199364056651305871.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4199364056651305871.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:41 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4199364056651305871.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4199364056651305871.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4199364056651305871.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:41 MarkDuplicates Start of doWork freeMemory: 1027930424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:41 MarkDuplicates Start of doWork freeMemory: 1027930424; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:41 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:41 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:41 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:41 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:22:41 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:22:41 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:41 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:22:41 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 973401128; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 973401128; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:42 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:42 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:42 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:42 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:42 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:42 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 488959568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 488959568; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:42 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:42 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:42 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:42 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:42 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:42 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:42 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:42 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:42 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:42 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:42 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:42 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:42 MarkDuplicates Before output close freeMemory: 758303216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:42 MarkDuplicates Before output close freeMemory: 758303216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:42 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:42 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:42 MarkDuplicates After output close freeMemory: 758443248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:42 MarkDuplicates After output close freeMemory: 758443248; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:42 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoMappedPairsWithOppositeOrientationsNumberTwo STANDARD_ERROR INFO 2024-07-02 11:22:42 MarkDuplicates Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17098309262031437744.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17098309262031437744.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17098309262031437744.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17098309262031437744.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17098309262031437744.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17098309262031437744.tmp/output.sam Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:42.911 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:42.911 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:42.911 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:42.911 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:42.912 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:42.912 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:42.912 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:42.912 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:42 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17098309262031437744.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17098309262031437744.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17098309262031437744.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:42 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17098309262031437744.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17098309262031437744.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17098309262031437744.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:43 MarkDuplicates Start of doWork freeMemory: 1027562952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:43 MarkDuplicates Start of doWork freeMemory: 1027562952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:43 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:43 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:43 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:43 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:22:43 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:22:43 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:43 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:22:43 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 973400320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 973400320; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:43 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:43 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:43 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:43 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:43 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:43 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 488958760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 488958760; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:43 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:43 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:43 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:43 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:43 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:43 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:43 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:43 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:43 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:43 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:43 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:43 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:43 MarkDuplicates Before output close freeMemory: 758302408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:43 MarkDuplicates Before output close freeMemory: 758302408; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:44 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:44 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:44 MarkDuplicates After output close freeMemory: 758442664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:44 MarkDuplicates After output close freeMemory: 758442664; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:44 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:44 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:44 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoMappedPairsWithSoftClipping STANDARD_ERROR INFO 2024-07-02 11:22:44 MarkDuplicates Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11786486926401684187.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11786486926401684187.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11786486926401684187.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11786486926401684187.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11786486926401684187.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11786486926401684187.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:44.230 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:44.230 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:44.230 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:44.230 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:44.230 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:44.230 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:44.230 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:44.230 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:44 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11786486926401684187.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11786486926401684187.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11786486926401684187.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:44 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11786486926401684187.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11786486926401684187.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11786486926401684187.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:44 MarkDuplicates Start of doWork freeMemory: 1027924088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:44 MarkDuplicates Start of doWork freeMemory: 1027924088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:44 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:44 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:44 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:44 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:22:44 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:22:44 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:44 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:22:44 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 973396808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 973396808; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:45 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:45 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:45 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:45 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:45 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:45 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 488955848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 488955848; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:45 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:45 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:45 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:45 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:45 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:45 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:45 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:45 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:45 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:45 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:45 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:45 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:45 MarkDuplicates Before output close freeMemory: 758299496; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:45 MarkDuplicates Before output close freeMemory: 758299496; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:45 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:45 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:45 MarkDuplicates After output close freeMemory: 758439752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:45 MarkDuplicates After output close freeMemory: 758439752; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:45 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoMappedPairsWithSoftClippingBoth STANDARD_ERROR INFO 2024-07-02 11:22:45 MarkDuplicates Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17084336135124889387.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17084336135124889387.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17084336135124889387.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17084336135124889387.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17084336135124889387.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17084336135124889387.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:45.422 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:45.422 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:45.422 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:45.422 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:45.422 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:45.422 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:45.422 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:45.422 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:45 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17084336135124889387.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17084336135124889387.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17084336135124889387.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:45 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17084336135124889387.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17084336135124889387.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17084336135124889387.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:45 MarkDuplicates Start of doWork freeMemory: 1027928800; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:45 MarkDuplicates Start of doWork freeMemory: 1027928800; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:45 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:45 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:45 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:45 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:22:45 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:22:45 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:45 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:22:45 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 973396672; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 973396672; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:45 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:45 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:45 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:45 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:45 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:45 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 488955112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 488955112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:46 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:46 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:46 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:46 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:46 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:46 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:46 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:46 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:46 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:46 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:46 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:46 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:46 MarkDuplicates Before output close freeMemory: 758298760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:46 MarkDuplicates Before output close freeMemory: 758298760; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:46 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:46 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:46 MarkDuplicates After output close freeMemory: 758438448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:46 MarkDuplicates After output close freeMemory: 758438448; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:46 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar STANDARD_ERROR INFO 2024-07-02 11:22:46 MarkDuplicates Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7800139953457469355.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7800139953457469355.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7800139953457469355.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7800139953457469355.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7800139953457469355.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7800139953457469355.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:46.440 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:46.440 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:46.440 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:46.440 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:46.440 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:46.440 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:46.440 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:46.440 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:46 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7800139953457469355.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7800139953457469355.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7800139953457469355.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:46 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7800139953457469355.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7800139953457469355.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7800139953457469355.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:46 MarkDuplicates Start of doWork freeMemory: 1027928856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:46 MarkDuplicates Start of doWork freeMemory: 1027928856; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:46 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:46 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:46 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:46 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:22:46 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:22:46 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:46 MarkDuplicates Read 2 records. 2 pairs never matched. INFO 2024-07-02 11:22:46 MarkDuplicates Read 2 records. 2 pairs never matched. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 973396872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 973396872; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:47 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:47 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:47 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:47 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:47 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:47 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 686088024; totalMemory: 1270874112; maxMemory: 2147483648 INFO 2024-07-02 11:22:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 686088024; totalMemory: 1270874112; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:47 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:22:47 MarkDuplicates Marking 0 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:47 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:22:47 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:47 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:47 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:47 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:47 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:47 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:47 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:47 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:47 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:47 MarkDuplicates Before output close freeMemory: 758299432; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:47 MarkDuplicates Before output close freeMemory: 758299432; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:47 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:47 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:47 MarkDuplicates After output close freeMemory: 758439568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:47 MarkDuplicates After output close freeMemory: 758439568; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:47 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:47 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:47 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoMappedPairsWithSupplementaryReads[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:22:47 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.18010842030902681669.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.18010842030902681669.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.18010842030902681669.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.18010842030902681669.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.18010842030902681669.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.18010842030902681669.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:47.635 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:47.635 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:47.635 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:47.635 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:47.636 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:47.636 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:47.636 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:47.636 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:47 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.18010842030902681669.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.18010842030902681669.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.18010842030902681669.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:47 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.18010842030902681669.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.18010842030902681669.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.18010842030902681669.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:47 MarkDuplicates Start of doWork freeMemory: 1027923280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:47 MarkDuplicates Start of doWork freeMemory: 1027923280; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:47 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:47 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:47 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:47 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:47 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:22:47 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 973393736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 973393736; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:48 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:48 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:48 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:48 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:48 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:48 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:48 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:48 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 488952208; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 488952208; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:48 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:48 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:48 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:22:48 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:48 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:48 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:48 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:48 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:48 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:48 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:48 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:48 MarkDuplicates Before output close freeMemory: 758295832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:48 MarkDuplicates Before output close freeMemory: 758295832; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:48 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:48 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:48 MarkDuplicates After output close freeMemory: 758436112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:48 MarkDuplicates After output close freeMemory: 758436112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:48 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:48 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:48 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoMappedPairsWithSupplementaryReads[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:22:48 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3550360335371822753.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3550360335371822753.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3550360335371822753.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3550360335371822753.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3550360335371822753.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3550360335371822753.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:48.856 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:48.856 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:48.856 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:48.856 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:48.856 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:48.856 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:48.856 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:48.856 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:48 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3550360335371822753.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3550360335371822753.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3550360335371822753.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:48 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3550360335371822753.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3550360335371822753.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3550360335371822753.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:48 MarkDuplicates Start of doWork freeMemory: 1027925016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:48 MarkDuplicates Start of doWork freeMemory: 1027925016; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:48 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:48 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:48 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:48 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:48 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:22:48 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 973026336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 973026336; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:49 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:49 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:49 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:49 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:49 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:49 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:49 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:49 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 488950808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 488950808; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:49 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:49 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:49 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:22:49 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:49 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:49 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:49 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:49 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:49 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:49 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:49 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:49 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:49 MarkDuplicates Before output close freeMemory: 758294752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:49 MarkDuplicates Before output close freeMemory: 758294752; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:49 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:49 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:49 MarkDuplicates After output close freeMemory: 758435408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:49 MarkDuplicates After output close freeMemory: 758435408; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:49 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoMappedPairsWithSupplementaryReads[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:22:49 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2927178095816713323.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2927178095816713323.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2927178095816713323.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2927178095816713323.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2927178095816713323.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2927178095816713323.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:49.837 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:49.837 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:49.837 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:49.837 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:49.837 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:49.837 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:49.837 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:49.837 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:49 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2927178095816713323.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2927178095816713323.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2927178095816713323.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:49 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2927178095816713323.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2927178095816713323.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2927178095816713323.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:49 MarkDuplicates Start of doWork freeMemory: 1027922504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:49 MarkDuplicates Start of doWork freeMemory: 1027922504; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:49 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:49 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:49 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:49 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:49 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:22:49 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 973392368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 973392368; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:50 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:50 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:50 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:50 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:50 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:50 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 488950872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 488950872; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:50 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:50 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:50 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:22:50 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:50 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:50 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:50 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:50 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:50 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:50 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:50 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:50 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:50 MarkDuplicates Before output close freeMemory: 758294496; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:50 MarkDuplicates Before output close freeMemory: 758294496; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:50 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:50 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:50 MarkDuplicates After output close freeMemory: 758434280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:50 MarkDuplicates After output close freeMemory: 758434280; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:50 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoMappedPairsWithSupplementaryReads[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:22:50 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5283595349999643590.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5283595349999643590.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5283595349999643590.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5283595349999643590.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5283595349999643590.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5283595349999643590.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:50.803 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:50.803 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:50.803 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:50.803 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:50.804 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:50.804 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:50.804 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:50.804 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:50 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5283595349999643590.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5283595349999643590.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5283595349999643590.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:50 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5283595349999643590.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5283595349999643590.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5283595349999643590.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:50 MarkDuplicates Start of doWork freeMemory: 1027924144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:50 MarkDuplicates Start of doWork freeMemory: 1027924144; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:50 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:50 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:50 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:50 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:50 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:22:50 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 973391952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 973391952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:51 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:51 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:51 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:51 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:51 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:51 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:51 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:51 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 488950240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 488950240; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:51 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:51 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:51 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:22:51 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:51 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:51 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:51 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:51 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:51 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:51 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:51 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:51 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:51 MarkDuplicates Before output close freeMemory: 757927600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:51 MarkDuplicates Before output close freeMemory: 757927600; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:51 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:51 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:51 MarkDuplicates After output close freeMemory: 758434072; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:51 MarkDuplicates After output close freeMemory: 758434072; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:51 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoMappedPairsWithSupplementaryReads[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:22:51 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2858272033297793486.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2858272033297793486.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2858272033297793486.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2858272033297793486.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2858272033297793486.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2858272033297793486.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:51.783 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:51.783 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:51.784 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:51.784 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:51.784 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:51.784 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:51.784 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:51.784 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:51 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2858272033297793486.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2858272033297793486.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2858272033297793486.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:51 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2858272033297793486.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2858272033297793486.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2858272033297793486.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:51 MarkDuplicates Start of doWork freeMemory: 1027923488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:51 MarkDuplicates Start of doWork freeMemory: 1027923488; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:51 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:51 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:51 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:51 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:52 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:22:52 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 973391296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 973391296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:53 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:53 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:53 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:53 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:53 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:53 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 703907664; totalMemory: 1288699904; maxMemory: 2147483648 INFO 2024-07-02 11:22:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 703907664; totalMemory: 1288699904; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:53 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:53 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:53 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:22:53 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:53 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:53 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:53 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:53 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:53 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:53 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:53 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:53 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:53 MarkDuplicates Before output close freeMemory: 758292800; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:53 MarkDuplicates Before output close freeMemory: 758292800; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:53 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:53 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:53 MarkDuplicates After output close freeMemory: 758432520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:53 MarkDuplicates After output close freeMemory: 758432520; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:22:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:53 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoMappedPairsWithSupplementaryReads[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:22:53 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7780588908512292151.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7780588908512292151.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7780588908512292151.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7780588908512292151.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7780588908512292151.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7780588908512292151.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:53.409 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:53.409 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:53.409 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:53.409 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:53.409 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:53.409 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:53.410 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:53.410 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:53 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7780588908512292151.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7780588908512292151.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7780588908512292151.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:53 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7780588908512292151.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7780588908512292151.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7780588908512292151.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:53 MarkDuplicates Start of doWork freeMemory: 1027922856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:53 MarkDuplicates Start of doWork freeMemory: 1027922856; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:53 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:53 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:53 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:53 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:53 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:22:53 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 973390664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 973390664; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:53 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:53 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:53 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:53 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:53 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:53 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 488948952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 488948952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:54 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:54 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:54 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:22:54 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:54 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:54 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:54 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:54 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:54 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:54 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:54 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:54 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:54 MarkDuplicates Before output close freeMemory: 758292576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:54 MarkDuplicates Before output close freeMemory: 758292576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:54 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:54 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:54 MarkDuplicates After output close freeMemory: 758432784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:54 MarkDuplicates After output close freeMemory: 758432784; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:54 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:22:54 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:54 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:22:54 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13503650562074686425.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13503650562074686425.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13503650562074686425.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13503650562074686425.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13503650562074686425.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13503650562074686425.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:54.280 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:54.280 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:54.280 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:54.280 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:54.280 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:54.280 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:54.280 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:54.280 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:54 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13503650562074686425.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13503650562074686425.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13503650562074686425.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:54 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13503650562074686425.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13503650562074686425.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13503650562074686425.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:54 MarkDuplicates Start of doWork freeMemory: 1027921704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:54 MarkDuplicates Start of doWork freeMemory: 1027921704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:54 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:54 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:54 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:54 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:54 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:22:54 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 973389296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 973389296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:54 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:54 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:54 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:54 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:54 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:54 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:54 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:54 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 488947800; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 488947800; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:54 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:54 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:54 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:22:54 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:54 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:54 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:54 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:54 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:54 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:54 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:54 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:54 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:55 MarkDuplicates Before output close freeMemory: 758290952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:55 MarkDuplicates Before output close freeMemory: 758290952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:55 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:55 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:55 MarkDuplicates After output close freeMemory: 758431704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:55 MarkDuplicates After output close freeMemory: 758431704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:55 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:22:55 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:55 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:22:55 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.14425070780973787685.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14425070780973787685.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14425070780973787685.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.14425070780973787685.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14425070780973787685.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14425070780973787685.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:55.196 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:55.196 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:55.196 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:55.196 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:55.196 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:55.196 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:55.196 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:55.196 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:55 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.14425070780973787685.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.14425070780973787685.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.14425070780973787685.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:55 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.14425070780973787685.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.14425070780973787685.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.14425070780973787685.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:55 MarkDuplicates Start of doWork freeMemory: 1027918232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:55 MarkDuplicates Start of doWork freeMemory: 1027918232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:55 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:55 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:55 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:55 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:55 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:22:55 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 973388656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 973388656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:55 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:55 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:55 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:55 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:55 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 488947160; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 488947160; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:55 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:55 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:55 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:22:55 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:55 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:55 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:55 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:55 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:55 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:55 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:55 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:55 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:56 MarkDuplicates Before output close freeMemory: 758289376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:56 MarkDuplicates Before output close freeMemory: 758289376; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:56 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:56 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:56 MarkDuplicates After output close freeMemory: 758431064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:56 MarkDuplicates After output close freeMemory: 758431064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:56 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:56 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:56 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:22:56 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9423125599199919923.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9423125599199919923.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9423125599199919923.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9423125599199919923.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9423125599199919923.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9423125599199919923.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:56.190 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:56.190 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:56.190 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:56.190 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:56.191 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:56.191 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:56.191 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:56.191 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:56 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9423125599199919923.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9423125599199919923.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9423125599199919923.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:56 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9423125599199919923.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9423125599199919923.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9423125599199919923.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:56 MarkDuplicates Start of doWork freeMemory: 1027920056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:56 MarkDuplicates Start of doWork freeMemory: 1027920056; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:56 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:56 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:56 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:56 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:56 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:22:56 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 973388040; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 973388040; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:56 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:56 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:56 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:56 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:56 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:56 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 488946544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 488946544; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:56 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:56 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:56 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:22:56 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:56 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:56 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:56 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:56 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:56 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:56 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:56 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:56 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:56 MarkDuplicates Before output close freeMemory: 758289696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:56 MarkDuplicates Before output close freeMemory: 758289696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:56 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:56 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:57 MarkDuplicates After output close freeMemory: 758429320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:57 MarkDuplicates After output close freeMemory: 758429320; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:57 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:22:57 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:57 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:22:57 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15090400345086167612.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15090400345086167612.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15090400345086167612.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15090400345086167612.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15090400345086167612.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15090400345086167612.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:57.065 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:57.065 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:57.066 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:57.066 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:57.066 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:57.066 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:57.066 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:57.066 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:57 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15090400345086167612.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15090400345086167612.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15090400345086167612.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:57 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15090400345086167612.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15090400345086167612.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15090400345086167612.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:57 MarkDuplicates Start of doWork freeMemory: 1027914376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:57 MarkDuplicates Start of doWork freeMemory: 1027914376; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:57 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:57 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:57 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:57 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:57 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:22:57 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 973387416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 973387416; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:57 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:57 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:57 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:57 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:57 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:57 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 488945920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 488945920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:57 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:57 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:57 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:22:57 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:57 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:57 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:57 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:57 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:57 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:57 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:57 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:57 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:57 MarkDuplicates Before output close freeMemory: 757922408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:57 MarkDuplicates Before output close freeMemory: 757922408; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:57 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:57 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:57 MarkDuplicates After output close freeMemory: 758429328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:57 MarkDuplicates After output close freeMemory: 758429328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:57 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:57 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:58 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:22:58 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3767205452759956927.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3767205452759956927.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3767205452759956927.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3767205452759956927.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3767205452759956927.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3767205452759956927.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:58.002 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:58.002 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:58.002 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:58.002 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:58.003 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:58.003 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:58.003 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:58.003 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:58 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3767205452759956927.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3767205452759956927.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3767205452759956927.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:58 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3767205452759956927.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3767205452759956927.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3767205452759956927.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:58 MarkDuplicates Start of doWork freeMemory: 1027918816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:58 MarkDuplicates Start of doWork freeMemory: 1027918816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:58 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:58 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:58 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:58 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:58 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:22:58 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 973386800; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 973386800; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:58 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:58 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:58 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:58 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:58 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:58 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 745846424; totalMemory: 1330642944; maxMemory: 2147483648 INFO 2024-07-02 11:22:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 745846424; totalMemory: 1330642944; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:58 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:58 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:58 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:22:58 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:58 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:58 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:58 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:58 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:58 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:58 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:58 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:58 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:58 MarkDuplicates Before output close freeMemory: 758289088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:58 MarkDuplicates Before output close freeMemory: 758289088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:58 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:58 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:58 MarkDuplicates After output close freeMemory: 758428712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:58 MarkDuplicates After output close freeMemory: 758428712; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:58 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:22:58 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7992500346876905469.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7992500346876905469.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7992500346876905469.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7992500346876905469.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7992500346876905469.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7992500346876905469.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:58.944 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:58.944 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:58.944 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:58.944 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:58.945 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:58.945 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:58.945 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:58.945 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:58 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7992500346876905469.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7992500346876905469.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7992500346876905469.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:58 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7992500346876905469.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7992500346876905469.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7992500346876905469.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:59 MarkDuplicates Start of doWork freeMemory: 1027918184; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:59 MarkDuplicates Start of doWork freeMemory: 1027918184; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:59 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:59 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:59 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:59 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:59 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:22:59 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 973386384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 973386384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:59 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:22:59 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:59 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:22:59 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:59 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:22:59 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:59 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:22:59 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 488944672; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 488944672; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:59 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:22:59 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:59 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:22:59 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:59 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:22:59 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:59 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:22:59 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:59 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:22:59 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:59 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:22:59 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:59 MarkDuplicates Before output close freeMemory: 758288456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:59 MarkDuplicates Before output close freeMemory: 758288456; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:59 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:22:59 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:59 MarkDuplicates After output close freeMemory: 758428504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:59 MarkDuplicates After output close freeMemory: 758428504; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:59 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:22:59 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:59 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoUnmappedFragments STANDARD_ERROR INFO 2024-07-02 11:22:59 MarkDuplicates Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2981418192705436839.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2981418192705436839.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2981418192705436839.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2981418192705436839.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2981418192705436839.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2981418192705436839.tmp/output.sam Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:59.880 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:59.880 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:59.881 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:59.881 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:59.881 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:22:59.881 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:22:59.881 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:22:59.881 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:59 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2981418192705436839.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2981418192705436839.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2981418192705436839.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:22:59 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2981418192705436839.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2981418192705436839.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2981418192705436839.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:22:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:22:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:59 MarkDuplicates Start of doWork freeMemory: 1027920272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:22:59 MarkDuplicates Start of doWork freeMemory: 1027920272; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:59 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:22:59 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:22:59 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:22:59 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:00 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2024-07-02 11:23:00 MarkDuplicates Read 0 records. 0 pairs never matched. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 973388904; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 973388904; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:00 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:00 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:00 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:00 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:00 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:00 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 488946992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 488946992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:00 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:23:00 MarkDuplicates Marking 0 records as duplicates. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:00 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:00 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:00 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:00 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:00 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:00 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:00 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:00 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:00 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:00 MarkDuplicates Getting Memory Stats. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:00 MarkDuplicates Before output close freeMemory: 758291032; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:00 MarkDuplicates Before output close freeMemory: 758291032; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:00 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:00 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:00 MarkDuplicates After output close freeMemory: 758430856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:00 MarkDuplicates After output close freeMemory: 758430856; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:00 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]}) STANDARD_ERROR INFO 2024-07-02 11:23:00 MarkDuplicates Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam -OUTPUT /tmp/MarkDuplicates.4479651510669196731.tmp/MarkDuplicates.sam -METRICS_FILE /tmp/MarkDuplicates.4479651510669196731.tmp/MarkDuplicates.duplicate_metrics -ADD_PG_TAG_TO_READS true ********** MarkDuplicates -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam -OUTPUT /tmp/MarkDuplicates.4479651510669196731.tmp/MarkDuplicates.sam -METRICS_FILE /tmp/MarkDuplicates.4479651510669196731.tmp/MarkDuplicates.duplicate_metrics -ADD_PG_TAG_TO_READS true Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:00.786 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:00.786 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:00.786 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:00.786 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:00.786 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:00.786 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:00.786 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:00.786 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:00 GMT+14:00 2024] MarkDuplicates ADD_PG_TAG_TO_READS=true INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.4479651510669196731.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.4479651510669196731.tmp/MarkDuplicates.duplicate_metrics MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:00 GMT+14:00 2024] MarkDuplicates ADD_PG_TAG_TO_READS=true INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.4479651510669196731.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.4479651510669196731.tmp/MarkDuplicates.duplicate_metrics MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:00 MarkDuplicates Start of doWork freeMemory: 1027922312; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:00 MarkDuplicates Start of doWork freeMemory: 1027922312; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:00 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:00 MarkDuplicates Reading input file and constructing read end information. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:00 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:23:00 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:00 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name '1AAXX.1.1'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. WARNING 2024-07-02 11:23:00 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name '1AAXX.1.1'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:00 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:23:00 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 965001144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 965001144; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:01 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:01 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:01 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:01 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:01 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:01 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:01 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:01 MarkDuplicates Sorting list of duplicate records. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 489997888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 489997888; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:01 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:23:01 MarkDuplicates Marking 4 records as duplicates. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:01 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:01 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:01 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:01 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:01 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:01 MarkDuplicates Writing complete. Closing input iterator. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:01 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:01 MarkDuplicates Duplicate Index cleanup. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:01 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:01 MarkDuplicates Getting Memory Stats. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:01 MarkDuplicates Before output close freeMemory: 1027773696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:01 MarkDuplicates Before output close freeMemory: 1027773696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:01 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:01 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:01 MarkDuplicates After output close freeMemory: 1027917296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:01 MarkDuplicates After output close freeMemory: 1027917296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:01 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:23:01 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51763432, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5ec0216e, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5220d161], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1b0e37ce, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7bb94739], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@24add271]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:01 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]}) STANDARD_ERROR INFO 2024-07-02 11:23:01 MarkDuplicates Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam -OUTPUT /tmp/MarkDuplicates.16058848636133591142.tmp/MarkDuplicates.sam -METRICS_FILE /tmp/MarkDuplicates.16058848636133591142.tmp/MarkDuplicates.duplicate_metrics -ADD_PG_TAG_TO_READS true -PROGRAM_RECORD_ID null ********** MarkDuplicates -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam -OUTPUT /tmp/MarkDuplicates.16058848636133591142.tmp/MarkDuplicates.sam -METRICS_FILE /tmp/MarkDuplicates.16058848636133591142.tmp/MarkDuplicates.duplicate_metrics -ADD_PG_TAG_TO_READS true -PROGRAM_RECORD_ID null Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:01.728 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:01.728 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:01.728 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:01.728 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:01.728 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:01.728 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:01.728 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:01.728 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:01 GMT+14:00 2024] MarkDuplicates ADD_PG_TAG_TO_READS=true INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.16058848636133591142.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.16058848636133591142.tmp/MarkDuplicates.duplicate_metrics PROGRAM_RECORD_ID=null MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:01 GMT+14:00 2024] MarkDuplicates ADD_PG_TAG_TO_READS=true INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.16058848636133591142.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.16058848636133591142.tmp/MarkDuplicates.duplicate_metrics PROGRAM_RECORD_ID=null MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:01 MarkDuplicates Start of doWork freeMemory: 1027924264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:01 MarkDuplicates Start of doWork freeMemory: 1027924264; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:01 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:01 MarkDuplicates Reading input file and constructing read end information. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:01 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:23:01 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:01 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name '1AAXX.1.1'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. WARNING 2024-07-02 11:23:01 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name '1AAXX.1.1'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:01 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:23:01 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 965001192; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 965001192; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:02 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:02 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:02 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:02 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:02 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:02 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:02 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:02 MarkDuplicates Sorting list of duplicate records. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 489997392; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 489997392; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:02 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:23:02 MarkDuplicates Marking 4 records as duplicates. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:02 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:02 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:02 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:02 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:02 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:02 MarkDuplicates Writing complete. Closing input iterator. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:02 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:02 MarkDuplicates Duplicate Index cleanup. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:02 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:02 MarkDuplicates Getting Memory Stats. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:02 MarkDuplicates Before output close freeMemory: 1027631912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:02 MarkDuplicates Before output close freeMemory: 1027631912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:02 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:02 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:02 MarkDuplicates After output close freeMemory: 1027264968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:02 MarkDuplicates After output close freeMemory: 1027264968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:02 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:23:02 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@44b7350d, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@567d74e], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f558731], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:02 MarkDuplicates Start of doWork freeMemory: 1027939376; totalMemory: 1073741824; maxMemory: 2147483648 Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1) STANDARD_ERROR INFO 2024-07-02 11:23:02 MarkDuplicates Start of doWork freeMemory: 1027939376; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:02 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:02 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:02 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:23:02 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:02 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:23:02 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 965018776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 965018776; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:02 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:02 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:03 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:03 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:03 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:03 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:03 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:03 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 653592104; totalMemory: 1237319680; maxMemory: 2147483648 INFO 2024-07-02 11:23:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 653592104; totalMemory: 1237319680; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:03 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:23:03 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:03 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:23:03 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:03 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:03 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:03 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:03 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:03 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:03 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:03 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:03 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:03 MarkDuplicates Before output close freeMemory: 1027746040; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:03 MarkDuplicates Before output close freeMemory: 1027746040; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:03 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:03 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:03 MarkDuplicates After output close freeMemory: 1027745544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:03 MarkDuplicates After output close freeMemory: 1027745544; totalMemory: 1073741824; maxMemory: 2147483648 Running Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:03 MarkDuplicates Start of doWork freeMemory: 1027938360; totalMemory: 1073741824; maxMemory: 2147483648 Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1) STANDARD_ERROR INFO 2024-07-02 11:23:03 MarkDuplicates Start of doWork freeMemory: 1027938360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:03 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:03 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:03 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:23:03 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:03 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:23:03 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 965017744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 965017744; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:03 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:03 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:04 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:04 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:04 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:04 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:04 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:04 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 490013216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 490013216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:04 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:23:04 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:04 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:23:04 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:04 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:04 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:04 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:04 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:04 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:04 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:04 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:04 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:04 MarkDuplicates Before output close freeMemory: 1027745032; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:04 MarkDuplicates Before output close freeMemory: 1027745032; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:04 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:04 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:04 MarkDuplicates After output close freeMemory: 1027746176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:04 MarkDuplicates After output close freeMemory: 1027746176; totalMemory: 1073741824; maxMemory: 2147483648 Running Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:04 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testTwoMappedPairsWithSoftClippingFirstOfPairOnly STANDARD_ERROR INFO 2024-07-02 11:23:04 MarkDuplicates Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13219995366262513881.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13219995366262513881.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13219995366262513881.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13219995366262513881.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13219995366262513881.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13219995366262513881.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:04.556 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:04.556 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:04.556 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:04.556 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:04.556 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:04.556 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:04.556 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:04.556 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:04 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13219995366262513881.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13219995366262513881.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13219995366262513881.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:04 GMT+14:00 2024] MarkDuplicates READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13219995366262513881.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13219995366262513881.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13219995366262513881.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:04 MarkDuplicates Start of doWork freeMemory: 1027913896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:04 MarkDuplicates Start of doWork freeMemory: 1027913896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:04 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:04 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:04 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:04 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:04 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:23:04 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:04 MarkDuplicates Read 2 records. 2 pairs never matched. INFO 2024-07-02 11:23:04 MarkDuplicates Read 2 records. 2 pairs never matched. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 973382048; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 973382048; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:04 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:04 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:05 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:05 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:05 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:05 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:05 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:05 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 488940312; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 488940312; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:05 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:23:05 MarkDuplicates Marking 0 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:05 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:05 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:05 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:05 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:05 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:05 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:05 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:05 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:05 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:05 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:05 MarkDuplicates Before output close freeMemory: 758283936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:05 MarkDuplicates Before output close freeMemory: 758283936; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:05 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:05 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:05 MarkDuplicates After output close freeMemory: 758423648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:05 MarkDuplicates After output close freeMemory: 758423648; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:05 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:05 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:05 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testWithBarcodeComplex STANDARD_ERROR INFO 2024-07-02 11:23:05 MarkDuplicates Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2388294961636624600.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2388294961636624600.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2388294961636624600.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2388294961636624600.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2388294961636624600.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2388294961636624600.tmp/output.sam Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:05.418 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:05.418 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:05.421 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:05.421 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:05.421 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:05.421 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:05.421 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:05.421 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:05 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2388294961636624600.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2388294961636624600.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2388294961636624600.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:05 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2388294961636624600.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2388294961636624600.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2388294961636624600.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:05 MarkDuplicates Start of doWork freeMemory: 1027910376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:05 MarkDuplicates Start of doWork freeMemory: 1027910376; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:05 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:05 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:05 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:05 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:05 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:23:05 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 973377704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 973377704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:05 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:05 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:05 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:05 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:05 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:05 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 488936448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 488936448; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:06 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:23:06 MarkDuplicates Marking 2 records as duplicates. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:06 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:06 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:06 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:06 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:06 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:06 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:06 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:06 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:06 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:06 MarkDuplicates Getting Memory Stats. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:06 MarkDuplicates Before output close freeMemory: 758280024; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:06 MarkDuplicates Before output close freeMemory: 758280024; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:06 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:06 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:06 MarkDuplicates After output close freeMemory: 758420352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:06 MarkDuplicates After output close freeMemory: 758420352; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:06 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:06 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:06 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testWithBarcodeDuplicate STANDARD_ERROR INFO 2024-07-02 11:23:06 MarkDuplicates Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15591937233454953503.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15591937233454953503.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15591937233454953503.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15591937233454953503.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15591937233454953503.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15591937233454953503.tmp/output.sam Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:06.322 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:06.322 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:06.322 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:06.322 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:06.322 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:06.322 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:06.322 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:06.322 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:06 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15591937233454953503.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15591937233454953503.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15591937233454953503.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:06 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15591937233454953503.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15591937233454953503.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15591937233454953503.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:06 MarkDuplicates Start of doWork freeMemory: 1027911008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:06 MarkDuplicates Start of doWork freeMemory: 1027911008; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:06 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:06 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:06 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:06 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:06 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:23:06 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 973378816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 973378816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:06 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:06 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:06 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:06 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:06 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:06 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:06 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:06 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 642029352; totalMemory: 1226833920; maxMemory: 2147483648 INFO 2024-07-02 11:23:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 642029352; totalMemory: 1226833920; maxMemory: 2147483648 Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:06 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:23:06 MarkDuplicates Marking 2 records as duplicates. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:06 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:06 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:06 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:06 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:06 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:06 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:06 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:06 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:06 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:06 MarkDuplicates Getting Memory Stats. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:07 MarkDuplicates Before output close freeMemory: 758280232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:07 MarkDuplicates Before output close freeMemory: 758280232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:07 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:07 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:07 MarkDuplicates After output close freeMemory: 758421160; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:07 MarkDuplicates After output close freeMemory: 758421160; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:07 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:07 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:07 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testWithBarcodeFragmentDuplicate STANDARD_ERROR INFO 2024-07-02 11:23:07 MarkDuplicates Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16060396903663839114.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16060396903663839114.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16060396903663839114.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16060396903663839114.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -READ_TWO_BARCODE_TAG RX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16060396903663839114.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16060396903663839114.tmp/output.sam Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:07.220 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:07.220 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:07.220 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:07.220 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:07.221 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:07.221 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:07.221 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:07.221 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:07 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16060396903663839114.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16060396903663839114.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16060396903663839114.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:07 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC READ_TWO_BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16060396903663839114.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16060396903663839114.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16060396903663839114.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:07 MarkDuplicates Start of doWork freeMemory: 1027911856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:07 MarkDuplicates Start of doWork freeMemory: 1027911856; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:07 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:07 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:07 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:07 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:23:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:07 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:23:07 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 973380200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 973380200; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:07 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:07 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:07 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:07 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:07 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:07 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:07 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:07 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 488938464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 488938464; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:07 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:23:07 MarkDuplicates Marking 1 records as duplicates. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:07 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:07 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:07 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:07 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:07 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:07 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:07 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:07 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:07 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:07 MarkDuplicates Getting Memory Stats. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:07 MarkDuplicates Before output close freeMemory: 757915360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:07 MarkDuplicates Before output close freeMemory: 757915360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:07 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:07 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:08 MarkDuplicates After output close freeMemory: 758055472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:08 MarkDuplicates After output close freeMemory: 758055472; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:08 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:08 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:08 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testWithIndividualReadBarcodes STANDARD_ERROR INFO 2024-07-02 11:23:08 MarkDuplicates Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7373902030604618290.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -READ_ONE_BARCODE_TAG BX -READ_TWO_BARCODE_TAG BX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7373902030604618290.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7373902030604618290.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7373902030604618290.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -READ_ONE_BARCODE_TAG BX -READ_TWO_BARCODE_TAG BX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7373902030604618290.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7373902030604618290.tmp/output.sam Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:08.131 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:08.131 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:08.131 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:08.131 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:08.131 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:08.131 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:08.131 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:08.131 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:08 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC READ_ONE_BARCODE_TAG=BX READ_TWO_BARCODE_TAG=BX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7373902030604618290.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7373902030604618290.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7373902030604618290.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:08 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC READ_ONE_BARCODE_TAG=BX READ_TWO_BARCODE_TAG=BX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7373902030604618290.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7373902030604618290.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7373902030604618290.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:08 MarkDuplicates Start of doWork freeMemory: 1027908184; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:08 MarkDuplicates Start of doWork freeMemory: 1027908184; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:08 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:08 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:08 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:08 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:08 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:23:08 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 973375512; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 973375512; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:08 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:08 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:08 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:08 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:08 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:08 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 488934256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 488934256; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:08 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:23:08 MarkDuplicates Marking 2 records as duplicates. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:08 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:08 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:08 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:08 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:08 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:08 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:08 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:08 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:08 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:08 MarkDuplicates Getting Memory Stats. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:08 MarkDuplicates Before output close freeMemory: 758277760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:08 MarkDuplicates Before output close freeMemory: 758277760; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:08 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:08 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:09 MarkDuplicates After output close freeMemory: 758417592; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:09 MarkDuplicates After output close freeMemory: 758417592; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:09 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:09 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:09 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true]) STANDARD_ERROR INFO 2024-07-02 11:23:09 MarkDuplicates Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2103995071147194115.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI false -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2103995071147194115.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2103995071147194115.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2103995071147194115.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI false -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2103995071147194115.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2103995071147194115.tmp/output.sam Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:09.054 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:09.054 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:09.054 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:09.054 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:09.055 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:09.055 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:09.055 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:09.055 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:09 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=false INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2103995071147194115.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2103995071147194115.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2103995071147194115.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:09 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=false INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2103995071147194115.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2103995071147194115.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2103995071147194115.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:09 MarkDuplicates Start of doWork freeMemory: 1027906376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:09 MarkDuplicates Start of doWork freeMemory: 1027906376; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:09 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:09 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:09 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:09 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:09 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. WARNING 2024-07-02 11:23:09 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:09 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:23:09 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 973374248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 973374248; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:09 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:09 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:09 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:09 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:09 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:09 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 488932688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 488932688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:09 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:23:09 MarkDuplicates Marking 2 records as duplicates. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:09 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:09 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:09 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:09 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:09 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:09 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:09 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:09 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:09 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:09 MarkDuplicates Getting Memory Stats. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:09 MarkDuplicates Before output close freeMemory: 758276008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:09 MarkDuplicates Before output close freeMemory: 758276008; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:09 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:09 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:09 MarkDuplicates After output close freeMemory: 758049016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:09 MarkDuplicates After output close freeMemory: 758049016; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:09 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:09 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:09 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true]) STANDARD_ERROR INFO 2024-07-02 11:23:09 MarkDuplicates Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.1118699134241394963.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI false -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1118699134241394963.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1118699134241394963.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.1118699134241394963.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI false -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1118699134241394963.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1118699134241394963.tmp/output.sam Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:09.972 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:09.972 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:09.972 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:09.972 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:09.973 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:09.973 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:09.973 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:09.973 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:09 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=false INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1118699134241394963.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1118699134241394963.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1118699134241394963.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:09 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=false INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1118699134241394963.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1118699134241394963.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1118699134241394963.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:10 MarkDuplicates Start of doWork freeMemory: 1027538776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:10 MarkDuplicates Start of doWork freeMemory: 1027538776; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:10 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:10 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:10 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:10 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:10 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. WARNING 2024-07-02 11:23:10 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:10 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:23:10 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 973373704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 973373704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:10 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:10 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:10 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:10 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:10 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:10 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 589595440; totalMemory: 1174405120; maxMemory: 2147483648 INFO 2024-07-02 11:23:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 589595440; totalMemory: 1174405120; maxMemory: 2147483648 Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:10 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:23:10 MarkDuplicates Marking 0 records as duplicates. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:10 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:10 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:10 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:10 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:10 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:10 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:10 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:10 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:10 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:10 MarkDuplicates Getting Memory Stats. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:10 MarkDuplicates Before output close freeMemory: 757907640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:10 MarkDuplicates Before output close freeMemory: 757907640; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:10 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:10 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:10 MarkDuplicates After output close freeMemory: 758415824; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:10 MarkDuplicates After output close freeMemory: 758415824; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:10 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:10 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:10 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false]) STANDARD_ERROR INFO 2024-07-02 11:23:10 MarkDuplicates Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.877557714980421876.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI true -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.877557714980421876.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.877557714980421876.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.877557714980421876.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI true -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.877557714980421876.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.877557714980421876.tmp/output.sam Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:10.892 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:10.892 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:10.892 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:10.892 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:10.894 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:10.894 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:10.894 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:10.894 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:10 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=true INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.877557714980421876.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.877557714980421876.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.877557714980421876.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:10 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=true INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.877557714980421876.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.877557714980421876.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.877557714980421876.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:11 MarkDuplicates Start of doWork freeMemory: 1027905192; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:11 MarkDuplicates Start of doWork freeMemory: 1027905192; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:11 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:11 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:11 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:11 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:11 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. WARNING 2024-07-02 11:23:11 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:11 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:23:11 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 973372848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 973372848; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:11 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:11 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:11 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:11 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 488931504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 488931504; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:11 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:23:11 MarkDuplicates Marking 2 records as duplicates. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:11 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:11 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:11 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:11 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:11 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:11 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:11 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:11 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:11 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:11 MarkDuplicates Getting Memory Stats. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:11 MarkDuplicates Before output close freeMemory: 758275232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:11 MarkDuplicates Before output close freeMemory: 758275232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:11 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:11 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:11 MarkDuplicates After output close freeMemory: 758414912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:11 MarkDuplicates After output close freeMemory: 758414912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:11 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:11 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:11 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest.testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false]) STANDARD_ERROR INFO 2024-07-02 11:23:11 MarkDuplicates Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4568423508483591979.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI true -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4568423508483591979.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4568423508483591979.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4568423508483591979.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI true -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4568423508483591979.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4568423508483591979.tmp/output.sam Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:11.795 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:11.795 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:11.795 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:11.795 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:11.796 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:11.796 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: 11:23:11.796 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:11.796 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:11 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=true INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4568423508483591979.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4568423508483591979.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4568423508483591979.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:11 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=true INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4568423508483591979.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4568423508483591979.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4568423508483591979.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:11 MarkDuplicates Start of doWork freeMemory: 1027904528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:11 MarkDuplicates Start of doWork freeMemory: 1027904528; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:11 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:11 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:11 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:11 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:11 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. WARNING 2024-07-02 11:23:11 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:11 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:23:11 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 973371800; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 973371800; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:12 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:12 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:12 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:12 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:12 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:12 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:12 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:12 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 488930144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 488930144; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:12 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:23:12 MarkDuplicates Marking 0 records as duplicates. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:12 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:12 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:12 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:12 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:12 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:12 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:12 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:12 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:12 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:12 MarkDuplicates Getting Memory Stats. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:12 MarkDuplicates Before output close freeMemory: 758274568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:12 MarkDuplicates Before output close freeMemory: 758274568; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:12 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:12 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:12 MarkDuplicates After output close freeMemory: 758414672; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:12 MarkDuplicates After output close freeMemory: 758414672; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:12 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:12 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:12 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testBulkFragmentsNoDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:23:12 MarkDuplicates Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9877934606012114224.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9877934606012114224.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9877934606012114224.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9877934606012114224.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9877934606012114224.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9877934606012114224.tmp/output.sam Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:12.775 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:12.775 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:12.775 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:12.775 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:12.776 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:12.776 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:12.776 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:12.776 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:12 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9877934606012114224.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9877934606012114224.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9877934606012114224.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:12 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9877934606012114224.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9877934606012114224.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9877934606012114224.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:12 MarkDuplicates Start of doWork freeMemory: 1020967872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:12 MarkDuplicates Start of doWork freeMemory: 1020967872; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:12 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:12 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:12 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:23:12 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:23:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:13 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2024-07-02 11:23:13 MarkDuplicates Read 10000 records. 0 pairs never matched. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 956960896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 956960896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:13 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:13 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:13 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:13 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:13 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:13 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:13 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:13 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 481994480; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 481994480; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:13 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:23:13 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:13 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:13 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:13 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:13 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:13 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:13 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:13 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:13 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:13 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:13 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:13 MarkDuplicates Before output close freeMemory: 750975104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:13 MarkDuplicates Before output close freeMemory: 750975104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:13 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:13 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:13 MarkDuplicates After output close freeMemory: 751477816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:13 MarkDuplicates After output close freeMemory: 751477816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:13 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:23:13 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:14 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testBulkFragmentsNoDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:23:14 MarkDuplicates Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13215740183584785944.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13215740183584785944.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13215740183584785944.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13215740183584785944.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13215740183584785944.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13215740183584785944.tmp/output.sam Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:14.191 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:14.191 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:14.191 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:14.191 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:14.191 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:14.191 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:14.191 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:14.191 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:14 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13215740183584785944.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13215740183584785944.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13215740183584785944.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:14 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13215740183584785944.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13215740183584785944.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13215740183584785944.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:14 MarkDuplicates Start of doWork freeMemory: 1020901392; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:14 MarkDuplicates Start of doWork freeMemory: 1020901392; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:14 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:14 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:14 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:23:14 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:14 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:23:14 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:14 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2024-07-02 11:23:14 MarkDuplicates Read 10000 records. 0 pairs never matched. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 957195256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 957195256; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:14 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:14 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:14 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:14 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:14 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:14 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:14 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 751476880; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:23:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 751476880; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:14 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:23:14 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:14 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:14 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:14 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:14 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:15 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:15 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:15 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:15 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:15 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:15 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:15 MarkDuplicates Before output close freeMemory: 775322320; totalMemory: 1097859072; maxMemory: 2147483648 INFO 2024-07-02 11:23:15 MarkDuplicates Before output close freeMemory: 775322320; totalMemory: 1097859072; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:15 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:15 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:15 MarkDuplicates After output close freeMemory: 775594048; totalMemory: 1097859072; maxMemory: 2147483648 INFO 2024-07-02 11:23:15 MarkDuplicates After output close freeMemory: 775594048; totalMemory: 1097859072; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:23:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1097859072 Runtime.totalMemory()=1097859072 Running Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:15 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testBulkFragmentsNoDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:23:15 MarkDuplicates Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9021263300666853347.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9021263300666853347.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9021263300666853347.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester5525915826584246252/input.fasta ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9021263300666853347.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9021263300666853347.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9021263300666853347.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester5525915826584246252/input.fasta Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:15.841 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:15.841 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:15.841 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:15.841 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:15.841 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:15.841 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:15.841 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:15.841 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:15 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9021263300666853347.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9021263300666853347.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9021263300666853347.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester5525915826584246252/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:15 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9021263300666853347.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9021263300666853347.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9021263300666853347.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester5525915826584246252/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:15 MarkDuplicates Start of doWork freeMemory: 1020964464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:15 MarkDuplicates Start of doWork freeMemory: 1020964464; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:15 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:15 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:15 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:23:15 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:16 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:23:16 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:16 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2024-07-02 11:23:16 MarkDuplicates Read 10000 records. 0 pairs never matched. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 956957216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 956957216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:16 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:16 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:16 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:16 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:16 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:16 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 481990968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 481990968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:16 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:23:16 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:16 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:16 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:16 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:16 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:16 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:16 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:16 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:16 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:16 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:16 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:17 MarkDuplicates Before output close freeMemory: 751334016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:17 MarkDuplicates Before output close freeMemory: 751334016; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:17 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:17 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:17 MarkDuplicates After output close freeMemory: 751474440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:17 MarkDuplicates After output close freeMemory: 751474440; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:17 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:23:17 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:17 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testBulkFragmentsWithDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:23:17 MarkDuplicates Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16483044545626772711.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16483044545626772711.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16483044545626772711.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16483044545626772711.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16483044545626772711.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16483044545626772711.tmp/output.sam Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:17.447 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:17.447 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:17.447 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:17.447 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:17.447 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:17.447 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:17.447 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:17.447 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:17 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16483044545626772711.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16483044545626772711.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16483044545626772711.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:17 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16483044545626772711.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16483044545626772711.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16483044545626772711.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:17 MarkDuplicates Start of doWork freeMemory: 1012770552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:17 MarkDuplicates Start of doWork freeMemory: 1012770552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:17 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:17 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:17 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:23:17 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:17 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:23:17 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:17 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2024-07-02 11:23:17 MarkDuplicates Read 21000 records. 0 pairs never matched. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 947972064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 947972064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:18 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:18 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:18 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:18 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:18 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:18 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 743281688; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:23:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 743281688; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:18 MarkDuplicates Marking 20000 records as duplicates. INFO 2024-07-02 11:23:18 MarkDuplicates Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:18 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:18 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:18 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:18 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:18 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:18 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:18 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:18 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:18 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:18 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:18 MarkDuplicates Before output close freeMemory: 791375224; totalMemory: 1121976320; maxMemory: 2147483648 INFO 2024-07-02 11:23:18 MarkDuplicates Before output close freeMemory: 791375224; totalMemory: 1121976320; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:18 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:18 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:18 MarkDuplicates After output close freeMemory: 784847560; totalMemory: 1115684864; maxMemory: 2147483648 INFO 2024-07-02 11:23:18 MarkDuplicates After output close freeMemory: 784847560; totalMemory: 1115684864; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:18 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:23:18 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1115684864 Runtime.totalMemory()=1115684864 Running Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:19 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testBulkFragmentsWithDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:23:19 MarkDuplicates Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11737316932618196766.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11737316932618196766.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11737316932618196766.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11737316932618196766.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11737316932618196766.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11737316932618196766.tmp/output.sam Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:19.350 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:19.350 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:19.350 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:19.350 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:19.350 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:19.350 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:19.350 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:19.350 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:19 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11737316932618196766.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11737316932618196766.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11737316932618196766.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:19 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11737316932618196766.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11737316932618196766.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11737316932618196766.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:19 MarkDuplicates Start of doWork freeMemory: 1012335264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:19 MarkDuplicates Start of doWork freeMemory: 1012335264; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:19 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:19 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:19 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:23:19 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:19 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:23:19 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:19 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2024-07-02 11:23:19 MarkDuplicates Read 21000 records. 0 pairs never matched. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 948206448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 948206448; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:20 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:20 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:20 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:20 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:20 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:20 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 743280752; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:23:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 743280752; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:20 MarkDuplicates Marking 20000 records as duplicates. INFO 2024-07-02 11:23:20 MarkDuplicates Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:20 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:20 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:20 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:20 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:20 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:20 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:20 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:20 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:20 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:20 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:20 MarkDuplicates Before output close freeMemory: 788096584; totalMemory: 1118830592; maxMemory: 2147483648 INFO 2024-07-02 11:23:20 MarkDuplicates Before output close freeMemory: 788096584; totalMemory: 1118830592; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:20 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:20 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:20 MarkDuplicates After output close freeMemory: 785091832; totalMemory: 1115684864; maxMemory: 2147483648 INFO 2024-07-02 11:23:20 MarkDuplicates After output close freeMemory: 785091832; totalMemory: 1115684864; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:20 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:23:20 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1115684864 Runtime.totalMemory()=1115684864 Running Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:21 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testBulkFragmentsWithDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:23:21 MarkDuplicates Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9834730609015331848.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9834730609015331848.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9834730609015331848.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester1184253132135366038/input.fasta ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9834730609015331848.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9834730609015331848.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9834730609015331848.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester1184253132135366038/input.fasta Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:21.761 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:21.761 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:21.761 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:21.761 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:21.761 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:21.761 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:21.761 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:21.761 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:21 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9834730609015331848.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9834730609015331848.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9834730609015331848.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester1184253132135366038/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:21 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9834730609015331848.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9834730609015331848.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9834730609015331848.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester1184253132135366038/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:21 MarkDuplicates Start of doWork freeMemory: 1012398344; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:21 MarkDuplicates Start of doWork freeMemory: 1012398344; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:21 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:21 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:21 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:23:21 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:22 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:23:22 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:22 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2024-07-02 11:23:22 MarkDuplicates Read 21000 records. 0 pairs never matched. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 948335520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 948335520; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:22 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:22 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:22 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:22 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:22 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:22 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 743278408; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:23:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 743278408; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:23 MarkDuplicates Marking 20000 records as duplicates. INFO 2024-07-02 11:23:23 MarkDuplicates Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:23 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:23 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:23 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:23 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:23 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:23 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:23 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:23 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:23 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:23 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:23 MarkDuplicates Before output close freeMemory: 801858416; totalMemory: 1132462080; maxMemory: 2147483648 INFO 2024-07-02 11:23:23 MarkDuplicates Before output close freeMemory: 801858416; totalMemory: 1132462080; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:23 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:23 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:23 MarkDuplicates After output close freeMemory: 788077144; totalMemory: 1118830592; maxMemory: 2147483648 INFO 2024-07-02 11:23:23 MarkDuplicates After output close freeMemory: 788077144; totalMemory: 1118830592; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:23 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:23:23 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1118830592 Runtime.totalMemory()=1118830592 Running Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:24 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testBulkPairsNoDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:23:24 MarkDuplicates Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6541349207085250765.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6541349207085250765.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6541349207085250765.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6541349207085250765.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6541349207085250765.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6541349207085250765.tmp/output.sam Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:24.192 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:24.192 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:24.192 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:24.192 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:24.192 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:24.192 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:24.192 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:24.192 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:24 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6541349207085250765.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6541349207085250765.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6541349207085250765.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:24 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6541349207085250765.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6541349207085250765.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6541349207085250765.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:24 MarkDuplicates Start of doWork freeMemory: 1012252400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:24 MarkDuplicates Start of doWork freeMemory: 1012252400; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:24 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:24 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:24 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:23:24 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:24 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:23:24 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:24 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2024-07-02 11:23:24 MarkDuplicates Read 20200 records. 0 pairs never matched. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 946792168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 946792168; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:24 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:24 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:25 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:25 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:25 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:25 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:25 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:25 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 473278816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 473278816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:25 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:23:25 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:25 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:25 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:25 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:25 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:25 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:25 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:25 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:25 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:25 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:25 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:25 MarkDuplicates Before output close freeMemory: 742622440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:25 MarkDuplicates Before output close freeMemory: 742622440; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:25 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:25 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:25 MarkDuplicates After output close freeMemory: 742762152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:25 MarkDuplicates After output close freeMemory: 742762152; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:25 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:23:25 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:26 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testBulkPairsNoDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:23:26 MarkDuplicates Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17326638401672949732.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17326638401672949732.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17326638401672949732.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17326638401672949732.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17326638401672949732.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17326638401672949732.tmp/output.sam Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:26.219 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:26.219 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:26.219 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:26.219 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:26.219 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:26.219 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:26.219 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:26.219 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:26 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17326638401672949732.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17326638401672949732.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17326638401672949732.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:26 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17326638401672949732.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17326638401672949732.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17326638401672949732.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:26 MarkDuplicates Start of doWork freeMemory: 1012186032; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:26 MarkDuplicates Start of doWork freeMemory: 1012186032; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:26 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:26 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:26 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:23:26 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:23:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:26 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2024-07-02 11:23:26 MarkDuplicates Read 20200 records. 0 pairs never matched. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 947018248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 947018248; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:27 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:27 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:27 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:27 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 742761752; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:23:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 742761752; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:27 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:23:27 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:27 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:27 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:27 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:27 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:27 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:27 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:27 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:27 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:27 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:27 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:27 MarkDuplicates Before output close freeMemory: 794918160; totalMemory: 1126170624; maxMemory: 2147483648 INFO 2024-07-02 11:23:27 MarkDuplicates Before output close freeMemory: 794918160; totalMemory: 1126170624; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:27 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:27 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:27 MarkDuplicates After output close freeMemory: 787463960; totalMemory: 1118830592; maxMemory: 2147483648 INFO 2024-07-02 11:23:27 MarkDuplicates After output close freeMemory: 787463960; totalMemory: 1118830592; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:27 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:23:27 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1118830592 Runtime.totalMemory()=1118830592 Running Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:28 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testBulkPairsNoDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:23:28 MarkDuplicates Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9682631195392373965.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9682631195392373965.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9682631195392373965.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester4010721779405202465/input.fasta ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9682631195392373965.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9682631195392373965.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9682631195392373965.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester4010721779405202465/input.fasta Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:28.865 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:28.865 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:28.865 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:28.865 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:28.865 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:28.865 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:28.865 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:28.865 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:28 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9682631195392373965.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9682631195392373965.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9682631195392373965.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester4010721779405202465/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:28 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9682631195392373965.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9682631195392373965.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9682631195392373965.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester4010721779405202465/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:28 MarkDuplicates Start of doWork freeMemory: 1012248592; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:28 MarkDuplicates Start of doWork freeMemory: 1012248592; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:28 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:28 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:28 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:23:28 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:29 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:23:29 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:29 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2024-07-02 11:23:29 MarkDuplicates Read 20200 records. 0 pairs never matched. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 947146688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 947146688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:30 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:30 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:30 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:30 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:30 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:30 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 473274976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 473274976; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:30 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:23:30 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:30 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:30 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:30 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:30 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:30 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:30 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:30 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:30 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:30 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:30 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:31 MarkDuplicates Before output close freeMemory: 742618888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:31 MarkDuplicates Before output close freeMemory: 742618888; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:31 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:31 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:31 MarkDuplicates After output close freeMemory: 742759048; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:31 MarkDuplicates After output close freeMemory: 742759048; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:31 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:23:31 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:31 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testBulkPairsWithDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:23:31 MarkDuplicates Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.14426703412214475839.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14426703412214475839.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14426703412214475839.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.14426703412214475839.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14426703412214475839.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14426703412214475839.tmp/output.sam Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:31.463 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:31.463 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:31.463 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:31.463 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:31.464 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:31.464 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:31.464 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:31.464 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:31 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.14426703412214475839.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.14426703412214475839.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.14426703412214475839.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:31 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.14426703412214475839.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.14426703412214475839.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.14426703412214475839.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:31 MarkDuplicates Start of doWork freeMemory: 1022769136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:31 MarkDuplicates Start of doWork freeMemory: 1022769136; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:31 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:31 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:31 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:23:31 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:31 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:23:31 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:31 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2024-07-02 11:23:31 MarkDuplicates Read 6820 records. 0 pairs never matched. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 959112472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 959112472; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:32 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:32 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:32 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:32 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:32 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:32 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 1022763616; totalMemory: 1612709888; maxMemory: 2147483648 INFO 2024-07-02 11:23:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 1022763616; totalMemory: 1612709888; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:32 MarkDuplicates Marking 6200 records as duplicates. INFO 2024-07-02 11:23:32 MarkDuplicates Marking 6200 records as duplicates. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:32 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:32 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:32 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:32 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:32 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:32 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:32 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:32 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:32 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:32 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:32 MarkDuplicates Before output close freeMemory: 763420872; totalMemory: 1084227584; maxMemory: 2147483648 INFO 2024-07-02 11:23:32 MarkDuplicates Before output close freeMemory: 763420872; totalMemory: 1084227584; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:32 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:32 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:32 MarkDuplicates After output close freeMemory: 763561584; totalMemory: 1084227584; maxMemory: 2147483648 INFO 2024-07-02 11:23:32 MarkDuplicates After output close freeMemory: 763561584; totalMemory: 1084227584; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:23:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:32 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testBulkPairsWithDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:23:32 MarkDuplicates Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.1232594745735143073.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1232594745735143073.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1232594745735143073.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.1232594745735143073.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1232594745735143073.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1232594745735143073.tmp/output.sam Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:32.939 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:32.939 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:32.940 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:32.940 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:32.940 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:32.940 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:32.940 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:32.940 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:32 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1232594745735143073.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1232594745735143073.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1232594745735143073.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:32 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1232594745735143073.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1232594745735143073.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1232594745735143073.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:33 MarkDuplicates Start of doWork freeMemory: 1022702824; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:33 MarkDuplicates Start of doWork freeMemory: 1022702824; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:33 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:33 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:33 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:23:33 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:33 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:23:33 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:33 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2024-07-02 11:23:33 MarkDuplicates Read 6820 records. 0 pairs never matched. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 958980080; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 958980080; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:33 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:33 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:33 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:33 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 1022762576; totalMemory: 1612709888; maxMemory: 2147483648 INFO 2024-07-02 11:23:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 1022762576; totalMemory: 1612709888; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:33 MarkDuplicates Marking 6200 records as duplicates. INFO 2024-07-02 11:23:33 MarkDuplicates Marking 6200 records as duplicates. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:33 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:33 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:33 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:33 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:33 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:33 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:33 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:33 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:33 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:33 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:33 MarkDuplicates Before output close freeMemory: 769783344; totalMemory: 1090519040; maxMemory: 2147483648 INFO 2024-07-02 11:23:33 MarkDuplicates Before output close freeMemory: 769783344; totalMemory: 1090519040; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:33 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:33 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:33 MarkDuplicates After output close freeMemory: 759437544; totalMemory: 1080033280; maxMemory: 2147483648 INFO 2024-07-02 11:23:33 MarkDuplicates After output close freeMemory: 759437544; totalMemory: 1080033280; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:33 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:23:33 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1080033280 Runtime.totalMemory()=1080033280 Running Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:34 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testBulkPairsWithDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:23:34 MarkDuplicates Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17901715246132492625.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17901715246132492625.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17901715246132492625.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester6453928107409095787/input.fasta ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17901715246132492625.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17901715246132492625.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17901715246132492625.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester6453928107409095787/input.fasta Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:34.471 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:34.471 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:34.471 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:34.471 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:34.471 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:34.471 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:34.471 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:34.471 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:34 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17901715246132492625.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17901715246132492625.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17901715246132492625.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester6453928107409095787/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:34 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17901715246132492625.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17901715246132492625.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17901715246132492625.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester6453928107409095787/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:34 MarkDuplicates Start of doWork freeMemory: 1022765688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:34 MarkDuplicates Start of doWork freeMemory: 1022765688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:34 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:34 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:34 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:23:34 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:34 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:23:34 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:34 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2024-07-02 11:23:34 MarkDuplicates Read 6820 records. 0 pairs never matched. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:34 MarkDuplicates After buildSortedReadEndLists freeMemory: 959108656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:34 MarkDuplicates After buildSortedReadEndLists freeMemory: 959108656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:35 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:35 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:35 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:35 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:35 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:35 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 483791896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 483791896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:35 MarkDuplicates Marking 6200 records as duplicates. INFO 2024-07-02 11:23:35 MarkDuplicates Marking 6200 records as duplicates. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:35 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:35 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:35 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:35 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:35 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:35 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:35 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:35 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:35 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:35 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:35 MarkDuplicates Before output close freeMemory: 753135568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:35 MarkDuplicates Before output close freeMemory: 753135568; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:35 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:35 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:35 MarkDuplicates After output close freeMemory: 753275648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:35 MarkDuplicates After output close freeMemory: 753275648; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:35 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:23:35 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:35 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testDifferentChromosomesInOppositeOrder STANDARD_ERROR INFO 2024-07-02 11:23:35 MarkDuplicates Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13162351283808980595.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13162351283808980595.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13162351283808980595.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13162351283808980595.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13162351283808980595.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13162351283808980595.tmp/output.sam Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:35.808 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:35.808 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:35.809 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:35.809 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:35.809 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:35.809 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:35.809 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:35.809 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:35 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13162351283808980595.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13162351283808980595.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13162351283808980595.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:35 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13162351283808980595.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13162351283808980595.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13162351283808980595.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:35 MarkDuplicates Start of doWork freeMemory: 1027887448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:35 MarkDuplicates Start of doWork freeMemory: 1027887448; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:35 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:35 MarkDuplicates Reading input file and constructing read end information. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:35 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:35 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:35 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:23:35 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 973355240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 973355240; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:36 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:36 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:36 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:36 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:36 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:36 MarkDuplicates Sorting list of duplicate records. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 488913528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 488913528; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:36 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:23:36 MarkDuplicates Marking 2 records as duplicates. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:36 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:23:36 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:36 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:36 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:36 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:36 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:36 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:36 MarkDuplicates Duplicate Index cleanup. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:36 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:36 MarkDuplicates Getting Memory Stats. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:36 MarkDuplicates Before output close freeMemory: 758256232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:36 MarkDuplicates Before output close freeMemory: 758256232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:36 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:36 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:36 MarkDuplicates After output close freeMemory: 758397136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:36 MarkDuplicates After output close freeMemory: 758397136; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:36 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:36 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:36 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:23:36 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9553494577551057783.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9553494577551057783.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9553494577551057783.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9553494577551057783.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9553494577551057783.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9553494577551057783.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:36.594 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:36.594 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:36.594 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:36.594 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:36.594 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:36.594 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:36.594 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:36.594 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:36 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9553494577551057783.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9553494577551057783.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9553494577551057783.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:36 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9553494577551057783.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9553494577551057783.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9553494577551057783.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:36 MarkDuplicates Start of doWork freeMemory: 1027880776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:36 MarkDuplicates Start of doWork freeMemory: 1027880776; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:36 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:36 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:36 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:36 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:36 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:23:36 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 973347576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 973347576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:37 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:37 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:37 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 488906872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 488906872; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:23:37 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:23:37 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:37 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:37 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:37 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:37 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Before output close freeMemory: 758250080; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:37 MarkDuplicates Before output close freeMemory: 758250080; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:37 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates After output close freeMemory: 758390776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:37 MarkDuplicates After output close freeMemory: 758390776; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:23:37 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.1195155402218815028.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1195155402218815028.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1195155402218815028.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.1195155402218815028.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1195155402218815028.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1195155402218815028.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:37.330 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:37.330 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:37.330 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:37.330 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:37.330 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:37.330 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:37.330 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:37.330 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:37 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1195155402218815028.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1195155402218815028.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1195155402218815028.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:37 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1195155402218815028.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1195155402218815028.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1195155402218815028.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Start of doWork freeMemory: 1027880096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:37 MarkDuplicates Start of doWork freeMemory: 1027880096; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:37 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:37 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:23:37 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 973346896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 973346896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:37 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:37 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:37 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 488906192; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 488906192; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:23:37 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:23:37 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:37 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:37 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:37 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:37 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Before output close freeMemory: 758249776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:37 MarkDuplicates Before output close freeMemory: 758249776; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:37 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates After output close freeMemory: 758390024; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:37 MarkDuplicates After output close freeMemory: 758390024; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:37 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:23:37 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2239806952944316197.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2239806952944316197.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2239806952944316197.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2239806952944316197.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2239806952944316197.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2239806952944316197.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:37.999 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:37.999 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:37.999 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:37.999 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:38.000 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:38.000 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:38.000 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:38.000 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:38 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2239806952944316197.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2239806952944316197.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2239806952944316197.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:38 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2239806952944316197.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2239806952944316197.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2239806952944316197.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:38 MarkDuplicates Start of doWork freeMemory: 1027879064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:38 MarkDuplicates Start of doWork freeMemory: 1027879064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:38 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:38 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:38 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:38 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:38 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:23:38 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 973346256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 973346256; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:38 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:38 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:38 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:38 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:38 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:38 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 488905552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 488905552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:38 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:23:38 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:38 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:23:38 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:38 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:38 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:38 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:38 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:38 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:38 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:38 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:38 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:38 MarkDuplicates Before output close freeMemory: 758249136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:38 MarkDuplicates Before output close freeMemory: 758249136; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:38 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:38 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:38 MarkDuplicates After output close freeMemory: 758389384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:38 MarkDuplicates After output close freeMemory: 758389384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:38 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:38 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:38 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:23:38 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.823558017309426165.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.823558017309426165.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.823558017309426165.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.823558017309426165.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.823558017309426165.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.823558017309426165.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:38.620 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:38.620 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:38.620 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:38.620 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:38.620 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:38.620 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:38.620 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:38.620 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:38 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.823558017309426165.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.823558017309426165.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.823558017309426165.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:38 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.823558017309426165.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.823558017309426165.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.823558017309426165.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:38 MarkDuplicates Start of doWork freeMemory: 1027877688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:38 MarkDuplicates Start of doWork freeMemory: 1027877688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:38 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:38 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:38 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:38 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:38 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:23:38 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 973344704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 973344704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:39 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:39 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:39 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 488903784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 488903784; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:23:39 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:23:39 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:39 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:39 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:39 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:39 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates Before output close freeMemory: 758246736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:39 MarkDuplicates Before output close freeMemory: 758246736; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:39 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates After output close freeMemory: 758387192; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:39 MarkDuplicates After output close freeMemory: 758387192; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:23:39 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17207233737645104069.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17207233737645104069.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17207233737645104069.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17207233737645104069.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17207233737645104069.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17207233737645104069.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:39.295 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:39.295 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:39.295 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:39.295 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:39.295 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:39.295 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:39.295 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:39.295 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:39 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17207233737645104069.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17207233737645104069.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17207233737645104069.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:39 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17207233737645104069.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17207233737645104069.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17207233737645104069.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates Start of doWork freeMemory: 1027871600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:39 MarkDuplicates Start of doWork freeMemory: 1027871600; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:39 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:39 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:23:39 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 973343832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 973343832; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:39 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:39 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:39 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 567546328; totalMemory: 1152385024; maxMemory: 2147483648 INFO 2024-07-02 11:23:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 567546328; totalMemory: 1152385024; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:23:39 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:23:39 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:39 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:39 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:39 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:39 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates Before output close freeMemory: 758246712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:39 MarkDuplicates Before output close freeMemory: 758246712; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:39 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:39 MarkDuplicates After output close freeMemory: 758153504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:39 MarkDuplicates After output close freeMemory: 758153504; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:40 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:23:40 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2911230109311879328.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2911230109311879328.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2911230109311879328.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2911230109311879328.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2911230109311879328.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2911230109311879328.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:40.019 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:40.019 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:40.020 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:40.020 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:40.020 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:40.020 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:40.020 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:40.020 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:40 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2911230109311879328.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2911230109311879328.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2911230109311879328.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:40 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2911230109311879328.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2911230109311879328.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2911230109311879328.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:40 MarkDuplicates Start of doWork freeMemory: 1027870992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:40 MarkDuplicates Start of doWork freeMemory: 1027870992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:40 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:40 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:40 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:40 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:40 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:23:40 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 973343424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 973343424; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:40 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:40 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:40 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:40 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:40 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 488902504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 488902504; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:40 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:23:40 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:40 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:23:40 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:40 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:40 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:40 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:40 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:40 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:40 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:40 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:40 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:40 MarkDuplicates Before output close freeMemory: 758246088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:40 MarkDuplicates Before output close freeMemory: 758246088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:40 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:40 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:40 MarkDuplicates After output close freeMemory: 758386336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:40 MarkDuplicates After output close freeMemory: 758386336; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:40 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:40 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:40 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testMappedFragmentAndMappedPairFirstOfPairNonPrimary STANDARD_ERROR INFO 2024-07-02 11:23:40 MarkDuplicates Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3649997253088042980.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3649997253088042980.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3649997253088042980.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3649997253088042980.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3649997253088042980.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3649997253088042980.tmp/output.sam Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:40.686 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:40.686 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:40.686 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:40.686 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:40.687 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:40.687 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:40.687 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:40.687 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:40 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3649997253088042980.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3649997253088042980.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3649997253088042980.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:40 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3649997253088042980.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3649997253088042980.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3649997253088042980.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:40 MarkDuplicates Start of doWork freeMemory: 1027882680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:40 MarkDuplicates Start of doWork freeMemory: 1027882680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:40 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:40 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:40 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:40 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:40 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:23:40 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:40 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:23:40 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 973351112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 973351112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:41 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:41 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:41 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 488772720; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 488772720; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:23:41 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:41 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:41 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:41 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:41 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:41 MarkDuplicates Getting Memory Stats. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates Before output close freeMemory: 758253048; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:41 MarkDuplicates Before output close freeMemory: 758253048; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:41 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates After output close freeMemory: 758392696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:41 MarkDuplicates After output close freeMemory: 758392696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:41 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:41 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testMappedFragmentAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:23:41 MarkDuplicates Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4349762444544501258.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4349762444544501258.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4349762444544501258.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4349762444544501258.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4349762444544501258.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4349762444544501258.tmp/output.sam Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:41.361 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:41.361 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:41.361 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:41.361 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:41.361 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:41.361 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:41.362 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:41.362 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:41 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4349762444544501258.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4349762444544501258.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4349762444544501258.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:41 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4349762444544501258.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4349762444544501258.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4349762444544501258.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates Start of doWork freeMemory: 1027881760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:41 MarkDuplicates Start of doWork freeMemory: 1027881760; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:41 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:41 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:41 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:23:41 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2024-07-02 11:23:41 MarkDuplicates Read 3 records. 0 pairs never matched. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 973349504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 973349504; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:41 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:41 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:41 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 488908368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 488908368; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:23:41 MarkDuplicates Marking 1 records as duplicates. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:41 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:41 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:41 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:41 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:41 MarkDuplicates Getting Memory Stats. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates Before output close freeMemory: 758250664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:41 MarkDuplicates Before output close freeMemory: 758250664; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:41 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:41 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:42 MarkDuplicates After output close freeMemory: 758392272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:42 MarkDuplicates After output close freeMemory: 758392272; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:42 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testMappedFragmentAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:23:42 MarkDuplicates Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4910822648114666769.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4910822648114666769.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4910822648114666769.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4910822648114666769.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4910822648114666769.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4910822648114666769.tmp/output.sam Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:42.032 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:42.032 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:42.033 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:42.033 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:42.033 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:42.033 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:42.033 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:42.033 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:42 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4910822648114666769.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4910822648114666769.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4910822648114666769.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:42 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4910822648114666769.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4910822648114666769.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4910822648114666769.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:42 MarkDuplicates Start of doWork freeMemory: 1027881224; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:42 MarkDuplicates Start of doWork freeMemory: 1027881224; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:42 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:42 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:42 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:42 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:42 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:23:42 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:42 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2024-07-02 11:23:42 MarkDuplicates Read 3 records. 0 pairs never matched. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 973348968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 973348968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:42 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:42 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:42 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:42 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:42 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:42 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 488907832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 488907832; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:42 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:23:42 MarkDuplicates Marking 1 records as duplicates. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:42 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:42 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:42 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:42 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:42 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:42 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:42 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:42 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:42 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:42 MarkDuplicates Getting Memory Stats. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:42 MarkDuplicates Before output close freeMemory: 758251696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:42 MarkDuplicates Before output close freeMemory: 758251696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:42 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:42 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:42 MarkDuplicates After output close freeMemory: 758154456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:42 MarkDuplicates After output close freeMemory: 758154456; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:42 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testMappedPairAndMappedFragmentAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:23:42 MarkDuplicates Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16608315925485944760.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16608315925485944760.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16608315925485944760.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16608315925485944760.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16608315925485944760.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16608315925485944760.tmp/output.sam Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:42.721 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:42.721 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:42.721 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:42.721 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:42.721 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:42.721 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:42.721 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:42.721 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:42 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16608315925485944760.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16608315925485944760.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16608315925485944760.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:42 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16608315925485944760.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16608315925485944760.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16608315925485944760.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:42 MarkDuplicates Start of doWork freeMemory: 1027640440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:42 MarkDuplicates Start of doWork freeMemory: 1027640440; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:42 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:42 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:42 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:42 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:42 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:23:42 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:42 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:23:42 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 973108576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 973108576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:43 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:43 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:43 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 488905480; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 488905480; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:23:43 MarkDuplicates Marking 2 records as duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:43 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:43 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:43 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:43 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:43 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Before output close freeMemory: 758249128; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:43 MarkDuplicates Before output close freeMemory: 758249128; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:43 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates After output close freeMemory: 758152104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:43 MarkDuplicates After output close freeMemory: 758152104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:43 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:43 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testMappedPairAndMappedFragmentAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:23:43 MarkDuplicates Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7987525051066380193.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7987525051066380193.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7987525051066380193.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7987525051066380193.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7987525051066380193.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7987525051066380193.tmp/output.sam Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:43.405 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:43.405 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:43.405 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:43.405 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:43.405 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:43.405 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:43.405 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:43.405 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:43 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7987525051066380193.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7987525051066380193.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7987525051066380193.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:43 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7987525051066380193.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7987525051066380193.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7987525051066380193.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Start of doWork freeMemory: 1027878344; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:43 MarkDuplicates Start of doWork freeMemory: 1027878344; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:43 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:43 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:43 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:23:43 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:23:43 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 973107752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 973107752; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:43 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:43 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:43 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 488904656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 488904656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:23:43 MarkDuplicates Marking 2 records as duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:43 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:43 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:43 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:43 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:43 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Before output close freeMemory: 758247896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:43 MarkDuplicates Before output close freeMemory: 758247896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:43 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:43 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:44 MarkDuplicates After output close freeMemory: 758388560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:44 MarkDuplicates After output close freeMemory: 758388560; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:44 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:44 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:44 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:23:44 MarkDuplicates Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16489633818108322398.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16489633818108322398.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16489633818108322398.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16489633818108322398.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16489633818108322398.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16489633818108322398.tmp/output.sam Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:44.062 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:44.062 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:44.062 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:44.062 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:44.062 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:44.062 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:44.062 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:44.062 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:44 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16489633818108322398.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16489633818108322398.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16489633818108322398.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:44 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16489633818108322398.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16489633818108322398.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16489633818108322398.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:44 MarkDuplicates Start of doWork freeMemory: 1027634288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:44 MarkDuplicates Start of doWork freeMemory: 1027634288; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:44 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:44 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:44 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:44 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:44 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:23:44 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:44 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:23:44 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 973345888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 973345888; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:44 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:44 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:44 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:44 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:44 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 488904368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 488904368; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:44 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:23:44 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:44 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:44 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:44 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:44 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:44 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:44 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:44 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:44 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:44 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:44 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:44 MarkDuplicates Before output close freeMemory: 758247968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:44 MarkDuplicates Before output close freeMemory: 758247968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:44 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:44 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:44 MarkDuplicates After output close freeMemory: 758150992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:44 MarkDuplicates After output close freeMemory: 758150992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:44 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:44 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:44 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testMappedPairAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:23:44 MarkDuplicates Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16427564610143406552.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16427564610143406552.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16427564610143406552.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16427564610143406552.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16427564610143406552.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16427564610143406552.tmp/output.sam Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:44.729 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:44.729 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:44.729 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:44.729 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:44.729 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:44.729 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:44.729 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:44.729 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:44 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16427564610143406552.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16427564610143406552.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16427564610143406552.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:44 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16427564610143406552.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16427564610143406552.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16427564610143406552.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:44 MarkDuplicates Start of doWork freeMemory: 1027872056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:44 MarkDuplicates Start of doWork freeMemory: 1027872056; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:44 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:44 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:44 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:44 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:44 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:23:44 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:44 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:23:44 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 973345536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 973345536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:45 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:45 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:45 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 488903104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 488903104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:23:45 MarkDuplicates Marking 1 records as duplicates. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:45 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:45 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:45 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:45 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:45 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates Before output close freeMemory: 758008008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:45 MarkDuplicates Before output close freeMemory: 758008008; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:45 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates After output close freeMemory: 758387704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:45 MarkDuplicates After output close freeMemory: 758387704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testMappedPairAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:23:45 MarkDuplicates Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.14853637869571828598.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14853637869571828598.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14853637869571828598.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.14853637869571828598.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14853637869571828598.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14853637869571828598.tmp/output.sam Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:45.407 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:45.407 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:45.407 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:45.407 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:45.407 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:45.407 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:45.407 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:45.407 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:45 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.14853637869571828598.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.14853637869571828598.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.14853637869571828598.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:45 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.14853637869571828598.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.14853637869571828598.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.14853637869571828598.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates Start of doWork freeMemory: 1027876800; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:45 MarkDuplicates Start of doWork freeMemory: 1027876800; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:45 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:45 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:45 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:23:45 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:23:45 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 973344848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 973344848; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:45 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:45 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:45 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 612634384; totalMemory: 1197473792; maxMemory: 2147483648 INFO 2024-07-02 11:23:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 612634384; totalMemory: 1197473792; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:23:45 MarkDuplicates Marking 1 records as duplicates. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:45 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:45 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:45 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:45 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:45 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:45 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:46 MarkDuplicates Before output close freeMemory: 758246760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:46 MarkDuplicates Before output close freeMemory: 758246760; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:46 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:46 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:46 MarkDuplicates After output close freeMemory: 758386520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:46 MarkDuplicates After output close freeMemory: 758386520; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:46 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testMappedPairWithFirstEndSamePositionAndOther STANDARD_ERROR INFO 2024-07-02 11:23:46 MarkDuplicates Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9033414369300196003.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9033414369300196003.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9033414369300196003.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9033414369300196003.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9033414369300196003.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9033414369300196003.tmp/output.sam Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:46.197 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:46.197 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:46.197 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:46.197 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:46.198 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:46.198 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:46.198 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:46.198 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:46 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9033414369300196003.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9033414369300196003.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9033414369300196003.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:46 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9033414369300196003.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9033414369300196003.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9033414369300196003.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:46 MarkDuplicates Start of doWork freeMemory: 1027875888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:46 MarkDuplicates Start of doWork freeMemory: 1027875888; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:46 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:46 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:46 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:46 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:46 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:23:46 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:46 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:23:46 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 973343544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 973343544; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:46 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:46 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:46 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:46 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:46 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:46 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 488902200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 488902200; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:46 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:23:46 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:46 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:46 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:46 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:46 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:46 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:46 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:46 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:46 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:46 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:46 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:46 MarkDuplicates Before output close freeMemory: 758244280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:46 MarkDuplicates Before output close freeMemory: 758244280; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:46 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:46 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:46 MarkDuplicates After output close freeMemory: 758383968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:46 MarkDuplicates After output close freeMemory: 758383968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:46 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testMappedPairWithSamePosition STANDARD_ERROR INFO 2024-07-02 11:23:46 MarkDuplicates Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6911045776593374928.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6911045776593374928.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6911045776593374928.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6911045776593374928.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6911045776593374928.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6911045776593374928.tmp/output.sam Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:46.896 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:46.896 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:46.896 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:46.896 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:46.896 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:46.896 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:46.896 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:46.896 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:46 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6911045776593374928.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6911045776593374928.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6911045776593374928.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:46 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6911045776593374928.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6911045776593374928.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6911045776593374928.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:46 MarkDuplicates Start of doWork freeMemory: 1027632784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:46 MarkDuplicates Start of doWork freeMemory: 1027632784; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:46 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:46 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:46 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:46 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:47 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:23:47 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:47 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:23:47 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 973344672; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 973344672; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:47 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:47 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:47 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:47 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:47 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:47 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 488902848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 488902848; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:47 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:23:47 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:47 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:47 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:47 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:47 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:47 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:47 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:47 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:47 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:47 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:47 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:47 MarkDuplicates Before output close freeMemory: 758246496; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:47 MarkDuplicates Before output close freeMemory: 758246496; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:47 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:47 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:47 MarkDuplicates After output close freeMemory: 758386752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:47 MarkDuplicates After output close freeMemory: 758386752; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:47 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:47 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:47 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testMappedPairWithSamePositionSameCigar STANDARD_ERROR INFO 2024-07-02 11:23:47 MarkDuplicates Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16854895898766051428.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16854895898766051428.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16854895898766051428.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16854895898766051428.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16854895898766051428.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16854895898766051428.tmp/output.sam Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:47.614 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:47.614 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:47.614 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:47.614 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:47.614 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:47.614 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:47.614 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:47.614 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:47 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16854895898766051428.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16854895898766051428.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16854895898766051428.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:47 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16854895898766051428.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16854895898766051428.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16854895898766051428.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:47 MarkDuplicates Start of doWork freeMemory: 1027875792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:47 MarkDuplicates Start of doWork freeMemory: 1027875792; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:47 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:47 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:47 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:47 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:47 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:23:47 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:47 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:23:47 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 973343928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 973343928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:48 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:48 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:48 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 488902104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 488902104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:23:48 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:48 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:48 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:48 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:48 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:48 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates Before output close freeMemory: 758245752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:48 MarkDuplicates Before output close freeMemory: 758245752; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:48 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates After output close freeMemory: 758385936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:48 MarkDuplicates After output close freeMemory: 758385936; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:48 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:48 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:23:48 MarkDuplicates Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10246037109804917948.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10246037109804917948.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10246037109804917948.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10246037109804917948.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10246037109804917948.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10246037109804917948.tmp/output.sam Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:48.352 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:48.352 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:48.352 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:48.352 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:48.352 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:48.352 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:48.352 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:48.352 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:48 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10246037109804917948.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10246037109804917948.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10246037109804917948.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:48 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10246037109804917948.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10246037109804917948.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10246037109804917948.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates Start of doWork freeMemory: 1027875224; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:48 MarkDuplicates Start of doWork freeMemory: 1027875224; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:48 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:48 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:48 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:23:48 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:23:48 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 973343656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 973343656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:48 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:48 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:48 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:48 MarkDuplicates Sorting list of duplicate records. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 488901832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 488901832; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:23:48 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:48 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:48 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:48 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:48 MarkDuplicates Duplicate Index cleanup. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:48 MarkDuplicates Getting Memory Stats. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates Before output close freeMemory: 758245592; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:48 MarkDuplicates Before output close freeMemory: 758245592; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:48 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:48 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:49 MarkDuplicates After output close freeMemory: 758385664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:49 MarkDuplicates After output close freeMemory: 758385664; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:49 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:23:49 MarkDuplicates Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2488619469176799271.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2488619469176799271.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2488619469176799271.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2488619469176799271.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2488619469176799271.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2488619469176799271.tmp/output.sam Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:49.046 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:49.046 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:49.046 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:49.046 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:49.046 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:49.046 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:49.046 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:49.046 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:49 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2488619469176799271.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2488619469176799271.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2488619469176799271.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:49 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2488619469176799271.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2488619469176799271.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2488619469176799271.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:49 MarkDuplicates Start of doWork freeMemory: 1027874624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:49 MarkDuplicates Start of doWork freeMemory: 1027874624; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:49 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:49 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:49 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:49 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:49 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:23:49 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:49 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:23:49 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 973343064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 973343064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:49 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:49 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:49 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:49 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:49 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:49 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:49 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:49 MarkDuplicates Sorting list of duplicate records. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 488901240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 488901240; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:49 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:23:49 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:49 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:49 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:49 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:49 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:49 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:49 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:49 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:49 MarkDuplicates Duplicate Index cleanup. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:49 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:49 MarkDuplicates Getting Memory Stats. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:49 MarkDuplicates Before output close freeMemory: 758245120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:49 MarkDuplicates Before output close freeMemory: 758245120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:49 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:49 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:49 MarkDuplicates After output close freeMemory: 758384648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:49 MarkDuplicates After output close freeMemory: 758384648; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:49 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testOpticalDuplicateBehaviorNullRegex STANDARD_ERROR INFO 2024-07-02 11:23:49 MarkDuplicates Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17137712870517466618.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_NAME_REGEX null -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17137712870517466618.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17137712870517466618.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17137712870517466618.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_NAME_REGEX null -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17137712870517466618.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17137712870517466618.tmp/output.sam Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:49.768 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:49.768 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:49.768 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:49.768 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:49.768 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:49.768 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:49.768 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:49.768 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:49 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17137712870517466618.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17137712870517466618.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17137712870517466618.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH READ_NAME_REGEX=null MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:49 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17137712870517466618.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17137712870517466618.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17137712870517466618.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH READ_NAME_REGEX=null MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:49 MarkDuplicates Start of doWork freeMemory: 1027632040; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:49 MarkDuplicates Start of doWork freeMemory: 1027632040; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:49 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:49 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:49 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:49 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:49 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:23:49 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 973101880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 973101880; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:50 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:50 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:50 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:50 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:50 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:50 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 573833016; totalMemory: 1158676480; maxMemory: 2147483648 INFO 2024-07-02 11:23:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 573833016; totalMemory: 1158676480; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:50 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:23:50 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:23:50 MarkDuplicates Skipped optical duplicate cluster discovery; library size estimation may be inaccurate! WARNING 2024-07-02 11:23:50 MarkDuplicates Skipped optical duplicate cluster discovery; library size estimation may be inaccurate! Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:50 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:50 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:50 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:50 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:50 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:50 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:50 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:50 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:50 MarkDuplicates Before output close freeMemory: 758242720; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:50 MarkDuplicates Before output close freeMemory: 758242720; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:50 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:50 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:50 MarkDuplicates After output close freeMemory: 758382408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:50 MarkDuplicates After output close freeMemory: 758382408; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:50 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testOpticalDuplicateClusterOneEndSamePositionOneCluster STANDARD_ERROR INFO 2024-07-02 11:23:50 MarkDuplicates Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9171541943597113557.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9171541943597113557.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9171541943597113557.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9171541943597113557.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9171541943597113557.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9171541943597113557.tmp/output.sam Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:50.500 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:50.500 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:50.500 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:50.500 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:50.500 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:50.500 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:50.500 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:50.500 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:50 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9171541943597113557.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9171541943597113557.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9171541943597113557.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:50 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9171541943597113557.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9171541943597113557.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9171541943597113557.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:50 MarkDuplicates Start of doWork freeMemory: 1027871520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:50 MarkDuplicates Start of doWork freeMemory: 1027871520; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:50 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:50 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:50 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:50 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:50 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:23:50 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 973339328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 973339328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:50 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:50 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:50 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:50 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:50 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:50 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 488897616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 488897616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:51 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:23:51 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:51 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:23:51 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:51 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:51 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:51 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:51 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:51 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:51 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:51 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:51 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:51 MarkDuplicates Before output close freeMemory: 758241176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:51 MarkDuplicates Before output close freeMemory: 758241176; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:51 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:51 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:51 MarkDuplicates After output close freeMemory: 758381520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:51 MarkDuplicates After output close freeMemory: 758381520; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:51 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:23:51 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.8211784385395260897.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8211784385395260897.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8211784385395260897.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.8211784385395260897.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8211784385395260897.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8211784385395260897.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:51.261 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:51.261 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:51.262 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:51.262 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:51.262 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:51.262 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:51.262 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:51.262 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:51 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8211784385395260897.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8211784385395260897.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8211784385395260897.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:51 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8211784385395260897.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8211784385395260897.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8211784385395260897.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:51 MarkDuplicates Start of doWork freeMemory: 1027869768; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:51 MarkDuplicates Start of doWork freeMemory: 1027869768; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:51 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:51 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:51 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:51 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:51 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:23:51 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 973337576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 973337576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:51 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:51 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:51 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:51 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:51 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:51 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:51 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:51 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 488896016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 488896016; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:51 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:23:51 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:51 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:51 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:51 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:51 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:51 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:51 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:51 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:51 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:51 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:51 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:52 MarkDuplicates Before output close freeMemory: 758239600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:52 MarkDuplicates Before output close freeMemory: 758239600; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:52 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:52 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:52 MarkDuplicates After output close freeMemory: 758141088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:52 MarkDuplicates After output close freeMemory: 758141088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:23:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:52 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:23:52 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.14343556742792295202.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14343556742792295202.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14343556742792295202.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.14343556742792295202.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14343556742792295202.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14343556742792295202.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:52.177 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:52.177 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:52.177 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:52.177 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:52.177 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:52.177 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:52.177 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:52.177 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:52 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.14343556742792295202.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.14343556742792295202.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.14343556742792295202.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:52 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.14343556742792295202.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.14343556742792295202.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.14343556742792295202.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:52 MarkDuplicates Start of doWork freeMemory: 1027868688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:52 MarkDuplicates Start of doWork freeMemory: 1027868688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:52 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:52 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:52 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:52 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:52 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:23:52 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 973336888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 973336888; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:52 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:52 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:52 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:52 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:52 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:52 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 488895328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 488895328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:53 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:23:53 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:53 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:53 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:53 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:53 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:53 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:53 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:53 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:53 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:53 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:53 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:53 MarkDuplicates Before output close freeMemory: 758237376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:53 MarkDuplicates Before output close freeMemory: 758237376; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:53 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:53 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:53 MarkDuplicates After output close freeMemory: 758379232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:53 MarkDuplicates After output close freeMemory: 758379232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:23:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:53 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:23:53 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15915502576945755194.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15915502576945755194.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15915502576945755194.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15915502576945755194.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15915502576945755194.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15915502576945755194.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:53.615 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:53.615 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:53.615 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:53.615 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:53.616 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:53.616 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:53.616 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:53.616 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:53 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15915502576945755194.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15915502576945755194.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15915502576945755194.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:53 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15915502576945755194.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15915502576945755194.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15915502576945755194.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:53 MarkDuplicates Start of doWork freeMemory: 1027868456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:53 MarkDuplicates Start of doWork freeMemory: 1027868456; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:53 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:53 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:53 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:53 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:53 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:23:53 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 973336048; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 973336048; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:54 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:54 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:54 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:54 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:54 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:54 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:54 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:54 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 488894704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 488894704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:54 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:23:54 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:54 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:54 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:54 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:54 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:54 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:54 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:54 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:54 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:54 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:54 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:55 MarkDuplicates Before output close freeMemory: 757998384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:55 MarkDuplicates Before output close freeMemory: 757998384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:55 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:55 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:55 MarkDuplicates After output close freeMemory: 758378312; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:55 MarkDuplicates After output close freeMemory: 758378312; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:55 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:23:55 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:55 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:23:55 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.1594184603250064508.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1594184603250064508.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1594184603250064508.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.1594184603250064508.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1594184603250064508.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.1594184603250064508.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:55.327 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:55.327 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:55.327 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:55.327 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:55.328 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:55.328 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:55.328 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:55.328 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:55 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1594184603250064508.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1594184603250064508.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1594184603250064508.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:55 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.1594184603250064508.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.1594184603250064508.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.1594184603250064508.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:55 MarkDuplicates Start of doWork freeMemory: 1027867848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:55 MarkDuplicates Start of doWork freeMemory: 1027867848; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:55 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:55 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:55 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:55 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:55 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:23:55 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 973335656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 973335656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:56 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:56 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:56 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:56 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:56 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:56 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 640937616; totalMemory: 1225785344; maxMemory: 2147483648 INFO 2024-07-02 11:23:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 640937616; totalMemory: 1225785344; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:56 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:23:56 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:56 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:56 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:56 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:56 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:56 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:56 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:56 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:56 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:56 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:56 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:56 MarkDuplicates Before output close freeMemory: 758237680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:56 MarkDuplicates Before output close freeMemory: 758237680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:56 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:56 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:57 MarkDuplicates After output close freeMemory: 758377432; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:57 MarkDuplicates After output close freeMemory: 758377432; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:57 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:23:57 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:57 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:23:57 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15106906297205611284.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15106906297205611284.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15106906297205611284.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15106906297205611284.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15106906297205611284.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15106906297205611284.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:57.192 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:57.192 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:57.192 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:57.192 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:57.192 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:57.192 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:57.192 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:57.192 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:57 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15106906297205611284.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15106906297205611284.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15106906297205611284.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:57 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15106906297205611284.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15106906297205611284.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15106906297205611284.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:57 MarkDuplicates Start of doWork freeMemory: 1027867208; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:57 MarkDuplicates Start of doWork freeMemory: 1027867208; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:57 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:57 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:57 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:57 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:57 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:23:57 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 973330920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 973330920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:57 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:57 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:57 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:57 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:57 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:57 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 488889360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 488889360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:58 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:23:58 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:58 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:58 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:58 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:58 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:58 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:58 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:58 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:58 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:58 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:58 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:58 MarkDuplicates Before output close freeMemory: 758232944; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:58 MarkDuplicates Before output close freeMemory: 758232944; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:58 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:23:58 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:58 MarkDuplicates After output close freeMemory: 758373192; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:58 MarkDuplicates After output close freeMemory: 758373192; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:23:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:58 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:23:58 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5882819843025324499.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5882819843025324499.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5882819843025324499.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5882819843025324499.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5882819843025324499.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5882819843025324499.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:58.579 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:58.579 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:58.580 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:58.580 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:58.580 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:23:58.580 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:23:58.580 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:23:58.580 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:58 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5882819843025324499.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5882819843025324499.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5882819843025324499.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:23:58 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5882819843025324499.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5882819843025324499.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5882819843025324499.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:23:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:23:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:58 MarkDuplicates Start of doWork freeMemory: 1027862504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:58 MarkDuplicates Start of doWork freeMemory: 1027862504; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:58 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:23:58 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:58 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:23:58 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:58 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:23:58 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 973330096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 973330096; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:59 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:23:59 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:59 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:23:59 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:59 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:23:59 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:59 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:23:59 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 488888752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:23:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 488888752; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:59 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:23:59 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:59 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:23:59 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:59 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:23:59 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:59 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:23:59 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:59 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:23:59 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:23:59 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:23:59 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:00 MarkDuplicates Before output close freeMemory: 758232336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:00 MarkDuplicates Before output close freeMemory: 758232336; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:00 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:00 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:00 MarkDuplicates After output close freeMemory: 758372584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:00 MarkDuplicates After output close freeMemory: 758372584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:24:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:00 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:24:00 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.912624006947232184.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.912624006947232184.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.912624006947232184.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.912624006947232184.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.912624006947232184.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.912624006947232184.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:00.400 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:00.400 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:00.400 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:00.400 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:00.400 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:00.400 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:00.400 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:00.400 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:00 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.912624006947232184.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.912624006947232184.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.912624006947232184.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:00 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.912624006947232184.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.912624006947232184.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.912624006947232184.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:00 MarkDuplicates Start of doWork freeMemory: 1027861888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:00 MarkDuplicates Start of doWork freeMemory: 1027861888; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:00 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:00 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:00 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:00 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:00 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:00 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 973329696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 973329696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:01 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:01 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:01 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:01 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:01 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:01 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 488888136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 488888136; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:01 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:01 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:01 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:01 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:01 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:01 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:01 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:01 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:01 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:01 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:01 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:01 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:01 MarkDuplicates Before output close freeMemory: 758231720; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:01 MarkDuplicates Before output close freeMemory: 758231720; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:01 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:01 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:01 MarkDuplicates After output close freeMemory: 758133208; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:01 MarkDuplicates After output close freeMemory: 758133208; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:01 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:24:01 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:01 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:24:01 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11231722383048955363.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11231722383048955363.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11231722383048955363.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11231722383048955363.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11231722383048955363.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11231722383048955363.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:01.846 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:01.846 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:01.846 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:01.846 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:01.847 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:01.847 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:01.847 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:01.847 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:01 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11231722383048955363.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11231722383048955363.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11231722383048955363.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:01 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11231722383048955363.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11231722383048955363.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11231722383048955363.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:02 MarkDuplicates Start of doWork freeMemory: 1027861240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:02 MarkDuplicates Start of doWork freeMemory: 1027861240; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:02 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:02 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:02 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:02 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:02 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:02 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 973329048; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 973329048; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:02 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:02 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:02 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:02 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:02 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:02 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:02 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:02 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 686019560; totalMemory: 1270874112; maxMemory: 2147483648 INFO 2024-07-02 11:24:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 686019560; totalMemory: 1270874112; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:03 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:03 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:03 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:03 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:03 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:03 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:03 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:03 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:03 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:03 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:03 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:03 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:03 MarkDuplicates Before output close freeMemory: 758231072; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:03 MarkDuplicates Before output close freeMemory: 758231072; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:03 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:03 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:03 MarkDuplicates After output close freeMemory: 758371320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:03 MarkDuplicates After output close freeMemory: 758371320; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:03 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:24:03 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:03 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:24:03 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7902062031356652534.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7902062031356652534.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7902062031356652534.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7902062031356652534.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7902062031356652534.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7902062031356652534.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:03.484 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:03.484 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:03.484 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:03.484 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:03.484 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:03.484 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:03.484 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:03.484 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:03 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7902062031356652534.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7902062031356652534.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7902062031356652534.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:03 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7902062031356652534.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7902062031356652534.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7902062031356652534.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:03 MarkDuplicates Start of doWork freeMemory: 1027860128; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:03 MarkDuplicates Start of doWork freeMemory: 1027860128; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:03 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:03 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:03 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:03 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:03 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:03 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 973328328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 973328328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:04 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:04 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:04 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:04 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:04 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:04 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:04 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:04 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 488886768; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 488886768; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:04 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:04 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:04 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:04 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:04 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:04 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:04 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:04 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:04 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:04 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:04 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:04 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:04 MarkDuplicates Before output close freeMemory: 758230352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:04 MarkDuplicates Before output close freeMemory: 758230352; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:04 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:04 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:04 MarkDuplicates After output close freeMemory: 758370600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:04 MarkDuplicates After output close freeMemory: 758370600; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:04 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:24:04 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:04 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:24:04 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17072775531249000808.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17072775531249000808.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17072775531249000808.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17072775531249000808.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17072775531249000808.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17072775531249000808.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:04.974 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:04.974 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:04.974 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:04.974 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:04.974 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:04.974 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:04.974 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:04.974 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:04 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17072775531249000808.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17072775531249000808.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17072775531249000808.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:04 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17072775531249000808.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17072775531249000808.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17072775531249000808.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:05 MarkDuplicates Start of doWork freeMemory: 1027854432; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:05 MarkDuplicates Start of doWork freeMemory: 1027854432; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:05 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:05 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:05 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:05 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:05 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:05 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 973327408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 973327408; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:05 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:05 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:05 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:05 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:05 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:05 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 488886064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 488886064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:06 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:06 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:06 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:06 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:06 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:06 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:06 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:06 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:06 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:06 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:06 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:06 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:06 MarkDuplicates Before output close freeMemory: 758229648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:06 MarkDuplicates Before output close freeMemory: 758229648; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:06 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:06 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:06 MarkDuplicates After output close freeMemory: 758369896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:06 MarkDuplicates After output close freeMemory: 758369896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:06 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:24:06 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:06 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756) STANDARD_ERROR INFO 2024-07-02 11:24:06 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6285383243360185969.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6285383243360185969.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6285383243360185969.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6285383243360185969.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6285383243360185969.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6285383243360185969.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:06.696 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:06.696 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:06.696 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:06.696 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:06.705 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:06.705 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:06.705 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:06.705 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:06 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6285383243360185969.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6285383243360185969.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6285383243360185969.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:06 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6285383243360185969.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6285383243360185969.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6285383243360185969.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:06 MarkDuplicates Start of doWork freeMemory: 1027859208; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:06 MarkDuplicates Start of doWork freeMemory: 1027859208; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:06 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:06 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:06 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:06 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:06 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:06 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 973327016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 973327016; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:07 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:07 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:08 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:08 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:08 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:08 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:08 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:08 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 488885456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 488885456; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:08 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:08 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:08 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:08 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:08 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:08 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:08 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:08 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:08 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:08 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:08 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:08 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:08 MarkDuplicates Before output close freeMemory: 758229040; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:08 MarkDuplicates Before output close freeMemory: 758229040; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:08 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:08 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:08 MarkDuplicates After output close freeMemory: 758369288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:08 MarkDuplicates After output close freeMemory: 758369288; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:08 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:24:08 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:08 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756) STANDARD_ERROR INFO 2024-07-02 11:24:08 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.8091250353195501955.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8091250353195501955.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8091250353195501955.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.8091250353195501955.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8091250353195501955.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8091250353195501955.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:08.857 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:08.857 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:08.857 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:08.857 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:08.857 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:08.857 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:08.857 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:08.857 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:08 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8091250353195501955.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8091250353195501955.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8091250353195501955.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:08 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8091250353195501955.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8091250353195501955.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8091250353195501955.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:09 MarkDuplicates Start of doWork freeMemory: 1027858560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:09 MarkDuplicates Start of doWork freeMemory: 1027858560; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:09 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:09 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:09 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:09 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:09 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:09 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 973326152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 973326152; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:09 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:09 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:09 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:09 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:09 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:09 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 710134344; totalMemory: 1294991360; maxMemory: 2147483648 INFO 2024-07-02 11:24:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 710134344; totalMemory: 1294991360; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:10 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:10 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:10 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:10 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:10 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:10 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:10 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:10 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:10 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:10 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:10 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:10 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:10 MarkDuplicates Before output close freeMemory: 758228392; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:10 MarkDuplicates Before output close freeMemory: 758228392; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:10 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:10 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:10 MarkDuplicates After output close freeMemory: 758368640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:10 MarkDuplicates After output close freeMemory: 758368640; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:10 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:24:10 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:10 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756) STANDARD_ERROR INFO 2024-07-02 11:24:10 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10677046736861332125.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10677046736861332125.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10677046736861332125.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10677046736861332125.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10677046736861332125.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10677046736861332125.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:10.767 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:10.767 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:10.767 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:10.767 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:10.767 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:10.767 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:10.767 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:10.767 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:10 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10677046736861332125.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10677046736861332125.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10677046736861332125.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:10 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10677046736861332125.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10677046736861332125.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10677046736861332125.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:11 MarkDuplicates Start of doWork freeMemory: 1027857920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:11 MarkDuplicates Start of doWork freeMemory: 1027857920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:11 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:11 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:11 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:11 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:11 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:11 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 973325728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 973325728; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:11 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:11 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:11 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:11 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 488884168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 488884168; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:11 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:11 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:11 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:11 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:11 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:11 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:11 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:11 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:11 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:11 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:11 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:11 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:12 MarkDuplicates Before output close freeMemory: 758227752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:12 MarkDuplicates Before output close freeMemory: 758227752; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:12 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:12 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:12 MarkDuplicates After output close freeMemory: 758368000; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:12 MarkDuplicates After output close freeMemory: 758368000; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:12 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:24:12 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:12 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756) STANDARD_ERROR INFO 2024-07-02 11:24:12 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.18366636079815686199.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.18366636079815686199.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.18366636079815686199.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.18366636079815686199.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.18366636079815686199.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.18366636079815686199.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:12.247 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:12.247 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:12.247 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:12.247 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:12.247 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:12.247 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:12.247 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:12.247 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:12 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.18366636079815686199.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.18366636079815686199.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.18366636079815686199.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:12 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.18366636079815686199.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.18366636079815686199.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.18366636079815686199.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:12 MarkDuplicates Start of doWork freeMemory: 1027857296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:12 MarkDuplicates Start of doWork freeMemory: 1027857296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:12 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:12 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:12 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:12 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:12 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:12 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 973086552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 973086552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:12 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:12 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:13 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:13 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:13 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:13 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:13 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:13 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 488883544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 488883544; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:13 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:13 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:13 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:13 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:13 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:13 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:13 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:13 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:13 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:13 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:13 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:13 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:13 MarkDuplicates Before output close freeMemory: 758226928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:13 MarkDuplicates Before output close freeMemory: 758226928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:13 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:13 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:13 MarkDuplicates After output close freeMemory: 758366680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:13 MarkDuplicates After output close freeMemory: 758366680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:13 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:24:13 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:13 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance STANDARD_ERROR INFO 2024-07-02 11:24:13 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5079379952989386151.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5079379952989386151.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5079379952989386151.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5079379952989386151.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5079379952989386151.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5079379952989386151.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:13.702 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:13.702 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:13.702 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:13.702 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:13.703 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:13.703 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:13.703 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:13.703 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:13 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5079379952989386151.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5079379952989386151.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5079379952989386151.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:13 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5079379952989386151.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5079379952989386151.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5079379952989386151.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:13 MarkDuplicates Start of doWork freeMemory: 1027854144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:13 MarkDuplicates Start of doWork freeMemory: 1027854144; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:13 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:13 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:13 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:13 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:13 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:13 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 973324768; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 973324768; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:14 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:14 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:14 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:14 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:14 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:14 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:14 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 488883208; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 488883208; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:14 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:14 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:14 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:14 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:14 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:14 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:14 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:14 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:14 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:14 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:14 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:14 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:14 MarkDuplicates Before output close freeMemory: 758226792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:14 MarkDuplicates Before output close freeMemory: 758226792; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:14 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:14 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:14 MarkDuplicates After output close freeMemory: 758366544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:14 MarkDuplicates After output close freeMemory: 758366544; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:14 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:24:14 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:14 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance STANDARD_ERROR INFO 2024-07-02 11:24:14 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7411015833135627635.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7411015833135627635.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7411015833135627635.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.7411015833135627635.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7411015833135627635.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.7411015833135627635.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:14.727 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:14.727 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:14.727 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:14.727 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:14.727 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:14.727 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:14.727 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:14.727 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:14 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7411015833135627635.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7411015833135627635.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7411015833135627635.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:14 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.7411015833135627635.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.7411015833135627635.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.7411015833135627635.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:14 MarkDuplicates Start of doWork freeMemory: 1027851352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:14 MarkDuplicates Start of doWork freeMemory: 1027851352; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:14 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:14 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:14 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:14 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:14 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:14 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 973324360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 973324360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:15 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:15 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:15 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:15 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 694403760; totalMemory: 1279262720; maxMemory: 2147483648 INFO 2024-07-02 11:24:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 694403760; totalMemory: 1279262720; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:15 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:24:15 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:15 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:15 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:15 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:15 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates Before output close freeMemory: 757987368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:15 MarkDuplicates Before output close freeMemory: 757987368; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:15 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates After output close freeMemory: 758366544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:15 MarkDuplicates After output close freeMemory: 758366544; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate STANDARD_ERROR INFO 2024-07-02 11:24:15 MarkDuplicates Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3382677187839996166.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3382677187839996166.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3382677187839996166.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3382677187839996166.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3382677187839996166.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3382677187839996166.tmp/output.sam Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:15.449 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:15.449 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:15.449 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:15.449 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:15.449 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:15.449 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:15.449 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:15.449 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:15 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3382677187839996166.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3382677187839996166.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3382677187839996166.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:15 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3382677187839996166.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3382677187839996166.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3382677187839996166.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates Start of doWork freeMemory: 1027853600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:15 MarkDuplicates Start of doWork freeMemory: 1027853600; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:15 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:15 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:15 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates After buildSortedReadEndLists freeMemory: 973085112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:15 MarkDuplicates After buildSortedReadEndLists freeMemory: 973085112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:15 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:15 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:15 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:15 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 488881952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 488881952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:15 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:24:15 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:15 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:15 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:15 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:15 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:15 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:16 MarkDuplicates Before output close freeMemory: 758225576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:16 MarkDuplicates Before output close freeMemory: 758225576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:16 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:16 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:16 MarkDuplicates After output close freeMemory: 758365856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:16 MarkDuplicates After output close freeMemory: 758365856; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:16 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:16 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:16 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testOpticalDuplicateFinding STANDARD_ERROR INFO 2024-07-02 11:24:16 MarkDuplicates Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2608974205540232031.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2608974205540232031.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2608974205540232031.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2608974205540232031.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2608974205540232031.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2608974205540232031.tmp/output.sam Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:16.137 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:16.137 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:16.137 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:16.137 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:16.137 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:16.137 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:16.137 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:16.137 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:16 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2608974205540232031.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2608974205540232031.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2608974205540232031.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:16 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2608974205540232031.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2608974205540232031.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2608974205540232031.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:16 MarkDuplicates Start of doWork freeMemory: 1027854136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:16 MarkDuplicates Start of doWork freeMemory: 1027854136; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:16 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:16 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:16 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:16 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:16 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:24:16 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 973321688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 973321688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:16 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:16 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:16 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:16 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:16 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:16 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 488880240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 488880240; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:16 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:24:16 MarkDuplicates Marking 4 records as duplicates. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:16 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:24:16 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:16 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:16 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:16 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:16 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:16 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:16 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:16 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:16 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:16 MarkDuplicates Before output close freeMemory: 758223928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:16 MarkDuplicates Before output close freeMemory: 758223928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:16 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:16 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:16 MarkDuplicates After output close freeMemory: 758364144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:16 MarkDuplicates After output close freeMemory: 758364144; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:16 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:16 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:16 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testPathologicalOrderingAtTheSamePosition STANDARD_ERROR INFO 2024-07-02 11:24:16 MarkDuplicates Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15377189442462987022.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15377189442462987022.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15377189442462987022.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15377189442462987022.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15377189442462987022.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15377189442462987022.tmp/output.sam Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:16.820 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:16.820 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:16.820 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:16.820 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:16.821 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:16.821 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:16.821 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:16.821 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:16 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15377189442462987022.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15377189442462987022.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15377189442462987022.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:16 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15377189442462987022.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15377189442462987022.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15377189442462987022.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:16 MarkDuplicates Start of doWork freeMemory: 1027854376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:16 MarkDuplicates Start of doWork freeMemory: 1027854376; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:16 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:16 MarkDuplicates Reading input file and constructing read end information. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:16 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:16 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:16 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:16 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 973322184; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 973322184; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:17 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:17 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:17 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:17 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:17 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:17 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:17 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:17 MarkDuplicates Sorting list of duplicate records. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 488880472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 488880472; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:17 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:17 MarkDuplicates Marking 2 records as duplicates. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:17 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:24:17 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:17 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:17 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:17 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:17 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:17 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:17 MarkDuplicates Duplicate Index cleanup. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:17 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:17 MarkDuplicates Getting Memory Stats. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:17 MarkDuplicates Before output close freeMemory: 758224120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:17 MarkDuplicates Before output close freeMemory: 758224120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:17 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:17 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:17 MarkDuplicates After output close freeMemory: 758364376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:17 MarkDuplicates After output close freeMemory: 758364376; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:17 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:17 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:17 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testSecondEndIsBeforeFirstInCoordinate STANDARD_ERROR INFO 2024-07-02 11:24:17 MarkDuplicates Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11353586458638623364.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11353586458638623364.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11353586458638623364.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11353586458638623364.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11353586458638623364.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11353586458638623364.tmp/output.sam Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:17.516 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:17.516 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:17.516 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:17.516 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:17.516 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:17.516 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:17.516 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:17.516 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:17 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11353586458638623364.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11353586458638623364.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11353586458638623364.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:17 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11353586458638623364.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11353586458638623364.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11353586458638623364.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:17 MarkDuplicates Start of doWork freeMemory: 1027854920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:17 MarkDuplicates Start of doWork freeMemory: 1027854920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:17 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:17 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:17 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:17 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:17 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:17 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:17 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:24:17 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 973323056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 973323056; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:18 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:18 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:18 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:18 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:18 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:18 MarkDuplicates Sorting list of duplicate records. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 488881232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 488881232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:18 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:24:18 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:18 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:18 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:18 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:18 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:18 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:18 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:18 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:18 MarkDuplicates Duplicate Index cleanup. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:18 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:18 MarkDuplicates Getting Memory Stats. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:18 MarkDuplicates Before output close freeMemory: 758224896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:18 MarkDuplicates Before output close freeMemory: 758224896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:18 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:18 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:18 MarkDuplicates After output close freeMemory: 758364912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:18 MarkDuplicates After output close freeMemory: 758364912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:18 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:24:18 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:18 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testSingleMappedFragment STANDARD_ERROR INFO 2024-07-02 11:24:18 MarkDuplicates Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13543963447238328957.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13543963447238328957.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13543963447238328957.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13543963447238328957.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13543963447238328957.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13543963447238328957.tmp/output.sam Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:18.861 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:18.861 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:18.861 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:18.861 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:18.861 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:18.861 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:18.861 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:18.861 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:18 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13543963447238328957.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13543963447238328957.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13543963447238328957.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:18 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13543963447238328957.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13543963447238328957.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13543963447238328957.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:18 MarkDuplicates Start of doWork freeMemory: 1027854952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:18 MarkDuplicates Start of doWork freeMemory: 1027854952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:18 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:18 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:18 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:18 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:18 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:18 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:18 MarkDuplicates Read 1 records. 0 pairs never matched. INFO 2024-07-02 11:24:18 MarkDuplicates Read 1 records. 0 pairs never matched. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 973322784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 973322784; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:19 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:19 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:19 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:19 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:19 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:19 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:19 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 488881560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 488881560; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:19 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:24:19 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:19 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:19 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:19 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:19 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:19 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:19 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:19 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:19 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:19 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:19 MarkDuplicates Getting Memory Stats. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:19 MarkDuplicates Before output close freeMemory: 758224760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:19 MarkDuplicates Before output close freeMemory: 758224760; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:19 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:19 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:19 MarkDuplicates After output close freeMemory: 758126224; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:19 MarkDuplicates After output close freeMemory: 758126224; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:19 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:24:19 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:19 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testSingleMappedFragmentAndSingleMappedPair STANDARD_ERROR INFO 2024-07-02 11:24:19 MarkDuplicates Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.8991326644188086097.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8991326644188086097.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8991326644188086097.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.8991326644188086097.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8991326644188086097.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8991326644188086097.tmp/output.sam Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:19.852 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:19.852 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:19.852 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:19.852 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:19.852 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:19.852 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:19.852 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:19.852 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:19 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8991326644188086097.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8991326644188086097.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8991326644188086097.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:19 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8991326644188086097.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8991326644188086097.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8991326644188086097.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:19 MarkDuplicates Start of doWork freeMemory: 1027614784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:19 MarkDuplicates Start of doWork freeMemory: 1027614784; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:19 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:19 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:19 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:19 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:19 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:19 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:19 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2024-07-02 11:24:19 MarkDuplicates Read 3 records. 0 pairs never matched. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 973321568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 973321568; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:20 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:20 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:20 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:20 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:20 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:20 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 488879832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 488879832; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:20 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:24:20 MarkDuplicates Marking 1 records as duplicates. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:20 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:20 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:20 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:20 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:20 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:20 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:20 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:20 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:20 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:20 MarkDuplicates Getting Memory Stats. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:20 MarkDuplicates Before output close freeMemory: 758223552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:20 MarkDuplicates Before output close freeMemory: 758223552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:20 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:20 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:20 MarkDuplicates After output close freeMemory: 758124904; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:20 MarkDuplicates After output close freeMemory: 758124904; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:20 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:20 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:20 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testSingleMappedFragmentAndTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:24:20 MarkDuplicates Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11190277176052770607.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11190277176052770607.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11190277176052770607.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11190277176052770607.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11190277176052770607.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11190277176052770607.tmp/output.sam Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:20.506 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:20.506 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:20.506 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:20.506 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:20.506 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:20.506 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:20.506 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:20.506 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:20 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11190277176052770607.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11190277176052770607.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11190277176052770607.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:20 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11190277176052770607.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11190277176052770607.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11190277176052770607.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:20 MarkDuplicates Start of doWork freeMemory: 1027612672; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:20 MarkDuplicates Start of doWork freeMemory: 1027612672; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:20 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:20 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:20 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:20 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:20 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:20 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:20 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:24:20 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 973318968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 973318968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:20 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:20 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:20 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:20 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:20 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:20 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 488738456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 488738456; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates Marking 3 records as duplicates. INFO 2024-07-02 11:24:21 MarkDuplicates Marking 3 records as duplicates. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:21 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:21 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:21 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:21 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:21 MarkDuplicates Getting Memory Stats. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates Before output close freeMemory: 758221432; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:21 MarkDuplicates Before output close freeMemory: 758221432; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:21 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates After output close freeMemory: 758122784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:21 MarkDuplicates After output close freeMemory: 758122784; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:21 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:21 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testSingleMappedPair STANDARD_ERROR INFO 2024-07-02 11:24:21 MarkDuplicates Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17096721504485929583.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17096721504485929583.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17096721504485929583.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17096721504485929583.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17096721504485929583.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17096721504485929583.tmp/output.sam Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:21.242 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:21.242 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:21.242 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:21.242 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:21.242 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:21.242 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:21.242 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:21.242 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:21 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17096721504485929583.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17096721504485929583.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17096721504485929583.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:21 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17096721504485929583.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17096721504485929583.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17096721504485929583.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates Start of doWork freeMemory: 1027850936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:21 MarkDuplicates Start of doWork freeMemory: 1027850936; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:21 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:21 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:21 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:21 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:24:21 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 973320176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 973320176; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:21 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:21 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:21 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:21 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 488878952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 488878952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:24:21 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:21 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:21 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:21 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:21 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:21 MarkDuplicates Getting Memory Stats. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates Before output close freeMemory: 758222672; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:21 MarkDuplicates Before output close freeMemory: 758222672; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:21 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates After output close freeMemory: 758362360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:21 MarkDuplicates After output close freeMemory: 758362360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:21 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:21 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:21 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testSingleUnmappedFragment STANDARD_ERROR INFO 2024-07-02 11:24:21 MarkDuplicates Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15097841466237896135.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15097841466237896135.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15097841466237896135.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15097841466237896135.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15097841466237896135.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15097841466237896135.tmp/output.sam Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:21.953 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:21.953 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:21.953 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:21.953 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:21.953 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:21.953 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:21.953 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:21.953 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:21 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15097841466237896135.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15097841466237896135.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15097841466237896135.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:21 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15097841466237896135.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15097841466237896135.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15097841466237896135.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:22 MarkDuplicates Start of doWork freeMemory: 1027852744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:22 MarkDuplicates Start of doWork freeMemory: 1027852744; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:22 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:22 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:22 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:22 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:22 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2024-07-02 11:24:22 MarkDuplicates Read 0 records. 0 pairs never matched. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 973082816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 973082816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:22 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:22 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:22 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:22 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:22 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:22 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 488879464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 488879464; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:22 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:24:22 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:22 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:22 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:22 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:22 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:22 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:22 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:22 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:22 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:22 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:22 MarkDuplicates Getting Memory Stats. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:22 MarkDuplicates Before output close freeMemory: 758223504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:22 MarkDuplicates Before output close freeMemory: 758223504; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:22 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:22 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:22 MarkDuplicates After output close freeMemory: 758124536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:22 MarkDuplicates After output close freeMemory: 758124536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:22 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:22 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:22 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testSingleUnmappedPair STANDARD_ERROR INFO 2024-07-02 11:24:22 MarkDuplicates Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16921806343384950418.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16921806343384950418.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16921806343384950418.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16921806343384950418.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16921806343384950418.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16921806343384950418.tmp/output.sam Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:22.678 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:22.678 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:22.678 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:22.678 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:22.678 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:22.678 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:22.678 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:22.678 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:22 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16921806343384950418.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16921806343384950418.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16921806343384950418.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:22 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16921806343384950418.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16921806343384950418.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16921806343384950418.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:22 MarkDuplicates Start of doWork freeMemory: 1027846272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:22 MarkDuplicates Start of doWork freeMemory: 1027846272; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:22 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:22 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:22 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:22 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:22 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2024-07-02 11:24:22 MarkDuplicates Read 0 records. 0 pairs never matched. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 973320336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 973320336; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:23 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:23 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:23 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 488878424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 488878424; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:24:23 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:23 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:23 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:23 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:23 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:23 MarkDuplicates Getting Memory Stats. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates Before output close freeMemory: 758222464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:23 MarkDuplicates Before output close freeMemory: 758222464; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:23 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates After output close freeMemory: 758362328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:23 MarkDuplicates After output close freeMemory: 758362328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:23 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:23 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testStackOverFlowPairSetSwap STANDARD_ERROR INFO 2024-07-02 11:24:23 MarkDuplicates Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9690718957673399307.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9690718957673399307.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9690718957673399307.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9690718957673399307.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9690718957673399307.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9690718957673399307.tmp/output.sam Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:23.403 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:23.403 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:23.403 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:23.403 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:23.404 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:23.404 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:23.404 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:23.404 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:23 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9690718957673399307.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9690718957673399307.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9690718957673399307.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:23 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9690718957673399307.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9690718957673399307.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9690718957673399307.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates Start of doWork freeMemory: 1027742040; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:23 MarkDuplicates Start of doWork freeMemory: 1027742040; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:23 MarkDuplicates Reading input file and constructing read end information. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:23 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:23 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 972942976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 972942976; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:23 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:23 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:23 MarkDuplicates Sorting list of duplicate records. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 488739824; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 488739824; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:23 MarkDuplicates Marking 2 records as duplicates. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:24:23 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:23 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:23 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:23 MarkDuplicates Duplicate Index cleanup. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:23 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:23 MarkDuplicates Getting Memory Stats. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:24 MarkDuplicates Before output close freeMemory: 758054976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:24 MarkDuplicates Before output close freeMemory: 758054976; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:24 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:24 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:24 MarkDuplicates After output close freeMemory: 758223728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:24 MarkDuplicates After output close freeMemory: 758223728; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:24 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:24 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:24 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:24:24 MarkDuplicates Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4031288906938577751.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4031288906938577751.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4031288906938577751.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4031288906938577751.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4031288906938577751.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4031288906938577751.tmp/output.sam Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:24.190 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:24.190 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:24.190 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:24.190 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:24.190 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:24.190 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:24.190 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:24.190 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:24 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4031288906938577751.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4031288906938577751.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4031288906938577751.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:24 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4031288906938577751.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4031288906938577751.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4031288906938577751.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:24 MarkDuplicates Start of doWork freeMemory: 1027837328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:24 MarkDuplicates Start of doWork freeMemory: 1027837328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:24 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:24 MarkDuplicates Reading input file and constructing read end information. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:24 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:24 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:24 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:24 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:24 MarkDuplicates Read 18 records. 0 pairs never matched. INFO 2024-07-02 11:24:24 MarkDuplicates Read 18 records. 0 pairs never matched. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 973304808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 973304808; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:24 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:24 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:24 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:24 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:24 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:24 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:24 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:24 MarkDuplicates Sorting list of duplicate records. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 488865096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 488865096; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:24 MarkDuplicates Marking 12 records as duplicates. INFO 2024-07-02 11:24:24 MarkDuplicates Marking 12 records as duplicates. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:24 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:24 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:24 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:24 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:24 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:24 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:24 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:24 MarkDuplicates Duplicate Index cleanup. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:24 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:24 MarkDuplicates Getting Memory Stats. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:24 MarkDuplicates Before output close freeMemory: 758208816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:24 MarkDuplicates Before output close freeMemory: 758208816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:24 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:24 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:24 MarkDuplicates After output close freeMemory: 758349000; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:24 MarkDuplicates After output close freeMemory: 758349000; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:24 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:24 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:24 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:24:24 MarkDuplicates Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16660504239066375733.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16660504239066375733.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16660504239066375733.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16660504239066375733.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16660504239066375733.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16660504239066375733.tmp/output.sam Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:24.944 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:24.944 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:24.944 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:24.944 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:24.945 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:24.945 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:24.945 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:24.945 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:24 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16660504239066375733.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16660504239066375733.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16660504239066375733.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:24 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16660504239066375733.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16660504239066375733.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16660504239066375733.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:25 MarkDuplicates Start of doWork freeMemory: 1027846272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:25 MarkDuplicates Start of doWork freeMemory: 1027846272; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:25 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:25 MarkDuplicates Reading input file and constructing read end information. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:25 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:25 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:25 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:25 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:25 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:24:25 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 973313880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 973313880; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:25 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:25 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:25 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:25 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:25 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:25 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:25 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:25 MarkDuplicates Sorting list of duplicate records. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 488872584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 488872584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:25 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:24:25 MarkDuplicates Marking 4 records as duplicates. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:25 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:25 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:25 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:25 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:25 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:25 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:25 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:25 MarkDuplicates Duplicate Index cleanup. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:25 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:25 MarkDuplicates Getting Memory Stats. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:25 MarkDuplicates Before output close freeMemory: 758216304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:25 MarkDuplicates Before output close freeMemory: 758216304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:25 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:25 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:25 MarkDuplicates After output close freeMemory: 758356416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:25 MarkDuplicates After output close freeMemory: 758356416; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:25 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:25 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:25 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testThreeMappedPairsWithMatchingSecondMate STANDARD_ERROR INFO 2024-07-02 11:24:25 MarkDuplicates Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4035158569619990218.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4035158569619990218.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4035158569619990218.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4035158569619990218.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4035158569619990218.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4035158569619990218.tmp/output.sam Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:25.696 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:25.696 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:25.696 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:25.696 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:25.696 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:25.696 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:25.696 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:25.696 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:25 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4035158569619990218.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4035158569619990218.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4035158569619990218.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:25 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4035158569619990218.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4035158569619990218.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4035158569619990218.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:25 MarkDuplicates Start of doWork freeMemory: 1027839992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:25 MarkDuplicates Start of doWork freeMemory: 1027839992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:25 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:25 MarkDuplicates Reading input file and constructing read end information. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:25 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:25 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:25 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:25 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:25 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:24:25 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 973312416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 973312416; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:26 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:26 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:26 MarkDuplicates Sorting list of duplicate records. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 488871544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 488871544; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:26 MarkDuplicates Marking 2 records as duplicates. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:26 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:26 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:26 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:26 MarkDuplicates Duplicate Index cleanup. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:26 MarkDuplicates Getting Memory Stats. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates Before output close freeMemory: 758215192; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:26 MarkDuplicates Before output close freeMemory: 758215192; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:26 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates After output close freeMemory: 758354952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:26 MarkDuplicates After output close freeMemory: 758354952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:26 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:26 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:24:26 MarkDuplicates Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16637576661080769497.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16637576661080769497.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16637576661080769497.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16637576661080769497.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16637576661080769497.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16637576661080769497.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:26.428 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:26.428 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:26.428 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:26.428 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:26.428 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:26.428 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:26.428 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:26.428 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:26 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16637576661080769497.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16637576661080769497.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16637576661080769497.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:26 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16637576661080769497.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16637576661080769497.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16637576661080769497.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates Start of doWork freeMemory: 1027840704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:26 MarkDuplicates Start of doWork freeMemory: 1027840704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:26 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:26 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates Read 12 records. 0 pairs never matched. INFO 2024-07-02 11:24:26 MarkDuplicates Read 12 records. 0 pairs never matched. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 973068848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 973068848; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:26 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:26 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:26 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 488866896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 488866896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:24:26 MarkDuplicates Marking 8 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:26 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:26 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:26 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:26 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:26 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:26 MarkDuplicates Getting Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:27 MarkDuplicates Before output close freeMemory: 758210616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:27 MarkDuplicates Before output close freeMemory: 758210616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:27 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:27 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:27 MarkDuplicates After output close freeMemory: 758111968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:27 MarkDuplicates After output close freeMemory: 758111968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:27 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:27 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:27 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoGroupsOnDifferentChromosomesOfTwoFragments STANDARD_ERROR INFO 2024-07-02 11:24:27 MarkDuplicates Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10229308611119344400.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10229308611119344400.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10229308611119344400.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10229308611119344400.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10229308611119344400.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10229308611119344400.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:27.206 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:27.206 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:27.206 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:27.206 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:27.206 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:27.206 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:27.207 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:27.207 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:27 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10229308611119344400.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10229308611119344400.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10229308611119344400.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:27 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10229308611119344400.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10229308611119344400.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10229308611119344400.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:27 MarkDuplicates Start of doWork freeMemory: 1027845448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:27 MarkDuplicates Start of doWork freeMemory: 1027845448; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:27 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:27 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:27 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:27 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:27 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:27 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:27 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:27 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 973313616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 973313616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:27 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:27 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:27 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:27 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 488872056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 488872056; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:27 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:27 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:27 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:27 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:27 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:27 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:27 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:27 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:27 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:27 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:27 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:27 MarkDuplicates Getting Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:27 MarkDuplicates Before output close freeMemory: 758215888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:27 MarkDuplicates Before output close freeMemory: 758215888; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:27 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:27 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:27 MarkDuplicates After output close freeMemory: 758117128; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:27 MarkDuplicates After output close freeMemory: 758117128; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:27 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:27 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:27 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:24:27 MarkDuplicates Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2128396504632772970.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2128396504632772970.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2128396504632772970.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2128396504632772970.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2128396504632772970.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2128396504632772970.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:27.890 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:27.890 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:27.891 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:27.891 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:27.891 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:27.891 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:27.891 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:27.891 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:27 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2128396504632772970.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2128396504632772970.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2128396504632772970.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:27 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2128396504632772970.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2128396504632772970.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2128396504632772970.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:27 MarkDuplicates Start of doWork freeMemory: 1027842016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:27 MarkDuplicates Start of doWork freeMemory: 1027842016; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:27 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:27 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:27 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:27 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:27 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:27 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:27 MarkDuplicates Read 8 records. 0 pairs never matched. INFO 2024-07-02 11:24:27 MarkDuplicates Read 8 records. 0 pairs never matched. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 973309240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 973309240; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:28 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:28 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:28 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:28 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:28 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:28 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 488868208; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 488868208; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:28 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:24:28 MarkDuplicates Marking 4 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:28 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:28 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:28 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:28 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:28 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:28 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:28 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:28 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:28 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:28 MarkDuplicates Getting Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:28 MarkDuplicates Before output close freeMemory: 758211928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:28 MarkDuplicates Before output close freeMemory: 758211928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:28 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:28 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:28 MarkDuplicates After output close freeMemory: 758351616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:28 MarkDuplicates After output close freeMemory: 758351616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:28 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:28 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:28 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoMappedFragments STANDARD_ERROR INFO 2024-07-02 11:24:28 MarkDuplicates Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3444691490914265298.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3444691490914265298.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3444691490914265298.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3444691490914265298.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3444691490914265298.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3444691490914265298.tmp/output.sam Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:28.621 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:28.621 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:28.621 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:28.621 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:28.621 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:28.621 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:28.621 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:28.621 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:28 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3444691490914265298.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3444691490914265298.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3444691490914265298.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:28 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3444691490914265298.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3444691490914265298.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3444691490914265298.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:28 MarkDuplicates Start of doWork freeMemory: 1027845256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:28 MarkDuplicates Start of doWork freeMemory: 1027845256; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:28 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:28 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:28 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:28 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:28 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:28 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:28 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:24:28 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 973313600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 973313600; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:29 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:29 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:29 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 488871864; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 488871864; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:24:29 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:29 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:29 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:29 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:29 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:29 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Before output close freeMemory: 758215696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:29 MarkDuplicates Before output close freeMemory: 758215696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:29 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates After output close freeMemory: 758355768; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:29 MarkDuplicates After output close freeMemory: 758355768; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoMappedPairWithSamePosition STANDARD_ERROR INFO 2024-07-02 11:24:29 MarkDuplicates Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16528579168046255756.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16528579168046255756.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16528579168046255756.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16528579168046255756.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16528579168046255756.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16528579168046255756.tmp/output.sam Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:29.314 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:29.314 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:29.314 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:29.314 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:29.314 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:29.314 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:29.315 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:29.315 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:29 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16528579168046255756.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16528579168046255756.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16528579168046255756.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:29 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16528579168046255756.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16528579168046255756.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16528579168046255756.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Start of doWork freeMemory: 1027843120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:29 MarkDuplicates Start of doWork freeMemory: 1027843120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:29 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:29 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:29 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:29 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:29 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 973310992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 973310992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:29 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:29 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:29 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 488869432; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 488869432; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:29 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:29 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:29 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:29 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:29 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:29 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Before output close freeMemory: 758213080; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:29 MarkDuplicates Before output close freeMemory: 758213080; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:29 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates After output close freeMemory: 758353336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:29 MarkDuplicates After output close freeMemory: 758353336; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:29 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoMappedPairWithSamePositionDifferentStrands STANDARD_ERROR INFO 2024-07-02 11:24:29 MarkDuplicates Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2541403663544631403.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2541403663544631403.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2541403663544631403.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2541403663544631403.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2541403663544631403.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2541403663544631403.tmp/output.sam Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:29.981 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:29.981 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:29.981 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:29.981 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:29.981 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:29.981 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:29.982 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:29.982 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:29 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2541403663544631403.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2541403663544631403.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2541403663544631403.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:29 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2541403663544631403.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2541403663544631403.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2541403663544631403.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:30 MarkDuplicates Start of doWork freeMemory: 1027842600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:30 MarkDuplicates Start of doWork freeMemory: 1027842600; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:30 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:30 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:30 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:30 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:30 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:30 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 973310472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 973310472; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:30 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:30 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:30 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:30 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:30 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:30 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 488902616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 488902616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:30 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:30 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:30 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:30 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:30 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:30 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:30 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:30 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:30 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:30 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:30 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:30 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:30 MarkDuplicates Before output close freeMemory: 758246336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:30 MarkDuplicates Before output close freeMemory: 758246336; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:30 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:30 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:30 MarkDuplicates After output close freeMemory: 758386520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:30 MarkDuplicates After output close freeMemory: 758386520; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:30 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:30 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:30 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoMappedPairWithSamePositionDifferentStrands2 STANDARD_ERROR INFO 2024-07-02 11:24:30 MarkDuplicates Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4906790881726187124.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4906790881726187124.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4906790881726187124.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4906790881726187124.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4906790881726187124.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4906790881726187124.tmp/output.sam Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:30.663 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:30.663 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:30.663 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:30.663 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:30.663 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:30.663 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:30.663 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:30.663 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:30 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4906790881726187124.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4906790881726187124.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4906790881726187124.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:30 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4906790881726187124.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4906790881726187124.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4906790881726187124.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:30 MarkDuplicates Start of doWork freeMemory: 1027875624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:30 MarkDuplicates Start of doWork freeMemory: 1027875624; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:30 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:30 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:30 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:30 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:30 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:30 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 973343496; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 973343496; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:31 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:31 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:31 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 488901936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 488901936; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:31 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:31 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:31 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:31 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:31 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:31 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates Before output close freeMemory: 758245656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:31 MarkDuplicates Before output close freeMemory: 758245656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:31 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates After output close freeMemory: 758385768; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:31 MarkDuplicates After output close freeMemory: 758385768; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:31 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:31 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:24:31 MarkDuplicates Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9185750550927255433.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9185750550927255433.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9185750550927255433.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.9185750550927255433.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9185750550927255433.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.9185750550927255433.tmp/output.sam Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:31.350 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:31.350 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:31.350 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:31.350 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:31.350 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:31.350 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:31.350 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:31.350 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:31 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9185750550927255433.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9185750550927255433.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9185750550927255433.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:31 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.9185750550927255433.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.9185750550927255433.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.9185750550927255433.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates Start of doWork freeMemory: 1027874704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:31 MarkDuplicates Start of doWork freeMemory: 1027874704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:31 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:31 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:31 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:31 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:31 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 973342576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 973342576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:31 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:31 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:31 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 918817176; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2024-07-02 11:24:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 918817176; totalMemory: 1503657984; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:31 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:31 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:31 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:31 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:31 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:31 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates Before output close freeMemory: 758244736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:31 MarkDuplicates Before output close freeMemory: 758244736; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:31 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:31 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:32 MarkDuplicates After output close freeMemory: 758384920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:32 MarkDuplicates After output close freeMemory: 758384920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:32 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoMappedPairsAndMappedSecondaryFragment STANDARD_ERROR INFO 2024-07-02 11:24:32 MarkDuplicates Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6079671273958533967.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6079671273958533967.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6079671273958533967.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6079671273958533967.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6079671273958533967.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6079671273958533967.tmp/output.sam Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:32.061 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:32.061 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:32.061 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:32.061 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:32.061 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:32.061 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:32.062 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:32.062 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:32 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6079671273958533967.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6079671273958533967.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6079671273958533967.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:32 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6079671273958533967.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6079671273958533967.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6079671273958533967.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:32 MarkDuplicates Start of doWork freeMemory: 1027873344; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:32 MarkDuplicates Start of doWork freeMemory: 1027873344; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:32 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:32 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:32 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:32 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:32 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:32 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:32 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:24:32 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 973341216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 973341216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:32 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:32 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:32 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:32 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:32 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:32 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 488899656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 488899656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:32 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:32 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:32 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:32 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:32 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:32 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:32 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:32 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:32 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:32 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:32 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:32 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:32 MarkDuplicates Before output close freeMemory: 758243488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:32 MarkDuplicates Before output close freeMemory: 758243488; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:32 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:32 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:32 MarkDuplicates After output close freeMemory: 758383064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:32 MarkDuplicates After output close freeMemory: 758383064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:32 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoMappedPairsAndTerminalUnmappedFragment STANDARD_ERROR INFO 2024-07-02 11:24:32 MarkDuplicates Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.338676962446242102.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.338676962446242102.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.338676962446242102.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.338676962446242102.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.338676962446242102.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.338676962446242102.tmp/output.sam Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:32.777 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:32.777 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:32.777 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:32.777 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:32.777 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:32.777 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:32.777 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:32.777 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:32 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.338676962446242102.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.338676962446242102.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.338676962446242102.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:32 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.338676962446242102.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.338676962446242102.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.338676962446242102.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:32 MarkDuplicates Start of doWork freeMemory: 1027872760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:32 MarkDuplicates Start of doWork freeMemory: 1027872760; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:32 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:32 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:32 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:32 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:32 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:32 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:32 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:32 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 973340040; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 973340040; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:33 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:33 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:33 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:33 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 488899080; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 488899080; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:33 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:33 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:33 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:33 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:33 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:33 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:33 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:33 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:33 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:33 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:33 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:33 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:33 MarkDuplicates Before output close freeMemory: 758243120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:33 MarkDuplicates Before output close freeMemory: 758243120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:33 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:33 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:33 MarkDuplicates After output close freeMemory: 758144152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:33 MarkDuplicates After output close freeMemory: 758144152; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:33 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:33 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:33 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoMappedPairsAndTerminalUnmappedPair STANDARD_ERROR INFO 2024-07-02 11:24:33 MarkDuplicates Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5782681124646402428.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5782681124646402428.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5782681124646402428.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5782681124646402428.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5782681124646402428.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5782681124646402428.tmp/output.sam Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:33.491 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:33.491 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:33.491 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:33.491 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:33.492 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:33.492 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:33.492 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:33.492 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:33 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5782681124646402428.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5782681124646402428.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5782681124646402428.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:33 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5782681124646402428.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5782681124646402428.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5782681124646402428.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:33 MarkDuplicates Start of doWork freeMemory: 1027869328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:33 MarkDuplicates Start of doWork freeMemory: 1027869328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:33 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:33 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:33 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:33 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:33 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:33 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:33 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:33 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 973339456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 973339456; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:33 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:33 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:33 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:33 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 488897896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 488897896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:34 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:34 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:34 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:34 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:34 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:34 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:34 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:34 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:34 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:34 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:34 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:34 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:34 MarkDuplicates Before output close freeMemory: 758241304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:34 MarkDuplicates Before output close freeMemory: 758241304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:34 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:34 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:34 MarkDuplicates After output close freeMemory: 758142720; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:34 MarkDuplicates After output close freeMemory: 758142720; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:34 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoMappedPairsMatesSoftClipped STANDARD_ERROR INFO 2024-07-02 11:24:34 MarkDuplicates Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.8161794120185708464.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8161794120185708464.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8161794120185708464.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.8161794120185708464.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8161794120185708464.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8161794120185708464.tmp/output.sam Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:34.400 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:34.400 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:34.400 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:34.400 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:34.401 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:34.401 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:34.401 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:34.401 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:34 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8161794120185708464.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8161794120185708464.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8161794120185708464.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:34 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8161794120185708464.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8161794120185708464.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8161794120185708464.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:34 MarkDuplicates Start of doWork freeMemory: 1027871752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:34 MarkDuplicates Start of doWork freeMemory: 1027871752; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:34 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:34 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:34 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:34 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:34 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:34 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:34 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:34 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:34 MarkDuplicates After buildSortedReadEndLists freeMemory: 973339624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:34 MarkDuplicates After buildSortedReadEndLists freeMemory: 973339624; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:34 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:34 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:34 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:34 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:34 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:34 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:34 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 488898064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 488898064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:34 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:24:34 MarkDuplicates Marking 0 records as duplicates. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:34 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:34 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:34 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:34 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:34 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:34 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:34 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:34 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:34 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:34 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:35 MarkDuplicates Before output close freeMemory: 758241712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:35 MarkDuplicates Before output close freeMemory: 758241712; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:35 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:35 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:35 MarkDuplicates After output close freeMemory: 758143408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:35 MarkDuplicates After output close freeMemory: 758143408; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:35 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:35 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:35 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoMappedPairsWithOppositeOrientations STANDARD_ERROR INFO 2024-07-02 11:24:35 MarkDuplicates Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6640677209530271101.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6640677209530271101.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6640677209530271101.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6640677209530271101.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6640677209530271101.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6640677209530271101.tmp/output.sam Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:35.225 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:35.225 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:35.225 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:35.225 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:35.226 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:35.226 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:35.226 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:35.226 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:35 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6640677209530271101.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6640677209530271101.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6640677209530271101.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:35 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6640677209530271101.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6640677209530271101.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6640677209530271101.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:35 MarkDuplicates Start of doWork freeMemory: 1027870488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:35 MarkDuplicates Start of doWork freeMemory: 1027870488; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:35 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:35 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:35 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:35 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:35 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:35 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:35 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:35 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 973338752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 973338752; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:35 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:35 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:35 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:35 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:35 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:35 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 488897192; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 488897192; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:35 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:35 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:35 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:35 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:35 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:35 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:35 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:35 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:35 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:35 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:35 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:35 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:36 MarkDuplicates Before output close freeMemory: 758240840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:36 MarkDuplicates Before output close freeMemory: 758240840; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:36 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:36 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:36 MarkDuplicates After output close freeMemory: 758142536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:36 MarkDuplicates After output close freeMemory: 758142536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:36 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:24:36 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:36 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoMappedPairsWithOppositeOrientationsNumberTwo STANDARD_ERROR INFO 2024-07-02 11:24:36 MarkDuplicates Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16763267092377034508.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16763267092377034508.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16763267092377034508.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.16763267092377034508.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16763267092377034508.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.16763267092377034508.tmp/output.sam Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:36.236 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:36.236 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:36.236 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:36.236 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:36.236 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:36.236 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:36.236 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:36.236 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:36 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16763267092377034508.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16763267092377034508.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16763267092377034508.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:36 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.16763267092377034508.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.16763267092377034508.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.16763267092377034508.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:36 MarkDuplicates Start of doWork freeMemory: 1027870128; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:36 MarkDuplicates Start of doWork freeMemory: 1027870128; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:36 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:36 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:36 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:36 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:36 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:36 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:36 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:36 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 973338000; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 973338000; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:36 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:36 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:36 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:36 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:36 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:36 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 488896440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 488896440; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:36 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:36 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:36 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:36 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:36 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:36 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:36 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:36 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:36 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:36 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:36 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:36 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:37 MarkDuplicates Before output close freeMemory: 758240088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:37 MarkDuplicates Before output close freeMemory: 758240088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:37 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:37 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:37 MarkDuplicates After output close freeMemory: 758380120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:37 MarkDuplicates After output close freeMemory: 758380120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:24:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:37 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoMappedPairsWithSoftClipping STANDARD_ERROR INFO 2024-07-02 11:24:37 MarkDuplicates Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12668912572949342915.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12668912572949342915.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12668912572949342915.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12668912572949342915.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12668912572949342915.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12668912572949342915.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:37.265 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:37.265 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:37.265 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:37.265 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:37.266 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:37.266 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:37.266 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:37.266 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:37 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12668912572949342915.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12668912572949342915.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12668912572949342915.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:37 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12668912572949342915.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12668912572949342915.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12668912572949342915.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:37 MarkDuplicates Start of doWork freeMemory: 1027868952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:37 MarkDuplicates Start of doWork freeMemory: 1027868952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:37 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:37 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:37 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:37 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:37 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:37 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:37 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:37 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 973337224; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 973337224; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:37 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:37 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:37 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:37 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 488895664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 488895664; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:37 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:37 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:37 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:37 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:37 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:37 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:37 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:37 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:37 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:37 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:37 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:37 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:37 MarkDuplicates Before output close freeMemory: 758239312; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:37 MarkDuplicates Before output close freeMemory: 758239312; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:37 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:37 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:37 MarkDuplicates After output close freeMemory: 758140736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:37 MarkDuplicates After output close freeMemory: 758140736; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:37 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoMappedPairsWithSoftClippingBoth STANDARD_ERROR INFO 2024-07-02 11:24:37 MarkDuplicates Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2545370237472741292.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2545370237472741292.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2545370237472741292.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2545370237472741292.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2545370237472741292.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2545370237472741292.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:37.853 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:37.853 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:37.853 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:37.853 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:37.853 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:37.853 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:37.853 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:37.853 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:37 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2545370237472741292.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2545370237472741292.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2545370237472741292.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:37 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2545370237472741292.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2545370237472741292.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2545370237472741292.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:37 MarkDuplicates Start of doWork freeMemory: 1027868632; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:37 MarkDuplicates Start of doWork freeMemory: 1027868632; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:37 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:37 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:37 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:37 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:37 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:37 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:37 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:37 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 973336504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 973336504; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:38 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:38 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:38 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:38 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:38 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:38 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 488894944; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 488894944; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:38 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:38 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:38 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:38 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:38 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:38 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:38 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:38 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:38 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:38 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:38 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:38 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:38 MarkDuplicates Before output close freeMemory: 758238592; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:38 MarkDuplicates Before output close freeMemory: 758238592; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:38 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:38 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:38 MarkDuplicates After output close freeMemory: 758378352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:38 MarkDuplicates After output close freeMemory: 758378352; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:38 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:38 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:38 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar STANDARD_ERROR INFO 2024-07-02 11:24:38 MarkDuplicates Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.8931268553528167047.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8931268553528167047.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8931268553528167047.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.8931268553528167047.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8931268553528167047.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8931268553528167047.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:38.532 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:38.532 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:38.532 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:38.532 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:38.532 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:38.532 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:38.532 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:38.532 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:38 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8931268553528167047.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8931268553528167047.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8931268553528167047.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:38 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8931268553528167047.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8931268553528167047.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8931268553528167047.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:38 MarkDuplicates Start of doWork freeMemory: 1027869064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:38 MarkDuplicates Start of doWork freeMemory: 1027869064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:38 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:38 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:38 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:38 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:38 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:38 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:38 MarkDuplicates Read 2 records. 2 pairs never matched. INFO 2024-07-02 11:24:38 MarkDuplicates Read 2 records. 2 pairs never matched. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 973337288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 973337288; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:38 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:38 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:38 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:38 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:38 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:38 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 488895552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 488895552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:24:39 MarkDuplicates Marking 0 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:39 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:39 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:39 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:39 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:39 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates Before output close freeMemory: 758239248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:39 MarkDuplicates Before output close freeMemory: 758239248; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:39 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates After output close freeMemory: 758140624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:39 MarkDuplicates After output close freeMemory: 758140624; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoMappedPairsWithSupplementaryReads[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:24:39 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10991296466265609753.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10991296466265609753.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10991296466265609753.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10991296466265609753.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10991296466265609753.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10991296466265609753.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:39.296 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:39.296 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:39.296 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:39.296 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:39.296 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:39.296 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:39.296 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:39.296 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:39 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10991296466265609753.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10991296466265609753.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10991296466265609753.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:39 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10991296466265609753.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10991296466265609753.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10991296466265609753.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates Start of doWork freeMemory: 1027865928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:39 MarkDuplicates Start of doWork freeMemory: 1027865928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:39 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:39 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:24:39 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 973333520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 973333520; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:39 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:39 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:39 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 488751968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 488751968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:39 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:24:39 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:39 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:39 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:39 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:39 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates Before output close freeMemory: 758235648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:39 MarkDuplicates Before output close freeMemory: 758235648; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:39 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:39 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:40 MarkDuplicates After output close freeMemory: 758375856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:40 MarkDuplicates After output close freeMemory: 758375856; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:40 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:40 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:40 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoMappedPairsWithSupplementaryReads[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:24:40 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3071191527215493469.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3071191527215493469.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3071191527215493469.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3071191527215493469.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3071191527215493469.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3071191527215493469.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:40.060 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:40.060 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:40.060 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:40.060 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:40.060 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:40.060 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:40.060 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:40.060 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:40 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3071191527215493469.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3071191527215493469.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3071191527215493469.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:40 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3071191527215493469.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3071191527215493469.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3071191527215493469.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:40 MarkDuplicates Start of doWork freeMemory: 1027865224; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:40 MarkDuplicates Start of doWork freeMemory: 1027865224; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:40 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:40 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:40 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:40 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:40 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:24:40 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 973333032; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 973333032; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:40 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:40 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:40 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:40 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:40 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 918807480; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2024-07-02 11:24:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 918807480; totalMemory: 1503657984; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:40 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:40 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:40 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:24:40 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:40 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:40 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:40 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:40 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:40 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:40 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:40 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:40 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:40 MarkDuplicates Before output close freeMemory: 764526400; totalMemory: 1080033280; maxMemory: 2147483648 INFO 2024-07-02 11:24:40 MarkDuplicates Before output close freeMemory: 764526400; totalMemory: 1080033280; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:40 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:40 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:40 MarkDuplicates After output close freeMemory: 758375152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:40 MarkDuplicates After output close freeMemory: 758375152; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:40 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:40 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:40 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoMappedPairsWithSupplementaryReads[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:24:40 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17051414218569123160.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17051414218569123160.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17051414218569123160.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17051414218569123160.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17051414218569123160.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17051414218569123160.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:40.815 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:40.815 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:40.816 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:40.816 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:40.816 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:40.816 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:40.816 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:40.816 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:40 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17051414218569123160.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17051414218569123160.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17051414218569123160.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:40 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17051414218569123160.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17051414218569123160.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17051414218569123160.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:40 MarkDuplicates Start of doWork freeMemory: 1027864576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:40 MarkDuplicates Start of doWork freeMemory: 1027864576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:40 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:40 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:40 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:40 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:40 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:24:40 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 973332384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 973332384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:41 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:41 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:41 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 488890672; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 488890672; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:41 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:24:41 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:41 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:41 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:41 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:41 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates Before output close freeMemory: 758234296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:41 MarkDuplicates Before output close freeMemory: 758234296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:41 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates After output close freeMemory: 758374504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:41 MarkDuplicates After output close freeMemory: 758374504; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:41 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:41 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoMappedPairsWithSupplementaryReads[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:24:41 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3626019705505564507.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3626019705505564507.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3626019705505564507.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3626019705505564507.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3626019705505564507.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3626019705505564507.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:41.496 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:41.496 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:41.496 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:41.496 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:41.496 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:41.496 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:41.496 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:41.496 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:41 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3626019705505564507.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3626019705505564507.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3626019705505564507.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:41 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3626019705505564507.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3626019705505564507.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3626019705505564507.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates Start of doWork freeMemory: 1027862808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:41 MarkDuplicates Start of doWork freeMemory: 1027862808; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:41 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:41 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:24:41 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 973330616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 973330616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:41 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:41 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:41 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 488888904; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 488888904; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:41 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:24:41 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:41 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:41 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:41 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:41 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:41 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:42 MarkDuplicates Before output close freeMemory: 758232528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:42 MarkDuplicates Before output close freeMemory: 758232528; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:42 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:42 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:42 MarkDuplicates After output close freeMemory: 758372808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:42 MarkDuplicates After output close freeMemory: 758372808; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:42 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoMappedPairsWithSupplementaryReads[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:24:42 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3547147269906262447.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3547147269906262447.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3547147269906262447.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3547147269906262447.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3547147269906262447.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3547147269906262447.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:42.174 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:42.174 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:42.174 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:42.174 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:42.174 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:42.174 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:42.174 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:42.174 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:42 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3547147269906262447.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3547147269906262447.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3547147269906262447.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:42 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3547147269906262447.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3547147269906262447.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3547147269906262447.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:42 MarkDuplicates Start of doWork freeMemory: 1027862176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:42 MarkDuplicates Start of doWork freeMemory: 1027862176; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:42 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:42 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:42 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:42 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:42 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:24:42 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 973329984; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 973329984; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:42 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:42 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:42 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:42 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:42 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:42 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 488888272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 488888272; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:42 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:42 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:42 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:24:42 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:42 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:42 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:42 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:42 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:42 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:42 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:42 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:42 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:42 MarkDuplicates Before output close freeMemory: 758231896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:42 MarkDuplicates Before output close freeMemory: 758231896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:42 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:42 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:42 MarkDuplicates After output close freeMemory: 758371680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:42 MarkDuplicates After output close freeMemory: 758371680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:42 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoMappedPairsWithSupplementaryReads[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:24:42 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5564384733058296083.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5564384733058296083.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5564384733058296083.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.5564384733058296083.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5564384733058296083.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.5564384733058296083.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:42.865 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:42.865 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:42.865 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:42.865 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:42.866 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:42.866 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:42.866 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:42.866 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:42 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5564384733058296083.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5564384733058296083.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5564384733058296083.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:42 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.5564384733058296083.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.5564384733058296083.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.5564384733058296083.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:42 MarkDuplicates Start of doWork freeMemory: 1027861576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:42 MarkDuplicates Start of doWork freeMemory: 1027861576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:42 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:42 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:42 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:42 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:42 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:24:42 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 973090824; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 973090824; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:43 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:43 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:43 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:43 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:43 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:43 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 488887672; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 488887672; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:43 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:43 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:43 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:24:43 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:43 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:43 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:43 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:43 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:43 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:43 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:43 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:43 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:43 MarkDuplicates Before output close freeMemory: 758231296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:43 MarkDuplicates Before output close freeMemory: 758231296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:43 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:43 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:43 MarkDuplicates After output close freeMemory: 758132744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:43 MarkDuplicates After output close freeMemory: 758132744; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:43 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:43 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:43 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:24:43 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4643734219758227329.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4643734219758227329.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4643734219758227329.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4643734219758227329.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4643734219758227329.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4643734219758227329.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:43.561 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:43.561 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:43.561 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:43.561 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:43.561 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:43.561 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:43.561 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:43.561 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:43 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4643734219758227329.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4643734219758227329.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4643734219758227329.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:43 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4643734219758227329.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4643734219758227329.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4643734219758227329.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:43 MarkDuplicates Start of doWork freeMemory: 1027621712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:43 MarkDuplicates Start of doWork freeMemory: 1027621712; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:43 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:43 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:43 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:43 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:43 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:24:43 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 973328040; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 973328040; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:43 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:43 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:43 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:43 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:43 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:43 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 488886544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 488886544; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:44 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:24:44 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:44 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:44 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:44 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:44 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates Before output close freeMemory: 758230328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:44 MarkDuplicates Before output close freeMemory: 758230328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:44 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates After output close freeMemory: 758131616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:44 MarkDuplicates After output close freeMemory: 758131616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:44 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:44 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:24:44 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13469852384034141979.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13469852384034141979.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13469852384034141979.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.13469852384034141979.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13469852384034141979.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.13469852384034141979.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:44.271 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:44.271 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:44.271 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:44.271 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:44.271 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:44.271 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:44.271 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:44.271 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:44 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13469852384034141979.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13469852384034141979.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13469852384034141979.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:44 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.13469852384034141979.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.13469852384034141979.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.13469852384034141979.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates Start of doWork freeMemory: 1027859792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:44 MarkDuplicates Start of doWork freeMemory: 1027859792; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:44 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:44 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:24:44 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 973327600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 973327600; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:44 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:44 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:44 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 488885888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 488885888; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:44 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:24:44 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:44 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:44 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:44 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:44 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates Before output close freeMemory: 757991520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:44 MarkDuplicates Before output close freeMemory: 757991520; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:44 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates After output close freeMemory: 758130960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:44 MarkDuplicates After output close freeMemory: 758130960; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:44 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:44 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:44 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:24:44 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11192679461190209276.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11192679461190209276.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11192679461190209276.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11192679461190209276.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11192679461190209276.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11192679461190209276.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:44.976 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:44.976 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:44.976 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:44.976 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:44.976 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:44.976 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:44.976 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:44.976 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:44 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11192679461190209276.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11192679461190209276.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11192679461190209276.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:44 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11192679461190209276.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11192679461190209276.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11192679461190209276.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:45 MarkDuplicates Start of doWork freeMemory: 1027859160; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:45 MarkDuplicates Start of doWork freeMemory: 1027859160; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:45 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:45 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:45 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:45 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:45 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:24:45 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 973088416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 973088416; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:45 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:45 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:45 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:45 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:45 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:45 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 660851720; totalMemory: 1245708288; maxMemory: 2147483648 INFO 2024-07-02 11:24:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 660851720; totalMemory: 1245708288; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:45 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:45 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:45 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:24:45 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:45 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:45 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:45 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:45 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:45 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:45 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:45 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:45 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:45 MarkDuplicates Before output close freeMemory: 758229040; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:45 MarkDuplicates Before output close freeMemory: 758229040; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:45 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:45 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:45 MarkDuplicates After output close freeMemory: 758368664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:45 MarkDuplicates After output close freeMemory: 758368664; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:45 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:24:45 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11062123390794132613.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11062123390794132613.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11062123390794132613.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.11062123390794132613.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11062123390794132613.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.11062123390794132613.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:45.730 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:45.730 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:45.731 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:45.731 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:45.731 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:45.731 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:45.731 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:45.731 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:45 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11062123390794132613.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11062123390794132613.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11062123390794132613.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:45 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.11062123390794132613.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.11062123390794132613.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.11062123390794132613.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:45 MarkDuplicates Start of doWork freeMemory: 1027856984; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:45 MarkDuplicates Start of doWork freeMemory: 1027856984; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:45 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:45 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:45 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:45 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:45 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:24:45 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 973324976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 973324976; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:46 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:46 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:46 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 488883480; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 488883480; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:46 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:24:46 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:46 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:46 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:46 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:46 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates Before output close freeMemory: 757988296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:46 MarkDuplicates Before output close freeMemory: 757988296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:46 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates After output close freeMemory: 758128824; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:46 MarkDuplicates After output close freeMemory: 758128824; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:24:46 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15872797807567805068.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15872797807567805068.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15872797807567805068.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.15872797807567805068.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15872797807567805068.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.15872797807567805068.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:46.466 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:46.466 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:46.466 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:46.466 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:46.467 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:46.467 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:46.467 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:46.467 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:46 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15872797807567805068.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15872797807567805068.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15872797807567805068.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:46 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.15872797807567805068.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.15872797807567805068.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.15872797807567805068.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates Start of doWork freeMemory: 1027856392; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:46 MarkDuplicates Start of doWork freeMemory: 1027856392; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:46 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:46 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:24:46 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 973086000; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 973086000; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:46 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:46 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:46 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 488882848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 488882848; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:46 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:24:46 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:46 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:46 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:46 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:46 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:46 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:47 MarkDuplicates Before output close freeMemory: 758226632; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:47 MarkDuplicates Before output close freeMemory: 758226632; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:47 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:47 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:47 MarkDuplicates After output close freeMemory: 758366184; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:47 MarkDuplicates After output close freeMemory: 758366184; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:47 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:47 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:47 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:24:47 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3981322256424059738.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3981322256424059738.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3981322256424059738.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3981322256424059738.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3981322256424059738.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3981322256424059738.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:47.188 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:47.188 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:47.189 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:47.189 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:47.189 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:47.189 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:47.189 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:47.189 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:47 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3981322256424059738.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3981322256424059738.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3981322256424059738.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:47 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3981322256424059738.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3981322256424059738.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3981322256424059738.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:47 MarkDuplicates Start of doWork freeMemory: 1027856136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:47 MarkDuplicates Start of doWork freeMemory: 1027856136; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:47 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:47 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:47 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:47 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:47 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:24:47 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 973085384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 973085384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:47 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:47 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:47 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:47 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:47 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:47 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 488882232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 488882232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:47 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:47 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:47 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:24:47 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:47 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:47 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:47 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:47 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:47 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:47 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:47 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:47 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:47 MarkDuplicates Before output close freeMemory: 758226016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:47 MarkDuplicates Before output close freeMemory: 758226016; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:47 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:47 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:47 MarkDuplicates After output close freeMemory: 758365568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:47 MarkDuplicates After output close freeMemory: 758365568; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:47 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:47 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:47 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoUnmappedFragments STANDARD_ERROR INFO 2024-07-02 11:24:47 MarkDuplicates Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6585299792024385928.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6585299792024385928.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6585299792024385928.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.6585299792024385928.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6585299792024385928.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.6585299792024385928.tmp/output.sam Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:47.902 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:47.902 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:47.902 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:47.902 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:47.902 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:47.902 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:47.902 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:47.902 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:47 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6585299792024385928.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6585299792024385928.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6585299792024385928.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:47 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.6585299792024385928.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.6585299792024385928.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.6585299792024385928.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:47 MarkDuplicates Start of doWork freeMemory: 1027858056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:47 MarkDuplicates Start of doWork freeMemory: 1027858056; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:47 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:47 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:47 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:47 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:48 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2024-07-02 11:24:48 MarkDuplicates Read 0 records. 0 pairs never matched. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 973326688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 973326688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:48 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:48 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:48 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:48 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:48 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:48 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:48 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:48 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 488884776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 488884776; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:48 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:24:48 MarkDuplicates Marking 0 records as duplicates. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:48 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:48 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:48 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:48 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:48 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:48 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:48 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:48 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:48 MarkDuplicates Getting Memory Stats. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:48 MarkDuplicates Before output close freeMemory: 758228816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:48 MarkDuplicates Before output close freeMemory: 758228816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:48 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:48 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:48 MarkDuplicates After output close freeMemory: 758129848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:48 MarkDuplicates After output close freeMemory: 758129848; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:48 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:48 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:48 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]}) STANDARD_ERROR INFO 2024-07-02 11:24:48 MarkDuplicates Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam -OUTPUT /tmp/MarkDuplicates.3396034087551145085.tmp/MarkDuplicates.sam -METRICS_FILE /tmp/MarkDuplicates.3396034087551145085.tmp/MarkDuplicates.duplicate_metrics -ADD_PG_TAG_TO_READS true ********** MarkDuplicates -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam -OUTPUT /tmp/MarkDuplicates.3396034087551145085.tmp/MarkDuplicates.sam -METRICS_FILE /tmp/MarkDuplicates.3396034087551145085.tmp/MarkDuplicates.duplicate_metrics -ADD_PG_TAG_TO_READS true Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:48.593 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:48.593 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:48.593 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:48.593 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:48.593 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:48.593 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:48.593 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:48.593 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:48 GMT+14:00 2024] MarkDuplicates ADD_PG_TAG_TO_READS=true INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.3396034087551145085.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.3396034087551145085.tmp/MarkDuplicates.duplicate_metrics MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:48 GMT+14:00 2024] MarkDuplicates ADD_PG_TAG_TO_READS=true INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.3396034087551145085.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.3396034087551145085.tmp/MarkDuplicates.duplicate_metrics MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:48 MarkDuplicates Start of doWork freeMemory: 1027861912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:48 MarkDuplicates Start of doWork freeMemory: 1027861912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:48 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:48 MarkDuplicates Reading input file and constructing read end information. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:48 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:24:48 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:48 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name '1AAXX.1.1'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. WARNING 2024-07-02 11:24:48 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name '1AAXX.1.1'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:48 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:24:48 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 964939272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 964939272; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:48 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:48 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:49 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:49 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:49 MarkDuplicates Sorting list of duplicate records. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 489935256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 489935256; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:24:49 MarkDuplicates Marking 4 records as duplicates. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:49 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:49 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:49 MarkDuplicates Writing complete. Closing input iterator. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:49 MarkDuplicates Duplicate Index cleanup. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:49 MarkDuplicates Getting Memory Stats. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates Before output close freeMemory: 1027711696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:49 MarkDuplicates Before output close freeMemory: 1027711696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:49 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates After output close freeMemory: 1027615616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:49 MarkDuplicates After output close freeMemory: 1027615616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@57554933, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@16a09519, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@185ff986], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@2fca013, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7f9d6dae], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@6d873719]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]}) STANDARD_ERROR INFO 2024-07-02 11:24:49 MarkDuplicates Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam -OUTPUT /tmp/MarkDuplicates.6724844418845806785.tmp/MarkDuplicates.sam -METRICS_FILE /tmp/MarkDuplicates.6724844418845806785.tmp/MarkDuplicates.duplicate_metrics -ADD_PG_TAG_TO_READS true -PROGRAM_RECORD_ID null ********** MarkDuplicates -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam -OUTPUT /tmp/MarkDuplicates.6724844418845806785.tmp/MarkDuplicates.sam -METRICS_FILE /tmp/MarkDuplicates.6724844418845806785.tmp/MarkDuplicates.duplicate_metrics -ADD_PG_TAG_TO_READS true -PROGRAM_RECORD_ID null Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:49.291 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:49.291 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:49.291 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:49.291 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:49.291 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:49.291 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:49.291 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:49.291 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:49 GMT+14:00 2024] MarkDuplicates ADD_PG_TAG_TO_READS=true INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.6724844418845806785.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.6724844418845806785.tmp/MarkDuplicates.duplicate_metrics PROGRAM_RECORD_ID=null MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:49 GMT+14:00 2024] MarkDuplicates ADD_PG_TAG_TO_READS=true INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.6724844418845806785.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.6724844418845806785.tmp/MarkDuplicates.duplicate_metrics PROGRAM_RECORD_ID=null MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates Start of doWork freeMemory: 1027861632; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:49 MarkDuplicates Start of doWork freeMemory: 1027861632; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:49 MarkDuplicates Reading input file and constructing read end information. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:24:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:49 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name '1AAXX.1.1'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. WARNING 2024-07-02 11:24:49 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name '1AAXX.1.1'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:24:49 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 964699680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 964699680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:49 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:49 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:49 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:49 MarkDuplicates Sorting list of duplicate records. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 555995048; totalMemory: 1139802112; maxMemory: 2147483648 INFO 2024-07-02 11:24:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 555995048; totalMemory: 1139802112; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:24:49 MarkDuplicates Marking 4 records as duplicates. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:49 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:49 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:49 MarkDuplicates Writing complete. Closing input iterator. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:49 MarkDuplicates Duplicate Index cleanup. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:49 MarkDuplicates Getting Memory Stats. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates Before output close freeMemory: 1027569280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:49 MarkDuplicates Before output close freeMemory: 1027569280; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:49 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:49 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:50 MarkDuplicates After output close freeMemory: 1027569280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:50 MarkDuplicates After output close freeMemory: 1027569280; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@413bc65a, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@307685cd], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7c51033f], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:50 MarkDuplicates Start of doWork freeMemory: 1027876744; totalMemory: 1073741824; maxMemory: 2147483648 Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1) STANDARD_ERROR INFO 2024-07-02 11:24:50 MarkDuplicates Start of doWork freeMemory: 1027876744; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:50 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:50 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:50 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:24:50 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:50 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:50 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 964956216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 964956216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:50 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:50 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:50 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:50 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:50 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:50 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:50 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:50 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 489951688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 489951688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:50 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:50 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:50 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:24:50 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:50 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:50 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:50 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:50 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:50 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:50 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:50 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:50 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:50 MarkDuplicates Before output close freeMemory: 1027685024; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:50 MarkDuplicates Before output close freeMemory: 1027685024; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:50 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:50 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:50 MarkDuplicates After output close freeMemory: 1027446264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:50 MarkDuplicates After output close freeMemory: 1027446264; totalMemory: 1073741824; maxMemory: 2147483648 Running Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:50 MarkDuplicates Start of doWork freeMemory: 1027875800; totalMemory: 1073741824; maxMemory: 2147483648 Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1) STANDARD_ERROR INFO 2024-07-02 11:24:50 MarkDuplicates Start of doWork freeMemory: 1027875800; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:50 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:50 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:50 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:24:50 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:50 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:50 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 964716624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 964716624; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:51 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:51 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:51 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:51 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:51 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:51 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:51 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:51 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 489950656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 489950656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:51 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:51 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:51 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:24:51 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:51 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:51 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:51 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:51 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:51 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:51 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:51 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:51 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:51 MarkDuplicates Before output close freeMemory: 1027684016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:51 MarkDuplicates Before output close freeMemory: 1027684016; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:51 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:51 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:51 MarkDuplicates After output close freeMemory: 1027684088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:51 MarkDuplicates After output close freeMemory: 1027684088; totalMemory: 1073741824; maxMemory: 2147483648 Running Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:51 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testTwoMappedPairsWithSoftClippingFirstOfPairOnly STANDARD_ERROR INFO 2024-07-02 11:24:51 MarkDuplicates Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17784872815205666869.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17784872815205666869.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17784872815205666869.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.17784872815205666869.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17784872815205666869.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.17784872815205666869.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:51.615 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:51.615 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:51.615 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:51.615 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:51.616 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:51.616 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:51.616 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:51.616 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:51 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17784872815205666869.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17784872815205666869.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17784872815205666869.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:51 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.17784872815205666869.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.17784872815205666869.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.17784872815205666869.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:51 MarkDuplicates Start of doWork freeMemory: 1027851816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:51 MarkDuplicates Start of doWork freeMemory: 1027851816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:51 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:51 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:51 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:51 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:51 MarkDuplicates Read 2 records. 2 pairs never matched. INFO 2024-07-02 11:24:51 MarkDuplicates Read 2 records. 2 pairs never matched. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 973319968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 973319968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:51 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:51 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:52 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:52 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:52 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:52 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:52 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:52 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:52 MarkDuplicates After generateDuplicateIndexes freeMemory: 488878232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:52 MarkDuplicates After generateDuplicateIndexes freeMemory: 488878232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:52 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:24:52 MarkDuplicates Marking 0 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:52 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:52 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:52 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:52 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:52 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:52 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:52 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:52 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:52 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:52 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:52 MarkDuplicates Before output close freeMemory: 758173824; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:52 MarkDuplicates Before output close freeMemory: 758173824; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:52 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:52 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:52 MarkDuplicates After output close freeMemory: 757935064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:52 MarkDuplicates After output close freeMemory: 757935064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:52 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testWithBarcodeComplex STANDARD_ERROR INFO 2024-07-02 11:24:52 MarkDuplicates Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2711776731980536500.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2711776731980536500.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2711776731980536500.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.2711776731980536500.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2711776731980536500.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.2711776731980536500.tmp/output.sam Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:52.502 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:52.502 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:52.502 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:52.502 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:52.502 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:52.502 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:52.502 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:52.502 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:52 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2711776731980536500.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2711776731980536500.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2711776731980536500.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:52 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.2711776731980536500.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.2711776731980536500.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.2711776731980536500.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:52 MarkDuplicates Start of doWork freeMemory: 1027848424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:52 MarkDuplicates Start of doWork freeMemory: 1027848424; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:52 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:52 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:52 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:52 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:52 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:24:52 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 973315752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 973315752; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:52 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:52 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:52 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:52 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:52 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:52 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 488874496; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 488874496; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:53 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:53 MarkDuplicates Marking 2 records as duplicates. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:53 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:53 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:53 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:53 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:53 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:53 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:53 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:53 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:53 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:53 MarkDuplicates Getting Memory Stats. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:53 MarkDuplicates Before output close freeMemory: 758169920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:53 MarkDuplicates Before output close freeMemory: 758169920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:53 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:53 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:53 MarkDuplicates After output close freeMemory: 758169992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:53 MarkDuplicates After output close freeMemory: 758169992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:24:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:53 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testWithBarcodeDuplicate STANDARD_ERROR INFO 2024-07-02 11:24:53 MarkDuplicates Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4180278335319644450.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4180278335319644450.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4180278335319644450.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.4180278335319644450.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4180278335319644450.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.4180278335319644450.tmp/output.sam Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:53.508 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:53.508 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:53.508 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:53.508 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:53.508 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:53.508 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:53.508 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:53.508 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:53 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4180278335319644450.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4180278335319644450.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4180278335319644450.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:53 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.4180278335319644450.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.4180278335319644450.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.4180278335319644450.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:53 MarkDuplicates Start of doWork freeMemory: 1027849072; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:53 MarkDuplicates Start of doWork freeMemory: 1027849072; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:53 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:53 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:53 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:53 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:53 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:53 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 973316672; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 973316672; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:53 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:53 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:53 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:53 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:53 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:53 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 488875328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 488875328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:53 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:53 MarkDuplicates Marking 2 records as duplicates. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:53 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:53 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:53 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:53 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:53 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:53 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:53 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:53 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:53 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:53 MarkDuplicates Getting Memory Stats. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:54 MarkDuplicates Before output close freeMemory: 758170816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:54 MarkDuplicates Before output close freeMemory: 758170816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:54 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:54 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:54 MarkDuplicates After output close freeMemory: 758170888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:54 MarkDuplicates After output close freeMemory: 758170888; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:54 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:54 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:54 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testWithBarcodeFragmentDuplicate STANDARD_ERROR INFO 2024-07-02 11:24:54 MarkDuplicates Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10983550452287270064.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10983550452287270064.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10983550452287270064.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.10983550452287270064.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10983550452287270064.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.10983550452287270064.tmp/output.sam Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:54.175 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:54.175 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:54.175 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:54.175 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:54.175 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:54.175 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:54.175 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:54.175 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:54 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10983550452287270064.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10983550452287270064.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10983550452287270064.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:54 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.10983550452287270064.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.10983550452287270064.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.10983550452287270064.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:54 MarkDuplicates Start of doWork freeMemory: 1027849912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:54 MarkDuplicates Start of doWork freeMemory: 1027849912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:54 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:54 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:54 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:54 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:54 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:54 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:54 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:24:54 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 973318256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 973318256; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:54 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:54 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:54 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:54 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:54 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:54 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:54 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:54 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 488876520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 488876520; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:54 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:24:54 MarkDuplicates Marking 1 records as duplicates. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:54 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:54 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:54 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:54 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:54 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:54 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:54 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:54 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:54 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:54 MarkDuplicates Getting Memory Stats. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:54 MarkDuplicates Before output close freeMemory: 758172456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:54 MarkDuplicates Before output close freeMemory: 758172456; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:54 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:54 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:54 MarkDuplicates After output close freeMemory: 758172528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:54 MarkDuplicates After output close freeMemory: 758172528; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:54 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:54 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:54 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testWithIndividualReadBarcodes STANDARD_ERROR INFO 2024-07-02 11:24:54 MarkDuplicates Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3853958621851147812.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -READ_ONE_BARCODE_TAG BX -READ_TWO_BARCODE_TAG BX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3853958621851147812.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3853958621851147812.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.3853958621851147812.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -READ_ONE_BARCODE_TAG BX -READ_TWO_BARCODE_TAG BX -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3853958621851147812.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.3853958621851147812.tmp/output.sam Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:54.860 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:54.860 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:54.861 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:54.861 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:54.861 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:54.861 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:54.861 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:54.861 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:54 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC READ_ONE_BARCODE_TAG=BX READ_TWO_BARCODE_TAG=BX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3853958621851147812.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3853958621851147812.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3853958621851147812.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:54 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC READ_ONE_BARCODE_TAG=BX READ_TWO_BARCODE_TAG=BX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.3853958621851147812.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.3853958621851147812.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.3853958621851147812.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:54 MarkDuplicates Start of doWork freeMemory: 1027846096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:54 MarkDuplicates Start of doWork freeMemory: 1027846096; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:54 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:54 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:54 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:54 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:54 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:24:54 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 973313640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 973313640; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:55 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:55 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:55 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:55 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:55 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 488872168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 488872168; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:55 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:55 MarkDuplicates Marking 2 records as duplicates. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:55 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:55 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:55 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:55 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:55 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:55 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:55 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:55 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:55 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:55 MarkDuplicates Getting Memory Stats. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:55 MarkDuplicates Before output close freeMemory: 758167520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:55 MarkDuplicates Before output close freeMemory: 758167520; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:55 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:55 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:55 MarkDuplicates After output close freeMemory: 758167592; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:55 MarkDuplicates After output close freeMemory: 758167592; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:55 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:55 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:55 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true]) STANDARD_ERROR INFO 2024-07-02 11:24:55 MarkDuplicates Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12744312247640102097.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI false -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12744312247640102097.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12744312247640102097.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.12744312247640102097.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI false -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12744312247640102097.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.12744312247640102097.tmp/output.sam Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:55.570 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:55.570 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:55.570 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:55.570 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:55.570 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:55.570 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:55.570 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:55.570 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:55 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=false INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12744312247640102097.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12744312247640102097.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12744312247640102097.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:55 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=false INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.12744312247640102097.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.12744312247640102097.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.12744312247640102097.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:55 MarkDuplicates Start of doWork freeMemory: 1027845312; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:55 MarkDuplicates Start of doWork freeMemory: 1027845312; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:55 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:55 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:55 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:55 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. WARNING 2024-07-02 11:24:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:55 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:55 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 973313184; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 973313184; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:55 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:55 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:55 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:55 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:55 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 488871624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 488871624; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:56 MarkDuplicates Marking 2 records as duplicates. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:56 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:56 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:56 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:56 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:56 MarkDuplicates Getting Memory Stats. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates Before output close freeMemory: 758167584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:56 MarkDuplicates Before output close freeMemory: 758167584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:56 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates After output close freeMemory: 758167096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:56 MarkDuplicates After output close freeMemory: 758167096; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:56 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:56 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true]) STANDARD_ERROR INFO 2024-07-02 11:24:56 MarkDuplicates Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.14078778671233592374.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI false -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14078778671233592374.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14078778671233592374.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.14078778671233592374.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI false -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14078778671233592374.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.14078778671233592374.tmp/output.sam Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:56.254 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:56.254 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:56.254 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:56.254 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:56.254 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:56.254 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:56.254 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:56.254 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:56 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=false INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.14078778671233592374.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.14078778671233592374.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.14078778671233592374.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:56 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=false INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.14078778671233592374.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.14078778671233592374.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.14078778671233592374.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates Start of doWork freeMemory: 1027841944; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:56 MarkDuplicates Start of doWork freeMemory: 1027841944; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:56 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:56 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:56 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. WARNING 2024-07-02 11:24:56 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:56 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 973312640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 973312640; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:56 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:56 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:56 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 488871080; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 488871080; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:24:56 MarkDuplicates Marking 0 records as duplicates. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:56 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:56 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:56 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:56 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:56 MarkDuplicates Getting Memory Stats. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates Before output close freeMemory: 758166840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:56 MarkDuplicates Before output close freeMemory: 758166840; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:56 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates After output close freeMemory: 757928552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:56 MarkDuplicates After output close freeMemory: 757928552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:56 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:56 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:56 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false]) STANDARD_ERROR INFO 2024-07-02 11:24:56 MarkDuplicates Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.8735841528876202540.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI true -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8735841528876202540.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8735841528876202540.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.8735841528876202540.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI true -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8735841528876202540.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.8735841528876202540.tmp/output.sam Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:56.993 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:56.993 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:56.994 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:56.994 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:56.994 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:56.994 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:56.994 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:56.994 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:56 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=true INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8735841528876202540.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8735841528876202540.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8735841528876202540.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:56 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=true INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.8735841528876202540.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.8735841528876202540.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.8735841528876202540.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:57 MarkDuplicates Start of doWork freeMemory: 1027843648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:57 MarkDuplicates Start of doWork freeMemory: 1027843648; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:57 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:57 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:57 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:57 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:57 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. WARNING 2024-07-02 11:24:57 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:57 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:57 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 973072976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 973072976; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:57 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:57 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:57 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:57 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:57 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:57 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 488870352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 488870352; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:57 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:24:57 MarkDuplicates Marking 2 records as duplicates. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:57 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:57 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:57 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:57 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:57 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:57 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:57 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:57 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:57 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:57 MarkDuplicates Getting Memory Stats. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:57 MarkDuplicates Before output close freeMemory: 758166304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:57 MarkDuplicates Before output close freeMemory: 758166304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:57 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:57 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:57 MarkDuplicates After output close freeMemory: 758165880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:57 MarkDuplicates After output close freeMemory: 758165880; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:57 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:57 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:57 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest.testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false]) STANDARD_ERROR INFO 2024-07-02 11:24:57 MarkDuplicates Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.364382359961744703.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI true -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.364382359961744703.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.364382359961744703.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesWithMissingBarcodesTester.364382359961744703.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI true -INPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.364382359961744703.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMissingBarcodesTester.364382359961744703.tmp/output.sam Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:57.687 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:57.687 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:57.687 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:57.687 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:57.687 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:57.687 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: 11:24:57.687 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:57.687 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:57 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=true INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.364382359961744703.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.364382359961744703.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.364382359961744703.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:57 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=true INPUT=[/tmp/MarkDuplicatesWithMissingBarcodesTester.364382359961744703.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMissingBarcodesTester.364382359961744703.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMissingBarcodesTester.364382359961744703.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:57 MarkDuplicates Start of doWork freeMemory: 1027843392; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:57 MarkDuplicates Start of doWork freeMemory: 1027843392; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:57 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:57 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:57 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:24:57 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: WARNING 2024-07-02 11:24:57 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. WARNING 2024-07-02 11:24:57 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:57 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:24:57 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 973072704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 973072704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:58 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:58 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:58 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:58 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:58 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:58 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 488869704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 488869704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:58 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:24:58 MarkDuplicates Marking 0 records as duplicates. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:58 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:58 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:58 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:58 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:58 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:58 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:58 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:58 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:58 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:58 MarkDuplicates Getting Memory Stats. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:58 MarkDuplicates Before output close freeMemory: 758165656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:58 MarkDuplicates Before output close freeMemory: 758165656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:58 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:58 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: INFO 2024-07-02 11:24:58 MarkDuplicates After output close freeMemory: 758165232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:58 MarkDuplicates After output close freeMemory: 758165232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: [Tue Jul 02 11:24:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:24:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:24:58 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testBulkFragmentsNoDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:24:58 MarkDuplicates Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.4118970325517094428.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4118970325517094428.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4118970325517094428.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.4118970325517094428.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4118970325517094428.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4118970325517094428.tmp/output.sam Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:24:58.420 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:58.420 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:24:58.420 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:58.420 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:24:58.420 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:58.420 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:24:58.420 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:58.420 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:24:58 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.4118970325517094428.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.4118970325517094428.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.4118970325517094428.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:58 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.4118970325517094428.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.4118970325517094428.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.4118970325517094428.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:24:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:24:58 MarkDuplicates Start of doWork freeMemory: 1020906480; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:58 MarkDuplicates Start of doWork freeMemory: 1020906480; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:24:58 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:58 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:24:58 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:24:58 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:24:58 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:58 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:24:58 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2024-07-02 11:24:58 MarkDuplicates Read 10000 records. 0 pairs never matched. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:24:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 957266168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 957266168; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:24:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:24:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:24:59 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:24:59 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:24:59 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:24:59 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:24:59 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:24:59 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:24:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 751417120; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:24:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 751417120; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:24:59 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:24:59 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:24:59 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:24:59 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:24:59 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:24:59 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:24:59 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:24:59 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:24:59 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:24:59 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:24:59 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:24:59 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:24:59 MarkDuplicates Before output close freeMemory: 772248344; totalMemory: 1094713344; maxMemory: 2147483648 INFO 2024-07-02 11:24:59 MarkDuplicates Before output close freeMemory: 772248344; totalMemory: 1094713344; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:24:59 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:24:59 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:24:59 MarkDuplicates After output close freeMemory: 765048480; totalMemory: 1087373312; maxMemory: 2147483648 INFO 2024-07-02 11:24:59 MarkDuplicates After output close freeMemory: 765048480; totalMemory: 1087373312; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:24:59 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:24:59 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1087373312 Runtime.totalMemory()=1087373312 Running Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:24:59 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testBulkFragmentsNoDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:24:59 MarkDuplicates Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.3386919932899246928.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.3386919932899246928.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.3386919932899246928.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.3386919932899246928.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.3386919932899246928.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.3386919932899246928.tmp/output.sam Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:24:59.745 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:59.745 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:24:59.745 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:59.745 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:24:59.745 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:24:59.745 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:24:59.745 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:24:59.745 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:24:59 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.3386919932899246928.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.3386919932899246928.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.3386919932899246928.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:24:59 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.3386919932899246928.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.3386919932899246928.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.3386919932899246928.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:24:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:24:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:24:59 MarkDuplicates Start of doWork freeMemory: 1020840448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:24:59 MarkDuplicates Start of doWork freeMemory: 1020840448; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:24:59 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:24:59 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:24:59 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:24:59 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:24:59 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:24:59 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:00 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2024-07-02 11:25:00 MarkDuplicates Read 10000 records. 0 pairs never matched. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 957134392; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 957134392; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:00 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:00 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:00 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:00 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:00 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:00 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 481932440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 481932440; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:00 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:25:00 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:00 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:25:00 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:00 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:00 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:00 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:00 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:00 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:00 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:00 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:00 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:00 MarkDuplicates Before output close freeMemory: 750907944; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:00 MarkDuplicates Before output close freeMemory: 750907944; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:00 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:00 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:00 MarkDuplicates After output close freeMemory: 751415928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:00 MarkDuplicates After output close freeMemory: 751415928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:25:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:01 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testBulkFragmentsNoDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:25:01 MarkDuplicates Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.6952209179563854893.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.6952209179563854893.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.6952209179563854893.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester10368283452956979024/input.fasta ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.6952209179563854893.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.6952209179563854893.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.6952209179563854893.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester10368283452956979024/input.fasta Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:01.275 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:01.275 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:01.275 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:01.275 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:01.275 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:01.275 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:01.275 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:01.275 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:01 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.6952209179563854893.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.6952209179563854893.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.6952209179563854893.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester10368283452956979024/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:01 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.6952209179563854893.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.6952209179563854893.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.6952209179563854893.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester10368283452956979024/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:01 MarkDuplicates Start of doWork freeMemory: 1020903024; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:01 MarkDuplicates Start of doWork freeMemory: 1020903024; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:01 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:01 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:01 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:01 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:25:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:25:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:01 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2024-07-02 11:25:01 MarkDuplicates Read 10000 records. 0 pairs never matched. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 957262688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 957262688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:02 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:02 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:02 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:02 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:02 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:02 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 751413576; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:25:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 751413576; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:02 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:25:02 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:02 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:25:02 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:02 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:02 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:02 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:02 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:02 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:02 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:02 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:02 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:02 MarkDuplicates Before output close freeMemory: 775390592; totalMemory: 1097859072; maxMemory: 2147483648 INFO 2024-07-02 11:25:02 MarkDuplicates Before output close freeMemory: 775390592; totalMemory: 1097859072; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:02 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:02 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:02 MarkDuplicates After output close freeMemory: 767951384; totalMemory: 1090519040; maxMemory: 2147483648 INFO 2024-07-02 11:25:02 MarkDuplicates After output close freeMemory: 767951384; totalMemory: 1090519040; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:02 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:25:02 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1090519040 Runtime.totalMemory()=1090519040 Running Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:02 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testBulkFragmentsWithDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:25:02 MarkDuplicates Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.2888089483223300274.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.2888089483223300274.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.2888089483223300274.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.2888089483223300274.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.2888089483223300274.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.2888089483223300274.tmp/output.sam Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:02.839 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:02.839 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:02.839 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:02.839 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:02.839 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:02.839 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:02.839 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:02.839 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:02 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.2888089483223300274.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.2888089483223300274.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.2888089483223300274.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:02 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.2888089483223300274.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.2888089483223300274.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.2888089483223300274.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:02 MarkDuplicates Start of doWork freeMemory: 1012468656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:02 MarkDuplicates Start of doWork freeMemory: 1012468656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:02 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:02 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:02 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:02 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:25:02 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:25:02 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:03 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2024-07-02 11:25:03 MarkDuplicates Read 21000 records. 0 pairs never matched. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 948277800; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 948277800; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:03 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:03 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:03 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:03 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:03 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:03 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:03 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:03 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 743220528; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:25:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 743220528; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:03 MarkDuplicates Marking 20000 records as duplicates. INFO 2024-07-02 11:25:03 MarkDuplicates Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:03 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:25:03 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:03 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:03 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:03 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:03 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:03 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:03 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:03 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:03 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:04 MarkDuplicates Before output close freeMemory: 784777672; totalMemory: 1115684864; maxMemory: 2147483648 INFO 2024-07-02 11:25:04 MarkDuplicates Before output close freeMemory: 784777672; totalMemory: 1115684864; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:04 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:04 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:04 MarkDuplicates After output close freeMemory: 784918272; totalMemory: 1115684864; maxMemory: 2147483648 INFO 2024-07-02 11:25:04 MarkDuplicates After output close freeMemory: 784918272; totalMemory: 1115684864; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:04 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:25:04 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1115684864 Runtime.totalMemory()=1115684864 Running Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:04 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testBulkFragmentsWithDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:25:04 MarkDuplicates Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.6904533466675016270.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.6904533466675016270.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.6904533466675016270.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.6904533466675016270.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.6904533466675016270.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.6904533466675016270.tmp/output.sam Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:04.680 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:04.680 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:04.680 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:04.680 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:04.680 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:04.680 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:04.680 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:04.680 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:04 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.6904533466675016270.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.6904533466675016270.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.6904533466675016270.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:04 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.6904533466675016270.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.6904533466675016270.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.6904533466675016270.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:04 MarkDuplicates Start of doWork freeMemory: 1012643576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:04 MarkDuplicates Start of doWork freeMemory: 1012643576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:04 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:04 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:04 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:04 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:25:04 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:25:04 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:05 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2024-07-02 11:25:05 MarkDuplicates Read 21000 records. 0 pairs never matched. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 947906952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 947906952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:05 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:05 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:05 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:05 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:05 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:05 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 473735568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 473735568; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:05 MarkDuplicates Marking 20000 records as duplicates. INFO 2024-07-02 11:25:05 MarkDuplicates Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:05 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:25:05 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:05 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:05 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:05 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:05 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:05 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:05 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:05 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:05 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:05 MarkDuplicates Before output close freeMemory: 742715304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:05 MarkDuplicates Before output close freeMemory: 742715304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:05 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:05 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:05 MarkDuplicates After output close freeMemory: 742986704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:05 MarkDuplicates After output close freeMemory: 742986704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:06 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:25:06 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:07 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testBulkFragmentsWithDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:25:07 MarkDuplicates Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.1428198642612413134.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1428198642612413134.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1428198642612413134.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester2112447478478799120/input.fasta ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.1428198642612413134.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1428198642612413134.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1428198642612413134.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester2112447478478799120/input.fasta Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:07.301 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:07.301 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:07.301 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:07.301 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:07.301 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:07.301 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:07.301 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:07.301 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:07 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.1428198642612413134.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.1428198642612413134.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.1428198642612413134.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester2112447478478799120/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:07 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.1428198642612413134.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.1428198642612413134.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.1428198642612413134.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester2112447478478799120/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:07 MarkDuplicates Start of doWork freeMemory: 1012706712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:07 MarkDuplicates Start of doWork freeMemory: 1012706712; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:07 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:07 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:07 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:07 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:25:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:25:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:08 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2024-07-02 11:25:08 MarkDuplicates Read 21000 records. 0 pairs never matched. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 948274360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 948274360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:08 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:08 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:08 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:08 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:08 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:08 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 743217248; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:25:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 743217248; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:08 MarkDuplicates Marking 20000 records as duplicates. INFO 2024-07-02 11:25:08 MarkDuplicates Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:08 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:25:08 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:08 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:08 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:09 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:09 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:09 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:09 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:09 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:09 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:09 MarkDuplicates Before output close freeMemory: 795505792; totalMemory: 1126170624; maxMemory: 2147483648 INFO 2024-07-02 11:25:09 MarkDuplicates Before output close freeMemory: 795505792; totalMemory: 1126170624; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:09 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:09 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:09 MarkDuplicates After output close freeMemory: 788305728; totalMemory: 1118830592; maxMemory: 2147483648 INFO 2024-07-02 11:25:09 MarkDuplicates After output close freeMemory: 788305728; totalMemory: 1118830592; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:09 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:25:09 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1118830592 Runtime.totalMemory()=1118830592 Running Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:10 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testBulkPairsNoDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:25:10 MarkDuplicates Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.7852010705075348233.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.7852010705075348233.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.7852010705075348233.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.7852010705075348233.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.7852010705075348233.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.7852010705075348233.tmp/output.sam Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:10.215 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:10.215 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:10.216 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:10.216 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:10.216 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:10.216 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:10.216 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:10.216 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:10 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.7852010705075348233.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.7852010705075348233.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.7852010705075348233.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:10 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.7852010705075348233.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.7852010705075348233.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.7852010705075348233.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:10 MarkDuplicates Start of doWork freeMemory: 1012190792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:10 MarkDuplicates Start of doWork freeMemory: 1012190792; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:10 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:10 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:10 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:10 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:25:10 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:25:10 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:10 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2024-07-02 11:25:10 MarkDuplicates Read 20200 records. 0 pairs never matched. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 947089088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 947089088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:11 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:11 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:11 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:11 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 742701240; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:25:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 742701240; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:11 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:25:11 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:11 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:25:11 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:11 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:11 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:11 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:11 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:11 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:11 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:11 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:11 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:11 MarkDuplicates Before output close freeMemory: 787435856; totalMemory: 1118830592; maxMemory: 2147483648 INFO 2024-07-02 11:25:11 MarkDuplicates Before output close freeMemory: 787435856; totalMemory: 1118830592; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:11 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:11 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:11 MarkDuplicates After output close freeMemory: 787789656; totalMemory: 1118830592; maxMemory: 2147483648 INFO 2024-07-02 11:25:11 MarkDuplicates After output close freeMemory: 787789656; totalMemory: 1118830592; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:11 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:25:11 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1118830592 Runtime.totalMemory()=1118830592 Running Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:12 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testBulkPairsNoDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:25:12 MarkDuplicates Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.3547753585028662496.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.3547753585028662496.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.3547753585028662496.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.3547753585028662496.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.3547753585028662496.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.3547753585028662496.tmp/output.sam Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:12.447 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:12.447 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:12.448 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:12.448 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:12.448 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:12.448 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:12.448 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:12.448 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:12 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.3547753585028662496.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.3547753585028662496.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.3547753585028662496.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:12 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.3547753585028662496.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.3547753585028662496.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.3547753585028662496.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:12 MarkDuplicates Start of doWork freeMemory: 1012124872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:12 MarkDuplicates Start of doWork freeMemory: 1012124872; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:12 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:12 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:12 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:12 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:25:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:25:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:12 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2024-07-02 11:25:12 MarkDuplicates Read 20200 records. 0 pairs never matched. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 946956872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 946956872; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:13 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:13 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:13 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:13 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:13 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:13 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:13 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:13 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 473216568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 473216568; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:13 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:25:13 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:13 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:25:13 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:13 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:13 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:13 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:13 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:13 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:13 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:13 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:13 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:13 MarkDuplicates Before output close freeMemory: 742427568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:13 MarkDuplicates Before output close freeMemory: 742427568; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:13 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:13 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:13 MarkDuplicates After output close freeMemory: 742699560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:13 MarkDuplicates After output close freeMemory: 742699560; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:13 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:25:13 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:15 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testBulkPairsNoDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:25:15 MarkDuplicates Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.9661966610549129666.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.9661966610549129666.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.9661966610549129666.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester3810394378401165564/input.fasta ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.9661966610549129666.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.9661966610549129666.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.9661966610549129666.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester3810394378401165564/input.fasta Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:15.091 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:15.091 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:15.091 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:15.091 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:15.091 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:15.091 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:15.091 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:15.091 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:15 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.9661966610549129666.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.9661966610549129666.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.9661966610549129666.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester3810394378401165564/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:15 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.9661966610549129666.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.9661966610549129666.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.9661966610549129666.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester3810394378401165564/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:15 MarkDuplicates Start of doWork freeMemory: 1012185696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:15 MarkDuplicates Start of doWork freeMemory: 1012185696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:15 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:15 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:15 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:15 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:25:15 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:25:15 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:15 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2024-07-02 11:25:15 MarkDuplicates Read 20200 records. 0 pairs never matched. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 947083632; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 947083632; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:16 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:16 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:16 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:16 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:16 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:16 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 742695944; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:25:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 742695944; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:16 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:25:16 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:16 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:25:16 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:16 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:16 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:16 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:16 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:16 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:16 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:16 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:16 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:17 MarkDuplicates Before output close freeMemory: 790790096; totalMemory: 1121976320; maxMemory: 2147483648 INFO 2024-07-02 11:25:17 MarkDuplicates Before output close freeMemory: 790790096; totalMemory: 1121976320; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:17 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:17 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:17 MarkDuplicates After output close freeMemory: 787649056; totalMemory: 1118830592; maxMemory: 2147483648 INFO 2024-07-02 11:25:17 MarkDuplicates After output close freeMemory: 787649056; totalMemory: 1118830592; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:17 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:25:17 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1118830592 Runtime.totalMemory()=1118830592 Running Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:17 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testBulkPairsWithDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:25:17 MarkDuplicates Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.13075239820190776720.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.13075239820190776720.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.13075239820190776720.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.13075239820190776720.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.13075239820190776720.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.13075239820190776720.tmp/output.sam Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:17.449 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:17.449 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:17.449 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:17.449 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:17.449 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:17.449 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:17.449 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:17.449 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:17 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.13075239820190776720.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.13075239820190776720.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.13075239820190776720.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:17 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.13075239820190776720.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.13075239820190776720.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.13075239820190776720.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:17 MarkDuplicates Start of doWork freeMemory: 1022704704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:17 MarkDuplicates Start of doWork freeMemory: 1022704704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:17 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:17 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:17 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:17 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:25:17 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:25:17 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:17 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2024-07-02 11:25:17 MarkDuplicates Read 6820 records. 0 pairs never matched. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 959048040; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 959048040; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:17 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:17 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:18 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:18 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:18 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:18 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:18 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:18 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 971318960; totalMemory: 1561329664; maxMemory: 2147483648 INFO 2024-07-02 11:25:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 971318960; totalMemory: 1561329664; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:18 MarkDuplicates Marking 6200 records as duplicates. INFO 2024-07-02 11:25:18 MarkDuplicates Marking 6200 records as duplicates. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:18 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:25:18 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:18 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:18 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:18 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:18 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:18 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:18 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:18 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:18 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:18 MarkDuplicates Before output close freeMemory: 763560480; totalMemory: 1084227584; maxMemory: 2147483648 INFO 2024-07-02 11:25:18 MarkDuplicates Before output close freeMemory: 763560480; totalMemory: 1084227584; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:18 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:18 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:18 MarkDuplicates After output close freeMemory: 756225312; totalMemory: 1076887552; maxMemory: 2147483648 INFO 2024-07-02 11:25:18 MarkDuplicates After output close freeMemory: 756225312; totalMemory: 1076887552; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:18 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:25:18 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1076887552 Runtime.totalMemory()=1076887552 Running Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:18 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testBulkPairsWithDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:25:18 MarkDuplicates Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.125234812738851327.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.125234812738851327.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.125234812738851327.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.125234812738851327.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.125234812738851327.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.125234812738851327.tmp/output.sam Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:18.658 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:18.658 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:18.659 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:18.659 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:18.659 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:18.659 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:18.659 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:18.659 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:18 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.125234812738851327.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.125234812738851327.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.125234812738851327.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:18 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.125234812738851327.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.125234812738851327.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.125234812738851327.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:18 MarkDuplicates Start of doWork freeMemory: 1022638400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:18 MarkDuplicates Start of doWork freeMemory: 1022638400; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:18 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:18 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:18 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:18 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:25:18 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:25:18 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:18 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2024-07-02 11:25:18 MarkDuplicates Read 6820 records. 0 pairs never matched. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 958915440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 958915440; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:19 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:19 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:19 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:19 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:19 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:19 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:19 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 1022698160; totalMemory: 1612709888; maxMemory: 2147483648 INFO 2024-07-02 11:25:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 1022698160; totalMemory: 1612709888; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:19 MarkDuplicates Marking 6200 records as duplicates. INFO 2024-07-02 11:25:19 MarkDuplicates Marking 6200 records as duplicates. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:19 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:25:19 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:19 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:19 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:19 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:19 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:19 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:19 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:19 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:19 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:19 MarkDuplicates Before output close freeMemory: 769577232; totalMemory: 1090519040; maxMemory: 2147483648 INFO 2024-07-02 11:25:19 MarkDuplicates Before output close freeMemory: 769577232; totalMemory: 1090519040; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:19 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:19 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:19 MarkDuplicates After output close freeMemory: 766844848; totalMemory: 1087373312; maxMemory: 2147483648 INFO 2024-07-02 11:25:19 MarkDuplicates After output close freeMemory: 766844848; totalMemory: 1087373312; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:19 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:25:19 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1087373312 Runtime.totalMemory()=1087373312 Running Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:20 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testBulkPairsWithDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:25:20 MarkDuplicates Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.5909722545358331151.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.5909722545358331151.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.5909722545358331151.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester12277264080889100372/input.fasta ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.5909722545358331151.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.5909722545358331151.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.5909722545358331151.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester12277264080889100372/input.fasta Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:20.223 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:20.223 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:20.223 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:20.223 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:20.224 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:20.224 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:20.224 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:20.224 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:20 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.5909722545358331151.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.5909722545358331151.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.5909722545358331151.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester12277264080889100372/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:20 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.5909722545358331151.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.5909722545358331151.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.5909722545358331151.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester12277264080889100372/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:20 MarkDuplicates Start of doWork freeMemory: 1022701384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:20 MarkDuplicates Start of doWork freeMemory: 1022701384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:20 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:20 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:20 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:20 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:25:20 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:25:20 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:20 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2024-07-02 11:25:20 MarkDuplicates Read 6820 records. 0 pairs never matched. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 959044136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 959044136; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:20 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:20 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:20 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:20 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:20 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:20 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 483727600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 483727600; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:21 MarkDuplicates Marking 6200 records as duplicates. INFO 2024-07-02 11:25:21 MarkDuplicates Marking 6200 records as duplicates. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:21 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:25:21 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:21 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:21 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:21 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:21 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:21 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:21 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:21 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:21 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:21 MarkDuplicates Before output close freeMemory: 753071264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:21 MarkDuplicates Before output close freeMemory: 753071264; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:21 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:21 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:21 MarkDuplicates After output close freeMemory: 753211120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:21 MarkDuplicates After output close freeMemory: 753211120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:21 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:25:21 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:21 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testDifferentChromosomesInOppositeOrder STANDARD_ERROR INFO 2024-07-02 11:25:21 MarkDuplicates Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.10192076488494408508.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.10192076488494408508.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.10192076488494408508.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.10192076488494408508.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.10192076488494408508.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.10192076488494408508.tmp/output.sam Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:21.606 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:21.606 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:21.606 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:21.606 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:21.606 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:21.606 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:21.606 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:21.606 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:21 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.10192076488494408508.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.10192076488494408508.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.10192076488494408508.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:21 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.10192076488494408508.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.10192076488494408508.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.10192076488494408508.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:21 MarkDuplicates Start of doWork freeMemory: 1027823304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:21 MarkDuplicates Start of doWork freeMemory: 1027823304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:21 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:21 MarkDuplicates Reading input file and constructing read end information. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:21 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:21 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:21 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:25:21 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 964902584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 964902584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:21 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:21 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:22 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:22 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:22 MarkDuplicates Sorting list of duplicate records. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 758333416; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:25:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 758333416; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:25:22 MarkDuplicates Marking 2 records as duplicates. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:25:22 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:22 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:22 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:22 MarkDuplicates Duplicate Index cleanup. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:22 MarkDuplicates Getting Memory Stats. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates Before output close freeMemory: 758192944; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:22 MarkDuplicates Before output close freeMemory: 758192944; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:22 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates After output close freeMemory: 758187248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:22 MarkDuplicates After output close freeMemory: 758187248; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:22 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:25:22 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:25:22 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.15109540252369180199.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.15109540252369180199.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.15109540252369180199.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.15109540252369180199.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.15109540252369180199.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.15109540252369180199.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:22.391 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:22.391 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:22.391 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:22.391 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:22.391 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:22.391 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:22.391 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:22.391 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:22 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.15109540252369180199.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.15109540252369180199.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.15109540252369180199.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:22 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.15109540252369180199.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.15109540252369180199.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.15109540252369180199.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates Start of doWork freeMemory: 1027816616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:22 MarkDuplicates Start of doWork freeMemory: 1027816616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:22 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:22 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:25:22 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 964740112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 964740112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:22 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:22 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:22 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 488842712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 488842712; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:25:22 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:25:22 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:22 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:22 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:22 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:22 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:22 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:23 MarkDuplicates Before output close freeMemory: 758186296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:23 MarkDuplicates Before output close freeMemory: 758186296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:23 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:23 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:23 MarkDuplicates After output close freeMemory: 758326424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:23 MarkDuplicates After output close freeMemory: 758326424; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:23 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:25:23 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:23 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:25:23 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.6764823486912523235.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.6764823486912523235.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.6764823486912523235.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.6764823486912523235.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.6764823486912523235.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.6764823486912523235.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:23.131 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:23.131 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:23.131 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:23.131 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:23.131 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:23.131 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:23.131 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:23.131 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:23 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.6764823486912523235.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.6764823486912523235.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.6764823486912523235.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:23 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.6764823486912523235.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.6764823486912523235.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.6764823486912523235.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:23 MarkDuplicates Start of doWork freeMemory: 1027815936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:23 MarkDuplicates Start of doWork freeMemory: 1027815936; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:23 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:23 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:23 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:23 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:23 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:25:23 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 964894584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 964894584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:23 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:23 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:23 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:23 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:23 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:23 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 488842032; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 488842032; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:23 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:25:23 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:23 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:25:23 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:23 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:23 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:23 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:23 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:23 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:23 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:23 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:23 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:23 MarkDuplicates Before output close freeMemory: 758185616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:23 MarkDuplicates Before output close freeMemory: 758185616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:23 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:23 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:23 MarkDuplicates After output close freeMemory: 758325936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:23 MarkDuplicates After output close freeMemory: 758325936; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:23 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:25:23 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:23 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:25:23 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.1050507977311708003.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1050507977311708003.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1050507977311708003.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.1050507977311708003.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1050507977311708003.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1050507977311708003.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:23.847 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:23.847 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:23.847 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:23.847 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:23.847 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:23.847 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:23.847 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:23.847 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:23 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.1050507977311708003.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.1050507977311708003.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.1050507977311708003.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:23 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.1050507977311708003.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.1050507977311708003.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.1050507977311708003.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:23 MarkDuplicates Start of doWork freeMemory: 1027815296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:23 MarkDuplicates Start of doWork freeMemory: 1027815296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:23 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:23 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:23 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:23 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:23 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:25:23 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 964893952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 964893952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:24 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:24 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:24 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:24 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:24 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:24 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:24 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:24 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 488841400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 488841400; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:24 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:25:24 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:24 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:25:24 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:24 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:24 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:24 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:24 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:24 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:24 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:24 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:24 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:24 MarkDuplicates Before output close freeMemory: 758184984; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:24 MarkDuplicates Before output close freeMemory: 758184984; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:24 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:24 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:24 MarkDuplicates After output close freeMemory: 758325304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:24 MarkDuplicates After output close freeMemory: 758325304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:24 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:25:24 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:24 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:25:24 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.9221470341290769335.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.9221470341290769335.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.9221470341290769335.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.9221470341290769335.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.9221470341290769335.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.9221470341290769335.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:24.613 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:24.613 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:24.613 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:24.613 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:24.613 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:24.613 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:24.613 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:24.613 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:24 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.9221470341290769335.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.9221470341290769335.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.9221470341290769335.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:24 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.9221470341290769335.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.9221470341290769335.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.9221470341290769335.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:24 MarkDuplicates Start of doWork freeMemory: 1027814680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:24 MarkDuplicates Start of doWork freeMemory: 1027814680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:24 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:24 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:24 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:24 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:24 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:25:24 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 964893328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 964893328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:24 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:24 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:25 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:25 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:25 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 488840776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 488840776; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:25:25 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:25:25 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:25 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:25 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:25 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:25 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates Before output close freeMemory: 758182792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:25 MarkDuplicates Before output close freeMemory: 758182792; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:25 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates After output close freeMemory: 758324680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:25 MarkDuplicates After output close freeMemory: 758324680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:25 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:25:25 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:25:25 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.8822950753081542354.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.8822950753081542354.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.8822950753081542354.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.8822950753081542354.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.8822950753081542354.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.8822950753081542354.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:25.379 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:25.379 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:25.379 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:25.379 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:25.379 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:25.379 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:25.379 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:25.379 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:25 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.8822950753081542354.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.8822950753081542354.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.8822950753081542354.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:25 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.8822950753081542354.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.8822950753081542354.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.8822950753081542354.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates Start of doWork freeMemory: 1027814048; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:25 MarkDuplicates Start of doWork freeMemory: 1027814048; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:25 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:25 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:25:25 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 964892696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 964892696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:25 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:25 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:25 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:25 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 488840144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 488840144; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:25:25 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:25:25 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:25 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:25 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:25 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:25 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:25 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:26 MarkDuplicates Before output close freeMemory: 758183728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:26 MarkDuplicates Before output close freeMemory: 758183728; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:26 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:26 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:26 MarkDuplicates After output close freeMemory: 758324048; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:26 MarkDuplicates After output close freeMemory: 758324048; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:26 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:25:26 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:26 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:25:26 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.15901722887008340751.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.15901722887008340751.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.15901722887008340751.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.15901722887008340751.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.15901722887008340751.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.15901722887008340751.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:26.181 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:26.181 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:26.181 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:26.181 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:26.181 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:26.181 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:26.181 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:26.181 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:26 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.15901722887008340751.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.15901722887008340751.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.15901722887008340751.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:26 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.15901722887008340751.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.15901722887008340751.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.15901722887008340751.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:26 MarkDuplicates Start of doWork freeMemory: 1027813408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:26 MarkDuplicates Start of doWork freeMemory: 1027813408; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:26 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:26 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:26 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:26 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:26 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:25:26 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 964891840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 964891840; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:26 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:26 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:26 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:26 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:26 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:26 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 488839504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 488839504; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:26 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:25:26 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:26 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:25:26 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:26 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:26 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:26 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:26 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:26 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:26 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:26 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:26 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:26 MarkDuplicates Before output close freeMemory: 758183088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:26 MarkDuplicates Before output close freeMemory: 758183088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:26 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:26 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:26 MarkDuplicates After output close freeMemory: 758170504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:26 MarkDuplicates After output close freeMemory: 758170504; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:26 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:25:26 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:26 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testMappedFragmentAndMappedPairFirstOfPairNonPrimary STANDARD_ERROR INFO 2024-07-02 11:25:26 MarkDuplicates Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.3435863613190816254.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.3435863613190816254.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.3435863613190816254.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.3435863613190816254.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.3435863613190816254.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.3435863613190816254.tmp/output.sam Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:26.968 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:26.968 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:26.968 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:26.968 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:26.968 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:26.968 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:26.968 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:26.968 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:26 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.3435863613190816254.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.3435863613190816254.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.3435863613190816254.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:26 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.3435863613190816254.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.3435863613190816254.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.3435863613190816254.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:27 MarkDuplicates Start of doWork freeMemory: 1027819680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:27 MarkDuplicates Start of doWork freeMemory: 1027819680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:27 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:27 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:27 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:27 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:25:27 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:25:27 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:27 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:25:27 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 964898920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 964898920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:27 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:27 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:27 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:27 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 488846288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 488846288; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:27 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:25:27 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:27 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:25:27 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:27 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:27 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:27 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:27 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:27 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:27 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:27 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:27 MarkDuplicates Getting Memory Stats. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:27 MarkDuplicates Before output close freeMemory: 758190048; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:27 MarkDuplicates Before output close freeMemory: 758190048; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:27 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:27 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:27 MarkDuplicates After output close freeMemory: 758330192; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:27 MarkDuplicates After output close freeMemory: 758330192; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:27 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:25:27 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:27 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testMappedFragmentAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:25:27 MarkDuplicates Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.18044462751963957619.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.18044462751963957619.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.18044462751963957619.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.18044462751963957619.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.18044462751963957619.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.18044462751963957619.tmp/output.sam Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:27.695 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:27.695 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:27.695 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:27.695 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:27.695 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:27.695 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:27.695 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:27.695 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:27 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.18044462751963957619.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.18044462751963957619.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.18044462751963957619.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:27 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.18044462751963957619.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.18044462751963957619.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.18044462751963957619.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:27 MarkDuplicates Start of doWork freeMemory: 1027818760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:27 MarkDuplicates Start of doWork freeMemory: 1027818760; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:27 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:27 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:27 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:27 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:25:27 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:25:27 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:27 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2024-07-02 11:25:27 MarkDuplicates Read 3 records. 0 pairs never matched. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 964898528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 964898528; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:28 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:28 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:28 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 488845368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 488845368; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:25:28 MarkDuplicates Marking 1 records as duplicates. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:25:28 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:28 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:28 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:28 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:28 MarkDuplicates Getting Memory Stats. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates Before output close freeMemory: 758189232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:28 MarkDuplicates Before output close freeMemory: 758189232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:28 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates After output close freeMemory: 758329272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:28 MarkDuplicates After output close freeMemory: 758329272; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:28 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:25:28 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testMappedFragmentAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:25:28 MarkDuplicates Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.12883132238076215692.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.12883132238076215692.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.12883132238076215692.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.12883132238076215692.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.12883132238076215692.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.12883132238076215692.tmp/output.sam Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:28.408 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:28.408 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:28.408 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:28.408 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:28.409 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:28.409 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:28.409 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:28.409 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:28 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.12883132238076215692.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.12883132238076215692.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.12883132238076215692.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:28 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.12883132238076215692.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.12883132238076215692.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.12883132238076215692.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates Start of doWork freeMemory: 1027818224; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:28 MarkDuplicates Start of doWork freeMemory: 1027818224; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:28 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:28 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:25:28 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:25:28 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2024-07-02 11:25:28 MarkDuplicates Read 3 records. 0 pairs never matched. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 964897992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 964897992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:28 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:28 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:28 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 488844832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 488844832; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:25:28 MarkDuplicates Marking 1 records as duplicates. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:25:28 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:28 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:28 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:28 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:28 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:28 MarkDuplicates Getting Memory Stats. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:29 MarkDuplicates Before output close freeMemory: 758188696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:29 MarkDuplicates Before output close freeMemory: 758188696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:29 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:29 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:29 MarkDuplicates After output close freeMemory: 758328736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:29 MarkDuplicates After output close freeMemory: 758328736; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:25:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:29 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testMappedPairAndMappedFragmentAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:25:29 MarkDuplicates Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.4359493780022726871.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4359493780022726871.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4359493780022726871.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.4359493780022726871.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4359493780022726871.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4359493780022726871.tmp/output.sam Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:29.124 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:29.124 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:29.124 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:29.124 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:29.124 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:29.124 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:29.124 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:29.124 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:29 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.4359493780022726871.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.4359493780022726871.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.4359493780022726871.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:29 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.4359493780022726871.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.4359493780022726871.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.4359493780022726871.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:29 MarkDuplicates Start of doWork freeMemory: 1027811000; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:29 MarkDuplicates Start of doWork freeMemory: 1027811000; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:29 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:29 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:29 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:29 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:25:29 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:25:29 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:29 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:25:29 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 964895616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 964895616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:29 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:29 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:29 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:29 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:29 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:29 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 488842496; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 488842496; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:29 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:25:29 MarkDuplicates Marking 2 records as duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:29 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:25:29 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:29 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:29 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:29 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:29 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:29 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:29 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:29 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:29 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:29 MarkDuplicates Before output close freeMemory: 758186144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:29 MarkDuplicates Before output close freeMemory: 758186144; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:29 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:29 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:29 MarkDuplicates After output close freeMemory: 758171656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:29 MarkDuplicates After output close freeMemory: 758171656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:25:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:29 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testMappedPairAndMappedFragmentAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:25:29 MarkDuplicates Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.14356436226538893967.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.14356436226538893967.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.14356436226538893967.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.14356436226538893967.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.14356436226538893967.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.14356436226538893967.tmp/output.sam Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:29.836 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:29.836 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:29.836 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:29.836 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:29.836 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:29.836 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:29.836 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:29.836 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:29 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.14356436226538893967.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.14356436226538893967.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.14356436226538893967.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:29 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.14356436226538893967.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.14356436226538893967.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.14356436226538893967.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:29 MarkDuplicates Start of doWork freeMemory: 1027815344; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:29 MarkDuplicates Start of doWork freeMemory: 1027815344; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:29 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:29 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:29 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:29 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:25:29 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:25:29 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:29 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:25:29 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 964894776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 964894776; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:30 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:30 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:30 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:30 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:30 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:30 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 562241976; totalMemory: 1147142144; maxMemory: 2147483648 INFO 2024-07-02 11:25:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 562241976; totalMemory: 1147142144; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:30 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:25:30 MarkDuplicates Marking 2 records as duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:30 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:25:30 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:30 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:30 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:30 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:30 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:30 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:30 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:30 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:30 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:30 MarkDuplicates Before output close freeMemory: 758185304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:30 MarkDuplicates Before output close freeMemory: 758185304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:30 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:30 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:30 MarkDuplicates After output close freeMemory: 758170568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:30 MarkDuplicates After output close freeMemory: 758170568; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:30 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:25:30 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:30 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:25:30 MarkDuplicates Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.1352474079040265241.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1352474079040265241.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1352474079040265241.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.1352474079040265241.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1352474079040265241.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1352474079040265241.tmp/output.sam Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:30.583 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:30.583 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:30.583 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:30.583 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:30.583 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:30.583 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:30.583 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:30.583 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:30 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.1352474079040265241.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.1352474079040265241.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.1352474079040265241.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:30 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.1352474079040265241.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.1352474079040265241.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.1352474079040265241.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:30 MarkDuplicates Start of doWork freeMemory: 1027815072; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:30 MarkDuplicates Start of doWork freeMemory: 1027815072; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:30 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:30 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:30 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:30 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:25:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:25:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:30 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:25:30 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 964893976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 964893976; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:31 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:31 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:31 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 488841384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 488841384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:25:31 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:25:31 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:31 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:31 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:31 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:31 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates Before output close freeMemory: 758183416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:31 MarkDuplicates Before output close freeMemory: 758183416; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:31 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates After output close freeMemory: 758324992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:31 MarkDuplicates After output close freeMemory: 758324992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:31 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:25:31 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testMappedPairAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:25:31 MarkDuplicates Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.8648953636765805662.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.8648953636765805662.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.8648953636765805662.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.8648953636765805662.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.8648953636765805662.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.8648953636765805662.tmp/output.sam Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:31.327 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:31.327 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:31.327 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:31.327 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:31.327 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:31.327 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:31.327 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:31.327 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:31 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.8648953636765805662.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.8648953636765805662.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.8648953636765805662.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:31 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.8648953636765805662.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.8648953636765805662.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.8648953636765805662.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates Start of doWork freeMemory: 1027814504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:31 MarkDuplicates Start of doWork freeMemory: 1027814504; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:31 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:31 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:25:31 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:25:31 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:25:31 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 964893408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 964893408; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:31 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:31 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:31 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 488840816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 488840816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:25:31 MarkDuplicates Marking 1 records as duplicates. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:25:31 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:31 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:31 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:31 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:31 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates Before output close freeMemory: 758184464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:31 MarkDuplicates Before output close freeMemory: 758184464; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:31 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:31 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:32 MarkDuplicates After output close freeMemory: 758324224; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:32 MarkDuplicates After output close freeMemory: 758324224; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:25:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:32 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testMappedPairAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:25:32 MarkDuplicates Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.7767029723255019421.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.7767029723255019421.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.7767029723255019421.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.7767029723255019421.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.7767029723255019421.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.7767029723255019421.tmp/output.sam Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:32.066 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:32.066 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:32.066 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:32.066 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:32.066 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:32.066 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:32.066 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:32.066 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:32 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.7767029723255019421.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.7767029723255019421.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.7767029723255019421.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:32 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.7767029723255019421.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.7767029723255019421.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.7767029723255019421.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:32 MarkDuplicates Start of doWork freeMemory: 1027813816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:32 MarkDuplicates Start of doWork freeMemory: 1027813816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:32 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:32 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:32 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:32 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:25:32 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:25:32 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:32 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:25:32 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 964893328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 964893328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:32 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:32 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:32 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:32 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:32 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:32 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 488840136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 488840136; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:32 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:25:32 MarkDuplicates Marking 1 records as duplicates. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:32 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:25:32 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:32 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:32 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:32 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:32 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:32 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:32 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:32 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:32 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:32 MarkDuplicates Before output close freeMemory: 758183784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:32 MarkDuplicates Before output close freeMemory: 758183784; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:32 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:32 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:32 MarkDuplicates After output close freeMemory: 758168864; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:32 MarkDuplicates After output close freeMemory: 758168864; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:25:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:32 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testMappedPairWithFirstEndSamePositionAndOther STANDARD_ERROR INFO 2024-07-02 11:25:32 MarkDuplicates Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.8774518754413085989.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.8774518754413085989.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.8774518754413085989.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.8774518754413085989.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.8774518754413085989.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.8774518754413085989.tmp/output.sam Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:32.755 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:32.755 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:32.755 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:32.755 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:32.755 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:32.755 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:32.755 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:32.755 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:32 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.8774518754413085989.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.8774518754413085989.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.8774518754413085989.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:32 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.8774518754413085989.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.8774518754413085989.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.8774518754413085989.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:32 MarkDuplicates Start of doWork freeMemory: 1027812896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:32 MarkDuplicates Start of doWork freeMemory: 1027812896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:32 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:32 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:32 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:32 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:25:32 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:25:32 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:32 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:25:32 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 964736728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 964736728; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:33 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:33 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:33 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:33 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 488839208; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 488839208; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:33 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:25:33 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:33 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:25:33 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:33 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:33 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:33 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:33 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:33 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:33 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:33 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:33 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:33 MarkDuplicates Before output close freeMemory: 758181288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:33 MarkDuplicates Before output close freeMemory: 758181288; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:33 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:33 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:33 MarkDuplicates After output close freeMemory: 758322616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:33 MarkDuplicates After output close freeMemory: 758322616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:33 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:25:33 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:33 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testMappedPairWithSamePosition STANDARD_ERROR INFO 2024-07-02 11:25:33 MarkDuplicates Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.4757035303835328720.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4757035303835328720.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4757035303835328720.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.4757035303835328720.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4757035303835328720.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4757035303835328720.tmp/output.sam Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:33.908 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:33.908 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:33.908 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:33.908 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:33.917 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:33.917 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:33.917 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:33.917 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:33 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.4757035303835328720.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.4757035303835328720.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.4757035303835328720.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:33 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.4757035303835328720.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.4757035303835328720.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.4757035303835328720.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:34 MarkDuplicates Start of doWork freeMemory: 1027811312; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:34 MarkDuplicates Start of doWork freeMemory: 1027811312; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:34 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:34 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:34 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:34 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:25:34 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:25:34 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:34 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:25:34 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 964892520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 964892520; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:36 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:36 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:36 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:36 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:36 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:36 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 488839856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 488839856; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:37 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:25:37 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:37 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:25:37 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:37 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:37 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:37 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:37 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:37 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:37 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:37 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:37 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:37 MarkDuplicates Before output close freeMemory: 758028168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:37 MarkDuplicates Before output close freeMemory: 758028168; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:37 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:37 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:37 MarkDuplicates After output close freeMemory: 758323688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:37 MarkDuplicates After output close freeMemory: 758323688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:25:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:38 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testMappedPairWithSamePositionSameCigar STANDARD_ERROR INFO 2024-07-02 11:25:38 MarkDuplicates Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.16362239096094113412.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16362239096094113412.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16362239096094113412.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.16362239096094113412.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16362239096094113412.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16362239096094113412.tmp/output.sam Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:38.051 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:38.051 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:38.051 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:38.051 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:38.052 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:38.052 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:38.052 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:38.052 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:38 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.16362239096094113412.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.16362239096094113412.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.16362239096094113412.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:38 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.16362239096094113412.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.16362239096094113412.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.16362239096094113412.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:38 MarkDuplicates Start of doWork freeMemory: 1027652440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:38 MarkDuplicates Start of doWork freeMemory: 1027652440; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:38 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:38 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:38 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:38 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:25:38 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:25:38 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:38 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:25:38 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 964736888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 964736888; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:39 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:39 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:39 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:39 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:39 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:39 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 488839128; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 488839128; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:39 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:25:39 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:39 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:25:39 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:39 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:39 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:39 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:39 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:39 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:39 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:39 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:39 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:39 MarkDuplicates Before output close freeMemory: 758182776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:39 MarkDuplicates Before output close freeMemory: 758182776; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:39 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:39 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:40 MarkDuplicates After output close freeMemory: 758322960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:40 MarkDuplicates After output close freeMemory: 758322960; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:40 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:25:40 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:40 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:25:40 MarkDuplicates Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.16880360355248776297.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16880360355248776297.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16880360355248776297.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.16880360355248776297.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16880360355248776297.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16880360355248776297.tmp/output.sam Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:40.143 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:40.143 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:40.143 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:40.143 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:40.143 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:40.143 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:40.143 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:40.143 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:40 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.16880360355248776297.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.16880360355248776297.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.16880360355248776297.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:40 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.16880360355248776297.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.16880360355248776297.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.16880360355248776297.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:40 MarkDuplicates Start of doWork freeMemory: 1027649680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:40 MarkDuplicates Start of doWork freeMemory: 1027649680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:40 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:40 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:40 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:40 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:25:40 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:25:40 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:40 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:25:40 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 964889896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 964889896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:41 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:41 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:41 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:41 MarkDuplicates Sorting list of duplicate records. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 488836664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 488836664; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:42 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:25:42 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:42 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:25:42 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:42 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:42 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:42 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:42 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:42 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:42 MarkDuplicates Duplicate Index cleanup. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:42 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:42 MarkDuplicates Getting Memory Stats. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:42 MarkDuplicates Before output close freeMemory: 758180424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:42 MarkDuplicates Before output close freeMemory: 758180424; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:42 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:42 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:42 MarkDuplicates After output close freeMemory: 758320496; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:42 MarkDuplicates After output close freeMemory: 758320496; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:25:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:42 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:25:42 MarkDuplicates Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.8804136645838498498.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.8804136645838498498.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.8804136645838498498.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.8804136645838498498.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.8804136645838498498.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.8804136645838498498.tmp/output.sam Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:42.981 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:42.981 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:42.981 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:42.981 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:42.982 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:42.982 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:42.982 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:42.982 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:42 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.8804136645838498498.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.8804136645838498498.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.8804136645838498498.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:42 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.8804136645838498498.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.8804136645838498498.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.8804136645838498498.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:43 MarkDuplicates Start of doWork freeMemory: 1027809440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:43 MarkDuplicates Start of doWork freeMemory: 1027809440; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:43 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:43 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:43 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:43 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:25:43 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:25:43 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:43 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:25:43 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 964889280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 964889280; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:44 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:44 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:44 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:44 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:44 MarkDuplicates Sorting list of duplicate records. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 673385424; totalMemory: 1258291200; maxMemory: 2147483648 INFO 2024-07-02 11:25:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 673385424; totalMemory: 1258291200; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:45 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:25:45 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:45 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:25:45 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:45 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:45 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:45 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:45 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:45 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:45 MarkDuplicates Duplicate Index cleanup. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:45 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:45 MarkDuplicates Getting Memory Stats. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:45 MarkDuplicates Before output close freeMemory: 758179928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:45 MarkDuplicates Before output close freeMemory: 758179928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:45 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:45 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:46 MarkDuplicates After output close freeMemory: 758319880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:46 MarkDuplicates After output close freeMemory: 758319880; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:25:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:46 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testOpticalDuplicateBehaviorNullRegex STANDARD_ERROR INFO 2024-07-02 11:25:46 MarkDuplicates Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.10944885783643964934.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_NAME_REGEX null -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.10944885783643964934.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.10944885783643964934.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.10944885783643964934.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_NAME_REGEX null -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.10944885783643964934.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.10944885783643964934.tmp/output.sam Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:46.181 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:46.181 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:46.189 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:46.189 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:46.189 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:46.189 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:46.189 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:46.189 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:46 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.10944885783643964934.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.10944885783643964934.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.10944885783643964934.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH READ_NAME_REGEX=null MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:46 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.10944885783643964934.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.10944885783643964934.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.10944885783643964934.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH READ_NAME_REGEX=null MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:46 MarkDuplicates Start of doWork freeMemory: 1027807392; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:46 MarkDuplicates Start of doWork freeMemory: 1027807392; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:46 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:46 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:46 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:46 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:46 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:25:46 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 964886752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 964886752; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:48 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:48 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:48 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:48 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:48 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:48 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 758317912; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:25:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 758317912; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:49 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:25:49 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:25:49 MarkDuplicates Skipped optical duplicate cluster discovery; library size estimation may be inaccurate! WARNING 2024-07-02 11:25:49 MarkDuplicates Skipped optical duplicate cluster discovery; library size estimation may be inaccurate! Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:49 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:49 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:49 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:49 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:49 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:49 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:49 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:49 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:49 MarkDuplicates Before output close freeMemory: 758177544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:49 MarkDuplicates Before output close freeMemory: 758177544; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:49 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:49 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:50 MarkDuplicates After output close freeMemory: 758317728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:50 MarkDuplicates After output close freeMemory: 758317728; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:25:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:50 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testOpticalDuplicateClusterOneEndSamePositionOneCluster STANDARD_ERROR INFO 2024-07-02 11:25:50 MarkDuplicates Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.6939140899498786932.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.6939140899498786932.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.6939140899498786932.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.6939140899498786932.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.6939140899498786932.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.6939140899498786932.tmp/output.sam Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:50.156 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:50.156 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:50.156 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:50.156 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:50.165 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:50.165 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:50.165 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:50.165 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:50 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.6939140899498786932.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.6939140899498786932.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.6939140899498786932.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:50 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.6939140899498786932.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.6939140899498786932.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.6939140899498786932.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:50 MarkDuplicates Start of doWork freeMemory: 1027806328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:50 MarkDuplicates Start of doWork freeMemory: 1027806328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:50 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:50 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:50 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:50 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:50 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:25:50 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 964885624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 964885624; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:52 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:52 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:52 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:52 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:52 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:52 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 488832424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 488832424; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:53 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:25:53 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:53 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:25:53 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:53 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:53 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:53 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:53 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:53 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:53 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:53 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:53 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:53 MarkDuplicates Before output close freeMemory: 758175984; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:53 MarkDuplicates Before output close freeMemory: 758175984; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:53 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:53 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:54 MarkDuplicates After output close freeMemory: 758316256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:54 MarkDuplicates After output close freeMemory: 758316256; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:54 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:25:54 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:54 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:25:54 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.10248103906731585979.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.10248103906731585979.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.10248103906731585979.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.10248103906731585979.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.10248103906731585979.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.10248103906731585979.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:54.101 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:54.101 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:54.101 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:54.101 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:54.102 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:54.102 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:54.102 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:54.102 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:54 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.10248103906731585979.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.10248103906731585979.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.10248103906731585979.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:54 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.10248103906731585979.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.10248103906731585979.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.10248103906731585979.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:54 MarkDuplicates Start of doWork freeMemory: 1027804528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:54 MarkDuplicates Start of doWork freeMemory: 1027804528; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:54 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:54 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:54 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:54 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:54 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:25:54 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 964883824; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 964883824; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:55 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:55 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:55 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:55 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:55 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 488830776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 488830776; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:56 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:25:56 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:56 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:25:56 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:56 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:56 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:56 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:56 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:56 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:56 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:56 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:56 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:56 MarkDuplicates Before output close freeMemory: 758174360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:56 MarkDuplicates Before output close freeMemory: 758174360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:56 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:56 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:56 MarkDuplicates After output close freeMemory: 758314608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:56 MarkDuplicates After output close freeMemory: 758314608; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:56 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:25:56 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:57 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:25:57 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.1113217003994172991.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1113217003994172991.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1113217003994172991.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.1113217003994172991.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1113217003994172991.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1113217003994172991.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:57.034 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:57.034 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:57.034 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:57.034 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:57.035 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:25:57.035 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:25:57.035 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:25:57.035 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:57 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.1113217003994172991.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.1113217003994172991.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.1113217003994172991.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:25:57 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.1113217003994172991.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.1113217003994172991.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.1113217003994172991.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:25:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:25:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:57 MarkDuplicates Start of doWork freeMemory: 1027803856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:57 MarkDuplicates Start of doWork freeMemory: 1027803856; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:57 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:25:57 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:57 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:25:57 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:57 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:25:57 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 964883152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 964883152; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:25:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:59 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:25:59 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:59 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:25:59 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:59 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:25:59 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 651359384; totalMemory: 1236271104; maxMemory: 2147483648 INFO 2024-07-02 11:25:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 651359384; totalMemory: 1236271104; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:59 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:25:59 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:59 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:25:59 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:59 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:25:59 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:59 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:25:59 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:59 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:25:59 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:59 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:25:59 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:59 MarkDuplicates Before output close freeMemory: 758173688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:25:59 MarkDuplicates Before output close freeMemory: 758173688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:25:59 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:25:59 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:00 MarkDuplicates After output close freeMemory: 758313440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:00 MarkDuplicates After output close freeMemory: 758313440; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:26:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:00 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:26:00 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.1864402665476293036.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1864402665476293036.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1864402665476293036.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.1864402665476293036.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1864402665476293036.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1864402665476293036.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:00.149 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:00.149 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:00.150 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:00.150 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:00.150 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:00.150 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:00.150 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:00.150 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:00 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.1864402665476293036.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.1864402665476293036.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.1864402665476293036.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:00 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.1864402665476293036.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.1864402665476293036.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.1864402665476293036.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:00 MarkDuplicates Start of doWork freeMemory: 1027800488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:00 MarkDuplicates Start of doWork freeMemory: 1027800488; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:00 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:00 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:00 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:00 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:00 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:26:00 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 964882576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 964882576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:02 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:02 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:02 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:02 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:02 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:02 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 488829528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 488829528; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:02 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:26:02 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:02 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:02 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:02 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:02 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:02 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:02 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:02 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:02 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:02 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:02 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:02 MarkDuplicates Before output close freeMemory: 758173112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:02 MarkDuplicates Before output close freeMemory: 758173112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:02 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:02 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:03 MarkDuplicates After output close freeMemory: 758312896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:03 MarkDuplicates After output close freeMemory: 758312896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:03 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:26:03 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:03 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:26:03 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.1659959172156402671.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1659959172156402671.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1659959172156402671.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.1659959172156402671.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1659959172156402671.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1659959172156402671.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:03.416 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:03.416 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:03.416 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:03.416 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:03.426 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:03.426 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:03.426 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:03.426 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:03 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.1659959172156402671.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.1659959172156402671.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.1659959172156402671.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:03 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.1659959172156402671.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.1659959172156402671.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.1659959172156402671.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:03 MarkDuplicates Start of doWork freeMemory: 1027800424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:03 MarkDuplicates Start of doWork freeMemory: 1027800424; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:03 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:03 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:03 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:03 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:04 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:26:04 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 964881952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 964881952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:05 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:05 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:05 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:05 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:05 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:05 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 488828904; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 488828904; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:06 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:26:06 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:06 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:06 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:06 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:06 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:06 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:06 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:06 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:06 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:06 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:06 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:06 MarkDuplicates Before output close freeMemory: 758172488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:06 MarkDuplicates Before output close freeMemory: 758172488; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:06 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:06 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:06 MarkDuplicates After output close freeMemory: 758312240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:06 MarkDuplicates After output close freeMemory: 758312240; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:06 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:26:06 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:06 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:26:06 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.15592820620540946453.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.15592820620540946453.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.15592820620540946453.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.15592820620540946453.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.15592820620540946453.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.15592820620540946453.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:06.784 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:06.784 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:06.784 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:06.784 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:06.784 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:06.784 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:06.785 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:06.785 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:06 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.15592820620540946453.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.15592820620540946453.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.15592820620540946453.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:06 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.15592820620540946453.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.15592820620540946453.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.15592820620540946453.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:07 MarkDuplicates Start of doWork freeMemory: 1027645400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:07 MarkDuplicates Start of doWork freeMemory: 1027645400; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:07 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:07 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:07 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:07 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:07 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:26:07 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 964726152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 964726152; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:07 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:07 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:08 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:08 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:08 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:08 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:08 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:08 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 488828256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 488828256; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:08 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:26:08 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:08 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:08 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:08 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:08 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:08 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:08 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:08 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:08 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:08 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:08 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:09 MarkDuplicates Before output close freeMemory: 758170280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:09 MarkDuplicates Before output close freeMemory: 758170280; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:09 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:09 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:09 MarkDuplicates After output close freeMemory: 758312088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:09 MarkDuplicates After output close freeMemory: 758312088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:09 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:26:09 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:09 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:26:09 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.17266467293471784289.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.17266467293471784289.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.17266467293471784289.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.17266467293471784289.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.17266467293471784289.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.17266467293471784289.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:09.524 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:09.524 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:09.524 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:09.524 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:09.524 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:09.524 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:09.524 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:09.524 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:09 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.17266467293471784289.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.17266467293471784289.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.17266467293471784289.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:09 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.17266467293471784289.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.17266467293471784289.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.17266467293471784289.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:09 MarkDuplicates Start of doWork freeMemory: 1027801384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:09 MarkDuplicates Start of doWork freeMemory: 1027801384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:09 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:09 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:09 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:09 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:09 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:26:09 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 964725560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 964725560; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:11 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:11 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:11 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:11 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 612559600; totalMemory: 1197473792; maxMemory: 2147483648 INFO 2024-07-02 11:26:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 612559600; totalMemory: 1197473792; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:11 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:26:11 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:11 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:11 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:11 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:11 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:11 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:11 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:11 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:11 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:11 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:11 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:11 MarkDuplicates Before output close freeMemory: 758171216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:11 MarkDuplicates Before output close freeMemory: 758171216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:11 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:11 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:12 MarkDuplicates After output close freeMemory: 758311464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:12 MarkDuplicates After output close freeMemory: 758311464; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:12 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:26:12 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:12 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:26:12 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.1905781569189043795.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1905781569189043795.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1905781569189043795.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.1905781569189043795.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1905781569189043795.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1905781569189043795.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:12.300 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:12.300 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:12.300 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:12.300 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:12.300 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:12.300 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:12.300 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:12.300 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:12 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.1905781569189043795.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.1905781569189043795.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.1905781569189043795.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:12 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.1905781569189043795.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.1905781569189043795.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.1905781569189043795.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:12 MarkDuplicates Start of doWork freeMemory: 1027800784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:12 MarkDuplicates Start of doWork freeMemory: 1027800784; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:12 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:12 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:12 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:12 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:12 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:26:12 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 964724928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 964724928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:13 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:13 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:14 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:14 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:14 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:14 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:14 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 488827032; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 488827032; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:14 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:26:14 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:14 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:14 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:14 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:14 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:14 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:14 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:14 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:14 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:14 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:14 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:14 MarkDuplicates Before output close freeMemory: 758170208; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:14 MarkDuplicates Before output close freeMemory: 758170208; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:14 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:14 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:15 MarkDuplicates After output close freeMemory: 758310368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:15 MarkDuplicates After output close freeMemory: 758310368; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:26:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:15 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:26:15 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.4643164142753154360.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4643164142753154360.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4643164142753154360.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.4643164142753154360.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4643164142753154360.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4643164142753154360.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:15.268 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:15.268 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:15.268 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:15.268 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:15.278 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:15.278 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:15.278 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:15.278 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:15 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.4643164142753154360.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.4643164142753154360.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.4643164142753154360.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:15 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.4643164142753154360.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.4643164142753154360.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.4643164142753154360.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:15 MarkDuplicates Start of doWork freeMemory: 1027643000; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:15 MarkDuplicates Start of doWork freeMemory: 1027643000; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:15 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:15 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:15 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:15 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:15 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:26:15 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 964879240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 964879240; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:16 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:16 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:16 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:16 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:16 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:16 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 488860112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 488860112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:17 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:26:17 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:17 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:17 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:17 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:17 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:17 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:17 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:17 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:17 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:17 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:17 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:17 MarkDuplicates Before output close freeMemory: 758203696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:17 MarkDuplicates Before output close freeMemory: 758203696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:17 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:17 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:18 MarkDuplicates After output close freeMemory: 758343944; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:18 MarkDuplicates After output close freeMemory: 758343944; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:18 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:26:18 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:18 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:26:18 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.10800458481329584844.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.10800458481329584844.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.10800458481329584844.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.10800458481329584844.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.10800458481329584844.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.10800458481329584844.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:18.094 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:18.094 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:18.095 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:18.095 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:18.095 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:18.095 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:18.095 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:18.095 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:18 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.10800458481329584844.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.10800458481329584844.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.10800458481329584844.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:18 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.10800458481329584844.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.10800458481329584844.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.10800458481329584844.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:18 MarkDuplicates Start of doWork freeMemory: 1027833240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:18 MarkDuplicates Start of doWork freeMemory: 1027833240; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:18 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:18 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:18 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:18 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:18 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:26:18 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 964912536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 964912536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:19 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:19 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:19 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:19 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:19 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:19 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:19 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 488859488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 488859488; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:19 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:26:19 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:19 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:19 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:19 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:19 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:19 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:19 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:19 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:19 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:19 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:19 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:20 MarkDuplicates Before output close freeMemory: 758203072; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:20 MarkDuplicates Before output close freeMemory: 758203072; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:20 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:20 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:20 MarkDuplicates After output close freeMemory: 758343320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:20 MarkDuplicates After output close freeMemory: 758343320; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:20 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:26:20 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:20 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:26:20 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.16502706110174552968.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16502706110174552968.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16502706110174552968.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.16502706110174552968.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16502706110174552968.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16502706110174552968.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:20.584 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:20.584 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:20.584 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:20.584 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:20.584 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:20.584 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:20.584 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:20.584 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:20 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.16502706110174552968.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.16502706110174552968.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.16502706110174552968.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:20 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.16502706110174552968.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.16502706110174552968.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.16502706110174552968.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:20 MarkDuplicates Start of doWork freeMemory: 1027827168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:20 MarkDuplicates Start of doWork freeMemory: 1027827168; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:20 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:20 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:20 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:20 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:21 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:26:21 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 964911848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 964911848; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:21 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:21 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:22 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:22 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:22 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:22 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:22 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:22 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 679699632; totalMemory: 1264582656; maxMemory: 2147483648 INFO 2024-07-02 11:26:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 679699632; totalMemory: 1264582656; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:22 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:26:22 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:22 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:22 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:22 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:22 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:22 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:22 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:22 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:22 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:22 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:22 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:22 MarkDuplicates Before output close freeMemory: 758202384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:22 MarkDuplicates Before output close freeMemory: 758202384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:22 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:22 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:23 MarkDuplicates After output close freeMemory: 758342632; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:23 MarkDuplicates After output close freeMemory: 758342632; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:23 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:26:23 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:23 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756) STANDARD_ERROR INFO 2024-07-02 11:26:23 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.7242618756147233220.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.7242618756147233220.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.7242618756147233220.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.7242618756147233220.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.7242618756147233220.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.7242618756147233220.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:23.292 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:23.292 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:23.292 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:23.292 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:23.292 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:23.292 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:23.292 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:23.292 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:23 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.7242618756147233220.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.7242618756147233220.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.7242618756147233220.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:23 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.7242618756147233220.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.7242618756147233220.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.7242618756147233220.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:23 MarkDuplicates Start of doWork freeMemory: 1027831928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:23 MarkDuplicates Start of doWork freeMemory: 1027831928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:23 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:23 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:23 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:23 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:23 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:26:23 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 964911224; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 964911224; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:25 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:25 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:25 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:25 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:25 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:25 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:25 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:25 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 488858176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 488858176; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:26 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:26:26 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:26 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:26 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:26 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:26 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:26 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:26 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:26 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:26 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:26 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:26 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:26 MarkDuplicates Before output close freeMemory: 758201760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:26 MarkDuplicates Before output close freeMemory: 758201760; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:26 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:26 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:27 MarkDuplicates After output close freeMemory: 758342008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:27 MarkDuplicates After output close freeMemory: 758342008; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:27 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:26:27 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:27 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756) STANDARD_ERROR INFO 2024-07-02 11:26:27 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.4585922001424716635.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4585922001424716635.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4585922001424716635.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.4585922001424716635.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4585922001424716635.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4585922001424716635.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:27.231 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:27.231 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:27.232 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:27.232 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:27.232 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:27.232 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:27.232 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:27.232 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:27 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.4585922001424716635.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.4585922001424716635.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.4585922001424716635.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:27 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.4585922001424716635.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.4585922001424716635.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.4585922001424716635.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:27 MarkDuplicates Start of doWork freeMemory: 1027831280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:27 MarkDuplicates Start of doWork freeMemory: 1027831280; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:27 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:27 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:27 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:27 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:27 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:26:27 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 964910576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 964910576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:29 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:29 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:29 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:29 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:29 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:29 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 488857528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 488857528; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:30 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:26:30 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:30 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:30 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:30 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:30 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:30 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:30 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:30 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:30 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:30 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:30 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:30 MarkDuplicates Before output close freeMemory: 758201112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:30 MarkDuplicates Before output close freeMemory: 758201112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:30 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:30 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:30 MarkDuplicates After output close freeMemory: 758341360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:30 MarkDuplicates After output close freeMemory: 758341360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:30 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:26:30 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:31 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756) STANDARD_ERROR INFO 2024-07-02 11:26:31 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.10381468587485283985.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.10381468587485283985.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.10381468587485283985.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.10381468587485283985.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.10381468587485283985.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.10381468587485283985.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:31.038 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:31.038 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:31.039 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:31.039 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:31.039 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:31.039 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:31.039 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:31.039 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:31 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.10381468587485283985.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.10381468587485283985.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.10381468587485283985.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:31 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.10381468587485283985.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.10381468587485283985.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.10381468587485283985.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:31 MarkDuplicates Start of doWork freeMemory: 1027827832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:31 MarkDuplicates Start of doWork freeMemory: 1027827832; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:31 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:31 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:31 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:31 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:31 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:26:31 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 964909928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 964909928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:33 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:33 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:33 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:33 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 488856880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 488856880; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:33 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:26:33 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:33 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:33 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:33 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:33 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:33 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:33 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:33 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:33 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:33 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:33 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:34 MarkDuplicates Before output close freeMemory: 758198896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:34 MarkDuplicates Before output close freeMemory: 758198896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:34 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:34 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:34 MarkDuplicates After output close freeMemory: 758340784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:34 MarkDuplicates After output close freeMemory: 758340784; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:26:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:34 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756) STANDARD_ERROR INFO 2024-07-02 11:26:34 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.18066309490684704192.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.18066309490684704192.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.18066309490684704192.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.18066309490684704192.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.18066309490684704192.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.18066309490684704192.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:34.641 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:34.641 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:34.642 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:34.642 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:34.642 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:34.642 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:34.642 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:34.642 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:34 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.18066309490684704192.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.18066309490684704192.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.18066309490684704192.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:34 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.18066309490684704192.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.18066309490684704192.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.18066309490684704192.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:35 MarkDuplicates Start of doWork freeMemory: 1027830008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:35 MarkDuplicates Start of doWork freeMemory: 1027830008; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:35 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:35 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:35 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:35 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:35 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:26:35 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 964909304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 964909304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:36 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:36 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:36 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:36 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:36 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:36 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 627268288; totalMemory: 1212153856; maxMemory: 2147483648 INFO 2024-07-02 11:26:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 627268288; totalMemory: 1212153856; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:37 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:26:37 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:37 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:37 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:37 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:37 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:37 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:37 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:37 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:37 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:37 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:37 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:37 MarkDuplicates Before output close freeMemory: 758199840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:37 MarkDuplicates Before output close freeMemory: 758199840; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:37 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:37 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:37 MarkDuplicates After output close freeMemory: 758340088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:37 MarkDuplicates After output close freeMemory: 758340088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:26:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:37 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance STANDARD_ERROR INFO 2024-07-02 11:26:37 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.4005881435718318319.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4005881435718318319.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4005881435718318319.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.4005881435718318319.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4005881435718318319.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4005881435718318319.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:37.695 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:37.695 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:37.695 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:37.695 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:37.695 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:37.695 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:37.696 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:37.696 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:37 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.4005881435718318319.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.4005881435718318319.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.4005881435718318319.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:37 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.4005881435718318319.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.4005881435718318319.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.4005881435718318319.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:37 MarkDuplicates Start of doWork freeMemory: 1027829680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:37 MarkDuplicates Start of doWork freeMemory: 1027829680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:37 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:37 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:37 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:37 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:38 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:26:38 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 964908760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 964908760; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:38 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:38 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:38 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:38 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:38 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:38 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 488855928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 488855928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:38 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:26:38 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:38 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:38 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:38 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:38 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:38 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:38 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:38 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:38 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:38 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:38 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:39 MarkDuplicates Before output close freeMemory: 758197944; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:39 MarkDuplicates Before output close freeMemory: 758197944; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:39 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:39 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:39 MarkDuplicates After output close freeMemory: 758339760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:39 MarkDuplicates After output close freeMemory: 758339760; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:26:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:39 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance STANDARD_ERROR INFO 2024-07-02 11:26:39 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.7228907933027498800.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.7228907933027498800.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.7228907933027498800.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.7228907933027498800.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.7228907933027498800.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.7228907933027498800.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:39.452 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:39.452 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:39.452 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:39.452 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:39.453 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:39.453 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:39.453 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:39.453 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:39 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.7228907933027498800.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.7228907933027498800.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.7228907933027498800.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:39 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.7228907933027498800.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.7228907933027498800.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.7228907933027498800.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:39 MarkDuplicates Start of doWork freeMemory: 1027829096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:39 MarkDuplicates Start of doWork freeMemory: 1027829096; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:39 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:39 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:39 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:39 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:39 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:26:39 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 964908568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 964908568; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:40 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:40 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:40 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:40 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:40 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 488855584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 488855584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:41 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:26:41 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:41 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:26:41 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:41 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:41 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:41 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:41 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:41 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:41 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:41 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:41 MarkDuplicates Before output close freeMemory: 758042784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:41 MarkDuplicates Before output close freeMemory: 758042784; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:41 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:41 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:41 MarkDuplicates After output close freeMemory: 758339416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:41 MarkDuplicates After output close freeMemory: 758339416; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:41 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:26:41 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:41 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate STANDARD_ERROR INFO 2024-07-02 11:26:41 MarkDuplicates Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.3473049402273605343.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.3473049402273605343.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.3473049402273605343.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.3473049402273605343.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.3473049402273605343.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.3473049402273605343.tmp/output.sam Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:41.503 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:41.503 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:41.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:41.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:41.504 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:41.504 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:41.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:41.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:41 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.3473049402273605343.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.3473049402273605343.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.3473049402273605343.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:41 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.3473049402273605343.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.3473049402273605343.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.3473049402273605343.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:41 MarkDuplicates Start of doWork freeMemory: 1027828184; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:41 MarkDuplicates Start of doWork freeMemory: 1027828184; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:41 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:41 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:41 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:41 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:41 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:26:41 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 964752728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 964752728; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:42 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:42 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:42 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:42 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:42 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:42 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 488854672; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 488854672; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:42 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:26:42 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:42 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:26:42 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:42 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:42 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:42 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:42 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:42 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:42 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:42 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:42 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:42 MarkDuplicates Before output close freeMemory: 758197888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:42 MarkDuplicates Before output close freeMemory: 758197888; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:42 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:42 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:42 MarkDuplicates After output close freeMemory: 758338504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:42 MarkDuplicates After output close freeMemory: 758338504; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:26:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:42 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testOpticalDuplicateFinding STANDARD_ERROR INFO 2024-07-02 11:26:42 MarkDuplicates Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.1607525962454174056.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1607525962454174056.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1607525962454174056.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.1607525962454174056.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1607525962454174056.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.1607525962454174056.tmp/output.sam Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:42.883 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:42.883 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:42.883 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:42.883 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:42.883 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:42.883 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:42.883 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:42.883 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:42 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.1607525962454174056.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.1607525962454174056.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.1607525962454174056.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:42 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.1607525962454174056.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.1607525962454174056.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.1607525962454174056.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:43 MarkDuplicates Start of doWork freeMemory: 1027671536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:43 MarkDuplicates Start of doWork freeMemory: 1027671536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:43 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:43 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:43 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:43 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:43 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:26:43 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 964750744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 964750744; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:43 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:43 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:43 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:43 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:43 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:43 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 488852912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 488852912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:43 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:26:43 MarkDuplicates Marking 4 records as duplicates. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:43 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:26:43 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:43 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:43 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:43 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:43 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:43 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:43 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:43 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:43 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:43 MarkDuplicates Before output close freeMemory: 758196600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:43 MarkDuplicates Before output close freeMemory: 758196600; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:43 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:43 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:44 MarkDuplicates After output close freeMemory: 758336320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:44 MarkDuplicates After output close freeMemory: 758336320; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:44 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:26:44 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:44 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testPathologicalOrderingAtTheSamePosition STANDARD_ERROR INFO 2024-07-02 11:26:44 MarkDuplicates Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.16633310987140019380.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16633310987140019380.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16633310987140019380.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.16633310987140019380.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16633310987140019380.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16633310987140019380.tmp/output.sam Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:44.099 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:44.099 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:44.099 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:44.099 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:44.099 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:44.099 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:44.099 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:44.099 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:44 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.16633310987140019380.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.16633310987140019380.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.16633310987140019380.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:44 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.16633310987140019380.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.16633310987140019380.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.16633310987140019380.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:44 MarkDuplicates Start of doWork freeMemory: 1027827064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:44 MarkDuplicates Start of doWork freeMemory: 1027827064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:44 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:44 MarkDuplicates Reading input file and constructing read end information. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:44 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:44 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:44 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:26:44 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 964751216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 964751216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:44 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:44 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:44 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:44 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:44 MarkDuplicates Sorting list of duplicate records. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 488762120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 488762120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:44 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:26:44 MarkDuplicates Marking 2 records as duplicates. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:44 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:26:44 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:44 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:44 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:44 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:44 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:44 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:44 MarkDuplicates Duplicate Index cleanup. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:44 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:44 MarkDuplicates Getting Memory Stats. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:45 MarkDuplicates Before output close freeMemory: 758196808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:45 MarkDuplicates Before output close freeMemory: 758196808; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:45 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:45 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:45 MarkDuplicates After output close freeMemory: 758336568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:45 MarkDuplicates After output close freeMemory: 758336568; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:26:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:45 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testSecondEndIsBeforeFirstInCoordinate STANDARD_ERROR INFO 2024-07-02 11:26:45 MarkDuplicates Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.6860082223751307212.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.6860082223751307212.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.6860082223751307212.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.6860082223751307212.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.6860082223751307212.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.6860082223751307212.tmp/output.sam Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:45.178 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:45.178 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:45.178 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:45.178 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:45.179 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:45.179 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:45.179 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:45.179 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:45 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.6860082223751307212.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.6860082223751307212.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.6860082223751307212.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:45 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.6860082223751307212.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.6860082223751307212.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.6860082223751307212.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:45 MarkDuplicates Start of doWork freeMemory: 1027827608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:45 MarkDuplicates Start of doWork freeMemory: 1027827608; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:45 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:45 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:45 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:45 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:26:45 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:26:45 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:45 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:26:45 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 964906584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 964906584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:45 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:45 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:45 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:45 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:45 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:45 MarkDuplicates Sorting list of duplicate records. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 488853920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 488853920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:45 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:26:45 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:45 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:45 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:45 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:45 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:45 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:45 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:45 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:45 MarkDuplicates Duplicate Index cleanup. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:45 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:45 MarkDuplicates Getting Memory Stats. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:46 MarkDuplicates Before output close freeMemory: 758197584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:46 MarkDuplicates Before output close freeMemory: 758197584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:46 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:46 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:46 MarkDuplicates After output close freeMemory: 758337824; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:46 MarkDuplicates After output close freeMemory: 758337824; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:26:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:46 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testSingleMappedFragment STANDARD_ERROR INFO 2024-07-02 11:26:46 MarkDuplicates Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.2852410315128377607.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.2852410315128377607.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.2852410315128377607.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.2852410315128377607.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.2852410315128377607.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.2852410315128377607.tmp/output.sam Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:46.222 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:46.222 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:46.222 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:46.222 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:46.223 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:46.223 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:46.223 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:46.223 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:46 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.2852410315128377607.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.2852410315128377607.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.2852410315128377607.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:46 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.2852410315128377607.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.2852410315128377607.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.2852410315128377607.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:46 MarkDuplicates Start of doWork freeMemory: 1027827640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:46 MarkDuplicates Start of doWork freeMemory: 1027827640; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:46 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:46 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:46 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:46 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:26:46 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:26:46 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:46 MarkDuplicates Read 1 records. 0 pairs never matched. INFO 2024-07-02 11:26:46 MarkDuplicates Read 1 records. 0 pairs never matched. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 964907480; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 964907480; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:46 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:46 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:46 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:46 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:46 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:46 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 488854248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 488854248; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:46 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:26:46 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:46 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:46 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:46 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:46 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:46 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:46 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:46 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:46 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:46 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:46 MarkDuplicates Getting Memory Stats. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:46 MarkDuplicates Before output close freeMemory: 758198080; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:46 MarkDuplicates Before output close freeMemory: 758198080; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:46 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:46 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:46 MarkDuplicates After output close freeMemory: 758182728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:46 MarkDuplicates After output close freeMemory: 758182728; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:26:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:47 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testSingleMappedFragmentAndSingleMappedPair STANDARD_ERROR INFO 2024-07-02 11:26:47 MarkDuplicates Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.308589691911317021.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.308589691911317021.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.308589691911317021.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.308589691911317021.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.308589691911317021.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.308589691911317021.tmp/output.sam Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:47.011 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:47.011 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:47.011 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:47.011 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:47.012 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:47.012 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:47.012 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:47.012 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:47 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.308589691911317021.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.308589691911317021.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.308589691911317021.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:47 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.308589691911317021.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.308589691911317021.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.308589691911317021.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:47 MarkDuplicates Start of doWork freeMemory: 1027825784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:47 MarkDuplicates Start of doWork freeMemory: 1027825784; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:47 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:47 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:47 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:47 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:26:47 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:26:47 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:47 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2024-07-02 11:26:47 MarkDuplicates Read 3 records. 0 pairs never matched. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 964905288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 964905288; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:47 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:47 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:47 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:47 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:47 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:47 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 488852096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 488852096; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:47 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:26:47 MarkDuplicates Marking 1 records as duplicates. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:47 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:47 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:47 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:47 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:47 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:47 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:47 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:47 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:47 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:47 MarkDuplicates Getting Memory Stats. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:47 MarkDuplicates Before output close freeMemory: 758195816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:47 MarkDuplicates Before output close freeMemory: 758195816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:47 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:47 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:47 MarkDuplicates After output close freeMemory: 758180576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:47 MarkDuplicates After output close freeMemory: 758180576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:47 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:26:47 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:47 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testSingleMappedFragmentAndTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:26:47 MarkDuplicates Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.4481533367551324764.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4481533367551324764.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4481533367551324764.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.4481533367551324764.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4481533367551324764.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4481533367551324764.tmp/output.sam Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:47.860 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:47.860 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:47.860 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:47.860 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:47.861 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:47.861 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:47.861 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:47.861 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:47 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.4481533367551324764.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.4481533367551324764.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.4481533367551324764.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:47 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.4481533367551324764.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.4481533367551324764.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.4481533367551324764.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:47 MarkDuplicates Start of doWork freeMemory: 1027821992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:47 MarkDuplicates Start of doWork freeMemory: 1027821992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:47 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:47 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:47 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:47 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:26:47 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:26:47 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:47 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:26:47 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 964902952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 964902952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:48 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:48 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:48 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:48 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:48 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:48 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:48 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:48 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 576930360; totalMemory: 1161822208; maxMemory: 2147483648 INFO 2024-07-02 11:26:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 576930360; totalMemory: 1161822208; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:48 MarkDuplicates Marking 3 records as duplicates. INFO 2024-07-02 11:26:48 MarkDuplicates Marking 3 records as duplicates. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:48 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:48 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:48 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:48 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:48 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:48 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:48 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:48 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:48 MarkDuplicates Getting Memory Stats. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:48 MarkDuplicates Before output close freeMemory: 758193696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:48 MarkDuplicates Before output close freeMemory: 758193696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:48 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:48 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:48 MarkDuplicates After output close freeMemory: 758178456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:48 MarkDuplicates After output close freeMemory: 758178456; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:48 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:26:48 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:48 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testSingleMappedPair STANDARD_ERROR INFO 2024-07-02 11:26:48 MarkDuplicates Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.7704421935276589543.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.7704421935276589543.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.7704421935276589543.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.7704421935276589543.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.7704421935276589543.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.7704421935276589543.tmp/output.sam Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:48.687 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:48.687 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:48.688 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:48.688 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:48.688 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:48.688 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:48.688 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:48.688 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:48 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.7704421935276589543.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.7704421935276589543.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.7704421935276589543.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:48 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.7704421935276589543.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.7704421935276589543.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.7704421935276589543.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:48 MarkDuplicates Start of doWork freeMemory: 1027824464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:48 MarkDuplicates Start of doWork freeMemory: 1027824464; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:48 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:48 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:48 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:48 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:26:48 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:26:48 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:48 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:26:48 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 964904432; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 964904432; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:49 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:49 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:49 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:49 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:49 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:49 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:49 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:49 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 488851168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 488851168; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:49 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:26:49 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:49 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:49 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:49 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:49 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:49 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:49 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:49 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:49 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:49 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:49 MarkDuplicates Getting Memory Stats. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:49 MarkDuplicates Before output close freeMemory: 758194888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:49 MarkDuplicates Before output close freeMemory: 758194888; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:49 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:49 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:49 MarkDuplicates After output close freeMemory: 758334576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:49 MarkDuplicates After output close freeMemory: 758334576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:26:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:49 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testSingleUnmappedFragment STANDARD_ERROR INFO 2024-07-02 11:26:49 MarkDuplicates Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.8894504532427271700.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.8894504532427271700.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.8894504532427271700.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.8894504532427271700.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.8894504532427271700.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.8894504532427271700.tmp/output.sam Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:49.486 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:49.486 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:49.486 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:49.486 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:49.486 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:49.486 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:49.486 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:49.486 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:49 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.8894504532427271700.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.8894504532427271700.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.8894504532427271700.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:49 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.8894504532427271700.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.8894504532427271700.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.8894504532427271700.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:49 MarkDuplicates Start of doWork freeMemory: 1027824960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:49 MarkDuplicates Start of doWork freeMemory: 1027824960; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:49 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:49 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:49 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2024-07-02 11:26:49 MarkDuplicates Read 0 records. 0 pairs never matched. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 964904768; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 964904768; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:49 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:49 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:49 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:49 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:49 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:49 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:49 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:49 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 488851680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 488851680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:26:50 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:50 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:50 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:50 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:50 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:50 MarkDuplicates Getting Memory Stats. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates Before output close freeMemory: 758195720; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:50 MarkDuplicates Before output close freeMemory: 758195720; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:50 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates After output close freeMemory: 758180160; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:50 MarkDuplicates After output close freeMemory: 758180160; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:26:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testSingleUnmappedPair STANDARD_ERROR INFO 2024-07-02 11:26:50 MarkDuplicates Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.15926889303112522810.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.15926889303112522810.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.15926889303112522810.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.15926889303112522810.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.15926889303112522810.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.15926889303112522810.tmp/output.sam Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:50.245 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:50.245 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:50.245 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:50.245 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:50.245 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:50.245 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:50.245 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:50.245 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:50 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.15926889303112522810.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.15926889303112522810.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.15926889303112522810.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:50 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.15926889303112522810.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.15926889303112522810.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.15926889303112522810.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates Start of doWork freeMemory: 1027823920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:50 MarkDuplicates Start of doWork freeMemory: 1027823920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:50 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:50 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2024-07-02 11:26:50 MarkDuplicates Read 0 records. 0 pairs never matched. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 964748792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 964748792; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:50 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:50 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:50 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 488850640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 488850640; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:26:50 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:50 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:50 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:50 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:50 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:50 MarkDuplicates Getting Memory Stats. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates Before output close freeMemory: 758194680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:50 MarkDuplicates Before output close freeMemory: 758194680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:50 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:50 MarkDuplicates After output close freeMemory: 758334544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:50 MarkDuplicates After output close freeMemory: 758334544; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:26:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:51 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testStackOverFlowPairSetSwap STANDARD_ERROR INFO 2024-07-02 11:26:51 MarkDuplicates Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.5313664054494585676.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.5313664054494585676.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.5313664054494585676.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.5313664054494585676.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.5313664054494585676.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.5313664054494585676.tmp/output.sam Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:51.013 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:51.013 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:51.013 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:51.013 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:51.013 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:51.013 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:51.013 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:51.013 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:51 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.5313664054494585676.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.5313664054494585676.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.5313664054494585676.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:51 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.5313664054494585676.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.5313664054494585676.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.5313664054494585676.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:51 MarkDuplicates Start of doWork freeMemory: 1027714240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:51 MarkDuplicates Start of doWork freeMemory: 1027714240; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:51 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:51 MarkDuplicates Reading input file and constructing read end information. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:51 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:51 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:51 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:26:51 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 964765216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 964765216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:51 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:51 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:51 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:51 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:51 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:51 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:51 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:51 MarkDuplicates Sorting list of duplicate records. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 488712016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 488712016; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:51 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:26:51 MarkDuplicates Marking 2 records as duplicates. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:51 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:26:51 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:51 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:51 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:51 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:51 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:51 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:51 MarkDuplicates Duplicate Index cleanup. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:51 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:51 MarkDuplicates Getting Memory Stats. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:51 MarkDuplicates Before output close freeMemory: 758027168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:51 MarkDuplicates Before output close freeMemory: 758027168; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:51 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:51 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:51 MarkDuplicates After output close freeMemory: 758195920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:51 MarkDuplicates After output close freeMemory: 758195920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:26:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:51 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:26:51 MarkDuplicates Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.12138337859164948435.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.12138337859164948435.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.12138337859164948435.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.12138337859164948435.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.12138337859164948435.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.12138337859164948435.tmp/output.sam Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:51.820 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:51.820 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:51.820 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:51.820 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:51.820 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:51.820 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:51.820 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:51.820 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:51 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.12138337859164948435.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.12138337859164948435.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.12138337859164948435.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:51 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.12138337859164948435.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.12138337859164948435.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.12138337859164948435.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:51 MarkDuplicates Start of doWork freeMemory: 1027811216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:51 MarkDuplicates Start of doWork freeMemory: 1027811216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:51 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:51 MarkDuplicates Reading input file and constructing read end information. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:51 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:51 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:26:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:26:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:51 MarkDuplicates Read 18 records. 0 pairs never matched. INFO 2024-07-02 11:26:51 MarkDuplicates Read 18 records. 0 pairs never matched. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 964888824; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 964888824; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:52 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:52 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:52 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:52 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:52 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:52 MarkDuplicates Sorting list of duplicate records. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:52 MarkDuplicates After generateDuplicateIndexes freeMemory: 488837288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:52 MarkDuplicates After generateDuplicateIndexes freeMemory: 488837288; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:52 MarkDuplicates Marking 12 records as duplicates. INFO 2024-07-02 11:26:52 MarkDuplicates Marking 12 records as duplicates. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:52 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:52 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:52 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:52 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:52 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:52 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:52 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:52 MarkDuplicates Duplicate Index cleanup. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:52 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:52 MarkDuplicates Getting Memory Stats. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:52 MarkDuplicates Before output close freeMemory: 758181008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:52 MarkDuplicates Before output close freeMemory: 758181008; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:52 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:52 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:52 MarkDuplicates After output close freeMemory: 758321192; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:52 MarkDuplicates After output close freeMemory: 758321192; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:26:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:52 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:26:52 MarkDuplicates Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.14200151813137530324.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.14200151813137530324.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.14200151813137530324.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.14200151813137530324.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.14200151813137530324.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.14200151813137530324.tmp/output.sam Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:52.554 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:52.554 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:52.555 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:52.555 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:52.555 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:52.555 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:52.555 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:52.555 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:52 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.14200151813137530324.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.14200151813137530324.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.14200151813137530324.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:52 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.14200151813137530324.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.14200151813137530324.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.14200151813137530324.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:52 MarkDuplicates Start of doWork freeMemory: 1027818480; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:52 MarkDuplicates Start of doWork freeMemory: 1027818480; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:52 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:52 MarkDuplicates Reading input file and constructing read end information. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:52 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:52 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:26:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:26:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:52 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:26:52 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 964897624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 964897624; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:52 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:52 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:52 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:52 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:52 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:52 MarkDuplicates Sorting list of duplicate records. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 488844792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 488844792; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:53 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:26:53 MarkDuplicates Marking 4 records as duplicates. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:53 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:53 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:53 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:53 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:53 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:53 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:53 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:53 MarkDuplicates Duplicate Index cleanup. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:53 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:53 MarkDuplicates Getting Memory Stats. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:53 MarkDuplicates Before output close freeMemory: 758188512; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:53 MarkDuplicates Before output close freeMemory: 758188512; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:53 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:53 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:53 MarkDuplicates After output close freeMemory: 758328696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:53 MarkDuplicates After output close freeMemory: 758328696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:26:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:53 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testThreeMappedPairsWithMatchingSecondMate STANDARD_ERROR INFO 2024-07-02 11:26:53 MarkDuplicates Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.8322772493019446229.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.8322772493019446229.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.8322772493019446229.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.8322772493019446229.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.8322772493019446229.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.8322772493019446229.tmp/output.sam Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:53.490 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:53.490 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:53.491 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:53.491 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:53.491 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:53.491 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:53.491 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:53.491 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:53 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.8322772493019446229.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.8322772493019446229.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.8322772493019446229.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:53 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.8322772493019446229.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.8322772493019446229.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.8322772493019446229.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:53 MarkDuplicates Start of doWork freeMemory: 1027817456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:53 MarkDuplicates Start of doWork freeMemory: 1027817456; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:53 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:53 MarkDuplicates Reading input file and constructing read end information. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:53 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:53 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:26:53 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:26:53 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:53 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:26:53 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 964896600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 964896600; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:53 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:53 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:53 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:53 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:53 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:53 MarkDuplicates Sorting list of duplicate records. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 488843592; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 488843592; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:53 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:26:53 MarkDuplicates Marking 2 records as duplicates. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:53 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:53 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:53 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:53 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:53 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:53 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:53 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:53 MarkDuplicates Duplicate Index cleanup. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:53 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:53 MarkDuplicates Getting Memory Stats. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:54 MarkDuplicates Before output close freeMemory: 758186608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:54 MarkDuplicates Before output close freeMemory: 758186608; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:54 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:54 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:54 MarkDuplicates After output close freeMemory: 758172592; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:54 MarkDuplicates After output close freeMemory: 758172592; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:54 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:26:54 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:54 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:26:54 MarkDuplicates Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.17211314210829845805.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.17211314210829845805.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.17211314210829845805.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.17211314210829845805.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.17211314210829845805.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.17211314210829845805.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:54.171 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:54.171 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:54.171 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:54.171 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:54.171 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:54.171 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:54.171 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:54.171 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:54 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.17211314210829845805.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.17211314210829845805.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.17211314210829845805.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:54 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.17211314210829845805.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.17211314210829845805.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.17211314210829845805.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:54 MarkDuplicates Start of doWork freeMemory: 1027812792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:54 MarkDuplicates Start of doWork freeMemory: 1027812792; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:54 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:54 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:54 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:54 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:26:54 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:26:54 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:54 MarkDuplicates Read 12 records. 0 pairs never matched. INFO 2024-07-02 11:26:54 MarkDuplicates Read 12 records. 0 pairs never matched. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 964891176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 964891176; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:54 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:54 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:54 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:54 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:54 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:54 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:54 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:54 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 488838992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 488838992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:54 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:26:54 MarkDuplicates Marking 8 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:54 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:54 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:54 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:54 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:54 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:54 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:54 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:54 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:54 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:54 MarkDuplicates Getting Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:54 MarkDuplicates Before output close freeMemory: 758027152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:54 MarkDuplicates Before output close freeMemory: 758027152; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:54 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:54 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:55 MarkDuplicates After output close freeMemory: 758322600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:55 MarkDuplicates After output close freeMemory: 758322600; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:55 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:26:55 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:55 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoGroupsOnDifferentChromosomesOfTwoFragments STANDARD_ERROR INFO 2024-07-02 11:26:55 MarkDuplicates Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.4995012509218660567.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4995012509218660567.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4995012509218660567.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.4995012509218660567.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4995012509218660567.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4995012509218660567.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:55.044 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:55.044 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:55.044 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:55.044 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:55.045 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:55.045 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:55.045 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:55.045 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:55 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.4995012509218660567.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.4995012509218660567.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.4995012509218660567.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:55 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.4995012509218660567.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.4995012509218660567.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.4995012509218660567.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:55 MarkDuplicates Start of doWork freeMemory: 1027817544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:55 MarkDuplicates Start of doWork freeMemory: 1027817544; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:55 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:55 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:55 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:55 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:26:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:26:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:55 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:26:55 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 964897168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 964897168; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:55 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:55 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:55 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:55 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:55 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 488844152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 488844152; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:55 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:26:55 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:55 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:55 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:55 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:55 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:55 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:55 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:55 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:55 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:55 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:55 MarkDuplicates Getting Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:55 MarkDuplicates Before output close freeMemory: 758187984; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:55 MarkDuplicates Before output close freeMemory: 758187984; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:55 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:55 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:55 MarkDuplicates After output close freeMemory: 758328056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:55 MarkDuplicates After output close freeMemory: 758328056; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:55 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:26:55 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:55 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:26:55 MarkDuplicates Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.308495907668863491.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.308495907668863491.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.308495907668863491.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.308495907668863491.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.308495907668863491.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.308495907668863491.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:55.968 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:55.968 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:55.969 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:55.969 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:55.969 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:55.969 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:55.969 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:55.969 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:55 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.308495907668863491.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.308495907668863491.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.308495907668863491.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:55 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.308495907668863491.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.308495907668863491.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.308495907668863491.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:56 MarkDuplicates Start of doWork freeMemory: 1027814120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:56 MarkDuplicates Start of doWork freeMemory: 1027814120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:56 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:56 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:56 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:56 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:26:56 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:26:56 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:56 MarkDuplicates Read 8 records. 0 pairs never matched. INFO 2024-07-02 11:26:56 MarkDuplicates Read 8 records. 0 pairs never matched. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 964892712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 964892712; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:56 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:56 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:56 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:56 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:56 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:56 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 488840312; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 488840312; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:56 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:26:56 MarkDuplicates Marking 4 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:56 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:56 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:56 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:56 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:56 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:56 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:56 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:56 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:56 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:56 MarkDuplicates Getting Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:56 MarkDuplicates Before output close freeMemory: 758184032; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:56 MarkDuplicates Before output close freeMemory: 758184032; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:56 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:56 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:56 MarkDuplicates After output close freeMemory: 758323720; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:56 MarkDuplicates After output close freeMemory: 758323720; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:56 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:26:56 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:56 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoMappedFragments STANDARD_ERROR INFO 2024-07-02 11:26:56 MarkDuplicates Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.4181304246251936650.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4181304246251936650.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4181304246251936650.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.4181304246251936650.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4181304246251936650.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4181304246251936650.tmp/output.sam Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:56.879 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:56.879 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:56.879 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:56.879 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:56.880 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:56.880 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:56.880 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:56.880 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:56 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.4181304246251936650.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.4181304246251936650.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.4181304246251936650.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:56 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.4181304246251936650.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.4181304246251936650.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.4181304246251936650.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:56 MarkDuplicates Start of doWork freeMemory: 1027817344; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:56 MarkDuplicates Start of doWork freeMemory: 1027817344; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:56 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:56 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:56 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:56 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:26:57 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:26:57 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:57 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:26:57 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 964897112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 964897112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:57 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:57 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:57 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:57 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:57 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:57 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 488843952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 488843952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:57 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:26:57 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:57 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:57 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:57 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:57 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:57 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:57 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:57 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:57 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:57 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:57 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:57 MarkDuplicates Before output close freeMemory: 758187784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:57 MarkDuplicates Before output close freeMemory: 758187784; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:57 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:57 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:57 MarkDuplicates After output close freeMemory: 758327632; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:57 MarkDuplicates After output close freeMemory: 758327632; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:57 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:26:57 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:57 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoMappedPairWithSamePosition STANDARD_ERROR INFO 2024-07-02 11:26:57 MarkDuplicates Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.4606303095663199274.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4606303095663199274.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4606303095663199274.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.4606303095663199274.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4606303095663199274.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4606303095663199274.tmp/output.sam Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:57.991 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:57.991 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:57.991 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:57.991 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:57.992 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:57.992 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:57.992 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:57.992 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:57 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.4606303095663199274.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.4606303095663199274.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.4606303095663199274.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:57 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.4606303095663199274.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.4606303095663199274.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.4606303095663199274.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:58 MarkDuplicates Start of doWork freeMemory: 1027812432; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:58 MarkDuplicates Start of doWork freeMemory: 1027812432; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:58 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:58 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:58 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:58 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:26:58 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:26:58 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:58 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:26:58 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 964894584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 964894584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:58 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:58 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:58 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:58 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:58 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:58 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 488841536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 488841536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:58 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:26:58 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:58 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:58 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:58 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:58 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:58 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:58 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:58 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:58 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:58 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:58 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:58 MarkDuplicates Before output close freeMemory: 758185184; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:58 MarkDuplicates Before output close freeMemory: 758185184; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:58 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:58 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:58 MarkDuplicates After output close freeMemory: 758325440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:58 MarkDuplicates After output close freeMemory: 758325440; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:26:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:58 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoMappedPairWithSamePositionDifferentStrands STANDARD_ERROR INFO 2024-07-02 11:26:58 MarkDuplicates Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.10753790407176850421.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.10753790407176850421.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.10753790407176850421.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.10753790407176850421.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.10753790407176850421.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.10753790407176850421.tmp/output.sam Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:58.971 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:58.971 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:58.971 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:58.971 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:58.971 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:58.971 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:58.971 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:58.971 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:58 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.10753790407176850421.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.10753790407176850421.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.10753790407176850421.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:58 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.10753790407176850421.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.10753790407176850421.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.10753790407176850421.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:59 MarkDuplicates Start of doWork freeMemory: 1027814688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:59 MarkDuplicates Start of doWork freeMemory: 1027814688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:59 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:59 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:59 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:59 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:26:59 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:26:59 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:59 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:26:59 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 964894048; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 964894048; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:59 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:26:59 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:59 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:26:59 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:59 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:26:59 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:59 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:26:59 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 488841000; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 488841000; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:59 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:26:59 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:59 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:26:59 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:59 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:26:59 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:59 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:26:59 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:59 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:26:59 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:59 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:26:59 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:59 MarkDuplicates Before output close freeMemory: 758184720; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:59 MarkDuplicates Before output close freeMemory: 758184720; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:59 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:26:59 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:59 MarkDuplicates After output close freeMemory: 758169408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:59 MarkDuplicates After output close freeMemory: 758169408; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:59 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:26:59 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:59 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoMappedPairWithSamePositionDifferentStrands2 STANDARD_ERROR INFO 2024-07-02 11:26:59 MarkDuplicates Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.9868643306444012409.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.9868643306444012409.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.9868643306444012409.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.9868643306444012409.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.9868643306444012409.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.9868643306444012409.tmp/output.sam Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:59.758 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:59.758 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:59.758 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:59.758 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:59.759 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:26:59.759 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:26:59.759 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:26:59.759 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:59 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.9868643306444012409.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.9868643306444012409.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.9868643306444012409.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:26:59 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.9868643306444012409.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.9868643306444012409.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.9868643306444012409.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:26:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:26:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:59 MarkDuplicates Start of doWork freeMemory: 1027813640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:59 MarkDuplicates Start of doWork freeMemory: 1027813640; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:59 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:26:59 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:59 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:26:59 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:26:59 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:26:59 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:59 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:26:59 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:26:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 964893392; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:26:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 964893392; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:00 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:00 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:00 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:00 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:00 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:00 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 488840344; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 488840344; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:00 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:27:00 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:00 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:27:00 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:00 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:00 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:00 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:00 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:00 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:00 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:00 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:00 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:00 MarkDuplicates Before output close freeMemory: 758184064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:00 MarkDuplicates Before output close freeMemory: 758184064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:00 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:00 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:00 MarkDuplicates After output close freeMemory: 758324248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:00 MarkDuplicates After output close freeMemory: 758324248; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:27:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:00 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:27:00 MarkDuplicates Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.18397626948180395818.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.18397626948180395818.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.18397626948180395818.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.18397626948180395818.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.18397626948180395818.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.18397626948180395818.tmp/output.sam Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:00.625 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:00.625 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:00.625 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:00.625 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:00.625 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:00.625 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:00.626 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:00.626 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:00 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.18397626948180395818.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.18397626948180395818.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.18397626948180395818.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:00 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.18397626948180395818.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.18397626948180395818.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.18397626948180395818.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:00 MarkDuplicates Start of doWork freeMemory: 1027813112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:00 MarkDuplicates Start of doWork freeMemory: 1027813112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:00 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:00 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:00 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:00 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:27:00 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:27:00 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:00 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:27:00 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 964892472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 964892472; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:01 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:01 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:01 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:01 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:01 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:01 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 918755584; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2024-07-02 11:27:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 918755584; totalMemory: 1503657984; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:01 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:27:01 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:01 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:27:01 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:01 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:01 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:01 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:01 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:01 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:01 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:01 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:01 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:01 MarkDuplicates Before output close freeMemory: 758183144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:01 MarkDuplicates Before output close freeMemory: 758183144; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:01 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:01 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:01 MarkDuplicates After output close freeMemory: 758323328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:01 MarkDuplicates After output close freeMemory: 758323328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:01 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:27:01 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:01 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoMappedPairsAndMappedSecondaryFragment STANDARD_ERROR INFO 2024-07-02 11:27:01 MarkDuplicates Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.2409417953365294023.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.2409417953365294023.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.2409417953365294023.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.2409417953365294023.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.2409417953365294023.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.2409417953365294023.tmp/output.sam Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:01.437 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:01.437 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:01.438 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:01.438 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:01.438 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:01.438 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:01.438 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:01.438 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:01 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.2409417953365294023.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.2409417953365294023.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.2409417953365294023.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:01 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.2409417953365294023.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.2409417953365294023.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.2409417953365294023.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:01 MarkDuplicates Start of doWork freeMemory: 1027811752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:01 MarkDuplicates Start of doWork freeMemory: 1027811752; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:01 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:01 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:01 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:01 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:27:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:27:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:01 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:27:01 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 964891112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 964891112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:01 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:01 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:01 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:01 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:01 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:01 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 488838064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 488838064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:02 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:27:02 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:02 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:27:02 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:02 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:02 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:02 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:02 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:02 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:02 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:02 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:02 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:02 MarkDuplicates Before output close freeMemory: 758181896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:02 MarkDuplicates Before output close freeMemory: 758181896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:02 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:02 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:02 MarkDuplicates After output close freeMemory: 758321968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:02 MarkDuplicates After output close freeMemory: 758321968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:02 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:27:02 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:02 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoMappedPairsAndTerminalUnmappedFragment STANDARD_ERROR INFO 2024-07-02 11:27:02 MarkDuplicates Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.13028125955198116700.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.13028125955198116700.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.13028125955198116700.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.13028125955198116700.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.13028125955198116700.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.13028125955198116700.tmp/output.sam Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:02.260 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:02.260 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:02.260 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:02.260 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:02.260 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:02.260 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:02.260 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:02.260 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:02 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.13028125955198116700.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.13028125955198116700.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.13028125955198116700.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:02 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.13028125955198116700.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.13028125955198116700.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.13028125955198116700.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:02 MarkDuplicates Start of doWork freeMemory: 1027811160; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:02 MarkDuplicates Start of doWork freeMemory: 1027811160; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:02 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:02 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:02 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:02 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:27:02 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:27:02 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:02 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:27:02 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 964890520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 964890520; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:02 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:02 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:02 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:02 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:02 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:02 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:02 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:02 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 488837472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 488837472; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:02 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:27:02 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:02 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:27:02 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:02 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:02 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:02 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:02 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:02 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:02 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:02 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:02 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:02 MarkDuplicates Before output close freeMemory: 758181512; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:02 MarkDuplicates Before output close freeMemory: 758181512; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:03 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:03 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:03 MarkDuplicates After output close freeMemory: 758321376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:03 MarkDuplicates After output close freeMemory: 758321376; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:03 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:27:03 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:03 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoMappedPairsAndTerminalUnmappedPair STANDARD_ERROR INFO 2024-07-02 11:27:03 MarkDuplicates Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.16865465034154244024.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16865465034154244024.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16865465034154244024.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.16865465034154244024.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16865465034154244024.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16865465034154244024.tmp/output.sam Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:03.211 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:03.211 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:03.211 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:03.211 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:03.211 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:03.211 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:03.211 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:03.211 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:03 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.16865465034154244024.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.16865465034154244024.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.16865465034154244024.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:03 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.16865465034154244024.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.16865465034154244024.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.16865465034154244024.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:03 MarkDuplicates Start of doWork freeMemory: 1027809984; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:03 MarkDuplicates Start of doWork freeMemory: 1027809984; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:03 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:03 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:03 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:03 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:27:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:27:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:03 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:27:03 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 964889344; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 964889344; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:03 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:03 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:03 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:03 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:03 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:03 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:03 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:03 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 488836296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 488836296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:03 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:27:03 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:03 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:27:03 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:03 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:03 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:03 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:03 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:03 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:03 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:03 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:03 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:03 MarkDuplicates Before output close freeMemory: 758180336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:03 MarkDuplicates Before output close freeMemory: 758180336; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:03 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:03 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:03 MarkDuplicates After output close freeMemory: 758320200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:03 MarkDuplicates After output close freeMemory: 758320200; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:03 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:27:03 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:03 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoMappedPairsMatesSoftClipped STANDARD_ERROR INFO 2024-07-02 11:27:03 MarkDuplicates Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.9266130940011497414.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.9266130940011497414.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.9266130940011497414.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.9266130940011497414.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.9266130940011497414.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.9266130940011497414.tmp/output.sam Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:03.967 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:03.967 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:03.967 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:03.967 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:03.967 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:03.967 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:03.967 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:03.967 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:03 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.9266130940011497414.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.9266130940011497414.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.9266130940011497414.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:03 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.9266130940011497414.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.9266130940011497414.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.9266130940011497414.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:04 MarkDuplicates Start of doWork freeMemory: 1027809824; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:04 MarkDuplicates Start of doWork freeMemory: 1027809824; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:04 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:04 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:04 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:04 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:27:04 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:27:04 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:04 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:27:04 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 964734032; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 964734032; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:04 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:04 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:04 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:04 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:04 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:04 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:04 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:04 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 488836136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 488836136; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:04 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:27:04 MarkDuplicates Marking 0 records as duplicates. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:04 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:27:04 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:04 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:04 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:04 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:04 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:04 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:04 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:04 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:04 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:04 MarkDuplicates Before output close freeMemory: 758179784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:04 MarkDuplicates Before output close freeMemory: 758179784; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:04 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:04 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:04 MarkDuplicates After output close freeMemory: 758319544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:04 MarkDuplicates After output close freeMemory: 758319544; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:04 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:27:04 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:04 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoMappedPairsWithOppositeOrientations STANDARD_ERROR INFO 2024-07-02 11:27:04 MarkDuplicates Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.16276920643128639647.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16276920643128639647.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16276920643128639647.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.16276920643128639647.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16276920643128639647.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16276920643128639647.tmp/output.sam Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:04.815 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:04.815 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:04.815 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:04.815 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:04.815 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:04.815 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:04.816 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:04.816 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:04 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.16276920643128639647.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.16276920643128639647.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.16276920643128639647.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:04 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.16276920643128639647.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.16276920643128639647.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.16276920643128639647.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:04 MarkDuplicates Start of doWork freeMemory: 1027808984; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:04 MarkDuplicates Start of doWork freeMemory: 1027808984; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:04 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:04 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:04 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:04 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:27:04 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:27:04 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:04 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:27:04 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 964888344; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 964888344; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:05 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:05 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:05 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:05 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:05 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:05 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 488835296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 488835296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:05 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:27:05 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:05 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:27:05 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:05 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:05 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:05 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:05 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:05 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:05 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:05 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:05 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:05 MarkDuplicates Before output close freeMemory: 758178088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:05 MarkDuplicates Before output close freeMemory: 758178088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:05 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:05 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:05 MarkDuplicates After output close freeMemory: 758319200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:05 MarkDuplicates After output close freeMemory: 758319200; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:05 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:27:05 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:05 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoMappedPairsWithOppositeOrientationsNumberTwo STANDARD_ERROR INFO 2024-07-02 11:27:05 MarkDuplicates Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.16099594094002389763.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16099594094002389763.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16099594094002389763.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.16099594094002389763.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16099594094002389763.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16099594094002389763.tmp/output.sam Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:05.624 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:05.624 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:05.624 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:05.624 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:05.625 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:05.625 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:05.625 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:05.625 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:05 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.16099594094002389763.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.16099594094002389763.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.16099594094002389763.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:05 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.16099594094002389763.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.16099594094002389763.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.16099594094002389763.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:05 MarkDuplicates Start of doWork freeMemory: 1027808248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:05 MarkDuplicates Start of doWork freeMemory: 1027808248; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:05 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:05 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:05 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:05 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:27:05 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:27:05 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:05 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:27:05 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 964887608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 964887608; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:06 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:06 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:06 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 488834560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 488834560; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:27:06 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:27:06 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:06 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:06 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:06 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:06 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates Before output close freeMemory: 758178208; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:06 MarkDuplicates Before output close freeMemory: 758178208; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:06 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates After output close freeMemory: 758163040; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:06 MarkDuplicates After output close freeMemory: 758163040; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:06 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:27:06 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoMappedPairsWithSoftClipping STANDARD_ERROR INFO 2024-07-02 11:27:06 MarkDuplicates Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.11258336832652325689.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.11258336832652325689.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.11258336832652325689.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.11258336832652325689.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.11258336832652325689.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.11258336832652325689.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:06.372 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:06.372 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:06.372 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:06.372 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:06.372 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:06.372 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:06.372 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:06.372 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:06 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.11258336832652325689.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.11258336832652325689.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.11258336832652325689.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:06 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.11258336832652325689.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.11258336832652325689.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.11258336832652325689.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates Start of doWork freeMemory: 1027807464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:06 MarkDuplicates Start of doWork freeMemory: 1027807464; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:06 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:06 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:27:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:27:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:27:06 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 964731296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 964731296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:06 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:06 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:06 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:06 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 488833776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 488833776; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:27:06 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:27:06 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:06 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:06 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:06 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:06 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:06 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:07 MarkDuplicates Before output close freeMemory: 758177424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:07 MarkDuplicates Before output close freeMemory: 758177424; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:07 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:07 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:07 MarkDuplicates After output close freeMemory: 758162256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:07 MarkDuplicates After output close freeMemory: 758162256; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:07 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:27:07 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:07 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoMappedPairsWithSoftClippingBoth STANDARD_ERROR INFO 2024-07-02 11:27:07 MarkDuplicates Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.10551974883528442611.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.10551974883528442611.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.10551974883528442611.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.10551974883528442611.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.10551974883528442611.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.10551974883528442611.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:07.135 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:07.135 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:07.135 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:07.135 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:07.135 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:07.135 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:07.135 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:07.135 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:07 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.10551974883528442611.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.10551974883528442611.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.10551974883528442611.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:07 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.10551974883528442611.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.10551974883528442611.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.10551974883528442611.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:07 MarkDuplicates Start of doWork freeMemory: 1027804488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:07 MarkDuplicates Start of doWork freeMemory: 1027804488; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:07 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:07 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:07 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:07 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:27:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:27:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:07 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:27:07 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 964886088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 964886088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:07 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:07 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:07 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:07 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:07 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:07 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:07 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:07 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 488833040; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 488833040; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:07 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:27:07 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:07 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:27:07 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:07 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:07 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:07 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:07 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:07 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:07 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:07 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:07 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:07 MarkDuplicates Before output close freeMemory: 758176688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:07 MarkDuplicates Before output close freeMemory: 758176688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:07 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:07 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:07 MarkDuplicates After output close freeMemory: 758316872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:07 MarkDuplicates After output close freeMemory: 758316872; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:07 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:27:07 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:07 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar STANDARD_ERROR INFO 2024-07-02 11:27:07 MarkDuplicates Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.2094425700270168379.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.2094425700270168379.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.2094425700270168379.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.2094425700270168379.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.2094425700270168379.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.2094425700270168379.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:07.909 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:07.909 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:07.910 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:07.910 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:07.910 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:07.910 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:07.910 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:07.910 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:07 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.2094425700270168379.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.2094425700270168379.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.2094425700270168379.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:07 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.2094425700270168379.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.2094425700270168379.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.2094425700270168379.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:08 MarkDuplicates Start of doWork freeMemory: 1027807160; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:08 MarkDuplicates Start of doWork freeMemory: 1027807160; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:08 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:08 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:08 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:08 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: WARNING 2024-07-02 11:27:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:27:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:08 MarkDuplicates Read 2 records. 2 pairs never matched. INFO 2024-07-02 11:27:08 MarkDuplicates Read 2 records. 2 pairs never matched. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 964886808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 964886808; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:08 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:08 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:08 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:08 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:08 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:08 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 594739824; totalMemory: 1179648000; maxMemory: 2147483648 INFO 2024-07-02 11:27:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 594739824; totalMemory: 1179648000; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:08 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:27:08 MarkDuplicates Marking 0 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:08 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:27:08 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:08 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:08 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:08 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:08 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:08 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:08 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:08 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:08 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:08 MarkDuplicates Before output close freeMemory: 758177344; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:08 MarkDuplicates Before output close freeMemory: 758177344; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:08 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:08 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:08 MarkDuplicates After output close freeMemory: 758317056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:08 MarkDuplicates After output close freeMemory: 758317056; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:08 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:27:08 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:08 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoMappedPairsWithSupplementaryReads[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:27:08 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.14278432486845803929.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.14278432486845803929.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.14278432486845803929.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.14278432486845803929.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.14278432486845803929.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.14278432486845803929.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:08.762 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:08.762 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:08.762 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:08.762 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:08.763 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:08.763 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:08.763 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:08.763 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:08 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.14278432486845803929.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.14278432486845803929.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.14278432486845803929.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:08 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.14278432486845803929.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.14278432486845803929.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.14278432486845803929.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:08 MarkDuplicates Start of doWork freeMemory: 1027804496; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:08 MarkDuplicates Start of doWork freeMemory: 1027804496; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:08 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:08 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:08 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:08 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:08 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:27:08 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 964883576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 964883576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:09 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:09 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:09 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:09 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:09 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:09 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 488830592; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 488830592; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:09 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:27:09 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:09 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:27:09 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:09 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:09 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:09 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:09 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:09 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:09 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:09 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:09 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:09 MarkDuplicates Before output close freeMemory: 758174216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:09 MarkDuplicates Before output close freeMemory: 758174216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:09 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:09 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:09 MarkDuplicates After output close freeMemory: 758159336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:09 MarkDuplicates After output close freeMemory: 758159336; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:09 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:27:09 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:09 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoMappedPairsWithSupplementaryReads[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:27:09 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.7219370097616719309.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.7219370097616719309.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.7219370097616719309.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.7219370097616719309.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.7219370097616719309.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.7219370097616719309.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:09.582 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:09.582 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:09.582 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:09.582 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:09.582 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:09.582 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:09.582 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:09.582 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:09 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.7219370097616719309.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.7219370097616719309.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.7219370097616719309.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:09 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.7219370097616719309.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.7219370097616719309.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.7219370097616719309.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:09 MarkDuplicates Start of doWork freeMemory: 1027803776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:09 MarkDuplicates Start of doWork freeMemory: 1027803776; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:09 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:09 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:09 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:09 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:09 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:27:09 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 964882856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 964882856; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:10 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:10 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:10 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:10 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:10 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:10 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 488738832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 488738832; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:10 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:27:10 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:10 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:27:10 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:10 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:10 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:10 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:10 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:10 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:10 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:10 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:10 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:10 MarkDuplicates Before output close freeMemory: 758173496; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:10 MarkDuplicates Before output close freeMemory: 758173496; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:10 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:10 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:10 MarkDuplicates After output close freeMemory: 758313552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:10 MarkDuplicates After output close freeMemory: 758313552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:10 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:27:10 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:10 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoMappedPairsWithSupplementaryReads[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:27:10 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.4731253273631430338.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4731253273631430338.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4731253273631430338.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.4731253273631430338.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4731253273631430338.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4731253273631430338.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:10.548 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:10.548 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:10.548 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:10.548 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:10.548 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:10.548 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:10.548 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:10.548 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:10 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.4731253273631430338.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.4731253273631430338.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.4731253273631430338.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:10 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.4731253273631430338.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.4731253273631430338.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.4731253273631430338.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:10 MarkDuplicates Start of doWork freeMemory: 1027803120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:10 MarkDuplicates Start of doWork freeMemory: 1027803120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:10 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:10 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:10 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:10 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:10 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:27:10 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 964882200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 964882200; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:11 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:11 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:11 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:11 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 488829216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 488829216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:11 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:27:11 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:11 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:27:11 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:11 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:11 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:11 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:11 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:11 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:11 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:11 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:11 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:11 MarkDuplicates Before output close freeMemory: 758172208; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:11 MarkDuplicates Before output close freeMemory: 758172208; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:11 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:11 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:11 MarkDuplicates After output close freeMemory: 758311920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:11 MarkDuplicates After output close freeMemory: 758311920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:11 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:27:11 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:11 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoMappedPairsWithSupplementaryReads[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:27:11 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.6125460428945844342.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.6125460428945844342.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.6125460428945844342.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.6125460428945844342.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.6125460428945844342.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.6125460428945844342.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:11.549 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:11.549 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:11.550 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:11.550 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:11.550 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:11.550 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:11.550 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:11.550 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:11 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.6125460428945844342.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.6125460428945844342.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.6125460428945844342.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:11 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.6125460428945844342.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.6125460428945844342.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.6125460428945844342.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:11 MarkDuplicates Start of doWork freeMemory: 1027802488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:11 MarkDuplicates Start of doWork freeMemory: 1027802488; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:11 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:11 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:11 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:11 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:11 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:27:11 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 964881784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 964881784; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:12 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:12 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:12 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:12 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:12 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:12 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:12 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:12 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 488828584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 488828584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:12 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:27:12 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:12 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:27:12 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:12 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:12 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:12 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:12 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:12 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:12 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:12 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:12 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:12 MarkDuplicates Before output close freeMemory: 758016896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:12 MarkDuplicates Before output close freeMemory: 758016896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:12 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:12 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:12 MarkDuplicates After output close freeMemory: 758312416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:12 MarkDuplicates After output close freeMemory: 758312416; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:12 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:27:12 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:12 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoMappedPairsWithSupplementaryReads[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:27:12 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.5928568448161626127.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.5928568448161626127.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.5928568448161626127.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.5928568448161626127.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.5928568448161626127.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.5928568448161626127.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:12.953 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:12.953 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:12.954 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:12.954 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:12.954 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:12.954 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:12.954 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:12.954 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:12 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.5928568448161626127.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.5928568448161626127.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.5928568448161626127.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:12 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.5928568448161626127.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.5928568448161626127.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.5928568448161626127.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:13 MarkDuplicates Start of doWork freeMemory: 1027801856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:13 MarkDuplicates Start of doWork freeMemory: 1027801856; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:13 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:13 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:13 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:13 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:13 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:27:13 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 964880936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 964880936; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:14 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:14 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:14 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:14 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:14 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:14 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:14 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 488827952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 488827952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:15 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:27:15 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:15 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:27:15 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:15 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:15 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:15 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:15 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:15 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:15 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:15 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:15 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:15 MarkDuplicates Before output close freeMemory: 758170008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:15 MarkDuplicates Before output close freeMemory: 758170008; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:15 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:15 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:15 MarkDuplicates After output close freeMemory: 758156704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:15 MarkDuplicates After output close freeMemory: 758156704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:27:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:15 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoMappedPairsWithSupplementaryReads[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:27:15 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.2710781749863947429.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.2710781749863947429.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.2710781749863947429.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.2710781749863947429.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.2710781749863947429.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.2710781749863947429.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:15.857 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:15.857 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:15.857 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:15.857 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:15.857 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:15.857 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:15.857 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:15.857 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:15 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.2710781749863947429.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.2710781749863947429.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.2710781749863947429.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:15 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.2710781749863947429.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.2710781749863947429.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.2710781749863947429.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:16 MarkDuplicates Start of doWork freeMemory: 1027801200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:16 MarkDuplicates Start of doWork freeMemory: 1027801200; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:16 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:16 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:16 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:16 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:16 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:27:16 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 964880496; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 964880496; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:17 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:17 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:17 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:17 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:17 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:17 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 488861000; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 488861000; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:17 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:27:17 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:17 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:27:17 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:17 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:17 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:17 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:17 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:17 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:17 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:17 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:17 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:17 MarkDuplicates Before output close freeMemory: 758204624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:17 MarkDuplicates Before output close freeMemory: 758204624; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:17 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:17 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:17 MarkDuplicates After output close freeMemory: 758344832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:17 MarkDuplicates After output close freeMemory: 758344832; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:17 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:27:17 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:17 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:27:17 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.12457444361234246063.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.12457444361234246063.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.12457444361234246063.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.12457444361234246063.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.12457444361234246063.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.12457444361234246063.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:17.969 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:17.969 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:17.969 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:17.969 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:17.969 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:17.969 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:17.969 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:17.969 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:17 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.12457444361234246063.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.12457444361234246063.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.12457444361234246063.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:17 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.12457444361234246063.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.12457444361234246063.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.12457444361234246063.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:18 MarkDuplicates Start of doWork freeMemory: 1027833768; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:18 MarkDuplicates Start of doWork freeMemory: 1027833768; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:18 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:18 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:18 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:18 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:18 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:27:18 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 964913064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 964913064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:18 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:18 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:18 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:18 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:18 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:18 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 613640408; totalMemory: 1198522368; maxMemory: 2147483648 INFO 2024-07-02 11:27:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 613640408; totalMemory: 1198522368; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:19 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:27:19 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:19 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:27:19 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:19 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:19 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:19 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:19 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:19 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:19 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:19 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:19 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:19 MarkDuplicates Before output close freeMemory: 758203016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:19 MarkDuplicates Before output close freeMemory: 758203016; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:19 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:19 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:19 MarkDuplicates After output close freeMemory: 758343280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:19 MarkDuplicates After output close freeMemory: 758343280; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:19 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:27:19 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:19 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:27:19 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.755477298374905681.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.755477298374905681.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.755477298374905681.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.755477298374905681.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.755477298374905681.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.755477298374905681.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:20.013 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:20.013 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:20.013 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:20.013 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:20.013 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:20.013 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:20.013 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:20.013 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:20 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.755477298374905681.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.755477298374905681.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.755477298374905681.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:20 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.755477298374905681.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.755477298374905681.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.755477298374905681.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:20 MarkDuplicates Start of doWork freeMemory: 1027830360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:20 MarkDuplicates Start of doWork freeMemory: 1027830360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:20 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:20 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:20 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:20 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:20 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:27:20 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 964912232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 964912232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:21 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:21 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:21 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:21 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:21 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:21 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 488859248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 488859248; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:21 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:27:21 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:21 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:27:21 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:21 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:21 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:21 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:21 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:21 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:21 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:21 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:21 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:21 MarkDuplicates Before output close freeMemory: 758201472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:21 MarkDuplicates Before output close freeMemory: 758201472; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:21 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:21 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:21 MarkDuplicates After output close freeMemory: 758343152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:21 MarkDuplicates After output close freeMemory: 758343152; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:21 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:27:21 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:21 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:27:21 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.11720821626565571412.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.11720821626565571412.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.11720821626565571412.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.11720821626565571412.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.11720821626565571412.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.11720821626565571412.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:22.003 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:22.003 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:22.003 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:22.003 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:22.003 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:22.003 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:22.003 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:22.003 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:22 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.11720821626565571412.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.11720821626565571412.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.11720821626565571412.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:22 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.11720821626565571412.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.11720821626565571412.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.11720821626565571412.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:22 MarkDuplicates Start of doWork freeMemory: 1027832552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:22 MarkDuplicates Start of doWork freeMemory: 1027832552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:22 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:22 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:22 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:22 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:22 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:27:22 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 964911848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 964911848; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:23 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:23 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:23 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:23 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:23 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:23 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 488858648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 488858648; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:23 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:27:23 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:23 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:27:23 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:23 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:23 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:23 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:23 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:23 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:23 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:23 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:23 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:23 MarkDuplicates Before output close freeMemory: 758202432; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:23 MarkDuplicates Before output close freeMemory: 758202432; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:23 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:23 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:23 MarkDuplicates After output close freeMemory: 758342480; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:23 MarkDuplicates After output close freeMemory: 758342480; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:23 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:27:23 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:23 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:27:23 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.16831449063848340504.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16831449063848340504.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16831449063848340504.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.16831449063848340504.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16831449063848340504.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.16831449063848340504.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:23.982 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:23.982 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:23.982 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:23.982 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:23.982 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:23.982 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:23.982 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:23.982 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:23 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.16831449063848340504.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.16831449063848340504.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.16831449063848340504.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:23 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.16831449063848340504.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.16831449063848340504.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.16831449063848340504.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:24 MarkDuplicates Start of doWork freeMemory: 1027831920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:24 MarkDuplicates Start of doWork freeMemory: 1027831920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:24 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:24 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:24 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:24 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:24 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:27:24 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 964911216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 964911216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:25 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:25 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:25 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:25 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:25 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:25 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:25 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:25 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 488858016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 488858016; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:25 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:27:25 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:25 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:27:25 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:25 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:25 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:25 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:25 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:25 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:25 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:25 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:25 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:26 MarkDuplicates Before output close freeMemory: 758200944; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:26 MarkDuplicates Before output close freeMemory: 758200944; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:26 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:26 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:26 MarkDuplicates After output close freeMemory: 758341456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:26 MarkDuplicates After output close freeMemory: 758341456; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:26 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:27:26 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:26 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:27:26 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.13546540827916527758.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.13546540827916527758.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.13546540827916527758.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.13546540827916527758.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.13546540827916527758.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.13546540827916527758.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:26.463 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:26.463 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:26.463 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:26.463 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:26.464 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:26.464 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:26.464 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:26.464 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:26 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.13546540827916527758.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.13546540827916527758.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.13546540827916527758.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:26 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.13546540827916527758.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.13546540827916527758.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.13546540827916527758.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:26 MarkDuplicates Start of doWork freeMemory: 1027831288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:26 MarkDuplicates Start of doWork freeMemory: 1027831288; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:26 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:26 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:26 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:26 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:26 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:27:26 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 964910584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 964910584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:27 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:27 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:27 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:27 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 488857384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 488857384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:28 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:27:28 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:28 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:27:28 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:28 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:28 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:28 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:28 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:28 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:28 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:28 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:28 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:28 MarkDuplicates Before output close freeMemory: 758045384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:28 MarkDuplicates Before output close freeMemory: 758045384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:28 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:28 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:28 MarkDuplicates After output close freeMemory: 758341216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:28 MarkDuplicates After output close freeMemory: 758341216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:28 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:27:28 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:28 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:27:28 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.11832218275243794522.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.11832218275243794522.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.11832218275243794522.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.11832218275243794522.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.11832218275243794522.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.11832218275243794522.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:28.714 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:28.714 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:28.714 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:28.714 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:28.715 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:28.715 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:28.715 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:28.715 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:28 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.11832218275243794522.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.11832218275243794522.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.11832218275243794522.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:28 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.11832218275243794522.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.11832218275243794522.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.11832218275243794522.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:28 MarkDuplicates Start of doWork freeMemory: 1027672880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:28 MarkDuplicates Start of doWork freeMemory: 1027672880; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:28 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:28 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:28 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:28 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:29 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:27:29 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 964754760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 964754760; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:30 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:30 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:30 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:30 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:30 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:30 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 669211776; totalMemory: 1254096896; maxMemory: 2147483648 INFO 2024-07-02 11:27:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 669211776; totalMemory: 1254096896; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:30 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:27:30 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:30 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:27:30 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:30 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:30 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:30 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:30 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:30 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:30 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:30 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:30 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:30 MarkDuplicates Before output close freeMemory: 758200488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:30 MarkDuplicates Before output close freeMemory: 758200488; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:30 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:30 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:31 MarkDuplicates After output close freeMemory: 758340536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:31 MarkDuplicates After output close freeMemory: 758340536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:31 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:27:31 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:31 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testTwoUnmappedFragments STANDARD_ERROR INFO 2024-07-02 11:27:31 MarkDuplicates Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.2715445393575879962.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.2715445393575879962.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.2715445393575879962.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.2715445393575879962.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.2715445393575879962.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.2715445393575879962.tmp/output.sam Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:31.130 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:31.130 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:31.130 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:31.130 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:31.131 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:31.131 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:31.131 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:31.131 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:31 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.2715445393575879962.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.2715445393575879962.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.2715445393575879962.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:31 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.2715445393575879962.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.2715445393575879962.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.2715445393575879962.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:31 MarkDuplicates Start of doWork freeMemory: 1027832208; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:31 MarkDuplicates Start of doWork freeMemory: 1027832208; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:31 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:31 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:31 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:31 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:31 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2024-07-02 11:27:31 MarkDuplicates Read 0 records. 0 pairs never matched. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 964912232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 964912232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:32 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:32 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:32 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:32 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:32 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:32 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 488858928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 488858928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:32 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:27:32 MarkDuplicates Marking 0 records as duplicates. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:32 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:27:32 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:32 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:32 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:32 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:32 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:32 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:32 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:32 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:32 MarkDuplicates Getting Memory Stats. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:32 MarkDuplicates Before output close freeMemory: 758201400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:32 MarkDuplicates Before output close freeMemory: 758201400; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:32 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:32 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:32 MarkDuplicates After output close freeMemory: 758342832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:32 MarkDuplicates After output close freeMemory: 758342832; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:27:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:32 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.TestSingleSet STANDARD_ERROR INFO 2024-07-02 11:27:32 MarkDuplicates Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.4287468642953048889.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4287468642953048889.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4287468642953048889.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.4287468642953048889.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4287468642953048889.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.4287468642953048889.tmp/output.sam Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:32.941 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:32.941 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:32.941 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:32.941 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:32.941 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:32.941 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:32.941 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:32.941 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:32 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.4287468642953048889.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.4287468642953048889.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.4287468642953048889.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:32 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.4287468642953048889.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.4287468642953048889.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.4287468642953048889.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:33 MarkDuplicates Start of doWork freeMemory: 1027827560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:33 MarkDuplicates Start of doWork freeMemory: 1027827560; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:33 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:33 MarkDuplicates Reading input file and constructing read end information. Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:33 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:33 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:33 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:27:33 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 964908872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 964908872; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:34 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:34 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:34 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:34 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:34 MarkDuplicates Sorting list of duplicate records. Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 488855888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 488855888; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:34 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:27:34 MarkDuplicates Marking 2 records as duplicates. Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:34 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:27:34 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:34 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:34 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:34 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:34 MarkDuplicates Writing complete. Closing input iterator. Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:34 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:34 MarkDuplicates Duplicate Index cleanup. Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:34 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:34 MarkDuplicates Getting Memory Stats. Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:34 MarkDuplicates Before output close freeMemory: 758198040; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:34 MarkDuplicates Before output close freeMemory: 758198040; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:34 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:34 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:34 MarkDuplicates After output close freeMemory: 758339568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:34 MarkDuplicates After output close freeMemory: 758339568; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:27:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method TestSingleSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:34 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testMultiRepresentativeReadTags STANDARD_ERROR INFO 2024-07-02 11:27:34 MarkDuplicates Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.14590886690936549354.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.14590886690936549354.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.14590886690936549354.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.14590886690936549354.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.14590886690936549354.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.14590886690936549354.tmp/output.sam Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:34.945 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:34.945 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:34.945 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:34.945 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:34.946 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:34.946 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:34.946 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:34.946 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:34 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.14590886690936549354.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.14590886690936549354.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.14590886690936549354.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:34 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.14590886690936549354.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.14590886690936549354.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.14590886690936549354.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:35 MarkDuplicates Start of doWork freeMemory: 1027823360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:35 MarkDuplicates Start of doWork freeMemory: 1027823360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:35 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:35 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:35 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:35 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:35 MarkDuplicates Read 12 records. 0 pairs never matched. INFO 2024-07-02 11:27:35 MarkDuplicates Read 12 records. 0 pairs never matched. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 964901792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 964901792; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:36 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:36 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:36 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:36 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:36 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:36 MarkDuplicates Sorting list of duplicate records. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 488848736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 488848736; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:36 MarkDuplicates Marking 6 records as duplicates. INFO 2024-07-02 11:27:36 MarkDuplicates Marking 6 records as duplicates. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:36 MarkDuplicates Found 3 optical duplicate clusters. INFO 2024-07-02 11:27:36 MarkDuplicates Found 3 optical duplicate clusters. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:36 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:36 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:36 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:36 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:36 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:36 MarkDuplicates Duplicate Index cleanup. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:36 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:36 MarkDuplicates Getting Memory Stats. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:36 MarkDuplicates Before output close freeMemory: 758192232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:36 MarkDuplicates Before output close freeMemory: 758192232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:36 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:36 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:36 MarkDuplicates After output close freeMemory: 758332120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:36 MarkDuplicates After output close freeMemory: 758332120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:36 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:27:36 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:37 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testOpticalAndNonOpticalSet STANDARD_ERROR INFO 2024-07-02 11:27:37 MarkDuplicates Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.14188785704769633259.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.14188785704769633259.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.14188785704769633259.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.14188785704769633259.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.14188785704769633259.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.14188785704769633259.tmp/output.sam Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:37.047 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:37.047 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:37.047 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:37.047 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:37.047 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:37.047 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:37.047 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:37.047 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:37 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.14188785704769633259.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.14188785704769633259.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.14188785704769633259.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:37 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.14188785704769633259.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.14188785704769633259.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.14188785704769633259.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:37 MarkDuplicates Start of doWork freeMemory: 1027664888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:37 MarkDuplicates Start of doWork freeMemory: 1027664888; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:37 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:37 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:37 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:37 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:37 MarkDuplicates Read 8 records. 0 pairs never matched. INFO 2024-07-02 11:27:37 MarkDuplicates Read 8 records. 0 pairs never matched. Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 964903880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 964903880; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:38 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:38 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:38 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:38 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:38 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:38 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 488851296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 488851296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:38 MarkDuplicates Marking 6 records as duplicates. INFO 2024-07-02 11:27:38 MarkDuplicates Marking 6 records as duplicates. Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:38 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:27:38 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:38 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:38 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:38 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:38 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:38 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:38 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:38 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:38 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:38 MarkDuplicates Before output close freeMemory: 758194992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:38 MarkDuplicates Before output close freeMemory: 758194992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:38 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:38 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:39 MarkDuplicates After output close freeMemory: 758335200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:39 MarkDuplicates After output close freeMemory: 758335200; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:27:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testOpticalAndNonOpticalSet(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:39 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest.testSingleton STANDARD_ERROR INFO 2024-07-02 11:27:39 MarkDuplicates Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.11136838449135787060.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.11136838449135787060.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.11136838449135787060.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesSetSizeHistogramTester.11136838449135787060.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesSetSizeHistogramTester.11136838449135787060.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesSetSizeHistogramTester.11136838449135787060.tmp/output.sam Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: ********** ********** Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:39.244 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:39.244 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:39.244 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:39.244 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:39.244 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:39.244 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: 11:27:39.244 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:39.244 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:39 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.11136838449135787060.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.11136838449135787060.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.11136838449135787060.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:39 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesSetSizeHistogramTester.11136838449135787060.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesSetSizeHistogramTester.11136838449135787060.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesSetSizeHistogramTester.11136838449135787060.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:39 MarkDuplicates Start of doWork freeMemory: 1027828232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:39 MarkDuplicates Start of doWork freeMemory: 1027828232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:39 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:39 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:39 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:39 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:39 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:27:39 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 964907744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 964907744; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:40 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:40 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:40 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:40 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:40 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 639849424; totalMemory: 1224736768; maxMemory: 2147483648 INFO 2024-07-02 11:27:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 639849424; totalMemory: 1224736768; maxMemory: 2147483648 Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:40 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:27:40 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:40 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:27:40 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:40 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:40 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:40 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:40 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:40 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:40 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:40 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:40 MarkDuplicates Getting Memory Stats. Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:41 MarkDuplicates Before output close freeMemory: 758196608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:41 MarkDuplicates Before output close freeMemory: 758196608; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:41 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:41 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: INFO 2024-07-02 11:27:41 MarkDuplicates After output close freeMemory: 758338384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:41 MarkDuplicates After output close freeMemory: 758338384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: [Tue Jul 02 11:27:41 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:27:41 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testSingleton(picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:41 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testBulkFragmentsNoDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:27:41 MarkDuplicates Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16740299262149515749.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16740299262149515749.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16740299262149515749.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16740299262149515749.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16740299262149515749.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16740299262149515749.tmp/output.sam Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:27:41.533 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:41.533 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:27:41.534 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:41.534 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:27:41.534 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:41.534 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:27:41.534 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:41.534 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:27:41 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16740299262149515749.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16740299262149515749.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16740299262149515749.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:41 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16740299262149515749.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16740299262149515749.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16740299262149515749.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:27:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:41 MarkDuplicates Start of doWork freeMemory: 1020889960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:41 MarkDuplicates Start of doWork freeMemory: 1020889960; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:41 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:41 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:41 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:41 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:27:41 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:27:41 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:42 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2024-07-02 11:27:42 MarkDuplicates Read 10000 records. 0 pairs never matched. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 957249872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 957249872; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:43 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:43 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:43 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:43 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:43 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:43 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 494496728; totalMemory: 1221591040; maxMemory: 2147483648 INFO 2024-07-02 11:27:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 494496728; totalMemory: 1221591040; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:43 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:27:43 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:43 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:27:43 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:43 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:43 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:43 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:43 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:43 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:43 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:43 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:27:43 MarkDuplicates Representative read Index cleanup. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:43 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:43 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:43 MarkDuplicates Before output close freeMemory: 763840600; totalMemory: 1221591040; maxMemory: 2147483648 INFO 2024-07-02 11:27:43 MarkDuplicates Before output close freeMemory: 763840600; totalMemory: 1221591040; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:43 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:43 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:44 MarkDuplicates After output close freeMemory: 763980696; totalMemory: 1221591040; maxMemory: 2147483648 INFO 2024-07-02 11:27:44 MarkDuplicates After output close freeMemory: 763980696; totalMemory: 1221591040; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:27:44 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:27:44 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1221591040 Runtime.totalMemory()=1221591040 Running Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:44 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testBulkFragmentsNoDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:27:44 MarkDuplicates Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14861716857013759055.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14861716857013759055.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14861716857013759055.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14861716857013759055.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14861716857013759055.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14861716857013759055.tmp/output.sam Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:27:44.651 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:44.651 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:27:44.651 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:44.651 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:27:44.651 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:44.651 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:27:44.651 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:44.651 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:27:44 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14861716857013759055.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14861716857013759055.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14861716857013759055.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:44 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14861716857013759055.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14861716857013759055.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14861716857013759055.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:27:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:44 MarkDuplicates Start of doWork freeMemory: 1020821192; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:44 MarkDuplicates Start of doWork freeMemory: 1020821192; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:44 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:44 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:44 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:44 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:27:45 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:27:45 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:45 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2024-07-02 11:27:45 MarkDuplicates Read 10000 records. 0 pairs never matched. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 957115120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 957115120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:46 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:46 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:46 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:46 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:46 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:46 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 491350192; totalMemory: 1218445312; maxMemory: 2147483648 INFO 2024-07-02 11:27:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 491350192; totalMemory: 1218445312; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:46 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:27:46 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:46 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:27:46 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:46 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:46 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:46 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:46 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:46 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:46 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:46 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:27:46 MarkDuplicates Representative read Index cleanup. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:46 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:46 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:47 MarkDuplicates Before output close freeMemory: 760561944; totalMemory: 1218445312; maxMemory: 2147483648 INFO 2024-07-02 11:27:47 MarkDuplicates Before output close freeMemory: 760561944; totalMemory: 1218445312; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:47 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:47 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:47 MarkDuplicates After output close freeMemory: 760701752; totalMemory: 1218445312; maxMemory: 2147483648 INFO 2024-07-02 11:27:47 MarkDuplicates After output close freeMemory: 760701752; totalMemory: 1218445312; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:27:47 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:27:47 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1218445312 Runtime.totalMemory()=1218445312 Running Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:48 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testBulkFragmentsNoDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:27:48 MarkDuplicates Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12884791810560517750.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12884791810560517750.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12884791810560517750.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester17405304647166010908/input.fasta ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12884791810560517750.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12884791810560517750.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12884791810560517750.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester17405304647166010908/input.fasta Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:27:48.701 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:48.701 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:27:48.701 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:48.701 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:27:48.702 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:48.702 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:27:48.702 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:48.702 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:27:48 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12884791810560517750.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12884791810560517750.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12884791810560517750.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester17405304647166010908/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:48 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12884791810560517750.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12884791810560517750.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12884791810560517750.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester17405304647166010908/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:27:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:49 MarkDuplicates Start of doWork freeMemory: 1020884376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:49 MarkDuplicates Start of doWork freeMemory: 1020884376; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:49 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:49 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:27:49 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:27:49 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:49 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2024-07-02 11:27:49 MarkDuplicates Read 10000 records. 0 pairs never matched. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 957243632; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 957243632; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:51 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:51 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:51 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:51 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:51 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:51 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 491347512; totalMemory: 1218445312; maxMemory: 2147483648 INFO 2024-07-02 11:27:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 491347512; totalMemory: 1218445312; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:51 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:27:51 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:51 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:27:51 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:51 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:51 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:52 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:52 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:52 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:52 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:52 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:27:52 MarkDuplicates Representative read Index cleanup. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:52 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:52 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:52 MarkDuplicates Before output close freeMemory: 760689704; totalMemory: 1218445312; maxMemory: 2147483648 INFO 2024-07-02 11:27:52 MarkDuplicates Before output close freeMemory: 760689704; totalMemory: 1218445312; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:52 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:52 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:52 MarkDuplicates After output close freeMemory: 760830072; totalMemory: 1218445312; maxMemory: 2147483648 INFO 2024-07-02 11:27:52 MarkDuplicates After output close freeMemory: 760830072; totalMemory: 1218445312; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:27:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:27:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1218445312 Runtime.totalMemory()=1218445312 Running Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:52 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testBulkFragmentsWithDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:27:52 MarkDuplicates Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3479271750407179963.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3479271750407179963.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3479271750407179963.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3479271750407179963.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3479271750407179963.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3479271750407179963.tmp/output.sam Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:27:52.899 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:52.899 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:27:52.899 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:52.899 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:27:52.899 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:52.899 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:27:52.899 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:52.899 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:27:52 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3479271750407179963.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3479271750407179963.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3479271750407179963.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:52 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3479271750407179963.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3479271750407179963.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3479271750407179963.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:27:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:53 MarkDuplicates Start of doWork freeMemory: 1012689952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:53 MarkDuplicates Start of doWork freeMemory: 1012689952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:53 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:53 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:53 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:53 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:27:53 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:27:53 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:53 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2024-07-02 11:27:53 MarkDuplicates Read 21000 records. 0 pairs never matched. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 948257864; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 948257864; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:54 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:54 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:54 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:54 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:54 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:54 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:54 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:54 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 496785072; totalMemory: 1232076800; maxMemory: 2147483648 INFO 2024-07-02 11:27:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 496785072; totalMemory: 1232076800; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:54 MarkDuplicates Marking 20000 records as duplicates. INFO 2024-07-02 11:27:54 MarkDuplicates Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:54 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:27:54 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:54 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:54 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:55 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:55 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:55 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:55 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:55 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:27:55 MarkDuplicates Representative read Index cleanup. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:55 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:55 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:55 MarkDuplicates Before output close freeMemory: 766128744; totalMemory: 1232076800; maxMemory: 2147483648 INFO 2024-07-02 11:27:55 MarkDuplicates Before output close freeMemory: 766128744; totalMemory: 1232076800; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:55 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:27:55 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:55 MarkDuplicates After output close freeMemory: 766268896; totalMemory: 1232076800; maxMemory: 2147483648 INFO 2024-07-02 11:27:55 MarkDuplicates After output close freeMemory: 766268896; totalMemory: 1232076800; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:27:55 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:27:55 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1232076800 Runtime.totalMemory()=1232076800 Running Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:56 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testBulkFragmentsWithDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:27:56 MarkDuplicates Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10005259307643304299.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10005259307643304299.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10005259307643304299.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10005259307643304299.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10005259307643304299.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10005259307643304299.tmp/output.sam Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:27:56.579 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:56.579 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:27:56.579 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:56.579 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:27:56.580 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:27:56.580 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:27:56.580 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:27:56.580 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:27:56 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10005259307643304299.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10005259307643304299.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10005259307643304299.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:27:56 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10005259307643304299.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10005259307643304299.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10005259307643304299.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:27:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:27:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:56 MarkDuplicates Start of doWork freeMemory: 1012623624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:56 MarkDuplicates Start of doWork freeMemory: 1012623624; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:56 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:27:56 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:56 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:27:56 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:27:56 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:27:56 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:57 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2024-07-02 11:27:57 MarkDuplicates Read 21000 records. 0 pairs never matched. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 948125552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:27:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 948125552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:27:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:58 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:27:58 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:58 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:27:58 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:58 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:27:58 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 495735536; totalMemory: 1231028224; maxMemory: 2147483648 INFO 2024-07-02 11:27:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 495735536; totalMemory: 1231028224; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:59 MarkDuplicates Marking 20000 records as duplicates. INFO 2024-07-02 11:27:59 MarkDuplicates Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:59 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:27:59 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:59 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:27:59 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:59 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:27:59 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:59 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:27:59 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:59 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:27:59 MarkDuplicates Representative read Index cleanup. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:27:59 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:27:59 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:00 MarkDuplicates Before output close freeMemory: 764939640; totalMemory: 1231028224; maxMemory: 2147483648 INFO 2024-07-02 11:28:00 MarkDuplicates Before output close freeMemory: 764939640; totalMemory: 1231028224; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:00 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:28:00 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:00 MarkDuplicates After output close freeMemory: 764939640; totalMemory: 1231028224; maxMemory: 2147483648 INFO 2024-07-02 11:28:00 MarkDuplicates After output close freeMemory: 764939640; totalMemory: 1231028224; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:28:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1231028224 Runtime.totalMemory()=1231028224 Running Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:01 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testBulkFragmentsWithDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:28:01 MarkDuplicates Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4582515049786842390.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4582515049786842390.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4582515049786842390.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester17702447519679410848/input.fasta ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4582515049786842390.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4582515049786842390.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4582515049786842390.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester17702447519679410848/input.fasta Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:01.911 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:01.911 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:01.911 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:01.911 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:01.911 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:01.911 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:01.911 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:01.911 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:01 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4582515049786842390.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4582515049786842390.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4582515049786842390.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester17702447519679410848/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:28:01 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4582515049786842390.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4582515049786842390.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4582515049786842390.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester17702447519679410848/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:28:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:02 MarkDuplicates Start of doWork freeMemory: 1012615304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:02 MarkDuplicates Start of doWork freeMemory: 1012615304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:02 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:28:02 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:02 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:28:02 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:28:02 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:28:02 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:03 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2024-07-02 11:28:03 MarkDuplicates Read 21000 records. 0 pairs never matched. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 948254248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 948254248; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:03 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:28:03 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:04 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:28:04 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:04 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:28:04 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:04 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:28:04 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 743196976; totalMemory: 1478492160; maxMemory: 2147483648 INFO 2024-07-02 11:28:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 743196976; totalMemory: 1478492160; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:04 MarkDuplicates Marking 20000 records as duplicates. INFO 2024-07-02 11:28:04 MarkDuplicates Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:04 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:28:04 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:04 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:28:04 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:05 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:28:05 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:05 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:28:05 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:05 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:28:05 MarkDuplicates Representative read Index cleanup. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:05 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:28:05 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:06 MarkDuplicates Before output close freeMemory: 1012539912; totalMemory: 1478492160; maxMemory: 2147483648 INFO 2024-07-02 11:28:06 MarkDuplicates Before output close freeMemory: 1012539912; totalMemory: 1478492160; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:06 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:28:06 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:06 MarkDuplicates After output close freeMemory: 1012680328; totalMemory: 1478492160; maxMemory: 2147483648 INFO 2024-07-02 11:28:06 MarkDuplicates After output close freeMemory: 1012680328; totalMemory: 1478492160; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:06 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:28:06 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1478492160 Runtime.totalMemory()=1478492160 Running Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:06 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testBulkPairsNoDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:28:06 MarkDuplicates Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2922717543509646025.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2922717543509646025.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2922717543509646025.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2922717543509646025.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2922717543509646025.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2922717543509646025.tmp/output.sam Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:06.907 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:06.907 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:06.907 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:06.907 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:06.907 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:06.907 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:06.907 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:06.907 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:06 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2922717543509646025.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2922717543509646025.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2922717543509646025.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:28:06 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2922717543509646025.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2922717543509646025.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2922717543509646025.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:28:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:07 MarkDuplicates Start of doWork freeMemory: 1012168408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:07 MarkDuplicates Start of doWork freeMemory: 1012168408; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:07 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:28:07 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:07 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:28:07 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:28:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:28:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:08 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2024-07-02 11:28:08 MarkDuplicates Read 20200 records. 0 pairs never matched. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 946914272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 946914272; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:28:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:09 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:28:09 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:09 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:28:09 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:09 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:28:09 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 496266056; totalMemory: 1232076800; maxMemory: 2147483648 INFO 2024-07-02 11:28:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 496266056; totalMemory: 1232076800; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:09 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:28:09 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:09 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:28:09 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:09 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:28:09 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:10 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:28:10 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:10 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:28:10 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:10 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:28:10 MarkDuplicates Representative read Index cleanup. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:10 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:28:10 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:11 MarkDuplicates Before output close freeMemory: 765609672; totalMemory: 1232076800; maxMemory: 2147483648 INFO 2024-07-02 11:28:11 MarkDuplicates Before output close freeMemory: 765609672; totalMemory: 1232076800; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:11 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:28:11 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:11 MarkDuplicates After output close freeMemory: 765749880; totalMemory: 1232076800; maxMemory: 2147483648 INFO 2024-07-02 11:28:11 MarkDuplicates After output close freeMemory: 765749880; totalMemory: 1232076800; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:11 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:28:11 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1232076800 Runtime.totalMemory()=1232076800 Running Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:12 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testBulkPairsNoDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:28:12 MarkDuplicates Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13020449679386227666.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13020449679386227666.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13020449679386227666.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13020449679386227666.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13020449679386227666.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13020449679386227666.tmp/output.sam Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:12.948 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:12.948 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:12.957 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:12.957 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:12.957 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:12.957 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:12.957 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:12.957 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:12 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13020449679386227666.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13020449679386227666.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13020449679386227666.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:28:12 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13020449679386227666.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13020449679386227666.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13020449679386227666.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:28:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:13 MarkDuplicates Start of doWork freeMemory: 1012104784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:13 MarkDuplicates Start of doWork freeMemory: 1012104784; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:13 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:28:13 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:13 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:28:13 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:28:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:28:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:14 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2024-07-02 11:28:14 MarkDuplicates Read 20200 records. 0 pairs never matched. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 946936992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 946936992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:15 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:28:15 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:15 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:28:15 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:15 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:28:15 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:15 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:28:15 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 498362128; totalMemory: 1234173952; maxMemory: 2147483648 INFO 2024-07-02 11:28:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 498362128; totalMemory: 1234173952; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:16 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:28:16 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:16 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:28:16 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:16 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:28:16 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:16 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:28:16 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:16 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:28:16 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:16 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:28:16 MarkDuplicates Representative read Index cleanup. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:16 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:28:16 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:17 MarkDuplicates Before output close freeMemory: 767573752; totalMemory: 1234173952; maxMemory: 2147483648 INFO 2024-07-02 11:28:17 MarkDuplicates Before output close freeMemory: 767573752; totalMemory: 1234173952; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:17 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:28:17 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:17 MarkDuplicates After output close freeMemory: 767714184; totalMemory: 1234173952; maxMemory: 2147483648 INFO 2024-07-02 11:28:17 MarkDuplicates After output close freeMemory: 767714184; totalMemory: 1234173952; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:17 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. [Tue Jul 02 11:28:17 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1234173952 Runtime.totalMemory()=1234173952 Running Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:19 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testBulkPairsNoDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:28:19 MarkDuplicates Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1775685663018071563.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1775685663018071563.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1775685663018071563.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester18308173136081678546/input.fasta ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1775685663018071563.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1775685663018071563.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1775685663018071563.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester18308173136081678546/input.fasta Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:19.862 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:19.862 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:19.862 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:19.862 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:19.862 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:19.862 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:19.862 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:19.862 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:19 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1775685663018071563.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1775685663018071563.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1775685663018071563.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester18308173136081678546/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:28:19 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1775685663018071563.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1775685663018071563.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1775685663018071563.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester18308173136081678546/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:28:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:20 MarkDuplicates Start of doWork freeMemory: 1012167760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:20 MarkDuplicates Start of doWork freeMemory: 1012167760; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:20 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:28:20 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:20 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:28:20 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:28:20 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:28:20 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:21 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2024-07-02 11:28:21 MarkDuplicates Read 20200 records. 0 pairs never matched. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 947065464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 947065464; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:28:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:22 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:28:22 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:22 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:28:22 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:22 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:28:22 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 607411536; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:28:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 607411536; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:22 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:28:22 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:22 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:28:22 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:22 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:28:22 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:23 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:28:23 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:23 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:28:23 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:23 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:28:23 MarkDuplicates Representative read Index cleanup. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:23 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:28:23 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:24 MarkDuplicates Before output close freeMemory: 876754376; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:28:24 MarkDuplicates Before output close freeMemory: 876754376; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:24 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:28:24 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:24 MarkDuplicates After output close freeMemory: 876895384; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:28:24 MarkDuplicates After output close freeMemory: 876895384; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:24 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:28:24 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1343225856 Runtime.totalMemory()=1343225856 Running Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:24 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testBulkPairsWithDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:28:24 MarkDuplicates Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16669550029531295471.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16669550029531295471.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16669550029531295471.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16669550029531295471.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16669550029531295471.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16669550029531295471.tmp/output.sam Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:24.624 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:24.624 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:24.624 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:24.624 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:24.625 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:24.625 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:24.625 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:24.625 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:24 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16669550029531295471.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16669550029531295471.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16669550029531295471.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:28:24 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16669550029531295471.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16669550029531295471.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16669550029531295471.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:28:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:24 MarkDuplicates Start of doWork freeMemory: 1022688016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:24 MarkDuplicates Start of doWork freeMemory: 1022688016; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:24 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:28:24 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:24 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:28:24 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:28:24 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:28:24 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:25 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2024-07-02 11:28:25 MarkDuplicates Read 6820 records. 0 pairs never matched. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 959031024; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 959031024; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:25 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:28:25 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:26 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:28:26 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:26 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:28:26 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:26 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:28:26 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 492905456; totalMemory: 1218445312; maxMemory: 2147483648 INFO 2024-07-02 11:28:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 492905456; totalMemory: 1218445312; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:26 MarkDuplicates Marking 6200 records as duplicates. INFO 2024-07-02 11:28:26 MarkDuplicates Marking 6200 records as duplicates. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:26 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:28:26 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:26 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:28:26 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:26 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:28:26 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:26 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:28:26 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:26 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:28:26 MarkDuplicates Representative read Index cleanup. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:26 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:28:26 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:27 MarkDuplicates Before output close freeMemory: 762493976; totalMemory: 1218445312; maxMemory: 2147483648 INFO 2024-07-02 11:28:27 MarkDuplicates Before output close freeMemory: 762493976; totalMemory: 1218445312; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:27 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:28:27 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:27 MarkDuplicates After output close freeMemory: 762633872; totalMemory: 1218445312; maxMemory: 2147483648 INFO 2024-07-02 11:28:27 MarkDuplicates After output close freeMemory: 762633872; totalMemory: 1218445312; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:27 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:28:27 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1218445312 Runtime.totalMemory()=1218445312 Running Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:27 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testBulkPairsWithDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:28:27 MarkDuplicates Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9288382627873094153.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9288382627873094153.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9288382627873094153.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9288382627873094153.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9288382627873094153.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9288382627873094153.tmp/output.sam Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:27.800 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:27.800 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:27.800 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:27.800 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:27.800 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:27.800 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:27.800 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:27.800 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:27 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9288382627873094153.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9288382627873094153.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9288382627873094153.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:28:27 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9288382627873094153.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9288382627873094153.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9288382627873094153.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:28:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:27 MarkDuplicates Start of doWork freeMemory: 1022621136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:27 MarkDuplicates Start of doWork freeMemory: 1022621136; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:27 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:28:27 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:27 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:28:27 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:28:28 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:28:28 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:28 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2024-07-02 11:28:28 MarkDuplicates Read 6820 records. 0 pairs never matched. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 958898552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 958898552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:28:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:28 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:28:28 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:28 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:28:28 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:28 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:28:28 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 490805920; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2024-07-02 11:28:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 490805920; totalMemory: 1216348160; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:29 MarkDuplicates Marking 6200 records as duplicates. INFO 2024-07-02 11:28:29 MarkDuplicates Marking 6200 records as duplicates. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:29 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:28:29 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:29 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:28:29 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:29 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:28:29 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:29 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:28:29 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:29 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:28:29 MarkDuplicates Representative read Index cleanup. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:29 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:28:29 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:29 MarkDuplicates Before output close freeMemory: 760264592; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2024-07-02 11:28:29 MarkDuplicates Before output close freeMemory: 760264592; totalMemory: 1216348160; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:29 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:28:29 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:29 MarkDuplicates After output close freeMemory: 760404912; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2024-07-02 11:28:29 MarkDuplicates After output close freeMemory: 760404912; totalMemory: 1216348160; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:28:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1216348160 Runtime.totalMemory()=1216348160 Running Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:30 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testBulkPairsWithDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:28:30 MarkDuplicates Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13256185280226708781.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13256185280226708781.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13256185280226708781.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester3388511615499732508/input.fasta ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13256185280226708781.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13256185280226708781.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13256185280226708781.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester3388511615499732508/input.fasta Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:30.175 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:30.175 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:30.175 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:30.175 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:30.175 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:30.175 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:30.175 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:30.175 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:30 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13256185280226708781.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13256185280226708781.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13256185280226708781.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester3388511615499732508/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:28:30 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13256185280226708781.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13256185280226708781.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13256185280226708781.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester3388511615499732508/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:28:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:30 MarkDuplicates Start of doWork freeMemory: 1022684504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:30 MarkDuplicates Start of doWork freeMemory: 1022684504; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:30 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:28:30 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:30 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:28:30 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:28:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:28:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:30 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2024-07-02 11:28:30 MarkDuplicates Read 6820 records. 0 pairs never matched. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 959027472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 959027472; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:28:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:31 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:28:31 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:31 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:28:31 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:31 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:28:31 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 495081208; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2024-07-02 11:28:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 495081208; totalMemory: 1220542464; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:31 MarkDuplicates Marking 6200 records as duplicates. INFO 2024-07-02 11:28:31 MarkDuplicates Marking 6200 records as duplicates. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:31 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:28:31 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:31 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:28:31 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:31 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:28:31 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:31 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:28:31 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:31 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:28:31 MarkDuplicates Representative read Index cleanup. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:31 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:28:31 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:31 MarkDuplicates Before output close freeMemory: 764587616; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2024-07-02 11:28:31 MarkDuplicates Before output close freeMemory: 764587616; totalMemory: 1220542464; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:31 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:28:31 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:32 MarkDuplicates After output close freeMemory: 764728632; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2024-07-02 11:28:32 MarkDuplicates After output close freeMemory: 764728632; totalMemory: 1220542464; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:28:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1220542464 Runtime.totalMemory()=1220542464 Running Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:32 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testDifferentChromosomesInOppositeOrder STANDARD_ERROR INFO 2024-07-02 11:28:32 MarkDuplicates Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3448687917837454156.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3448687917837454156.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3448687917837454156.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3448687917837454156.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3448687917837454156.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3448687917837454156.tmp/output.sam Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:32.165 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:32.165 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:32.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:32.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:32.166 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:32.166 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:32.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:32.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:32 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3448687917837454156.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3448687917837454156.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3448687917837454156.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:28:32 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3448687917837454156.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3448687917837454156.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3448687917837454156.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:28:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:32 MarkDuplicates Start of doWork freeMemory: 1027806360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:32 MarkDuplicates Start of doWork freeMemory: 1027806360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:32 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:28:32 MarkDuplicates Reading input file and constructing read end information. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:32 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:28:32 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:32 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:28:32 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 964885536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 964885536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:28:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:32 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:28:32 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:32 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:28:32 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:32 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:28:32 MarkDuplicates Sorting list of duplicate records. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 489796672; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:28:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 489796672; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:32 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:28:32 MarkDuplicates Marking 2 records as duplicates. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:32 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:28:32 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:32 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:28:32 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:32 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:28:32 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:32 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:28:32 MarkDuplicates Duplicate Index cleanup. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:32 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:28:32 MarkDuplicates Representative read Index cleanup. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:32 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:28:32 MarkDuplicates Getting Memory Stats. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:33 MarkDuplicates Before output close freeMemory: 759224256; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:28:33 MarkDuplicates Before output close freeMemory: 759224256; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:33 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:28:33 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:33 MarkDuplicates After output close freeMemory: 759364080; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:28:33 MarkDuplicates After output close freeMemory: 759364080; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:33 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:28:33 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1210056704 Runtime.totalMemory()=1210056704 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:33 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:28:33 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18127013321698365178.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18127013321698365178.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18127013321698365178.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18127013321698365178.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18127013321698365178.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18127013321698365178.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:33.283 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:33.283 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:33.283 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:33.283 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:33.283 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:33.283 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:33.283 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:33.283 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:33 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18127013321698365178.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18127013321698365178.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18127013321698365178.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:28:33 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18127013321698365178.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18127013321698365178.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18127013321698365178.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:28:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:33 MarkDuplicates Start of doWork freeMemory: 1027799880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:33 MarkDuplicates Start of doWork freeMemory: 1027799880; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:33 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:28:33 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:33 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:28:33 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:33 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:28:33 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 964878528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 964878528; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:28:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:28:34 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:34 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:28:34 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:34 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:28:34 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 489789168; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:28:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 489789168; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:34 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:28:34 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:34 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:28:34 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:34 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:28:34 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:34 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:28:34 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:34 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:28:34 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:34 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:28:34 MarkDuplicates Representative read Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:34 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:28:34 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:34 MarkDuplicates Before output close freeMemory: 759217896; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:28:34 MarkDuplicates Before output close freeMemory: 759217896; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:34 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:28:34 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:34 MarkDuplicates After output close freeMemory: 759357792; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:28:34 MarkDuplicates After output close freeMemory: 759357792; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:28:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1210056704 Runtime.totalMemory()=1210056704 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:34 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:28:34 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13512616399095955946.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13512616399095955946.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13512616399095955946.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13512616399095955946.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13512616399095955946.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13512616399095955946.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:34.646 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:34.646 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:34.646 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:34.646 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:34.647 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:34.647 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:34.647 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:34.647 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:34 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13512616399095955946.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13512616399095955946.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13512616399095955946.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:28:34 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13512616399095955946.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13512616399095955946.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13512616399095955946.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:28:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:34 MarkDuplicates Start of doWork freeMemory: 1027799184; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:34 MarkDuplicates Start of doWork freeMemory: 1027799184; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:34 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:28:34 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:34 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:28:34 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:34 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:28:34 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 964877832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 964877832; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:28:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:35 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:28:35 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:35 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:28:35 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:35 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:28:35 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 485679152; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:28:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 485679152; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:35 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:28:35 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:35 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:28:35 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:35 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:28:35 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:35 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:28:35 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:35 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:28:35 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:35 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:28:35 MarkDuplicates Representative read Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:35 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:28:35 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:35 MarkDuplicates Before output close freeMemory: 755022896; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:28:35 MarkDuplicates Before output close freeMemory: 755022896; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:35 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:28:35 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:35 MarkDuplicates After output close freeMemory: 755163288; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:28:35 MarkDuplicates After output close freeMemory: 755163288; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:35 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:28:35 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1205862400 Runtime.totalMemory()=1205862400 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:35 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:28:35 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8961717297918564700.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8961717297918564700.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8961717297918564700.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8961717297918564700.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8961717297918564700.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8961717297918564700.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:35.916 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:35.916 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:35.916 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:35.916 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:35.917 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:35.917 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:35.917 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:35.917 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:35 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8961717297918564700.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8961717297918564700.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8961717297918564700.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:28:35 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8961717297918564700.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8961717297918564700.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8961717297918564700.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:28:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:36 MarkDuplicates Start of doWork freeMemory: 1027798544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:36 MarkDuplicates Start of doWork freeMemory: 1027798544; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:36 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:28:36 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:36 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:28:36 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:36 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:28:36 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 964877192; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 964877192; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:28:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:36 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:28:36 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:36 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:28:36 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:36 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:28:36 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 783474096; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2024-07-02 11:28:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 783474096; totalMemory: 1503657984; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:36 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:28:36 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:36 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:28:36 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:36 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:28:36 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:36 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:28:36 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:36 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:28:36 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:36 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:28:36 MarkDuplicates Representative read Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:36 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:28:36 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:36 MarkDuplicates Before output close freeMemory: 1052817840; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2024-07-02 11:28:36 MarkDuplicates Before output close freeMemory: 1052817840; totalMemory: 1503657984; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:36 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:28:36 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:36 MarkDuplicates After output close freeMemory: 1052958008; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2024-07-02 11:28:36 MarkDuplicates After output close freeMemory: 1052958008; totalMemory: 1503657984; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:28:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1503657984 Runtime.totalMemory()=1503657984 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:37 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:28:37 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8450759842680615642.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8450759842680615642.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8450759842680615642.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8450759842680615642.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8450759842680615642.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8450759842680615642.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:37.036 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:37.036 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:37.037 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:37.037 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:37.037 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:37.037 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:37.037 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:37.037 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:37 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8450759842680615642.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8450759842680615642.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8450759842680615642.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:28:37 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8450759842680615642.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8450759842680615642.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8450759842680615642.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:28:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:37 MarkDuplicates Start of doWork freeMemory: 1027797912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:37 MarkDuplicates Start of doWork freeMemory: 1027797912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:37 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:28:37 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:37 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:28:37 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:37 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:28:37 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 964876344; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 964876344; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:28:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:28:37 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:28:37 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:37 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:28:37 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 487775032; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:28:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 487775032; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:37 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:28:37 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:37 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:28:37 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:37 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:28:37 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:37 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:28:37 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:37 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:28:37 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:37 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:28:37 MarkDuplicates Representative read Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:37 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:28:37 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:37 MarkDuplicates Before output close freeMemory: 757116992; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:28:37 MarkDuplicates Before output close freeMemory: 757116992; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:37 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:28:37 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:37 MarkDuplicates After output close freeMemory: 757256816; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:28:37 MarkDuplicates After output close freeMemory: 757256816; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:28:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1207959552 Runtime.totalMemory()=1207959552 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:38 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:28:38 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.470107076024233485.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.470107076024233485.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.470107076024233485.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.470107076024233485.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.470107076024233485.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.470107076024233485.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:38.004 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:38.004 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:38.005 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:38.005 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:38.005 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:38.005 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:38.005 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:38.005 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:38 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.470107076024233485.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.470107076024233485.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.470107076024233485.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:28:38 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.470107076024233485.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.470107076024233485.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.470107076024233485.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:28:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:38 MarkDuplicates Start of doWork freeMemory: 1027797272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:38 MarkDuplicates Start of doWork freeMemory: 1027797272; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:38 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:28:38 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:38 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:28:38 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:38 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:28:38 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 964875704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 964875704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:28:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:38 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:28:38 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:38 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:28:38 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:38 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:28:38 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 489871544; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:28:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 489871544; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:38 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:28:38 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:38 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:28:38 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:38 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:28:38 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:38 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:28:38 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:38 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:28:38 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:38 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:28:38 MarkDuplicates Representative read Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:38 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:28:38 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:38 MarkDuplicates Before output close freeMemory: 759215288; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:28:38 MarkDuplicates Before output close freeMemory: 759215288; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:38 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:28:38 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:39 MarkDuplicates After output close freeMemory: 759204792; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:28:39 MarkDuplicates After output close freeMemory: 759204792; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:28:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1210056704 Runtime.totalMemory()=1210056704 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:39 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:28:39 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9179379414306332742.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9179379414306332742.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9179379414306332742.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9179379414306332742.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9179379414306332742.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9179379414306332742.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:39.050 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:39.050 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:39.050 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:39.050 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:39.051 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:39.051 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:39.051 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:39.051 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:39 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9179379414306332742.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9179379414306332742.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9179379414306332742.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:28:39 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9179379414306332742.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9179379414306332742.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9179379414306332742.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:28:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:39 MarkDuplicates Start of doWork freeMemory: 1027796672; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:39 MarkDuplicates Start of doWork freeMemory: 1027796672; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:39 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:28:39 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:39 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:28:39 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:39 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:28:39 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 964875320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 964875320; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:28:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:39 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:28:39 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:39 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:28:39 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:39 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:28:39 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 489870248; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:28:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 489870248; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:39 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:28:39 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:39 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:28:39 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:39 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:28:39 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:39 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:28:39 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:39 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:28:39 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:39 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:28:39 MarkDuplicates Representative read Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:39 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:28:39 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:39 MarkDuplicates Before output close freeMemory: 759214688; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:28:39 MarkDuplicates Before output close freeMemory: 759214688; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:39 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:28:39 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:40 MarkDuplicates After output close freeMemory: 759203440; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:28:40 MarkDuplicates After output close freeMemory: 759203440; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:40 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:28:40 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1210056704 Runtime.totalMemory()=1210056704 Running Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:40 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testMappedFragmentAndMappedPairFirstOfPairNonPrimary STANDARD_ERROR INFO 2024-07-02 11:28:40 MarkDuplicates Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13054656311921708619.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13054656311921708619.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13054656311921708619.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13054656311921708619.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13054656311921708619.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13054656311921708619.tmp/output.sam Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:40.144 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:40.144 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:40.145 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:40.145 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:40.145 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:40.145 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:40.145 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:40.145 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:40 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13054656311921708619.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13054656311921708619.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13054656311921708619.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:28:40 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13054656311921708619.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13054656311921708619.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13054656311921708619.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:28:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:40 MarkDuplicates Start of doWork freeMemory: 1027644864; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:40 MarkDuplicates Start of doWork freeMemory: 1027644864; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:40 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:28:40 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:40 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:28:40 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:28:40 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:28:40 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:40 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:28:40 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 964881848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 964881848; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:28:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:40 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:28:40 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:28:40 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:40 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:28:40 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 487693728; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:28:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 487693728; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:40 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:28:40 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:40 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:28:40 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:40 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:28:40 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:40 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:28:40 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:40 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:28:40 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:40 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:28:40 MarkDuplicates Representative read Index cleanup. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:40 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:28:40 MarkDuplicates Getting Memory Stats. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:41 MarkDuplicates Before output close freeMemory: 757123160; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:28:41 MarkDuplicates Before output close freeMemory: 757123160; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:41 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:28:41 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:41 MarkDuplicates After output close freeMemory: 757264376; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:28:41 MarkDuplicates After output close freeMemory: 757264376; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:41 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:28:41 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1207959552 Runtime.totalMemory()=1207959552 Running Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:41 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testMappedFragmentAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:28:41 MarkDuplicates Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6691931744043228463.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6691931744043228463.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6691931744043228463.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6691931744043228463.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6691931744043228463.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6691931744043228463.tmp/output.sam Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:41.178 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:41.178 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:41.179 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:41.179 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:41.179 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:41.179 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:41.179 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:41.179 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:41 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6691931744043228463.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6691931744043228463.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6691931744043228463.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:28:41 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6691931744043228463.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6691931744043228463.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6691931744043228463.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:28:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:41 MarkDuplicates Start of doWork freeMemory: 1027796144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:41 MarkDuplicates Start of doWork freeMemory: 1027796144; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:41 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:28:41 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:41 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:28:41 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:28:41 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:28:41 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:41 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2024-07-02 11:28:41 MarkDuplicates Read 3 records. 0 pairs never matched. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 964881360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 964881360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:28:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:28:41 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:28:41 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:41 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:28:41 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 484633736; totalMemory: 1204813824; maxMemory: 2147483648 INFO 2024-07-02 11:28:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 484633736; totalMemory: 1204813824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:41 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:28:41 MarkDuplicates Marking 1 records as duplicates. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:41 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:28:41 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:28:41 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:41 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:28:41 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:41 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:28:41 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:41 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:28:41 MarkDuplicates Representative read Index cleanup. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:41 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:28:41 MarkDuplicates Getting Memory Stats. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:42 MarkDuplicates Before output close freeMemory: 753977568; totalMemory: 1204813824; maxMemory: 2147483648 INFO 2024-07-02 11:28:42 MarkDuplicates Before output close freeMemory: 753977568; totalMemory: 1204813824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:42 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:28:42 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:42 MarkDuplicates After output close freeMemory: 754117136; totalMemory: 1204813824; maxMemory: 2147483648 INFO 2024-07-02 11:28:42 MarkDuplicates After output close freeMemory: 754117136; totalMemory: 1204813824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:28:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1204813824 Runtime.totalMemory()=1204813824 Running Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:42 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testMappedFragmentAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:28:42 MarkDuplicates Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3810112838769327902.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3810112838769327902.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3810112838769327902.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3810112838769327902.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3810112838769327902.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3810112838769327902.tmp/output.sam Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:42.272 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:42.272 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:42.272 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:42.272 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:42.272 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:42.272 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:42.272 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:42.272 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:42 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3810112838769327902.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3810112838769327902.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3810112838769327902.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:28:42 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3810112838769327902.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3810112838769327902.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3810112838769327902.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:28:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:42 MarkDuplicates Start of doWork freeMemory: 1027800968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:42 MarkDuplicates Start of doWork freeMemory: 1027800968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:42 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:28:42 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:42 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:28:42 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:28:42 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:28:42 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:42 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2024-07-02 11:28:42 MarkDuplicates Read 3 records. 0 pairs never matched. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 964880736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 964880736; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:28:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:42 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:28:42 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:42 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:28:42 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:42 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:28:42 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 487778840; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:28:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 487778840; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:43 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:28:43 MarkDuplicates Marking 1 records as duplicates. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:43 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:28:43 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:43 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:28:43 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:43 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:28:43 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:43 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:28:43 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:43 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:28:43 MarkDuplicates Representative read Index cleanup. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:43 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:28:43 MarkDuplicates Getting Memory Stats. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:43 MarkDuplicates Before output close freeMemory: 757122672; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:28:43 MarkDuplicates Before output close freeMemory: 757122672; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:43 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:28:43 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:43 MarkDuplicates After output close freeMemory: 757262736; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:28:43 MarkDuplicates After output close freeMemory: 757262736; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:43 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:28:43 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1207959552 Runtime.totalMemory()=1207959552 Running Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:43 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testMappedPairAndMappedFragmentAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:28:43 MarkDuplicates Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5955204974929589290.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5955204974929589290.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5955204974929589290.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5955204974929589290.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5955204974929589290.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5955204974929589290.tmp/output.sam Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:43.324 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:43.324 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:43.324 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:43.324 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:43.324 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:43.324 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:43.324 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:43.324 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:43 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5955204974929589290.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5955204974929589290.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5955204974929589290.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:28:43 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5955204974929589290.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5955204974929589290.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5955204974929589290.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:28:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:43 MarkDuplicates Start of doWork freeMemory: 1027798920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:43 MarkDuplicates Start of doWork freeMemory: 1027798920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:43 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:28:43 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:43 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:28:43 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:28:43 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:28:43 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:43 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:28:43 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 964878352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 964878352; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:28:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:43 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:28:43 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:43 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:28:43 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:43 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:28:43 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 489873648; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:28:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 489873648; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:44 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:28:44 MarkDuplicates Marking 2 records as duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:44 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:28:44 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:44 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:28:44 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:44 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:28:44 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:44 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:28:44 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:44 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:28:44 MarkDuplicates Representative read Index cleanup. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:44 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:28:44 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:44 MarkDuplicates Before output close freeMemory: 759217288; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:28:44 MarkDuplicates Before output close freeMemory: 759217288; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:44 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:28:44 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:44 MarkDuplicates After output close freeMemory: 759357544; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:28:44 MarkDuplicates After output close freeMemory: 759357544; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:44 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:28:44 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1210056704 Runtime.totalMemory()=1210056704 Running Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:44 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testMappedPairAndMappedFragmentAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:28:44 MarkDuplicates Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15338193763341902712.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15338193763341902712.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15338193763341902712.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15338193763341902712.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15338193763341902712.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15338193763341902712.tmp/output.sam Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:44.379 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:44.379 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:44.379 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:44.379 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:44.379 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:44.379 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:44.379 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:44.379 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:44 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15338193763341902712.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15338193763341902712.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15338193763341902712.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:28:44 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15338193763341902712.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15338193763341902712.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15338193763341902712.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:28:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:44 MarkDuplicates Start of doWork freeMemory: 1027798120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:44 MarkDuplicates Start of doWork freeMemory: 1027798120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:44 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:28:44 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:44 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:28:44 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:28:44 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:28:44 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:44 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:28:44 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 964877552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 964877552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:28:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:47 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:28:47 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:47 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:28:47 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:47 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:28:47 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 489872848; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:28:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 489872848; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:47 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:28:47 MarkDuplicates Marking 2 records as duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:47 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:28:47 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:47 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:28:47 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:47 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:28:47 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:47 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:28:47 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:47 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:28:47 MarkDuplicates Representative read Index cleanup. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:47 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:28:47 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:48 MarkDuplicates Before output close freeMemory: 759216488; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:28:48 MarkDuplicates Before output close freeMemory: 759216488; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:48 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:28:48 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:49 MarkDuplicates After output close freeMemory: 759356744; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:28:49 MarkDuplicates After output close freeMemory: 759356744; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. [Tue Jul 02 11:28:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1210056704 Runtime.totalMemory()=1210056704 Running Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:49 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:28:49 MarkDuplicates Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6083820902308484831.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6083820902308484831.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6083820902308484831.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6083820902308484831.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6083820902308484831.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6083820902308484831.tmp/output.sam Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:49.196 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:49.196 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:49.196 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:49.196 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:49.196 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:49.196 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:49.196 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:49.196 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:49 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6083820902308484831.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6083820902308484831.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6083820902308484831.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:28:49 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6083820902308484831.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6083820902308484831.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6083820902308484831.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:28:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:49 MarkDuplicates Start of doWork freeMemory: 1027797848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:49 MarkDuplicates Start of doWork freeMemory: 1027797848; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:49 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:28:49 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:28:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:28:49 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:28:49 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:49 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:28:49 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 964877352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 964877352; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:28:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:50 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:28:50 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:50 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:28:50 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:50 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:28:50 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 487775424; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:28:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 487775424; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:51 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:28:51 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:51 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:28:51 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:51 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:28:51 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:51 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:28:51 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:51 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:28:51 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:51 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:28:51 MarkDuplicates Representative read Index cleanup. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:51 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:28:51 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:51 MarkDuplicates Before output close freeMemory: 757119016; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:28:51 MarkDuplicates Before output close freeMemory: 757119016; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:51 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:28:51 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:51 MarkDuplicates After output close freeMemory: 757259248; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:28:51 MarkDuplicates After output close freeMemory: 757259248; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:28:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1207959552 Runtime.totalMemory()=1207959552 Running Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:51 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testMappedPairAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:28:51 MarkDuplicates Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3162716456584204198.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3162716456584204198.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3162716456584204198.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3162716456584204198.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3162716456584204198.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3162716456584204198.tmp/output.sam Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:51.877 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:51.877 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:51.877 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:51.877 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:51.877 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:51.877 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:51.877 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:51.877 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:51 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3162716456584204198.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3162716456584204198.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3162716456584204198.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:28:51 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3162716456584204198.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3162716456584204198.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3162716456584204198.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:28:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:52 MarkDuplicates Start of doWork freeMemory: 1027797368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:52 MarkDuplicates Start of doWork freeMemory: 1027797368; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:52 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:28:52 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:52 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:28:52 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:28:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:28:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:52 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:28:52 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 964876872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 964876872; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:28:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:53 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:28:53 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:53 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:28:53 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:53 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:28:53 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 485677792; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:28:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 485677792; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:54 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:28:54 MarkDuplicates Marking 1 records as duplicates. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:54 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:28:54 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:54 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:28:54 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:54 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:28:54 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:54 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:28:54 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:54 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:28:54 MarkDuplicates Representative read Index cleanup. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:54 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:28:54 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:54 MarkDuplicates Before output close freeMemory: 755021432; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:28:54 MarkDuplicates Before output close freeMemory: 755021432; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:54 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:28:54 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:55 MarkDuplicates After output close freeMemory: 755161616; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:28:55 MarkDuplicates After output close freeMemory: 755161616; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:55 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:28:55 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1205862400 Runtime.totalMemory()=1205862400 Running Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:55 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testMappedPairAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:28:55 MarkDuplicates Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11971913316235809349.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11971913316235809349.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11971913316235809349.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11971913316235809349.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11971913316235809349.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11971913316235809349.tmp/output.sam Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:55.585 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:55.585 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:55.586 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:55.586 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:55.587 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:28:55.587 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:28:55.587 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:28:55.587 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:55 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11971913316235809349.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11971913316235809349.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11971913316235809349.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:28:55 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11971913316235809349.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11971913316235809349.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11971913316235809349.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:28:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:28:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:56 MarkDuplicates Start of doWork freeMemory: 1027796616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:56 MarkDuplicates Start of doWork freeMemory: 1027796616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:56 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:28:56 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:56 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:28:56 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:28:56 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:28:56 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:56 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:28:56 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 964875520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:28:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 964875520; totalMemory: 1073741824; maxMemory: 2147483648 Gradle is still running, please be patient... Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:28:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:28:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:01 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:29:01 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:01 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:29:01 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:01 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:29:01 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 783472624; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2024-07-02 11:29:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 783472624; totalMemory: 1503657984; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:01 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:29:01 MarkDuplicates Marking 1 records as duplicates. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:01 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:29:01 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:01 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:29:01 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:01 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:29:01 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:01 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:29:01 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:01 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:29:01 MarkDuplicates Representative read Index cleanup. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:01 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:29:01 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:02 MarkDuplicates Before output close freeMemory: 1052816264; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2024-07-02 11:29:02 MarkDuplicates Before output close freeMemory: 1052816264; totalMemory: 1503657984; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:02 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:29:02 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:03 MarkDuplicates After output close freeMemory: 1052956448; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2024-07-02 11:29:03 MarkDuplicates After output close freeMemory: 1052956448; totalMemory: 1503657984; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:03 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.13 minutes. [Tue Jul 02 11:29:03 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.13 minutes. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1503657984 Runtime.totalMemory()=1503657984 Running Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:03 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testMappedPairWithFirstEndSamePositionAndOther STANDARD_ERROR INFO 2024-07-02 11:29:03 MarkDuplicates Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3532401320979289205.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3532401320979289205.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3532401320979289205.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3532401320979289205.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3532401320979289205.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3532401320979289205.tmp/output.sam Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:03.424 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:03.424 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:03.437 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:03.437 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:03.438 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:03.438 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:03.438 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:03.438 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:03 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3532401320979289205.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3532401320979289205.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3532401320979289205.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:29:03 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3532401320979289205.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3532401320979289205.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.3532401320979289205.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:29:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:03 MarkDuplicates Start of doWork freeMemory: 1027795640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:03 MarkDuplicates Start of doWork freeMemory: 1027795640; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:03 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:29:03 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:03 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:29:03 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:29:04 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:29:04 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:04 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:29:04 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 964875000; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 964875000; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:29:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:06 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:29:06 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:06 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:29:06 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:06 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:29:06 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 487773216; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:29:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 487773216; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:07 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:29:07 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:07 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:29:07 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:07 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:29:07 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:07 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:29:07 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:07 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:29:07 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:07 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:29:07 MarkDuplicates Representative read Index cleanup. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:07 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:29:07 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:07 MarkDuplicates Before output close freeMemory: 757116856; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:29:07 MarkDuplicates Before output close freeMemory: 757116856; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:07 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:29:07 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:07 MarkDuplicates After output close freeMemory: 757257040; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:29:07 MarkDuplicates After output close freeMemory: 757257040; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:07 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:29:07 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1207959552 Runtime.totalMemory()=1207959552 Running Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:07 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testMappedPairWithSamePosition STANDARD_ERROR INFO 2024-07-02 11:29:07 MarkDuplicates Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17534523114730643807.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17534523114730643807.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17534523114730643807.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17534523114730643807.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17534523114730643807.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17534523114730643807.tmp/output.sam Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:07.884 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:07.884 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:07.884 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:07.884 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:07.884 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:07.884 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:07.884 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:07.884 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:07 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17534523114730643807.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17534523114730643807.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17534523114730643807.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:29:07 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17534523114730643807.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17534523114730643807.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17534523114730643807.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:29:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:08 MarkDuplicates Start of doWork freeMemory: 1027796280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:08 MarkDuplicates Start of doWork freeMemory: 1027796280; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:08 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:29:08 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:08 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:29:08 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:29:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:29:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:08 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:29:08 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 964875856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 964875856; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:29:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:10 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:29:10 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:10 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:29:10 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:10 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:29:10 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 489871008; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:29:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 489871008; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:10 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:29:10 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:10 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:29:10 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:10 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:29:10 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:10 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:29:10 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:10 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:29:10 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:10 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:29:10 MarkDuplicates Representative read Index cleanup. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:10 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:29:10 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:11 MarkDuplicates Before output close freeMemory: 759214648; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:29:11 MarkDuplicates Before output close freeMemory: 759214648; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:11 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:29:11 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:11 MarkDuplicates After output close freeMemory: 759354904; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:29:11 MarkDuplicates After output close freeMemory: 759354904; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:11 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:29:11 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1210056704 Runtime.totalMemory()=1210056704 Running Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:12 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testMappedPairWithSamePositionSameCigar STANDARD_ERROR INFO 2024-07-02 11:29:12 MarkDuplicates Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8214823512243431483.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8214823512243431483.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8214823512243431483.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8214823512243431483.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8214823512243431483.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8214823512243431483.tmp/output.sam Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:12.032 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:12.032 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:12.035 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:12.035 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:12.035 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:12.035 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:12.035 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:12.035 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:12 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8214823512243431483.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8214823512243431483.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8214823512243431483.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:29:12 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8214823512243431483.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8214823512243431483.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8214823512243431483.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:29:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:12 MarkDuplicates Start of doWork freeMemory: 1027795592; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:12 MarkDuplicates Start of doWork freeMemory: 1027795592; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:12 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:29:12 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:12 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:29:12 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:29:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:29:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:12 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:29:12 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 964875168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 964875168; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:13 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:29:13 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:29:14 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:14 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:29:14 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:14 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:29:14 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 487773168; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:29:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 487773168; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:14 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:29:14 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:14 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:29:14 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:14 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:29:14 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:14 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:29:14 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:14 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:29:14 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:14 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:29:14 MarkDuplicates Representative read Index cleanup. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:14 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:29:14 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:15 MarkDuplicates Before output close freeMemory: 757116808; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:29:15 MarkDuplicates Before output close freeMemory: 757116808; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:15 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:29:15 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:15 MarkDuplicates After output close freeMemory: 757104936; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:29:15 MarkDuplicates After output close freeMemory: 757104936; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:29:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1207959552 Runtime.totalMemory()=1207959552 Running Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:15 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:29:15 MarkDuplicates Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6208396504449345092.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6208396504449345092.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6208396504449345092.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6208396504449345092.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6208396504449345092.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6208396504449345092.tmp/output.sam Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:15.735 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:15.735 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:15.735 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:15.735 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:15.736 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:15.736 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:15.736 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:15.736 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:15 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6208396504449345092.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6208396504449345092.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6208396504449345092.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:29:15 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6208396504449345092.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6208396504449345092.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6208396504449345092.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:29:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:16 MarkDuplicates Start of doWork freeMemory: 1027794704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:16 MarkDuplicates Start of doWork freeMemory: 1027794704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:16 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:29:16 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:16 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:29:16 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:29:16 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:29:16 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:16 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:29:16 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 964874544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 964874544; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:29:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:16 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:29:16 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:16 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:29:16 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:16 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:29:16 MarkDuplicates Sorting list of duplicate records. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 485675424; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:29:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 485675424; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:17 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:29:17 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:17 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:29:17 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:17 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:29:17 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:17 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:29:17 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:17 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:29:17 MarkDuplicates Duplicate Index cleanup. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:17 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:29:17 MarkDuplicates Representative read Index cleanup. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:17 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:29:17 MarkDuplicates Getting Memory Stats. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:17 MarkDuplicates Before output close freeMemory: 755019176; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:29:17 MarkDuplicates Before output close freeMemory: 755019176; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:17 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:29:17 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:17 MarkDuplicates After output close freeMemory: 755158752; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:29:17 MarkDuplicates After output close freeMemory: 755158752; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:17 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:29:17 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1205862400 Runtime.totalMemory()=1205862400 Running Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:17 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:29:17 MarkDuplicates Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5948661045951839343.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5948661045951839343.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5948661045951839343.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5948661045951839343.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5948661045951839343.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5948661045951839343.tmp/output.sam Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:17.769 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:17.769 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:17.769 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:17.769 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:17.769 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:17.769 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:17.769 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:17.769 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:17 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5948661045951839343.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5948661045951839343.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5948661045951839343.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:29:17 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5948661045951839343.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5948661045951839343.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5948661045951839343.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:29:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:17 MarkDuplicates Start of doWork freeMemory: 1027794056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:17 MarkDuplicates Start of doWork freeMemory: 1027794056; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:17 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:29:17 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:17 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:29:17 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:29:18 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:29:18 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:18 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:29:18 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 964873896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 964873896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:29:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:18 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:29:18 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:18 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:29:18 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:18 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:29:18 MarkDuplicates Sorting list of duplicate records. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 489869080; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:29:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 489869080; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:19 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:29:19 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:19 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:29:19 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:19 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:29:19 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:19 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:29:19 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:19 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:29:19 MarkDuplicates Duplicate Index cleanup. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:19 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:29:19 MarkDuplicates Representative read Index cleanup. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:19 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:29:19 MarkDuplicates Getting Memory Stats. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:19 MarkDuplicates Before output close freeMemory: 759212952; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:29:19 MarkDuplicates Before output close freeMemory: 759212952; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:19 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:29:19 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:19 MarkDuplicates After output close freeMemory: 759352904; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:29:19 MarkDuplicates After output close freeMemory: 759352904; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:19 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:29:19 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1210056704 Runtime.totalMemory()=1210056704 Running Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:19 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testOpticalDuplicateBehaviorNullRegex STANDARD_ERROR INFO 2024-07-02 11:29:19 MarkDuplicates Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.28135395698852343.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -READ_NAME_REGEX null -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.28135395698852343.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.28135395698852343.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.28135395698852343.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -READ_NAME_REGEX null -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.28135395698852343.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.28135395698852343.tmp/output.sam Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:19.940 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:19.940 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:19.940 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:19.940 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:19.945 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:19.945 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:19.945 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:19.945 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:19 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.28135395698852343.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.28135395698852343.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.28135395698852343.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH READ_NAME_REGEX=null MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:29:19 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.28135395698852343.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.28135395698852343.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.28135395698852343.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH READ_NAME_REGEX=null MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:29:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:20 MarkDuplicates Start of doWork freeMemory: 1027792024; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:20 MarkDuplicates Start of doWork freeMemory: 1027792024; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:20 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:29:20 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:20 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:29:20 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:20 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:29:20 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 964871384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 964871384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:21 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:29:21 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:21 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:29:21 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:21 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:29:21 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:21 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:29:21 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 487769680; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:29:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 487769680; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:22 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:29:22 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:29:22 MarkDuplicates Skipped optical duplicate cluster discovery; library size estimation may be inaccurate! WARNING 2024-07-02 11:29:22 MarkDuplicates Skipped optical duplicate cluster discovery; library size estimation may be inaccurate! Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:22 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:29:22 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:22 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:29:22 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:22 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:29:22 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:22 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:29:22 MarkDuplicates Representative read Index cleanup. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:22 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:29:22 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:22 MarkDuplicates Before output close freeMemory: 757113360; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:29:22 MarkDuplicates Before output close freeMemory: 757113360; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:22 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:29:22 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:22 MarkDuplicates After output close freeMemory: 757253120; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:29:22 MarkDuplicates After output close freeMemory: 757253120; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:22 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:29:22 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1207959552 Runtime.totalMemory()=1207959552 Running Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:22 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testOpticalDuplicateClusterOneEndSamePositionOneCluster STANDARD_ERROR INFO 2024-07-02 11:29:22 MarkDuplicates Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5666660426183677024.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5666660426183677024.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5666660426183677024.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5666660426183677024.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5666660426183677024.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5666660426183677024.tmp/output.sam Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:22.893 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:22.893 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:22.893 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:22.893 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:22.894 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:22.894 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:22.894 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:22.894 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:22 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5666660426183677024.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5666660426183677024.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5666660426183677024.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:29:22 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5666660426183677024.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5666660426183677024.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5666660426183677024.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:29:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:23 MarkDuplicates Start of doWork freeMemory: 1027824664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:23 MarkDuplicates Start of doWork freeMemory: 1027824664; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:23 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:29:23 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:23 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:29:23 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:23 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:29:23 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 964903960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 964903960; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:29:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:24 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:29:24 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:24 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:29:24 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:24 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:29:24 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 554910792; totalMemory: 1275068416; maxMemory: 2147483648 INFO 2024-07-02 11:29:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 554910792; totalMemory: 1275068416; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:24 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:29:24 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:24 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:29:24 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:24 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:29:24 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:24 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:29:24 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:24 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:29:24 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:24 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:29:24 MarkDuplicates Representative read Index cleanup. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:24 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:29:24 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:25 MarkDuplicates Before output close freeMemory: 824254392; totalMemory: 1275068416; maxMemory: 2147483648 INFO 2024-07-02 11:29:25 MarkDuplicates Before output close freeMemory: 824254392; totalMemory: 1275068416; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:25 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:29:25 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:25 MarkDuplicates After output close freeMemory: 824394712; totalMemory: 1275068416; maxMemory: 2147483648 INFO 2024-07-02 11:29:25 MarkDuplicates After output close freeMemory: 824394712; totalMemory: 1275068416; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:25 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:29:25 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1275068416 Runtime.totalMemory()=1275068416 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:25 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:29:25 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1720312383459069082.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1720312383459069082.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1720312383459069082.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1720312383459069082.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1720312383459069082.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1720312383459069082.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:25.419 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:25.419 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:25.419 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:25.419 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:25.419 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:25.419 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:25.419 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:25.419 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:25 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1720312383459069082.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1720312383459069082.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1720312383459069082.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:29:25 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1720312383459069082.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1720312383459069082.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1720312383459069082.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:29:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:25 MarkDuplicates Start of doWork freeMemory: 1027823216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:25 MarkDuplicates Start of doWork freeMemory: 1027823216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:25 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:29:25 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:25 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:29:25 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:25 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:29:25 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 964902520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 964902520; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:29:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:26 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:29:26 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:26 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:29:26 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:26 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:29:26 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 487800640; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:29:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 487800640; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:27 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:29:27 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:27 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:29:27 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:27 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:29:27 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:27 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:29:27 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:27 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:29:27 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:27 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:29:27 MarkDuplicates Representative read Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:27 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:29:27 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:27 MarkDuplicates Before output close freeMemory: 757144240; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:29:27 MarkDuplicates Before output close freeMemory: 757144240; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:27 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:29:27 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:27 MarkDuplicates After output close freeMemory: 757284632; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:29:27 MarkDuplicates After output close freeMemory: 757284632; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:27 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:29:27 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1207959552 Runtime.totalMemory()=1207959552 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:27 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:29:27 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4166545614848424596.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4166545614848424596.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4166545614848424596.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4166545614848424596.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4166545614848424596.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4166545614848424596.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:27.897 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:27.897 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:27.898 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:27.898 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:27.898 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:27.898 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:27.898 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:27.898 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:27 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4166545614848424596.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4166545614848424596.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4166545614848424596.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:29:27 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4166545614848424596.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4166545614848424596.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4166545614848424596.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:29:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:28 MarkDuplicates Start of doWork freeMemory: 1027822536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:28 MarkDuplicates Start of doWork freeMemory: 1027822536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:28 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:29:28 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:28 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:29:28 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:28 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:29:28 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 964901832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 964901832; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:29:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:29 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:29:29 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:29 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:29:29 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:29 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:29:29 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 490945680; totalMemory: 1211105280; maxMemory: 2147483648 INFO 2024-07-02 11:29:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 490945680; totalMemory: 1211105280; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:29 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:29:29 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:29 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:29:29 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:29 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:29:29 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:29 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:29:29 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:29 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:29:29 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:29 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:29:29 MarkDuplicates Representative read Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:29 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:29:29 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:30 MarkDuplicates Before output close freeMemory: 760289280; totalMemory: 1211105280; maxMemory: 2147483648 INFO 2024-07-02 11:29:30 MarkDuplicates Before output close freeMemory: 760289280; totalMemory: 1211105280; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:30 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:29:30 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:30 MarkDuplicates After output close freeMemory: 760429600; totalMemory: 1211105280; maxMemory: 2147483648 INFO 2024-07-02 11:29:30 MarkDuplicates After output close freeMemory: 760429600; totalMemory: 1211105280; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:30 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:29:30 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1211105280 Runtime.totalMemory()=1211105280 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:30 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:29:30 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2681349467732994630.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2681349467732994630.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2681349467732994630.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2681349467732994630.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2681349467732994630.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2681349467732994630.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:30.494 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:30.494 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:30.494 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:30.494 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:30.494 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:30.494 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:30.494 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:30.494 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:30 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2681349467732994630.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2681349467732994630.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2681349467732994630.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:29:30 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2681349467732994630.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2681349467732994630.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2681349467732994630.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:29:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:30 MarkDuplicates Start of doWork freeMemory: 1027821904; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:30 MarkDuplicates Start of doWork freeMemory: 1027821904; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:30 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:29:30 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:30 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:29:30 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:30 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:29:30 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 964901200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 964901200; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:29:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:32 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:29:32 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:32 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:29:32 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:32 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:29:32 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 485702168; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:29:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 485702168; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:32 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:29:32 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:32 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:29:32 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:32 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:29:32 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:32 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:29:32 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:32 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:29:32 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:32 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:29:32 MarkDuplicates Representative read Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:32 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:29:32 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:32 MarkDuplicates Before output close freeMemory: 755045768; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:29:32 MarkDuplicates Before output close freeMemory: 755045768; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:32 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:29:32 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:33 MarkDuplicates After output close freeMemory: 755186088; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:29:33 MarkDuplicates After output close freeMemory: 755186088; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:33 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:29:33 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1205862400 Runtime.totalMemory()=1205862400 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:33 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:29:33 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9201066479338759886.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9201066479338759886.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9201066479338759886.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9201066479338759886.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9201066479338759886.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9201066479338759886.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:33.347 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:33.347 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:33.347 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:33.347 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:33.348 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:33.348 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:33.348 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:33.348 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:33 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9201066479338759886.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9201066479338759886.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9201066479338759886.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:29:33 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9201066479338759886.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9201066479338759886.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9201066479338759886.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:29:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:33 MarkDuplicates Start of doWork freeMemory: 1027815800; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:33 MarkDuplicates Start of doWork freeMemory: 1027815800; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:33 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:29:33 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:33 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:29:33 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:33 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:29:33 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:34 MarkDuplicates After buildSortedReadEndLists freeMemory: 964900544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:34 MarkDuplicates After buildSortedReadEndLists freeMemory: 964900544; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:34 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:29:34 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:29:34 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:34 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:29:34 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:34 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:29:34 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 568539016; totalMemory: 1288699904; maxMemory: 2147483648 INFO 2024-07-02 11:29:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 568539016; totalMemory: 1288699904; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:35 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:29:35 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:35 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:29:35 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:35 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:29:35 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:35 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:29:35 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:35 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:29:35 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:35 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:29:35 MarkDuplicates Representative read Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:35 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:29:35 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:35 MarkDuplicates Before output close freeMemory: 837882616; totalMemory: 1288699904; maxMemory: 2147483648 INFO 2024-07-02 11:29:35 MarkDuplicates Before output close freeMemory: 837882616; totalMemory: 1288699904; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:35 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:29:35 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:35 MarkDuplicates After output close freeMemory: 838022712; totalMemory: 1288699904; maxMemory: 2147483648 INFO 2024-07-02 11:29:35 MarkDuplicates After output close freeMemory: 838022712; totalMemory: 1288699904; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:35 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:29:35 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1288699904 Runtime.totalMemory()=1288699904 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:36 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:29:36 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13323315033542841656.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13323315033542841656.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13323315033542841656.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13323315033542841656.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13323315033542841656.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13323315033542841656.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:36.015 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:36.015 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:36.015 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:36.015 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:36.015 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:36.015 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:36.015 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:36.015 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:36 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13323315033542841656.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13323315033542841656.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13323315033542841656.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:29:36 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13323315033542841656.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13323315033542841656.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13323315033542841656.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:29:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:36 MarkDuplicates Start of doWork freeMemory: 1027815160; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:36 MarkDuplicates Start of doWork freeMemory: 1027815160; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:36 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:29:36 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:36 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:29:36 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:36 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:29:36 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 964899912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 964899912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:29:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:29:37 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:29:37 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:37 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:29:37 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 484652304; totalMemory: 1204813824; maxMemory: 2147483648 INFO 2024-07-02 11:29:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 484652304; totalMemory: 1204813824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:37 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:29:37 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:37 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:29:37 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:37 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:29:37 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:37 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:29:37 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:37 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:29:37 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:37 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:29:37 MarkDuplicates Representative read Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:37 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:29:37 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:37 MarkDuplicates Before output close freeMemory: 753994120; totalMemory: 1204813824; maxMemory: 2147483648 INFO 2024-07-02 11:29:37 MarkDuplicates Before output close freeMemory: 753994120; totalMemory: 1204813824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:37 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:29:37 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:38 MarkDuplicates After output close freeMemory: 754136080; totalMemory: 1204813824; maxMemory: 2147483648 INFO 2024-07-02 11:29:38 MarkDuplicates After output close freeMemory: 754136080; totalMemory: 1204813824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:38 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:29:38 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1204813824 Runtime.totalMemory()=1204813824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:38 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:29:38 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17441364283755194201.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17441364283755194201.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17441364283755194201.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17441364283755194201.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17441364283755194201.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17441364283755194201.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:38.195 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:38.195 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:38.195 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:38.195 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:38.195 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:38.195 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:38.195 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:38.195 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:38 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17441364283755194201.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17441364283755194201.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17441364283755194201.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:29:38 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17441364283755194201.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17441364283755194201.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17441364283755194201.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:29:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:38 MarkDuplicates Start of doWork freeMemory: 1027819800; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:38 MarkDuplicates Start of doWork freeMemory: 1027819800; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:38 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:29:38 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:38 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:29:38 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:38 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:29:38 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 964899096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 964899096; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:29:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:39 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:29:39 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:39 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:29:39 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:39 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:29:39 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 487797216; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:29:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 487797216; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:39 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:29:39 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:39 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:29:39 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:39 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:29:39 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:39 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:29:39 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:39 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:29:39 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:39 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:29:39 MarkDuplicates Representative read Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:39 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:29:39 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:39 MarkDuplicates Before output close freeMemory: 757139064; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:29:39 MarkDuplicates Before output close freeMemory: 757139064; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:39 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:29:39 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:40 MarkDuplicates After output close freeMemory: 757278888; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:29:40 MarkDuplicates After output close freeMemory: 757278888; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:40 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:29:40 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1207959552 Runtime.totalMemory()=1207959552 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:40 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:29:40 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17615149223287471476.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17615149223287471476.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17615149223287471476.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17615149223287471476.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17615149223287471476.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17615149223287471476.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:40.049 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:40.049 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:40.049 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:40.049 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:40.049 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:40.049 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:40.049 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:40.049 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:40 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17615149223287471476.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17615149223287471476.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17615149223287471476.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:29:40 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17615149223287471476.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17615149223287471476.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17615149223287471476.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:29:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:40 MarkDuplicates Start of doWork freeMemory: 1027816912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:40 MarkDuplicates Start of doWork freeMemory: 1027816912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:40 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:29:40 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:40 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:29:40 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:40 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:29:40 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 964898464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 964898464; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:29:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:40 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:29:40 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:29:40 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:40 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:29:40 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 485699432; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:29:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 485699432; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:41 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:29:41 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:41 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:29:41 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:29:41 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:41 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:29:41 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:41 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:29:41 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:41 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:29:41 MarkDuplicates Representative read Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:41 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:29:41 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:41 MarkDuplicates Before output close freeMemory: 754891040; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:29:41 MarkDuplicates Before output close freeMemory: 754891040; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:41 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:29:41 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:41 MarkDuplicates After output close freeMemory: 755183424; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:29:41 MarkDuplicates After output close freeMemory: 755183424; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:41 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:29:41 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1205862400 Runtime.totalMemory()=1205862400 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:41 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:29:41 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12035594424836596898.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12035594424836596898.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12035594424836596898.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12035594424836596898.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12035594424836596898.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12035594424836596898.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:41.603 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:41.603 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:41.603 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:41.603 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:41.603 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:41.603 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:41.603 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:41.603 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:41 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12035594424836596898.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12035594424836596898.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12035594424836596898.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:29:41 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12035594424836596898.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12035594424836596898.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12035594424836596898.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:29:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:41 MarkDuplicates Start of doWork freeMemory: 1027818536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:41 MarkDuplicates Start of doWork freeMemory: 1027818536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:41 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:29:41 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:41 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:29:41 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:41 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:29:41 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 964897832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 964897832; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:29:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:42 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:29:42 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:42 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:29:42 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:42 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:29:42 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 489893104; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:29:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 489893104; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:43 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:29:43 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:43 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:29:43 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:43 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:29:43 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:43 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:29:43 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:43 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:29:43 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:43 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:29:43 MarkDuplicates Representative read Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:43 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:29:43 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:43 MarkDuplicates Before output close freeMemory: 759236704; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:29:43 MarkDuplicates Before output close freeMemory: 759236704; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:43 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:29:43 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:43 MarkDuplicates After output close freeMemory: 759377024; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:29:43 MarkDuplicates After output close freeMemory: 759377024; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:43 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:29:43 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1210056704 Runtime.totalMemory()=1210056704 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:43 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:29:43 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4798547979198780048.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4798547979198780048.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4798547979198780048.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4798547979198780048.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4798547979198780048.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4798547979198780048.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:43.753 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:43.753 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:43.753 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:43.753 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:43.754 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:43.754 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:43.754 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:43.754 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:43 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4798547979198780048.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4798547979198780048.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4798547979198780048.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:29:43 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4798547979198780048.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4798547979198780048.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4798547979198780048.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:29:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:44 MarkDuplicates Start of doWork freeMemory: 1027817912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:44 MarkDuplicates Start of doWork freeMemory: 1027817912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:44 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:29:44 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:44 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:29:44 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:44 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:29:44 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 964897208; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 964897208; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:29:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:45 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:29:45 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:45 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:29:45 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:45 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:29:45 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 522398336; totalMemory: 1242562560; maxMemory: 2147483648 INFO 2024-07-02 11:29:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 522398336; totalMemory: 1242562560; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:45 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:29:45 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:45 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:29:45 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:45 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:29:45 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:45 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:29:45 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:45 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:29:45 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:45 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:29:45 MarkDuplicates Representative read Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:45 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:29:45 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:46 MarkDuplicates Before output close freeMemory: 791741936; totalMemory: 1242562560; maxMemory: 2147483648 INFO 2024-07-02 11:29:46 MarkDuplicates Before output close freeMemory: 791741936; totalMemory: 1242562560; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:46 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:29:46 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:46 MarkDuplicates After output close freeMemory: 791882256; totalMemory: 1242562560; maxMemory: 2147483648 INFO 2024-07-02 11:29:46 MarkDuplicates After output close freeMemory: 791882256; totalMemory: 1242562560; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:29:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1242562560 Runtime.totalMemory()=1242562560 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:46 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:29:46 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4022152269790130781.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4022152269790130781.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4022152269790130781.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4022152269790130781.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4022152269790130781.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4022152269790130781.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:46.542 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:46.542 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:46.542 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:46.542 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:46.542 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:46.542 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:46.542 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:46.542 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:46 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4022152269790130781.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4022152269790130781.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4022152269790130781.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:29:46 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4022152269790130781.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4022152269790130781.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4022152269790130781.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:29:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:46 MarkDuplicates Start of doWork freeMemory: 1027817256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:46 MarkDuplicates Start of doWork freeMemory: 1027817256; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:46 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:29:46 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:46 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:29:46 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:46 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:29:46 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 964896552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 964896552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:29:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:48 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:29:48 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:48 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:29:48 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:48 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:29:48 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 489891824; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:29:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 489891824; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:48 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:29:48 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:48 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:29:48 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:29:48 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:48 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:29:48 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:48 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:29:48 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:48 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:29:48 MarkDuplicates Representative read Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:48 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:29:48 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:48 MarkDuplicates Before output close freeMemory: 759235424; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:29:48 MarkDuplicates Before output close freeMemory: 759235424; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:48 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:29:48 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:49 MarkDuplicates After output close freeMemory: 759375744; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:29:49 MarkDuplicates After output close freeMemory: 759375744; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:29:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1210056704 Runtime.totalMemory()=1210056704 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:49 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756) STANDARD_ERROR INFO 2024-07-02 11:29:49 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17356558815154898922.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17356558815154898922.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17356558815154898922.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17356558815154898922.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17356558815154898922.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17356558815154898922.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:49.329 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:49.329 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:49.329 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:49.329 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:49.329 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:49.329 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:49.329 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:49.329 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:49 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17356558815154898922.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17356558815154898922.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17356558815154898922.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:29:49 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17356558815154898922.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17356558815154898922.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17356558815154898922.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:29:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:49 MarkDuplicates Start of doWork freeMemory: 1027816616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:49 MarkDuplicates Start of doWork freeMemory: 1027816616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:49 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:29:49 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:29:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:49 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:29:49 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 964895912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 964895912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:29:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:50 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:29:50 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:50 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:29:50 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:50 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:29:50 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 487794032; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:29:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 487794032; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:50 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:29:50 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:50 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:29:50 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:50 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:29:50 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:50 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:29:50 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:50 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:29:50 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:50 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:29:50 MarkDuplicates Representative read Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:50 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:29:50 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:50 MarkDuplicates Before output close freeMemory: 757137632; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:29:50 MarkDuplicates Before output close freeMemory: 757137632; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:50 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:29:50 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:51 MarkDuplicates After output close freeMemory: 757277456; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:29:51 MarkDuplicates After output close freeMemory: 757277456; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:29:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1207959552 Runtime.totalMemory()=1207959552 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:51 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756) STANDARD_ERROR INFO 2024-07-02 11:29:51 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5056882725370523490.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5056882725370523490.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5056882725370523490.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5056882725370523490.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5056882725370523490.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5056882725370523490.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:51.243 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:51.243 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:51.243 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:51.243 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:51.243 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:51.243 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:51.243 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:51.243 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:51 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5056882725370523490.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5056882725370523490.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5056882725370523490.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:29:51 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5056882725370523490.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5056882725370523490.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.5056882725370523490.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:29:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:51 MarkDuplicates Start of doWork freeMemory: 1027815968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:51 MarkDuplicates Start of doWork freeMemory: 1027815968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:51 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:29:51 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:51 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:29:51 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:51 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:29:51 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 964895264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 964895264; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:29:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:52 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:29:52 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:52 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:29:52 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:52 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:29:52 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:52 MarkDuplicates After generateDuplicateIndexes freeMemory: 489890536; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:29:52 MarkDuplicates After generateDuplicateIndexes freeMemory: 489890536; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:52 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:29:52 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:52 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:29:52 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:52 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:29:52 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:53 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:29:53 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:53 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:29:53 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:53 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:29:53 MarkDuplicates Representative read Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:53 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:29:53 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:53 MarkDuplicates Before output close freeMemory: 759233288; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:29:53 MarkDuplicates Before output close freeMemory: 759233288; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:53 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:29:53 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:53 MarkDuplicates After output close freeMemory: 759374456; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:29:53 MarkDuplicates After output close freeMemory: 759374456; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:29:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1210056704 Runtime.totalMemory()=1210056704 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:53 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756) STANDARD_ERROR INFO 2024-07-02 11:29:53 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17022766303505080451.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17022766303505080451.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17022766303505080451.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17022766303505080451.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17022766303505080451.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17022766303505080451.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:53.663 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:53.663 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:53.663 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:53.663 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:53.663 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:53.663 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:53.663 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:53.663 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:53 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17022766303505080451.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17022766303505080451.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17022766303505080451.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:29:53 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17022766303505080451.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17022766303505080451.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17022766303505080451.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:29:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:53 MarkDuplicates Start of doWork freeMemory: 1027815376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:53 MarkDuplicates Start of doWork freeMemory: 1027815376; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:53 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:29:53 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:53 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:29:53 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:53 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:29:53 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 964894672; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 964894672; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:54 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:29:54 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:29:55 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:55 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:29:55 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:55 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:29:55 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 490937824; totalMemory: 1211105280; maxMemory: 2147483648 INFO 2024-07-02 11:29:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 490937824; totalMemory: 1211105280; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:55 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:29:55 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:55 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:29:55 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:55 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:29:55 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:55 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:29:55 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:55 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:29:55 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:55 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:29:55 MarkDuplicates Representative read Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:55 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:29:55 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:55 MarkDuplicates Before output close freeMemory: 760128712; totalMemory: 1211105280; maxMemory: 2147483648 INFO 2024-07-02 11:29:55 MarkDuplicates Before output close freeMemory: 760128712; totalMemory: 1211105280; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:55 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:29:55 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:56 MarkDuplicates After output close freeMemory: 760422440; totalMemory: 1211105280; maxMemory: 2147483648 INFO 2024-07-02 11:29:56 MarkDuplicates After output close freeMemory: 760422440; totalMemory: 1211105280; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:56 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:29:56 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1211105280 Runtime.totalMemory()=1211105280 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:56 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756) STANDARD_ERROR INFO 2024-07-02 11:29:56 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9918562191429482460.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9918562191429482460.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9918562191429482460.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9918562191429482460.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9918562191429482460.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9918562191429482460.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:56.087 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:56.087 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:56.087 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:56.087 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:56.087 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:56.087 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:56.087 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:56.087 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:56 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9918562191429482460.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9918562191429482460.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9918562191429482460.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:29:56 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9918562191429482460.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9918562191429482460.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9918562191429482460.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:29:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:56 MarkDuplicates Start of doWork freeMemory: 1027809336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:56 MarkDuplicates Start of doWork freeMemory: 1027809336; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:56 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:29:56 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:56 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:29:56 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:56 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:29:56 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 964894048; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 964894048; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:29:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:57 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:29:57 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:57 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:29:57 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:57 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:29:57 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 568531824; totalMemory: 1288699904; maxMemory: 2147483648 INFO 2024-07-02 11:29:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 568531824; totalMemory: 1288699904; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:57 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:29:57 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:57 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:29:57 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:57 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:29:57 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:57 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:29:57 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:57 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:29:57 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:57 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:29:57 MarkDuplicates Representative read Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:57 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:29:57 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:58 MarkDuplicates Before output close freeMemory: 837876120; totalMemory: 1288699904; maxMemory: 2147483648 INFO 2024-07-02 11:29:58 MarkDuplicates Before output close freeMemory: 837876120; totalMemory: 1288699904; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:58 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:29:58 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:58 MarkDuplicates After output close freeMemory: 837846408; totalMemory: 1288699904; maxMemory: 2147483648 INFO 2024-07-02 11:29:58 MarkDuplicates After output close freeMemory: 837846408; totalMemory: 1288699904; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:29:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1288699904 Runtime.totalMemory()=1288699904 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:58 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance STANDARD_ERROR INFO 2024-07-02 11:29:58 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8463143105204383578.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8463143105204383578.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8463143105204383578.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8463143105204383578.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8463143105204383578.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8463143105204383578.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:58.453 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:58.453 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:58.453 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:58.453 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:58.454 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:29:58.454 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:29:58.454 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:29:58.454 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:58 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8463143105204383578.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8463143105204383578.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8463143105204383578.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:29:58 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8463143105204383578.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8463143105204383578.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8463143105204383578.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:29:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:29:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:58 MarkDuplicates Start of doWork freeMemory: 1027814152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:58 MarkDuplicates Start of doWork freeMemory: 1027814152; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:58 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:29:58 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:58 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:29:58 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:58 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:29:58 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 964893448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:29:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 964893448; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:29:59 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:29:59 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:00 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:30:00 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:00 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:30:00 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:00 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:30:00 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 489888720; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:30:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 489888720; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:00 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:30:00 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:00 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:30:00 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:00 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:30:00 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:00 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:30:00 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:00 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:30:00 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:00 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:30:00 MarkDuplicates Representative read Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:00 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:30:00 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:00 MarkDuplicates Before output close freeMemory: 759232320; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:30:00 MarkDuplicates Before output close freeMemory: 759232320; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:00 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:30:00 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:01 MarkDuplicates After output close freeMemory: 759372640; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:30:01 MarkDuplicates After output close freeMemory: 759372640; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:01 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:30:01 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1210056704 Runtime.totalMemory()=1210056704 Running Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:01 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance STANDARD_ERROR INFO 2024-07-02 11:30:01 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13851756660716730830.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13851756660716730830.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13851756660716730830.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13851756660716730830.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13851756660716730830.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13851756660716730830.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:01.391 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:01.391 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:01.391 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:01.391 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:01.391 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:01.391 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:01.391 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:01.391 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:01 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13851756660716730830.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13851756660716730830.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13851756660716730830.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:30:01 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13851756660716730830.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13851756660716730830.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13851756660716730830.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:30:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:01 MarkDuplicates Start of doWork freeMemory: 1027813944; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:01 MarkDuplicates Start of doWork freeMemory: 1027813944; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:01 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:30:01 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:01 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:30:01 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:01 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:30:01 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 964893240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 964893240; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:02 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:30:02 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:03 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:30:03 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:03 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:30:03 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:03 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:30:03 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 485694056; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:30:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 485694056; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:03 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:30:03 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:03 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:30:03 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:03 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:30:03 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:03 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:30:03 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:03 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:30:03 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:03 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:30:03 MarkDuplicates Representative read Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:03 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:30:03 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:04 MarkDuplicates Before output close freeMemory: 755037792; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:30:04 MarkDuplicates Before output close freeMemory: 755037792; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:04 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:30:04 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:04 MarkDuplicates After output close freeMemory: 755178048; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:30:04 MarkDuplicates After output close freeMemory: 755178048; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:04 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:30:04 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1205862400 Runtime.totalMemory()=1205862400 Running Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:04 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate STANDARD_ERROR INFO 2024-07-02 11:30:04 MarkDuplicates Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10091009112665220759.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10091009112665220759.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10091009112665220759.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10091009112665220759.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10091009112665220759.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10091009112665220759.tmp/output.sam Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:04.474 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:04.474 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:04.474 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:04.474 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:04.474 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:04.474 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:04.474 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:04.474 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:04 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10091009112665220759.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10091009112665220759.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10091009112665220759.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:30:04 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10091009112665220759.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10091009112665220759.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10091009112665220759.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:30:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:04 MarkDuplicates Start of doWork freeMemory: 1027812912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:04 MarkDuplicates Start of doWork freeMemory: 1027812912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:04 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:30:04 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:04 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:30:04 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:04 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:30:04 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 964892208; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 964892208; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:30:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:06 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:30:06 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:06 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:30:06 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:06 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:30:06 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 487790176; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:30:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 487790176; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:06 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:30:06 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:06 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:30:06 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:06 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:30:06 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:06 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:30:06 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:06 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:30:06 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:06 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:30:06 MarkDuplicates Representative read Index cleanup. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:06 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:30:06 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:06 MarkDuplicates Before output close freeMemory: 757133840; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:30:06 MarkDuplicates Before output close freeMemory: 757133840; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:06 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:30:06 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:07 MarkDuplicates After output close freeMemory: 757274096; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:30:07 MarkDuplicates After output close freeMemory: 757274096; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:07 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:30:07 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1207959552 Runtime.totalMemory()=1207959552 Running Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:07 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testOpticalDuplicateFinding STANDARD_ERROR INFO 2024-07-02 11:30:07 MarkDuplicates Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2702091071938292818.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2702091071938292818.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2702091071938292818.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2702091071938292818.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2702091071938292818.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2702091071938292818.tmp/output.sam Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:07.429 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:07.429 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:07.429 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:07.429 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:07.429 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:07.429 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:07.429 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:07.429 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:07 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2702091071938292818.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2702091071938292818.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2702091071938292818.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:30:07 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2702091071938292818.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2702091071938292818.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2702091071938292818.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:30:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:07 MarkDuplicates Start of doWork freeMemory: 1027811248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:07 MarkDuplicates Start of doWork freeMemory: 1027811248; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:07 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:30:07 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:07 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:30:07 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:07 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:30:07 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 964890336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 964890336; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:30:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:09 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:30:09 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:09 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:30:09 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:09 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:30:09 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 539168696; totalMemory: 1259339776; maxMemory: 2147483648 INFO 2024-07-02 11:30:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 539168696; totalMemory: 1259339776; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:09 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:30:09 MarkDuplicates Marking 4 records as duplicates. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:09 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:30:09 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:09 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:30:09 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:09 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:30:09 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:09 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:30:09 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:09 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:30:09 MarkDuplicates Representative read Index cleanup. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:09 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:30:09 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:10 MarkDuplicates Before output close freeMemory: 808510688; totalMemory: 1259339776; maxMemory: 2147483648 INFO 2024-07-02 11:30:10 MarkDuplicates Before output close freeMemory: 808510688; totalMemory: 1259339776; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:10 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:30:10 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:10 MarkDuplicates After output close freeMemory: 808652664; totalMemory: 1259339776; maxMemory: 2147483648 INFO 2024-07-02 11:30:10 MarkDuplicates After output close freeMemory: 808652664; totalMemory: 1259339776; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:10 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:30:10 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1259339776 Runtime.totalMemory()=1259339776 Running Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:10 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testPathologicalOrderingAtTheSamePosition STANDARD_ERROR INFO 2024-07-02 11:30:10 MarkDuplicates Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13282563367654366000.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13282563367654366000.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13282563367654366000.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13282563367654366000.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13282563367654366000.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13282563367654366000.tmp/output.sam Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:10.487 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:10.487 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:10.487 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:10.487 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:10.487 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:10.487 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:10.487 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:10.487 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:10 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13282563367654366000.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13282563367654366000.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13282563367654366000.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:30:10 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13282563367654366000.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13282563367654366000.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13282563367654366000.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:30:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:10 MarkDuplicates Start of doWork freeMemory: 1027811432; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:10 MarkDuplicates Start of doWork freeMemory: 1027811432; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:10 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:30:10 MarkDuplicates Reading input file and constructing read end information. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:10 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:30:10 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:10 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:30:10 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 964890728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 964890728; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:30:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:12 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:30:12 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:12 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:30:12 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:12 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:30:12 MarkDuplicates Sorting list of duplicate records. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 489885848; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:30:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 489885848; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:12 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:30:12 MarkDuplicates Marking 2 records as duplicates. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:12 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:30:12 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:12 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:30:12 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:12 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:30:12 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:12 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:30:12 MarkDuplicates Duplicate Index cleanup. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:12 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:30:12 MarkDuplicates Representative read Index cleanup. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:12 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:30:12 MarkDuplicates Getting Memory Stats. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:13 MarkDuplicates Before output close freeMemory: 759229536; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:30:13 MarkDuplicates Before output close freeMemory: 759229536; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:13 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:30:13 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:13 MarkDuplicates After output close freeMemory: 759369768; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:30:13 MarkDuplicates After output close freeMemory: 759369768; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:13 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:30:13 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1210056704 Runtime.totalMemory()=1210056704 Running Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:13 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testSecondEndIsBeforeFirstInCoordinate STANDARD_ERROR INFO 2024-07-02 11:30:13 MarkDuplicates Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1695470519473333603.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1695470519473333603.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1695470519473333603.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1695470519473333603.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1695470519473333603.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1695470519473333603.tmp/output.sam Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:13.736 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:13.736 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:13.749 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:13.749 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:13.749 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:13.749 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:13.749 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:13.749 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:13 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1695470519473333603.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1695470519473333603.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1695470519473333603.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:30:13 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1695470519473333603.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1695470519473333603.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1695470519473333603.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:30:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:14 MarkDuplicates Start of doWork freeMemory: 1027812008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:14 MarkDuplicates Start of doWork freeMemory: 1027812008; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:14 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:30:14 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:14 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:30:14 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:30:14 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:30:14 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:14 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:30:14 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 964891584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 964891584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:15 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:30:15 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:16 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:30:16 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:16 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:30:16 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:16 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:30:16 MarkDuplicates Sorting list of duplicate records. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 485692432; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:30:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 485692432; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:16 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:30:16 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:16 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:30:16 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:16 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:30:16 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:16 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:30:16 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:16 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:30:16 MarkDuplicates Duplicate Index cleanup. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:16 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:30:16 MarkDuplicates Representative read Index cleanup. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:16 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:30:16 MarkDuplicates Getting Memory Stats. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:17 MarkDuplicates Before output close freeMemory: 755036088; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:30:17 MarkDuplicates Before output close freeMemory: 755036088; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:17 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:30:17 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:17 MarkDuplicates After output close freeMemory: 755176256; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:30:17 MarkDuplicates After output close freeMemory: 755176256; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:17 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:30:17 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1205862400 Runtime.totalMemory()=1205862400 Running Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:17 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testSingleMappedFragment STANDARD_ERROR INFO 2024-07-02 11:30:17 MarkDuplicates Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16381331453438592089.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16381331453438592089.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16381331453438592089.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16381331453438592089.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16381331453438592089.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16381331453438592089.tmp/output.sam Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:17.648 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:17.648 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:17.648 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:17.648 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:17.648 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:17.648 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:17.648 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:17.648 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:17 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16381331453438592089.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16381331453438592089.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16381331453438592089.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:30:17 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16381331453438592089.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16381331453438592089.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16381331453438592089.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:30:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:17 MarkDuplicates Start of doWork freeMemory: 1027806552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:17 MarkDuplicates Start of doWork freeMemory: 1027806552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:18 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:30:18 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:18 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:30:18 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:30:18 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:30:18 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:18 MarkDuplicates Read 1 records. 0 pairs never matched. INFO 2024-07-02 11:30:18 MarkDuplicates Read 1 records. 0 pairs never matched. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 964891840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 964891840; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:19 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:30:19 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:20 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:30:20 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:20 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:30:20 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:20 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:30:20 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 487789872; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:30:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 487789872; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:20 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:30:20 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:20 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:30:20 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:20 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:30:20 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:20 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:30:20 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:20 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:30:20 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:20 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:30:20 MarkDuplicates Representative read Index cleanup. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:20 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:30:20 MarkDuplicates Getting Memory Stats. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:21 MarkDuplicates Before output close freeMemory: 757131912; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:30:21 MarkDuplicates Before output close freeMemory: 757131912; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:21 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:30:21 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:21 MarkDuplicates After output close freeMemory: 757273768; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:30:21 MarkDuplicates After output close freeMemory: 757273768; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:21 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:30:21 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1207959552 Runtime.totalMemory()=1207959552 Running Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:21 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testSingleMappedFragmentAndSingleMappedPair STANDARD_ERROR INFO 2024-07-02 11:30:21 MarkDuplicates Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14280084069835792221.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14280084069835792221.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14280084069835792221.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14280084069835792221.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14280084069835792221.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14280084069835792221.tmp/output.sam Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:21.416 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:21.416 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:21.417 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:21.417 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:21.417 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:21.417 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:21.417 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:21.417 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:21 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14280084069835792221.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14280084069835792221.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14280084069835792221.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:30:21 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14280084069835792221.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14280084069835792221.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14280084069835792221.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:30:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:21 MarkDuplicates Start of doWork freeMemory: 1027810056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:21 MarkDuplicates Start of doWork freeMemory: 1027810056; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:21 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:30:21 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:21 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:30:21 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:30:21 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:30:21 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:21 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2024-07-02 11:30:21 MarkDuplicates Read 3 records. 0 pairs never matched. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 964889560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 964889560; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:30:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:23 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:30:23 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:23 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:30:23 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:23 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:30:23 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 503549976; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2024-07-02 11:30:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 503549976; totalMemory: 1223688192; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:23 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:30:23 MarkDuplicates Marking 1 records as duplicates. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:23 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:30:23 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:23 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:30:23 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:23 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:30:23 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:23 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:30:23 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:23 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:30:23 MarkDuplicates Representative read Index cleanup. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:23 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:30:23 MarkDuplicates Getting Memory Stats. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:24 MarkDuplicates Before output close freeMemory: 772893688; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2024-07-02 11:30:24 MarkDuplicates Before output close freeMemory: 772893688; totalMemory: 1223688192; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:24 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:30:24 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:24 MarkDuplicates After output close freeMemory: 773033800; totalMemory: 1223688192; maxMemory: 2147483648 INFO 2024-07-02 11:30:24 MarkDuplicates After output close freeMemory: 773033800; totalMemory: 1223688192; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:24 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:30:24 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1223688192 Runtime.totalMemory()=1223688192 Running Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:24 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testSingleMappedFragmentAndTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:30:24 MarkDuplicates Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16297720768282746976.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16297720768282746976.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16297720768282746976.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16297720768282746976.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16297720768282746976.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16297720768282746976.tmp/output.sam Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:24.659 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:24.659 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:24.659 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:24.659 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:24.659 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:24.659 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:24.659 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:24.659 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:24 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16297720768282746976.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16297720768282746976.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16297720768282746976.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:30:24 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16297720768282746976.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16297720768282746976.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16297720768282746976.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:30:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:24 MarkDuplicates Start of doWork freeMemory: 1027838856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:24 MarkDuplicates Start of doWork freeMemory: 1027838856; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:24 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:30:24 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:24 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:30:24 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:30:25 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:30:25 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:25 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:30:25 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 964920960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 964920960; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:25 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:30:25 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:26 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:30:26 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:26 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:30:26 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:26 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:30:26 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 485722000; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:30:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 485722000; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:27 MarkDuplicates Marking 3 records as duplicates. INFO 2024-07-02 11:30:27 MarkDuplicates Marking 3 records as duplicates. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:27 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:30:27 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:27 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:30:27 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:27 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:30:27 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:27 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:30:27 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:27 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:30:27 MarkDuplicates Representative read Index cleanup. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:27 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:30:27 MarkDuplicates Getting Memory Stats. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:27 MarkDuplicates Before output close freeMemory: 755065736; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:30:27 MarkDuplicates Before output close freeMemory: 755065736; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:27 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:30:27 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:27 MarkDuplicates After output close freeMemory: 755205424; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:30:27 MarkDuplicates After output close freeMemory: 755205424; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:27 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:30:27 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1205862400 Runtime.totalMemory()=1205862400 Running Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:27 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testSingleMappedPair STANDARD_ERROR INFO 2024-07-02 11:30:27 MarkDuplicates Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18033517587824737043.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18033517587824737043.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18033517587824737043.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18033517587824737043.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18033517587824737043.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18033517587824737043.tmp/output.sam Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:27.840 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:27.840 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:27.840 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:27.840 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:27.840 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:27.840 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:27.840 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:27.840 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:27 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18033517587824737043.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18033517587824737043.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18033517587824737043.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:30:27 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18033517587824737043.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18033517587824737043.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18033517587824737043.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:30:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:28 MarkDuplicates Start of doWork freeMemory: 1027842808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:28 MarkDuplicates Start of doWork freeMemory: 1027842808; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:28 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:30:28 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:28 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:30:28 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:30:28 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:30:28 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:28 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:30:28 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 964922384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 964922384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:30:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:29 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:30:29 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:29 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:30:29 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:29 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:30:29 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 487820384; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:30:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 487820384; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:29 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:30:29 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:29 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:30:29 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:29 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:30:29 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:29 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:30:29 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:29 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:30:29 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:29 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:30:29 MarkDuplicates Representative read Index cleanup. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:29 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:30:29 MarkDuplicates Getting Memory Stats. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:29 MarkDuplicates Before output close freeMemory: 757164096; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:30:29 MarkDuplicates Before output close freeMemory: 757164096; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:30 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:30:30 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:30 MarkDuplicates After output close freeMemory: 757304280; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:30:30 MarkDuplicates After output close freeMemory: 757304280; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:30 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:30:30 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1207959552 Runtime.totalMemory()=1207959552 Running Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:30 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testSingleUnmappedFragment STANDARD_ERROR INFO 2024-07-02 11:30:30 MarkDuplicates Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12336154067646916215.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12336154067646916215.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12336154067646916215.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12336154067646916215.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12336154067646916215.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12336154067646916215.tmp/output.sam Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:30.504 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:30.504 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:30.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:30.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:30.505 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:30.505 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:30.505 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:30.505 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:30 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12336154067646916215.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12336154067646916215.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12336154067646916215.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:30:30 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12336154067646916215.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12336154067646916215.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.12336154067646916215.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:30:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:30 MarkDuplicates Start of doWork freeMemory: 1027842904; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:30 MarkDuplicates Start of doWork freeMemory: 1027842904; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:30 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:30:30 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:30 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:30:30 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:30 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2024-07-02 11:30:30 MarkDuplicates Read 0 records. 0 pairs never matched. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 964922928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 964922928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:30:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:32 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:30:32 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:32 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:30:32 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:32 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:30:32 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 489918040; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:30:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 489918040; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:32 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:30:32 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:32 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:30:32 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:32 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:30:32 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:32 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:30:32 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:32 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:30:32 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:32 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:30:32 MarkDuplicates Representative read Index cleanup. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:32 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:30:32 MarkDuplicates Getting Memory Stats. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:32 MarkDuplicates Before output close freeMemory: 759262072; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:30:32 MarkDuplicates Before output close freeMemory: 759262072; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:32 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:30:32 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:33 MarkDuplicates After output close freeMemory: 759401864; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:30:33 MarkDuplicates After output close freeMemory: 759401864; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:33 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:30:33 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1210056704 Runtime.totalMemory()=1210056704 Running Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:33 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testSingleUnmappedPair STANDARD_ERROR INFO 2024-07-02 11:30:33 MarkDuplicates Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10848680271095970894.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10848680271095970894.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10848680271095970894.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10848680271095970894.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10848680271095970894.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10848680271095970894.tmp/output.sam Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:33.373 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:33.373 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:33.373 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:33.373 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:33.374 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:33.374 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:33.374 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:33.374 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:33 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10848680271095970894.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10848680271095970894.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10848680271095970894.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:30:33 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10848680271095970894.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10848680271095970894.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10848680271095970894.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:30:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:33 MarkDuplicates Start of doWork freeMemory: 1027841920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:33 MarkDuplicates Start of doWork freeMemory: 1027841920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:33 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:30:33 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:33 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:30:33 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:33 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2024-07-02 11:30:33 MarkDuplicates Read 0 records. 0 pairs never matched. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:34 MarkDuplicates After buildSortedReadEndLists freeMemory: 964921944; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:34 MarkDuplicates After buildSortedReadEndLists freeMemory: 964921944; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:34 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:30:34 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:35 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:30:35 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:35 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:30:35 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:35 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:30:35 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 485722752; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:30:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 485722752; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:35 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:30:35 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:35 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:30:35 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:35 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:30:35 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:35 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:30:35 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:35 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:30:35 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:35 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:30:35 MarkDuplicates Representative read Index cleanup. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:35 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:30:35 MarkDuplicates Getting Memory Stats. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:35 MarkDuplicates Before output close freeMemory: 755065000; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:30:35 MarkDuplicates Before output close freeMemory: 755065000; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:35 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:30:35 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:36 MarkDuplicates After output close freeMemory: 755206576; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:30:36 MarkDuplicates After output close freeMemory: 755206576; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:36 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:30:36 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1205862400 Runtime.totalMemory()=1205862400 Running Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:36 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testStackOverFlowPairSetSwap STANDARD_ERROR INFO 2024-07-02 11:30:36 MarkDuplicates Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16749438786373885000.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16749438786373885000.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16749438786373885000.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16749438786373885000.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16749438786373885000.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16749438786373885000.tmp/output.sam Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:36.331 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:36.331 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:36.331 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:36.331 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:36.332 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:36.332 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:36.332 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:36.332 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:36 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16749438786373885000.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16749438786373885000.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16749438786373885000.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:30:36 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16749438786373885000.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16749438786373885000.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16749438786373885000.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:30:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:36 MarkDuplicates Start of doWork freeMemory: 1027726976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:36 MarkDuplicates Start of doWork freeMemory: 1027726976; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:36 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:30:36 MarkDuplicates Reading input file and constructing read end information. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:36 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:30:36 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:36 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:30:36 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 964783216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 964783216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:30:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:38 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:30:38 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:38 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:30:38 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:38 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:30:38 MarkDuplicates Sorting list of duplicate records. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 487681184; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:30:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 487681184; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:38 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:30:38 MarkDuplicates Marking 2 records as duplicates. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:38 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:30:38 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:38 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:30:38 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:38 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:30:38 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:38 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:30:38 MarkDuplicates Duplicate Index cleanup. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:38 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:30:38 MarkDuplicates Representative read Index cleanup. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:38 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:30:38 MarkDuplicates Getting Memory Stats. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:38 MarkDuplicates Before output close freeMemory: 756996416; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:30:38 MarkDuplicates Before output close freeMemory: 756996416; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:38 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:30:38 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:39 MarkDuplicates After output close freeMemory: 757165104; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:30:39 MarkDuplicates After output close freeMemory: 757165104; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:30:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1207959552 Runtime.totalMemory()=1207959552 Running Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:39 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:30:39 MarkDuplicates Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18178537531958170568.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18178537531958170568.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18178537531958170568.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18178537531958170568.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18178537531958170568.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18178537531958170568.tmp/output.sam Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:39.460 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:39.460 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:39.460 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:39.460 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:39.460 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:39.460 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:39.460 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:39.460 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:39 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18178537531958170568.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18178537531958170568.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18178537531958170568.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:30:39 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18178537531958170568.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18178537531958170568.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18178537531958170568.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:30:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:39 MarkDuplicates Start of doWork freeMemory: 1027829344; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:39 MarkDuplicates Start of doWork freeMemory: 1027829344; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:39 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:30:39 MarkDuplicates Reading input file and constructing read end information. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:39 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:30:39 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:30:39 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:30:39 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:39 MarkDuplicates Read 18 records. 0 pairs never matched. INFO 2024-07-02 11:30:39 MarkDuplicates Read 18 records. 0 pairs never matched. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 964906952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 964906952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:30:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:30:41 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:30:41 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:41 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:30:41 MarkDuplicates Sorting list of duplicate records. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 487806248; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:30:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 487806248; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:41 MarkDuplicates Marking 12 records as duplicates. INFO 2024-07-02 11:30:41 MarkDuplicates Marking 12 records as duplicates. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:41 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:30:41 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:30:41 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:41 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:30:41 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:41 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:30:41 MarkDuplicates Duplicate Index cleanup. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:41 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:30:41 MarkDuplicates Representative read Index cleanup. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:41 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:30:41 MarkDuplicates Getting Memory Stats. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:42 MarkDuplicates Before output close freeMemory: 757150320; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:30:42 MarkDuplicates Before output close freeMemory: 757150320; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:42 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:30:42 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:42 MarkDuplicates After output close freeMemory: 757290504; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:30:42 MarkDuplicates After output close freeMemory: 757290504; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:30:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1207959552 Runtime.totalMemory()=1207959552 Running Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:42 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:30:42 MarkDuplicates Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8139300604778510170.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8139300604778510170.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8139300604778510170.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8139300604778510170.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8139300604778510170.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8139300604778510170.tmp/output.sam Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:42.515 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:42.515 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:42.515 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:42.515 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:42.516 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:42.516 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:42.516 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:42.516 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:42 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8139300604778510170.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8139300604778510170.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8139300604778510170.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:30:42 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8139300604778510170.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8139300604778510170.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8139300604778510170.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:30:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:42 MarkDuplicates Start of doWork freeMemory: 1027831048; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:42 MarkDuplicates Start of doWork freeMemory: 1027831048; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:42 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:30:42 MarkDuplicates Reading input file and constructing read end information. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:42 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:30:42 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:30:42 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:30:42 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:42 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:30:42 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 964915640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 964915640; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:30:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:30:44 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:44 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:30:44 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:44 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:30:44 MarkDuplicates Sorting list of duplicate records. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 487813928; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:30:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 487813928; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:44 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:30:44 MarkDuplicates Marking 4 records as duplicates. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:44 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:30:44 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:44 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:30:44 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:44 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:30:44 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:44 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:30:44 MarkDuplicates Duplicate Index cleanup. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:44 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:30:44 MarkDuplicates Representative read Index cleanup. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:44 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:30:44 MarkDuplicates Getting Memory Stats. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:45 MarkDuplicates Before output close freeMemory: 757157712; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:30:45 MarkDuplicates Before output close freeMemory: 757157712; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:45 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:30:45 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:45 MarkDuplicates After output close freeMemory: 757297896; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:30:45 MarkDuplicates After output close freeMemory: 757297896; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:30:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1207959552 Runtime.totalMemory()=1207959552 Running Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:45 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testThreeMappedPairsWithMatchingSecondMate STANDARD_ERROR INFO 2024-07-02 11:30:45 MarkDuplicates Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6498356452291535612.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6498356452291535612.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6498356452291535612.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6498356452291535612.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6498356452291535612.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6498356452291535612.tmp/output.sam Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:45.554 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:45.554 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:45.554 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:45.554 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:45.555 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:45.555 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:45.555 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:45.555 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:45 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6498356452291535612.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6498356452291535612.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6498356452291535612.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:30:45 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6498356452291535612.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6498356452291535612.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6498356452291535612.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:30:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:45 MarkDuplicates Start of doWork freeMemory: 1027832792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:45 MarkDuplicates Start of doWork freeMemory: 1027832792; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:45 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:30:45 MarkDuplicates Reading input file and constructing read end information. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:45 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:30:45 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:30:45 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:30:45 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:45 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:30:45 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 964914752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 964914752; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:30:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:47 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:30:47 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:47 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:30:47 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:47 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:30:47 MarkDuplicates Sorting list of duplicate records. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 485715760; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:30:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 485715760; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:48 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:30:48 MarkDuplicates Marking 2 records as duplicates. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:48 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:30:48 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:30:48 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:48 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:30:48 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:48 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:30:48 MarkDuplicates Duplicate Index cleanup. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:48 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:30:48 MarkDuplicates Representative read Index cleanup. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:48 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:30:48 MarkDuplicates Getting Memory Stats. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:48 MarkDuplicates Before output close freeMemory: 755059424; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:30:48 MarkDuplicates Before output close freeMemory: 755059424; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:48 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:30:48 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:49 MarkDuplicates After output close freeMemory: 755199680; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:30:49 MarkDuplicates After output close freeMemory: 755199680; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:30:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1205862400 Runtime.totalMemory()=1205862400 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:49 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:30:49 MarkDuplicates Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2007599307231301492.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2007599307231301492.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2007599307231301492.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2007599307231301492.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2007599307231301492.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2007599307231301492.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:49.259 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:49.259 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:49.260 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:49.260 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:49.260 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:49.260 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:49.260 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:49.260 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:49 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2007599307231301492.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2007599307231301492.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2007599307231301492.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:30:49 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2007599307231301492.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2007599307231301492.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2007599307231301492.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:30:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:49 MarkDuplicates Start of doWork freeMemory: 1027825560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:49 MarkDuplicates Start of doWork freeMemory: 1027825560; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:49 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:30:49 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:30:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:30:49 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:30:49 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:49 MarkDuplicates Read 12 records. 0 pairs never matched. INFO 2024-07-02 11:30:49 MarkDuplicates Read 12 records. 0 pairs never matched. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 964909352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 964909352; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:30:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:51 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:30:51 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:51 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:30:51 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:51 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:30:51 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 505633936; totalMemory: 1225785344; maxMemory: 2147483648 INFO 2024-07-02 11:30:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 505633936; totalMemory: 1225785344; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:51 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:30:51 MarkDuplicates Marking 8 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:51 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:30:51 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:51 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:30:51 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:51 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:30:51 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:51 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:30:51 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:51 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:30:51 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:51 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:30:51 MarkDuplicates Getting Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:52 MarkDuplicates Before output close freeMemory: 774977864; totalMemory: 1225785344; maxMemory: 2147483648 INFO 2024-07-02 11:30:52 MarkDuplicates Before output close freeMemory: 774977864; totalMemory: 1225785344; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:52 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:30:52 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:52 MarkDuplicates After output close freeMemory: 775118048; totalMemory: 1225785344; maxMemory: 2147483648 INFO 2024-07-02 11:30:52 MarkDuplicates After output close freeMemory: 775118048; totalMemory: 1225785344; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:30:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1225785344 Runtime.totalMemory()=1225785344 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:52 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoGroupsOnDifferentChromosomesOfTwoFragments STANDARD_ERROR INFO 2024-07-02 11:30:52 MarkDuplicates Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17255865404429140475.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17255865404429140475.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17255865404429140475.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17255865404429140475.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17255865404429140475.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17255865404429140475.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:52.536 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:52.536 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:52.536 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:52.536 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:52.536 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:52.536 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:52.536 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:52.536 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:52 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17255865404429140475.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17255865404429140475.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17255865404429140475.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:30:52 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17255865404429140475.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17255865404429140475.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.17255865404429140475.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:30:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:52 MarkDuplicates Start of doWork freeMemory: 1027835640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:52 MarkDuplicates Start of doWork freeMemory: 1027835640; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:52 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:30:52 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:52 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:30:52 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:30:53 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:30:53 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:53 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:30:53 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 964915264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 964915264; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:30:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:54 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:30:54 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:54 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:30:54 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:54 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:30:54 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 485716360; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:30:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 485716360; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:54 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:30:54 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:54 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:30:54 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:54 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:30:54 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:54 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:30:54 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:54 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:30:54 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:54 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:30:54 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:54 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:30:54 MarkDuplicates Getting Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:55 MarkDuplicates Before output close freeMemory: 755060160; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:30:55 MarkDuplicates Before output close freeMemory: 755060160; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:55 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:30:55 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:55 MarkDuplicates After output close freeMemory: 755200184; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:30:55 MarkDuplicates After output close freeMemory: 755200184; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:55 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:30:55 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1205862400 Runtime.totalMemory()=1205862400 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:55 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:30:55 MarkDuplicates Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2373277523301102337.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2373277523301102337.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2373277523301102337.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2373277523301102337.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2373277523301102337.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2373277523301102337.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:55.644 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:55.644 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:55.644 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:55.644 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:55.644 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:55.644 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:55.644 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:55.644 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:55 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2373277523301102337.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2373277523301102337.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2373277523301102337.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:30:55 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2373277523301102337.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2373277523301102337.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2373277523301102337.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:30:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:56 MarkDuplicates Start of doWork freeMemory: 1027832176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:56 MarkDuplicates Start of doWork freeMemory: 1027832176; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:56 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:30:56 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:56 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:30:56 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:30:56 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:30:56 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:56 MarkDuplicates Read 8 records. 0 pairs never matched. INFO 2024-07-02 11:30:56 MarkDuplicates Read 8 records. 0 pairs never matched. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 964910984; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 964910984; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:30:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:57 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:30:57 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:57 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:30:57 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:57 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:30:57 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 485712288; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:30:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 485712288; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:57 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:30:57 MarkDuplicates Marking 4 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:57 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:30:57 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:57 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:30:57 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:57 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:30:57 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:57 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:30:57 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:57 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:30:57 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:57 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:30:57 MarkDuplicates Getting Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:58 MarkDuplicates Before output close freeMemory: 755056120; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:30:58 MarkDuplicates Before output close freeMemory: 755056120; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:58 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:30:58 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:58 MarkDuplicates After output close freeMemory: 755196304; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:30:58 MarkDuplicates After output close freeMemory: 755196304; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:30:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1205862400 Runtime.totalMemory()=1205862400 Running Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:58 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoMappedFragments STANDARD_ERROR INFO 2024-07-02 11:30:58 MarkDuplicates Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6919866418550977100.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6919866418550977100.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6919866418550977100.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6919866418550977100.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6919866418550977100.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6919866418550977100.tmp/output.sam Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:58.676 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:58.676 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:58.676 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:58.676 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:58.676 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:30:58.676 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:30:58.676 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:30:58.676 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:58 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6919866418550977100.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6919866418550977100.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6919866418550977100.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:30:58 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6919866418550977100.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6919866418550977100.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6919866418550977100.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:30:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:30:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:59 MarkDuplicates Start of doWork freeMemory: 1027835400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:59 MarkDuplicates Start of doWork freeMemory: 1027835400; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:59 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:30:59 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:59 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:30:59 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:30:59 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:30:59 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:59 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:30:59 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 964915168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:30:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 964915168; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:30:59 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:30:59 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:00 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:31:00 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:00 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:31:00 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:00 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:31:00 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 487813272; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:31:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 487813272; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:01 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:31:01 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:01 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:31:01 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:01 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:31:01 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:01 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:31:01 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:01 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:31:01 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:01 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:31:01 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:01 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:31:01 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:01 MarkDuplicates Before output close freeMemory: 757157072; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:31:01 MarkDuplicates Before output close freeMemory: 757157072; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:01 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:31:01 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:02 MarkDuplicates After output close freeMemory: 757297096; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:31:02 MarkDuplicates After output close freeMemory: 757297096; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:02 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:31:02 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1207959552 Runtime.totalMemory()=1207959552 Running Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:02 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoMappedPairWithSamePosition STANDARD_ERROR INFO 2024-07-02 11:31:02 MarkDuplicates Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1090046797304916719.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1090046797304916719.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1090046797304916719.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1090046797304916719.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1090046797304916719.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1090046797304916719.tmp/output.sam Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:02.528 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:02.528 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:02.528 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:02.528 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:02.528 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:02.528 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:02.528 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:02.528 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:02 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1090046797304916719.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1090046797304916719.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1090046797304916719.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:31:02 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1090046797304916719.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1090046797304916719.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1090046797304916719.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:31:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:03 MarkDuplicates Start of doWork freeMemory: 1027833256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:03 MarkDuplicates Start of doWork freeMemory: 1027833256; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:03 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:31:03 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:03 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:31:03 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:31:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:31:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:03 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:31:03 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 964912616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 964912616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:04 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:31:04 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:05 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:31:05 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:05 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:31:05 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:05 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:31:05 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 496199344; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2024-07-02 11:31:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 496199344; totalMemory: 1216348160; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:05 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:31:05 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:05 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:31:05 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:05 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:31:05 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:05 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:31:05 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:05 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:31:05 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:05 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:31:05 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:05 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:31:05 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:06 MarkDuplicates Before output close freeMemory: 765543008; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2024-07-02 11:31:06 MarkDuplicates Before output close freeMemory: 765543008; totalMemory: 1216348160; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:06 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:31:06 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:06 MarkDuplicates After output close freeMemory: 765683264; totalMemory: 1216348160; maxMemory: 2147483648 INFO 2024-07-02 11:31:06 MarkDuplicates After output close freeMemory: 765683264; totalMemory: 1216348160; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:06 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:31:06 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1216348160 Runtime.totalMemory()=1216348160 Running Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:07 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoMappedPairWithSamePositionDifferentStrands STANDARD_ERROR INFO 2024-07-02 11:31:07 MarkDuplicates Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13271470646228457918.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13271470646228457918.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13271470646228457918.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13271470646228457918.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13271470646228457918.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13271470646228457918.tmp/output.sam Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:07.068 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:07.068 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:07.068 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:07.068 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:07.087 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:07.087 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:07.087 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:07.087 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:07 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13271470646228457918.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13271470646228457918.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13271470646228457918.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:31:07 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13271470646228457918.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13271470646228457918.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13271470646228457918.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:31:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:07 MarkDuplicates Start of doWork freeMemory: 1027832816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:07 MarkDuplicates Start of doWork freeMemory: 1027832816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:07 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:31:07 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:07 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:31:07 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:31:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:31:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:07 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:31:07 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 964912176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 964912176; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:31:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:09 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:31:09 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:09 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:31:09 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:09 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:31:09 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 485713144; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:31:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 485713144; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:09 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:31:09 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:09 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:31:09 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:09 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:31:09 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:09 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:31:09 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:09 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:31:09 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:09 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:31:09 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:09 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:31:09 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:10 MarkDuplicates Before output close freeMemory: 755056880; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:31:10 MarkDuplicates Before output close freeMemory: 755056880; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:10 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:31:10 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:10 MarkDuplicates After output close freeMemory: 755197064; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:31:10 MarkDuplicates After output close freeMemory: 755197064; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:10 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:31:10 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1205862400 Runtime.totalMemory()=1205862400 Running Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:10 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoMappedPairWithSamePositionDifferentStrands2 STANDARD_ERROR INFO 2024-07-02 11:31:10 MarkDuplicates Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4179484410108213778.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4179484410108213778.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4179484410108213778.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4179484410108213778.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4179484410108213778.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4179484410108213778.tmp/output.sam Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:10.949 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:10.949 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:10.957 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:10.957 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:10.958 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:10.958 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:10.958 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:10.958 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:10 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4179484410108213778.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4179484410108213778.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4179484410108213778.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:31:10 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4179484410108213778.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4179484410108213778.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4179484410108213778.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:31:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:11 MarkDuplicates Start of doWork freeMemory: 1027829264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:11 MarkDuplicates Start of doWork freeMemory: 1027829264; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:11 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:31:11 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:11 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:31:11 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:31:11 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:31:11 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:11 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:31:11 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 964911440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 964911440; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:12 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:31:12 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:31:14 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:14 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:31:14 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:14 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:31:14 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 485712408; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:31:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 485712408; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:14 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:31:14 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:14 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:31:14 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:14 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:31:14 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:14 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:31:14 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:14 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:31:14 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:14 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:31:14 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:14 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:31:14 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:15 MarkDuplicates Before output close freeMemory: 755056144; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:31:15 MarkDuplicates Before output close freeMemory: 755056144; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:15 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:31:15 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:15 MarkDuplicates After output close freeMemory: 755196328; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:31:15 MarkDuplicates After output close freeMemory: 755196328; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. [Tue Jul 02 11:31:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1205862400 Runtime.totalMemory()=1205862400 Running Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:15 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:31:15 MarkDuplicates Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8749703438082716853.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8749703438082716853.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8749703438082716853.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8749703438082716853.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8749703438082716853.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8749703438082716853.tmp/output.sam Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:15.753 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:15.753 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:15.761 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:15.761 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:15.761 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:15.761 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:15.761 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:15.761 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:15 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8749703438082716853.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8749703438082716853.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8749703438082716853.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:31:15 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8749703438082716853.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8749703438082716853.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8749703438082716853.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:31:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:16 MarkDuplicates Start of doWork freeMemory: 1027831144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:16 MarkDuplicates Start of doWork freeMemory: 1027831144; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:16 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:31:16 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:16 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:31:16 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:31:16 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:31:16 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:16 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:31:16 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 964910504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 964910504; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:17 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:31:17 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:18 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:31:18 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:18 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:31:18 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:18 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:31:18 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 487808624; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:31:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 487808624; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:19 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:31:19 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:19 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:31:19 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:19 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:31:19 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:19 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:31:19 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:19 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:31:19 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:19 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:31:19 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:19 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:31:19 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:19 MarkDuplicates Before output close freeMemory: 757152360; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:31:19 MarkDuplicates Before output close freeMemory: 757152360; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:19 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:31:19 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:20 MarkDuplicates After output close freeMemory: 757292544; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:31:20 MarkDuplicates After output close freeMemory: 757292544; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:20 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. [Tue Jul 02 11:31:20 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1207959552 Runtime.totalMemory()=1207959552 Running Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:20 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoMappedPairsAndMappedSecondaryFragment STANDARD_ERROR INFO 2024-07-02 11:31:20 MarkDuplicates Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10592485155496344685.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10592485155496344685.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10592485155496344685.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10592485155496344685.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10592485155496344685.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10592485155496344685.tmp/output.sam Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:20.438 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:20.438 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:20.438 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:20.438 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:20.438 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:20.438 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:20.438 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:20.438 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:20 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10592485155496344685.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10592485155496344685.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10592485155496344685.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:31:20 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10592485155496344685.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10592485155496344685.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10592485155496344685.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:31:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:20 MarkDuplicates Start of doWork freeMemory: 1027829760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:20 MarkDuplicates Start of doWork freeMemory: 1027829760; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:20 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:31:20 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:20 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:31:20 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:31:21 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:31:21 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:21 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:31:21 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 964909120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 964909120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:31:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:23 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:31:23 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:23 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:31:23 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:23 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:31:23 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 489938088; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:31:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 489938088; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:24 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:31:24 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:24 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:31:24 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:24 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:31:24 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:24 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:31:24 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:24 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:31:24 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:24 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:31:24 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:24 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:31:24 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:24 MarkDuplicates Before output close freeMemory: 759282008; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:31:24 MarkDuplicates Before output close freeMemory: 759282008; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:24 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:31:24 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:25 MarkDuplicates After output close freeMemory: 759422008; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:31:25 MarkDuplicates After output close freeMemory: 759422008; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:25 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. [Tue Jul 02 11:31:25 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1210056704 Runtime.totalMemory()=1210056704 Running Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:25 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoMappedPairsAndTerminalUnmappedFragment STANDARD_ERROR INFO 2024-07-02 11:31:25 MarkDuplicates Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11509384397914841095.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11509384397914841095.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11509384397914841095.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11509384397914841095.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11509384397914841095.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11509384397914841095.tmp/output.sam Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:25.295 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:25.295 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:25.295 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:25.295 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:25.296 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:25.296 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:25.296 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:25.296 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:25 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11509384397914841095.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11509384397914841095.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11509384397914841095.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:31:25 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11509384397914841095.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11509384397914841095.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11509384397914841095.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:31:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:25 MarkDuplicates Start of doWork freeMemory: 1027862840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:25 MarkDuplicates Start of doWork freeMemory: 1027862840; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:25 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:31:25 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:25 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:31:25 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:31:25 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:31:25 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:25 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:31:25 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 964942200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 964942200; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:31:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:26 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:31:26 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:26 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:31:26 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:26 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:31:26 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 485743168; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:31:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 485743168; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:27 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:31:27 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:27 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:31:27 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:27 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:31:27 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:27 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:31:27 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:27 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:31:27 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:27 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:31:27 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:27 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:31:27 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:27 MarkDuplicates Before output close freeMemory: 755087296; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:31:27 MarkDuplicates Before output close freeMemory: 755087296; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:27 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:31:27 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:28 MarkDuplicates After output close freeMemory: 755226592; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:31:28 MarkDuplicates After output close freeMemory: 755226592; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:28 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:31:28 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1205862400 Runtime.totalMemory()=1205862400 Running Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:28 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoMappedPairsAndTerminalUnmappedPair STANDARD_ERROR INFO 2024-07-02 11:31:28 MarkDuplicates Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13967487478765153694.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13967487478765153694.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13967487478765153694.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13967487478765153694.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13967487478765153694.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13967487478765153694.tmp/output.sam Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:28.161 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:28.161 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:28.173 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:28.173 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:28.174 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:28.174 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:28.174 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:28.174 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:28 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13967487478765153694.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13967487478765153694.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13967487478765153694.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:31:28 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13967487478765153694.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13967487478765153694.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13967487478765153694.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:31:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:28 MarkDuplicates Start of doWork freeMemory: 1027858824; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:28 MarkDuplicates Start of doWork freeMemory: 1027858824; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:28 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:31:28 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:28 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:31:28 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:31:28 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:31:28 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:28 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:31:28 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 964785472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 964785472; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:31:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:29 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:31:29 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:29 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:31:29 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:29 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:31:29 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 487839120; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:31:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 487839120; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:30 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:31:30 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:30 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:31:30 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:30 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:31:30 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:30 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:31:30 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:30 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:31:30 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:30 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:31:30 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:30 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:31:30 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:30 MarkDuplicates Before output close freeMemory: 757182400; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:31:30 MarkDuplicates Before output close freeMemory: 757182400; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:30 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:31:30 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:30 MarkDuplicates After output close freeMemory: 757170712; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:31:30 MarkDuplicates After output close freeMemory: 757170712; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:30 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:31:30 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1207959552 Runtime.totalMemory()=1207959552 Running Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:30 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoMappedPairsMatesSoftClipped STANDARD_ERROR INFO 2024-07-02 11:31:30 MarkDuplicates Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11530232224117981973.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11530232224117981973.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11530232224117981973.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11530232224117981973.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11530232224117981973.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11530232224117981973.tmp/output.sam Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:30.922 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:30.922 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:30.922 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:30.922 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:30.922 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:30.922 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:30.922 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:30.922 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:30 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11530232224117981973.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11530232224117981973.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11530232224117981973.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:31:30 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11530232224117981973.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11530232224117981973.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11530232224117981973.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:31:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:31 MarkDuplicates Start of doWork freeMemory: 1027858968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:31 MarkDuplicates Start of doWork freeMemory: 1027858968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:31 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:31:31 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:31 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:31:31 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:31:31 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:31:31 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:31 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:31:31 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 964941144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 964941144; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:31:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:32 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:31:32 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:32 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:31:32 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:32 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:31:32 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 489936512; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:31:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 489936512; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:32 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:31:32 MarkDuplicates Marking 0 records as duplicates. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:32 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:31:32 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:32 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:31:32 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:32 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:31:32 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:32 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:31:32 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:32 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:31:32 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:32 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:31:32 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:32 MarkDuplicates Before output close freeMemory: 759280152; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:31:32 MarkDuplicates Before output close freeMemory: 759280152; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:32 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:31:32 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:33 MarkDuplicates After output close freeMemory: 759419840; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:31:33 MarkDuplicates After output close freeMemory: 759419840; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:33 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:31:33 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1210056704 Runtime.totalMemory()=1210056704 Running Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:33 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoMappedPairsWithOppositeOrientations STANDARD_ERROR INFO 2024-07-02 11:31:33 MarkDuplicates Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10874175715129865472.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10874175715129865472.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10874175715129865472.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10874175715129865472.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10874175715129865472.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10874175715129865472.tmp/output.sam Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:33.282 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:33.282 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:33.282 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:33.282 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:33.283 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:33.283 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:33.283 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:33.283 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:33 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10874175715129865472.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10874175715129865472.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10874175715129865472.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:31:33 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10874175715129865472.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10874175715129865472.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10874175715129865472.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:31:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:33 MarkDuplicates Start of doWork freeMemory: 1027700552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:33 MarkDuplicates Start of doWork freeMemory: 1027700552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:33 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:31:33 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:33 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:31:33 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:31:33 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:31:33 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:33 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:31:33 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 964940352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 964940352; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:34 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:31:34 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:31:34 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:34 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:31:34 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:34 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:31:34 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 489935624; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:31:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 489935624; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:34 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:31:34 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:34 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:31:34 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:34 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:31:34 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:34 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:31:34 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:34 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:31:34 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:34 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:31:34 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:34 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:31:34 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:35 MarkDuplicates Before output close freeMemory: 759279312; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:31:35 MarkDuplicates Before output close freeMemory: 759279312; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:35 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:31:35 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:35 MarkDuplicates After output close freeMemory: 759419544; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:31:35 MarkDuplicates After output close freeMemory: 759419544; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:35 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:31:35 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1210056704 Runtime.totalMemory()=1210056704 Running Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:35 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoMappedPairsWithOppositeOrientationsNumberTwo STANDARD_ERROR INFO 2024-07-02 11:31:35 MarkDuplicates Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15142497916796004065.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15142497916796004065.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15142497916796004065.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15142497916796004065.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15142497916796004065.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15142497916796004065.tmp/output.sam Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:35.534 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:35.534 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:35.534 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:35.534 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:35.535 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:35.535 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:35.535 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:35.535 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:35 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15142497916796004065.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15142497916796004065.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15142497916796004065.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:31:35 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15142497916796004065.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15142497916796004065.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15142497916796004065.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:31:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:35 MarkDuplicates Start of doWork freeMemory: 1027860248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:35 MarkDuplicates Start of doWork freeMemory: 1027860248; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:35 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:31:35 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:35 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:31:35 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:31:35 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:31:35 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:35 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:31:35 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 964939608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 964939608; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:31:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:36 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:31:36 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:36 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:31:36 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:36 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:31:36 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 489934880; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:31:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 489934880; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:37 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:31:37 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:37 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:31:37 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:37 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:31:37 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:37 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:31:37 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:37 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:31:37 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:37 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:31:37 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:37 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:31:37 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:37 MarkDuplicates Before output close freeMemory: 759276760; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:31:37 MarkDuplicates Before output close freeMemory: 759276760; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:37 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:31:37 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:37 MarkDuplicates After output close freeMemory: 759266224; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:31:37 MarkDuplicates After output close freeMemory: 759266224; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:31:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1210056704 Runtime.totalMemory()=1210056704 Running Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:37 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoMappedPairsWithSoftClipping STANDARD_ERROR INFO 2024-07-02 11:31:37 MarkDuplicates Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13905844937019706310.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13905844937019706310.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13905844937019706310.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13905844937019706310.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13905844937019706310.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13905844937019706310.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:37.814 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:37.814 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:37.814 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:37.814 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:37.814 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:37.814 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:37.815 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:37.815 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:37 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13905844937019706310.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13905844937019706310.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13905844937019706310.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:31:37 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13905844937019706310.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13905844937019706310.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13905844937019706310.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:31:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:38 MarkDuplicates Start of doWork freeMemory: 1027856664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:38 MarkDuplicates Start of doWork freeMemory: 1027856664; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:38 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:31:38 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:38 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:31:38 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:31:38 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:31:38 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:38 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:31:38 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 964938840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 964938840; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:31:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:39 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:31:39 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:39 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:31:39 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:39 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:31:39 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 490894928; totalMemory: 1211105280; maxMemory: 2147483648 INFO 2024-07-02 11:31:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 490894928; totalMemory: 1211105280; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:39 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:31:39 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:39 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:31:39 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:39 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:31:39 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:39 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:31:39 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:39 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:31:39 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:39 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:31:39 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:39 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:31:39 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:39 MarkDuplicates Before output close freeMemory: 760325280; totalMemory: 1211105280; maxMemory: 2147483648 INFO 2024-07-02 11:31:39 MarkDuplicates Before output close freeMemory: 760325280; totalMemory: 1211105280; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:39 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:31:39 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:40 MarkDuplicates After output close freeMemory: 760466608; totalMemory: 1211105280; maxMemory: 2147483648 INFO 2024-07-02 11:31:40 MarkDuplicates After output close freeMemory: 760466608; totalMemory: 1211105280; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:40 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:31:40 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1211105280 Runtime.totalMemory()=1211105280 Running Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:40 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoMappedPairsWithSoftClippingBoth STANDARD_ERROR INFO 2024-07-02 11:31:40 MarkDuplicates Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18442327706423229901.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18442327706423229901.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18442327706423229901.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18442327706423229901.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18442327706423229901.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18442327706423229901.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:40.255 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:40.255 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:40.255 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:40.255 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:40.256 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:40.256 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:40.256 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:40.256 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:40 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18442327706423229901.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18442327706423229901.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18442327706423229901.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:31:40 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18442327706423229901.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18442327706423229901.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.18442327706423229901.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:31:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:40 MarkDuplicates Start of doWork freeMemory: 1027858736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:40 MarkDuplicates Start of doWork freeMemory: 1027858736; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:40 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:31:40 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:40 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:31:40 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:31:40 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:31:40 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:40 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:31:40 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 964938096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 964938096; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:31:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:31:41 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:31:41 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:41 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:31:41 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 489933368; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:31:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 489933368; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:41 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:31:41 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:41 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:31:41 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:31:41 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:41 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:31:41 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:41 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:31:41 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:41 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:31:41 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:41 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:31:41 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:42 MarkDuplicates Before output close freeMemory: 759277056; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:31:42 MarkDuplicates Before output close freeMemory: 759277056; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:42 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:31:42 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:42 MarkDuplicates After output close freeMemory: 759416792; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:31:42 MarkDuplicates After output close freeMemory: 759416792; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:31:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1210056704 Runtime.totalMemory()=1210056704 Running Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:42 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar STANDARD_ERROR INFO 2024-07-02 11:31:42 MarkDuplicates Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11659350254887361193.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11659350254887361193.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11659350254887361193.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11659350254887361193.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11659350254887361193.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11659350254887361193.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:42.559 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:42.559 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:42.559 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:42.559 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:42.559 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:42.559 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:42.559 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:42.559 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:42 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11659350254887361193.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11659350254887361193.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11659350254887361193.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:31:42 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11659350254887361193.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11659350254887361193.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.11659350254887361193.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:31:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:42 MarkDuplicates Start of doWork freeMemory: 1027858768; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:42 MarkDuplicates Start of doWork freeMemory: 1027858768; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:42 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:31:42 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:42 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:31:42 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: WARNING 2024-07-02 11:31:43 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:31:43 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:43 MarkDuplicates Read 2 records. 2 pairs never matched. INFO 2024-07-02 11:31:43 MarkDuplicates Read 2 records. 2 pairs never matched. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 964938808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 964938808; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:31:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:31:44 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:44 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:31:44 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:44 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:31:44 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 568576576; totalMemory: 1288699904; maxMemory: 2147483648 INFO 2024-07-02 11:31:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 568576576; totalMemory: 1288699904; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:44 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:31:44 MarkDuplicates Marking 0 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:44 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:31:44 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:44 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:31:44 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:44 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:31:44 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:44 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:31:44 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:44 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:31:44 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:44 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:31:44 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:44 MarkDuplicates Before output close freeMemory: 837920104; totalMemory: 1288699904; maxMemory: 2147483648 INFO 2024-07-02 11:31:44 MarkDuplicates Before output close freeMemory: 837920104; totalMemory: 1288699904; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:44 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:31:44 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:45 MarkDuplicates After output close freeMemory: 838061160; totalMemory: 1288699904; maxMemory: 2147483648 INFO 2024-07-02 11:31:45 MarkDuplicates After output close freeMemory: 838061160; totalMemory: 1288699904; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:31:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1288699904 Runtime.totalMemory()=1288699904 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:45 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoMappedPairsWithSupplementaryReads[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:31:45 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14292379939930322846.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14292379939930322846.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14292379939930322846.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14292379939930322846.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14292379939930322846.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14292379939930322846.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:45.313 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:45.313 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:45.313 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:45.313 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:45.313 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:45.313 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:45.313 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:45.313 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:45 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14292379939930322846.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14292379939930322846.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14292379939930322846.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:31:45 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14292379939930322846.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14292379939930322846.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14292379939930322846.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:31:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:45 MarkDuplicates Start of doWork freeMemory: 1027853520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:45 MarkDuplicates Start of doWork freeMemory: 1027853520; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:45 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:31:45 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:45 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:31:45 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:45 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:31:45 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 964935632; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 964935632; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:31:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:46 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:31:46 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:46 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:31:46 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:46 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:31:46 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 487833600; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:31:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 487833600; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:47 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:31:47 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:47 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:31:47 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:47 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:31:47 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:47 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:31:47 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:47 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:31:47 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:47 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:31:47 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:47 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:31:47 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:47 MarkDuplicates Before output close freeMemory: 757177264; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:31:47 MarkDuplicates Before output close freeMemory: 757177264; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:47 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:31:47 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:47 MarkDuplicates After output close freeMemory: 757317520; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:31:47 MarkDuplicates After output close freeMemory: 757317520; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:47 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:31:47 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1207959552 Runtime.totalMemory()=1207959552 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:48 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoMappedPairsWithSupplementaryReads[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:31:48 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1501116128831983707.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1501116128831983707.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1501116128831983707.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1501116128831983707.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1501116128831983707.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1501116128831983707.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:48.015 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:48.015 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:48.015 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:48.015 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:48.016 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:48.016 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:48.016 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:48.016 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:48 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1501116128831983707.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1501116128831983707.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1501116128831983707.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:31:48 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1501116128831983707.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1501116128831983707.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1501116128831983707.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:31:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:48 MarkDuplicates Start of doWork freeMemory: 1027855592; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:48 MarkDuplicates Start of doWork freeMemory: 1027855592; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:48 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:31:48 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:48 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:31:48 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:48 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:31:48 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 964934888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:48 MarkDuplicates After buildSortedReadEndLists freeMemory: 964934888; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:48 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:31:48 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:49 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:31:49 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:49 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:31:49 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:49 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:31:49 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 487832856; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:31:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 487832856; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:49 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:31:49 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:49 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:31:49 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:49 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:31:49 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:49 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:31:49 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:49 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:31:49 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:49 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:31:49 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:49 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:31:49 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:50 MarkDuplicates Before output close freeMemory: 757176520; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:31:50 MarkDuplicates Before output close freeMemory: 757176520; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:50 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:31:50 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:50 MarkDuplicates After output close freeMemory: 757316776; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:31:50 MarkDuplicates After output close freeMemory: 757316776; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:31:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1207959552 Runtime.totalMemory()=1207959552 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:50 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoMappedPairsWithSupplementaryReads[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:31:50 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6867644752958311101.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6867644752958311101.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6867644752958311101.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6867644752958311101.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6867644752958311101.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6867644752958311101.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:50.490 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:50.490 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:50.490 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:50.490 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:50.491 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:50.491 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:50.491 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:50.491 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:50 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6867644752958311101.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6867644752958311101.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6867644752958311101.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:31:50 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6867644752958311101.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6867644752958311101.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6867644752958311101.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:31:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:50 MarkDuplicates Start of doWork freeMemory: 1027852136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:50 MarkDuplicates Start of doWork freeMemory: 1027852136; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:50 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:31:50 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:50 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:31:50 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:50 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:31:50 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 964934248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 964934248; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:31:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:53 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:31:53 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:53 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:31:53 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:53 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:31:53 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 485647560; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:31:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 485647560; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:53 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:31:53 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:53 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:31:53 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:53 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:31:53 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:54 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:31:54 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:54 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:31:54 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:54 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:31:54 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:54 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:31:54 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:54 MarkDuplicates Before output close freeMemory: 755077880; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:31:54 MarkDuplicates Before output close freeMemory: 755077880; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:54 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:31:54 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:55 MarkDuplicates After output close freeMemory: 755218984; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:31:55 MarkDuplicates After output close freeMemory: 755218984; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:55 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. [Tue Jul 02 11:31:55 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1205862400 Runtime.totalMemory()=1205862400 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:55 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoMappedPairsWithSupplementaryReads[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:31:55 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6492532704943733132.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6492532704943733132.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6492532704943733132.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6492532704943733132.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6492532704943733132.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6492532704943733132.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:55.278 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:55.278 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:55.278 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:55.278 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:55.278 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:55.278 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:55.278 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:55.278 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:55 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6492532704943733132.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6492532704943733132.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6492532704943733132.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:31:55 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6492532704943733132.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6492532704943733132.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.6492532704943733132.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:31:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:55 MarkDuplicates Start of doWork freeMemory: 1027854312; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:55 MarkDuplicates Start of doWork freeMemory: 1027854312; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:55 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:31:55 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:55 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:31:55 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:55 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:31:55 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 964933616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 964933616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:31:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:57 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:31:57 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:57 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:31:57 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:57 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:31:57 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 568571936; totalMemory: 1288699904; maxMemory: 2147483648 INFO 2024-07-02 11:31:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 568571936; totalMemory: 1288699904; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:58 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:31:58 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:58 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:31:58 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:58 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:31:58 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:58 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:31:58 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:58 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:31:58 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:58 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:31:58 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:58 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:31:58 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:58 MarkDuplicates Before output close freeMemory: 837915600; totalMemory: 1288699904; maxMemory: 2147483648 INFO 2024-07-02 11:31:58 MarkDuplicates Before output close freeMemory: 837915600; totalMemory: 1288699904; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:58 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:31:58 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:59 MarkDuplicates After output close freeMemory: 838055856; totalMemory: 1288699904; maxMemory: 2147483648 INFO 2024-07-02 11:31:59 MarkDuplicates After output close freeMemory: 838055856; totalMemory: 1288699904; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:59 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:31:59 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1288699904 Runtime.totalMemory()=1288699904 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:59 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoMappedPairsWithSupplementaryReads[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:31:59 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13803999612087824756.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13803999612087824756.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13803999612087824756.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13803999612087824756.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13803999612087824756.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13803999612087824756.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:59.109 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:59.109 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:59.109 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:59.109 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:59.110 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:31:59.110 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:31:59.110 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:31:59.110 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:59 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13803999612087824756.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13803999612087824756.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13803999612087824756.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:31:59 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13803999612087824756.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13803999612087824756.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.13803999612087824756.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:31:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:31:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:59 MarkDuplicates Start of doWork freeMemory: 1027853672; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:31:59 MarkDuplicates Start of doWork freeMemory: 1027853672; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:59 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:31:59 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:59 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:31:59 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:31:59 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:31:59 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 964932968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:32:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 964932968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:32:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:01 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:32:01 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:01 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:32:01 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:01 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:32:01 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 485733784; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:32:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 485733784; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:02 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:32:02 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:02 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:32:02 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:02 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:32:02 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:02 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:32:02 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:02 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:32:02 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:02 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:32:02 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:02 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:32:02 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:02 MarkDuplicates Before output close freeMemory: 755075664; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:32:02 MarkDuplicates Before output close freeMemory: 755075664; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:02 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:32:02 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:02 MarkDuplicates After output close freeMemory: 755217280; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:32:02 MarkDuplicates After output close freeMemory: 755217280; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:02 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:32:02 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1205862400 Runtime.totalMemory()=1205862400 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:03 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoMappedPairsWithSupplementaryReads[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:32:03 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10121909303509525888.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10121909303509525888.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10121909303509525888.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10121909303509525888.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10121909303509525888.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10121909303509525888.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:03.039 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:32:03.039 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:03.039 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:32:03.039 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:03.039 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:32:03.039 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:03.039 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:32:03.039 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:03 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10121909303509525888.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10121909303509525888.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10121909303509525888.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:32:03 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10121909303509525888.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10121909303509525888.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.10121909303509525888.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:32:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:03 MarkDuplicates Start of doWork freeMemory: 1027847584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:32:03 MarkDuplicates Start of doWork freeMemory: 1027847584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:03 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:32:03 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:03 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:32:03 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:03 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:32:03 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 964932328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:32:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 964932328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:32:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:07 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:32:07 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:07 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:32:07 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:07 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:32:07 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 485733144; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:32:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 485733144; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:08 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:32:08 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:08 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:32:08 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:08 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:32:08 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:08 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:32:08 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:08 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:32:08 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:08 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:32:08 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:08 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:32:08 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:08 MarkDuplicates Before output close freeMemory: 755076808; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:32:08 MarkDuplicates Before output close freeMemory: 755076808; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:08 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:32:08 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:09 MarkDuplicates After output close freeMemory: 755217064; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:32:09 MarkDuplicates After output close freeMemory: 755217064; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:09 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.11 minutes. [Tue Jul 02 11:32:09 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.11 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1205862400 Runtime.totalMemory()=1205862400 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:09 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:32:09 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16612252712260693389.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16612252712260693389.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16612252712260693389.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16612252712260693389.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16612252712260693389.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16612252712260693389.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:09.480 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:32:09.480 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:09.480 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:32:09.480 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:09.480 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:32:09.480 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:09.480 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:32:09.480 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:09 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16612252712260693389.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16612252712260693389.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16612252712260693389.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:32:09 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16612252712260693389.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16612252712260693389.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.16612252712260693389.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:32:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:10 MarkDuplicates Start of doWork freeMemory: 1027851888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:32:10 MarkDuplicates Start of doWork freeMemory: 1027851888; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:10 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:32:10 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:10 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:32:10 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:10 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:32:10 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 964931184; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:32:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 964931184; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:12 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:32:12 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:32:14 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:14 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:32:14 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:14 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:32:14 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 487829152; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:32:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 487829152; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:14 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:32:14 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:14 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:32:14 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:14 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:32:14 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:14 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:32:14 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:14 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:32:14 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:14 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:32:14 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:14 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:32:14 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:15 MarkDuplicates Before output close freeMemory: 757173024; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:32:15 MarkDuplicates Before output close freeMemory: 757173024; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:15 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:32:15 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:15 MarkDuplicates After output close freeMemory: 757313144; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:32:15 MarkDuplicates After output close freeMemory: 757313144; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.11 minutes. [Tue Jul 02 11:32:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.11 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1207959552 Runtime.totalMemory()=1207959552 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:16 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:32:16 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4077778698055157902.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4077778698055157902.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4077778698055157902.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4077778698055157902.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4077778698055157902.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4077778698055157902.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:16.089 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:32:16.089 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:16.090 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:32:16.090 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:16.090 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:32:16.090 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:16.090 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:32:16.090 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:16 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4077778698055157902.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4077778698055157902.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4077778698055157902.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:32:16 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4077778698055157902.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4077778698055157902.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.4077778698055157902.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:32:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:16 MarkDuplicates Start of doWork freeMemory: 1027851200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:32:16 MarkDuplicates Start of doWork freeMemory: 1027851200; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:16 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:32:16 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:16 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:32:16 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:16 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:32:16 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 964930496; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:32:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 964930496; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:32:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:32:19 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:19 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:32:19 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:19 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:32:19 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 487828464; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:32:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 487828464; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:19 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:32:19 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:19 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:32:19 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:19 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:32:19 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:19 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:32:19 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:19 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:32:19 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:19 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:32:19 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:19 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:32:19 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:20 MarkDuplicates Before output close freeMemory: 757172336; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:32:20 MarkDuplicates Before output close freeMemory: 757172336; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:20 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:32:20 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:20 MarkDuplicates After output close freeMemory: 757312384; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:32:20 MarkDuplicates After output close freeMemory: 757312384; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:20 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. [Tue Jul 02 11:32:20 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1207959552 Runtime.totalMemory()=1207959552 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:20 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:32:20 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8258031314961821411.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8258031314961821411.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8258031314961821411.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8258031314961821411.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8258031314961821411.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8258031314961821411.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:20.780 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:32:20.780 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:20.780 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:32:20.780 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:20.780 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:32:20.780 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:20.780 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:32:20.780 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:20 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8258031314961821411.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8258031314961821411.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8258031314961821411.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:32:20 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8258031314961821411.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8258031314961821411.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8258031314961821411.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:32:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:21 MarkDuplicates Start of doWork freeMemory: 1027850560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:32:21 MarkDuplicates Start of doWork freeMemory: 1027850560; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:21 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:32:21 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:21 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:32:21 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:21 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:32:21 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 964929856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:32:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 964929856; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:32:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:24 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:32:24 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:24 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:32:24 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:24 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:32:24 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 485764376; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:32:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 485764376; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:24 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:32:24 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:24 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:32:24 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:24 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:32:24 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:24 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:32:24 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:24 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:32:24 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:24 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:32:24 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:24 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:32:24 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:25 MarkDuplicates Before output close freeMemory: 755107400; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:32:25 MarkDuplicates Before output close freeMemory: 755107400; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:25 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:32:25 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:25 MarkDuplicates After output close freeMemory: 755247872; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:32:25 MarkDuplicates After output close freeMemory: 755247872; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:25 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.09 minutes. [Tue Jul 02 11:32:25 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.09 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1205862400 Runtime.totalMemory()=1205862400 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:26 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:32:26 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9827082140072361767.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9827082140072361767.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9827082140072361767.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9827082140072361767.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9827082140072361767.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9827082140072361767.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:26.056 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:32:26.056 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:26.056 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:32:26.056 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:26.065 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:32:26.065 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:26.065 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:32:26.065 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:26 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9827082140072361767.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9827082140072361767.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9827082140072361767.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:32:26 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9827082140072361767.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9827082140072361767.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.9827082140072361767.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:32:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:26 MarkDuplicates Start of doWork freeMemory: 1027883624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:32:26 MarkDuplicates Start of doWork freeMemory: 1027883624; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:26 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:32:26 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:26 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:32:26 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:26 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:32:26 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 964962920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:32:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 964962920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:32:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:28 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:32:28 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:28 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:32:28 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:28 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:32:28 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 489958040; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:32:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 489958040; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:29 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:32:29 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:29 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:32:29 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:29 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:32:29 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:29 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:32:29 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:29 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:32:29 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:29 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:32:29 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:29 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:32:29 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:29 MarkDuplicates Before output close freeMemory: 759301912; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:32:29 MarkDuplicates Before output close freeMemory: 759301912; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:29 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:32:29 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:30 MarkDuplicates After output close freeMemory: 759441960; totalMemory: 1210056704; maxMemory: 2147483648 INFO 2024-07-02 11:32:30 MarkDuplicates After output close freeMemory: 759441960; totalMemory: 1210056704; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:30 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:32:30 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1210056704 Runtime.totalMemory()=1210056704 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:30 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:32:30 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1256580692258327393.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1256580692258327393.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1256580692258327393.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1256580692258327393.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1256580692258327393.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1256580692258327393.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:30.110 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:32:30.110 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:30.110 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:32:30.110 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:30.110 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:32:30.110 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:30.110 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:32:30.110 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:30 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1256580692258327393.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1256580692258327393.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1256580692258327393.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:32:30 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1256580692258327393.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1256580692258327393.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.1256580692258327393.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:32:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:30 MarkDuplicates Start of doWork freeMemory: 1027882984; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:32:30 MarkDuplicates Start of doWork freeMemory: 1027882984; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:30 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:32:30 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:30 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:32:30 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:30 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:32:30 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 964962280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:32:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 964962280; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:32:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:32 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:32:32 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:32 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:32:32 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:32 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:32:32 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 485763096; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:32:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 485763096; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:33 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:32:33 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:33 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:32:33 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:33 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:32:33 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:33 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:32:33 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:33 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:32:33 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:33 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:32:33 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:33 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:32:33 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:33 MarkDuplicates Before output close freeMemory: 755106968; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:32:33 MarkDuplicates Before output close freeMemory: 755106968; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:33 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:32:33 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:34 MarkDuplicates After output close freeMemory: 755247016; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:32:34 MarkDuplicates After output close freeMemory: 755247016; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:32:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1205862400 Runtime.totalMemory()=1205862400 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:34 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:32:34 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8167038412742918890.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8167038412742918890.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8167038412742918890.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8167038412742918890.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8167038412742918890.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8167038412742918890.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:34.283 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:32:34.283 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:34.284 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:32:34.284 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:34.284 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:32:34.284 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:34.284 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:32:34.284 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:34 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8167038412742918890.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8167038412742918890.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8167038412742918890.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:32:34 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8167038412742918890.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8167038412742918890.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.8167038412742918890.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:32:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:34 MarkDuplicates Start of doWork freeMemory: 1027882320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:32:34 MarkDuplicates Start of doWork freeMemory: 1027882320; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:34 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:32:34 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:34 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:32:34 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:34 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:32:34 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 964961616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:32:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 964961616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:32:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:32:37 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:32:37 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:37 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:32:37 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 487859584; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:32:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 487859584; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:38 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:32:38 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:38 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:32:38 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:38 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:32:38 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:38 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:32:38 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:38 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:32:38 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:38 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:32:38 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:38 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:32:38 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:38 MarkDuplicates Before output close freeMemory: 757203456; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:32:38 MarkDuplicates Before output close freeMemory: 757203456; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:38 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:32:38 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:39 MarkDuplicates After output close freeMemory: 757343504; totalMemory: 1207959552; maxMemory: 2147483648 INFO 2024-07-02 11:32:39 MarkDuplicates After output close freeMemory: 757343504; totalMemory: 1207959552; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.09 minutes. [Tue Jul 02 11:32:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.09 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1207959552 Runtime.totalMemory()=1207959552 Running Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:39 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testTwoUnmappedFragments STANDARD_ERROR INFO 2024-07-02 11:32:39 MarkDuplicates Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2009691328696717452.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2009691328696717452.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2009691328696717452.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2009691328696717452.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2009691328696717452.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2009691328696717452.tmp/output.sam Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:39.722 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:32:39.722 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:39.722 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:32:39.722 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:39.722 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:32:39.722 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:39.722 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:32:39.722 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:39 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2009691328696717452.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2009691328696717452.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2009691328696717452.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:32:39 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2009691328696717452.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2009691328696717452.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.2009691328696717452.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:32:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:40 MarkDuplicates Start of doWork freeMemory: 1027883840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:32:40 MarkDuplicates Start of doWork freeMemory: 1027883840; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:40 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:32:40 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:40 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:32:40 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:40 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2024-07-02 11:32:40 MarkDuplicates Read 0 records. 0 pairs never matched. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 964963864; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:32:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 964963864; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:32:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:43 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:32:43 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:43 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:32:43 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:43 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:32:43 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 484716096; totalMemory: 1204813824; maxMemory: 2147483648 INFO 2024-07-02 11:32:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 484716096; totalMemory: 1204813824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:43 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:32:43 MarkDuplicates Marking 0 records as duplicates. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:43 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:32:43 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:43 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:32:43 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:43 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:32:43 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:43 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:32:43 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:43 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:32:43 MarkDuplicates Representative read Index cleanup. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:43 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:32:43 MarkDuplicates Getting Memory Stats. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:44 MarkDuplicates Before output close freeMemory: 754060128; totalMemory: 1204813824; maxMemory: 2147483648 INFO 2024-07-02 11:32:44 MarkDuplicates Before output close freeMemory: 754060128; totalMemory: 1204813824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:44 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:32:44 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:45 MarkDuplicates After output close freeMemory: 754199920; totalMemory: 1204813824; maxMemory: 2147483648 INFO 2024-07-02 11:32:45 MarkDuplicates After output close freeMemory: 754199920; totalMemory: 1204813824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.09 minutes. [Tue Jul 02 11:32:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.09 minutes. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1204813824 Runtime.totalMemory()=1204813824 Running Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:45 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testMultiRepresentativeReadTags STANDARD_ERROR INFO 2024-07-02 11:32:45 MarkDuplicates Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15103043885224510539.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15103043885224510539.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15103043885224510539.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15103043885224510539.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15103043885224510539.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15103043885224510539.tmp/output.sam Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:45.337 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:32:45.337 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:45.338 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:32:45.338 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:45.338 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:32:45.338 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:45.338 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:32:45.338 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:45 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15103043885224510539.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15103043885224510539.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15103043885224510539.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:32:45 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15103043885224510539.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15103043885224510539.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.15103043885224510539.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:32:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:46 MarkDuplicates Start of doWork freeMemory: 1027876096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:32:46 MarkDuplicates Start of doWork freeMemory: 1027876096; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:46 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:32:46 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:46 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:32:46 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:46 MarkDuplicates Read 12 records. 0 pairs never matched. INFO 2024-07-02 11:32:46 MarkDuplicates Read 12 records. 0 pairs never matched. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 964954528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:32:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 964954528; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:32:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:49 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:32:49 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:49 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:32:49 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:49 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:32:49 MarkDuplicates Sorting list of duplicate records. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 485755104; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:32:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 485755104; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:50 MarkDuplicates Marking 6 records as duplicates. INFO 2024-07-02 11:32:50 MarkDuplicates Marking 6 records as duplicates. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:50 MarkDuplicates Found 3 optical duplicate clusters. INFO 2024-07-02 11:32:50 MarkDuplicates Found 3 optical duplicate clusters. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:50 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:32:50 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:50 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:32:50 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:50 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:32:50 MarkDuplicates Duplicate Index cleanup. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:50 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:32:50 MarkDuplicates Representative read Index cleanup. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:50 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:32:50 MarkDuplicates Getting Memory Stats. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:50 MarkDuplicates Before output close freeMemory: 755099656; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:32:50 MarkDuplicates Before output close freeMemory: 755099656; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:50 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:32:50 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:51 MarkDuplicates After output close freeMemory: 755239368; totalMemory: 1205862400; maxMemory: 2147483648 INFO 2024-07-02 11:32:51 MarkDuplicates After output close freeMemory: 755239368; totalMemory: 1205862400; maxMemory: 2147483648 Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.10 minutes. [Tue Jul 02 11:32:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.10 minutes. Test: Test method testMultiRepresentativeReadTags(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1205862400 Runtime.totalMemory()=1205862400 Running Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:51 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest.testRepresentativeReadTag STANDARD_ERROR INFO 2024-07-02 11:32:51 MarkDuplicates Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14867145489637905778.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14867145489637905778.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14867145489637905778.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14867145489637905778.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY All -TAG_DUPLICATE_SET_MEMBERS true -INPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14867145489637905778.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14867145489637905778.tmp/output.sam Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: ********** ********** Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:51.656 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:32:51.656 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:51.656 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:32:51.656 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:51.673 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:32:51.673 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: 11:32:51.673 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:32:51.673 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:51 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14867145489637905778.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14867145489637905778.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14867145489637905778.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:32:51 GMT+14:00 2024] MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14867145489637905778.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14867145489637905778.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTagRepresentativeReadIndexTester.14867145489637905778.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:32:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:52 MarkDuplicates Start of doWork freeMemory: 1027878432; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:32:52 MarkDuplicates Start of doWork freeMemory: 1027878432; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:52 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:32:52 MarkDuplicates Reading input file and constructing read end information. Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:52 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:32:52 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:52 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:32:52 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 964959984; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:32:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 964959984; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:32:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:32:55 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:55 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:32:55 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:55 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:32:55 MarkDuplicates Sorting list of duplicate records. Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 482615072; totalMemory: 1202716672; maxMemory: 2147483648 INFO 2024-07-02 11:32:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 482615072; totalMemory: 1202716672; maxMemory: 2147483648 Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:55 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:32:55 MarkDuplicates Marking 2 records as duplicates. Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:55 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:32:55 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:55 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:32:55 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:55 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:32:55 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:55 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:32:55 MarkDuplicates Duplicate Index cleanup. Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:55 MarkDuplicates Representative read Index cleanup. INFO 2024-07-02 11:32:55 MarkDuplicates Representative read Index cleanup. Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:55 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:32:55 MarkDuplicates Getting Memory Stats. Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:56 MarkDuplicates Before output close freeMemory: 751958832; totalMemory: 1202716672; maxMemory: 2147483648 INFO 2024-07-02 11:32:56 MarkDuplicates Before output close freeMemory: 751958832; totalMemory: 1202716672; maxMemory: 2147483648 Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:56 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:32:56 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: INFO 2024-07-02 11:32:57 MarkDuplicates After output close freeMemory: 752098992; totalMemory: 1202716672; maxMemory: 2147483648 INFO 2024-07-02 11:32:57 MarkDuplicates After output close freeMemory: 752098992; totalMemory: 1202716672; maxMemory: 2147483648 Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: [Tue Jul 02 11:32:57 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.09 minutes. [Tue Jul 02 11:32:57 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.09 minutes. Test: Test method testRepresentativeReadTag(picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest) produced standard out/err: Runtime.totalMemory()=1202716672 Runtime.totalMemory()=1202716672 Running Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:32:57 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testBulkFragmentsNoDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:32:57 MarkDuplicates Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.12373672078286359662.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.12373672078286359662.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.12373672078286359662.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.12373672078286359662.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.12373672078286359662.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.12373672078286359662.tmp/output.sam Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:32:58.001 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:32:58.001 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:32:58.001 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:32:58.001 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:32:58.002 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:32:58.002 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:32:58.002 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:32:58.002 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:32:58 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.12373672078286359662.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.12373672078286359662.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.12373672078286359662.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:32:58 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.12373672078286359662.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.12373672078286359662.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.12373672078286359662.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:32:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:32:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:32:58 MarkDuplicates Start of doWork freeMemory: 1020942952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:32:58 MarkDuplicates Start of doWork freeMemory: 1020942952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:32:58 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:32:58 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:32:58 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:32:58 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:32:58 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:32:58 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:00 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2024-07-02 11:33:00 MarkDuplicates Read 10000 records. 0 pairs never matched. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 957302864; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:33:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 957302864; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:33:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:03 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:33:03 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:03 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:33:03 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:03 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:33:03 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 800736664; totalMemory: 1392508928; maxMemory: 2147483648 INFO 2024-07-02 11:33:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 800736664; totalMemory: 1392508928; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:03 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:33:03 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:03 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:33:03 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:03 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:33:03 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:04 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:33:04 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:04 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:33:04 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:04 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:33:04 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:05 MarkDuplicates Before output close freeMemory: 761799072; totalMemory: 1084227584; maxMemory: 2147483648 INFO 2024-07-02 11:33:05 MarkDuplicates Before output close freeMemory: 761799072; totalMemory: 1084227584; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:05 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:33:05 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:05 MarkDuplicates After output close freeMemory: 761939168; totalMemory: 1084227584; maxMemory: 2147483648 INFO 2024-07-02 11:33:05 MarkDuplicates After output close freeMemory: 761939168; totalMemory: 1084227584; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:33:05 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.13 minutes. [Tue Jul 02 11:33:05 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.13 minutes. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:07 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testBulkFragmentsNoDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:33:07 MarkDuplicates Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.15244705431684404916.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.15244705431684404916.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesTester.15244705431684404916.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.15244705431684404916.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.15244705431684404916.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesTester.15244705431684404916.tmp/output.sam Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:33:07.108 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:33:07.108 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:33:07.108 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:33:07.108 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:33:07.108 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:33:07.108 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:33:07.108 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:33:07.108 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:33:07 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.15244705431684404916.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesTester.15244705431684404916.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.15244705431684404916.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:33:07 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.15244705431684404916.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesTester.15244705431684404916.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.15244705431684404916.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:33:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:33:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:07 MarkDuplicates Start of doWork freeMemory: 1020876584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:33:07 MarkDuplicates Start of doWork freeMemory: 1020876584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:07 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:33:07 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:07 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:33:07 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:33:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:33:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:09 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2024-07-02 11:33:09 MarkDuplicates Read 10000 records. 0 pairs never matched. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 957162352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:33:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 957162352; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:33:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:33:11 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:33:11 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:11 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:33:11 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 481960400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:33:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 481960400; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:12 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:33:12 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:12 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:33:12 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:12 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:33:12 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:12 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:33:12 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:12 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:33:12 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:12 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:33:12 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:13 MarkDuplicates Before output close freeMemory: 751171560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:33:13 MarkDuplicates Before output close freeMemory: 751171560; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:13 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:33:13 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:14 MarkDuplicates After output close freeMemory: 751289768; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:33:14 MarkDuplicates After output close freeMemory: 751289768; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:33:14 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.12 minutes. [Tue Jul 02 11:33:14 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.12 minutes. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:18 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testBulkFragmentsNoDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:33:18 MarkDuplicates Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.11834938110526401597.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.11834938110526401597.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesTester.11834938110526401597.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester14290138882661042311/input.fasta ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.11834938110526401597.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.11834938110526401597.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesTester.11834938110526401597.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester14290138882661042311/input.fasta Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:33:18.857 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:33:18.857 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:33:18.857 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:33:18.857 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:33:18.858 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:33:18.858 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:33:18.858 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:33:18.858 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:33:18 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.11834938110526401597.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesTester.11834938110526401597.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.11834938110526401597.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester14290138882661042311/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:33:18 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.11834938110526401597.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesTester.11834938110526401597.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.11834938110526401597.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester14290138882661042311/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:33:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:33:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:19 MarkDuplicates Start of doWork freeMemory: 1020928392; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:33:19 MarkDuplicates Start of doWork freeMemory: 1020928392; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:19 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:33:19 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:19 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:33:19 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:33:21 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:33:21 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:22 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2024-07-02 11:33:22 MarkDuplicates Read 10000 records. 0 pairs never matched. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 957290608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:33:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 957290608; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:33:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:24 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:33:24 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:24 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:33:24 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:24 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:33:24 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 481957688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:33:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 481957688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:25 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:33:25 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:25 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:33:25 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:25 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:33:25 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:26 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:33:26 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:26 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:33:26 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:26 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:33:26 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:27 MarkDuplicates Before output close freeMemory: 751300912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:33:27 MarkDuplicates Before output close freeMemory: 751300912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:27 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:33:27 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:27 MarkDuplicates After output close freeMemory: 751441064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:33:27 MarkDuplicates After output close freeMemory: 751441064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:33:27 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.15 minutes. [Tue Jul 02 11:33:27 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.15 minutes. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:29 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testBulkFragmentsWithDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:33:29 MarkDuplicates Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.16544053134975797479.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.16544053134975797479.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.16544053134975797479.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.16544053134975797479.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.16544053134975797479.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.16544053134975797479.tmp/output.sam Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:33:29.640 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:33:29.640 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:33:29.640 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:33:29.640 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:33:29.640 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:33:29.640 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:33:29.640 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:33:29.640 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:33:29 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.16544053134975797479.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.16544053134975797479.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.16544053134975797479.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:33:29 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.16544053134975797479.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.16544053134975797479.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.16544053134975797479.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:33:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:33:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:30 MarkDuplicates Start of doWork freeMemory: 1012736304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:33:30 MarkDuplicates Start of doWork freeMemory: 1012736304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:30 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:33:30 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:30 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:33:30 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:33:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:33:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:32 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2024-07-02 11:33:32 MarkDuplicates Read 21000 records. 0 pairs never matched. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 948149560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:33:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 948149560; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:33:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:33:34 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:34 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:33:34 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:34 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:33:34 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 473763408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:33:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 473763408; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:35 MarkDuplicates Marking 20000 records as duplicates. INFO 2024-07-02 11:33:35 MarkDuplicates Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:35 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:33:35 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:35 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:33:35 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:36 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:33:36 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:36 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:33:36 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:36 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:33:36 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:37 MarkDuplicates Before output close freeMemory: 743059200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:33:37 MarkDuplicates Before output close freeMemory: 743059200; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:37 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:33:37 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:37 MarkDuplicates After output close freeMemory: 743059200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:33:37 MarkDuplicates After output close freeMemory: 743059200; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:33:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.14 minutes. [Tue Jul 02 11:33:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.14 minutes. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:41 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testBulkFragmentsWithDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:33:41 MarkDuplicates Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.13014291393922014374.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.13014291393922014374.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesTester.13014291393922014374.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.13014291393922014374.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.13014291393922014374.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesTester.13014291393922014374.tmp/output.sam Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:33:41.099 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:33:41.099 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:33:41.100 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:33:41.100 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:33:41.100 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:33:41.100 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:33:41.100 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:33:41.100 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:33:41 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.13014291393922014374.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesTester.13014291393922014374.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.13014291393922014374.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:33:41 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.13014291393922014374.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesTester.13014291393922014374.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.13014291393922014374.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:33:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:33:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:41 MarkDuplicates Start of doWork freeMemory: 1012670504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:33:41 MarkDuplicates Start of doWork freeMemory: 1012670504; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:41 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:33:41 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:41 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:33:41 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:33:42 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:33:42 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:44 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2024-07-02 11:33:44 MarkDuplicates Read 21000 records. 0 pairs never matched. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 948172240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:33:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 948172240; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:33:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:46 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:33:46 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:46 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:33:46 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:46 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:33:46 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 473762512; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:33:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 473762512; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:47 MarkDuplicates Marking 20000 records as duplicates. INFO 2024-07-02 11:33:47 MarkDuplicates Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:47 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:33:47 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:47 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:33:47 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:48 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:33:48 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:48 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:33:48 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:48 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:33:48 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:49 MarkDuplicates Before output close freeMemory: 742974264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:33:49 MarkDuplicates Before output close freeMemory: 742974264; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:49 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:33:49 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:49 MarkDuplicates After output close freeMemory: 743114608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:33:49 MarkDuplicates After output close freeMemory: 743114608; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:33:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.14 minutes. [Tue Jul 02 11:33:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.14 minutes. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:57 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testBulkFragmentsWithDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:33:57 MarkDuplicates Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.940019330217509035.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.940019330217509035.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesTester.940019330217509035.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester456410698587443886/input.fasta ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.940019330217509035.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.940019330217509035.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesTester.940019330217509035.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester456410698587443886/input.fasta Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:33:57.517 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:33:57.517 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:33:57.517 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:33:57.517 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:33:57.518 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:33:57.518 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:33:57.518 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:33:57.518 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:33:57 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.940019330217509035.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesTester.940019330217509035.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.940019330217509035.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester456410698587443886/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:33:57 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.940019330217509035.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesTester.940019330217509035.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.940019330217509035.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester456410698587443886/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:33:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:33:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:58 MarkDuplicates Start of doWork freeMemory: 1012730928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:33:58 MarkDuplicates Start of doWork freeMemory: 1012730928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:58 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:33:58 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:33:58 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:33:58 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:33:59 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:33:59 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:02 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2024-07-02 11:34:02 MarkDuplicates Read 21000 records. 0 pairs never matched. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 948301408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:34:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 948301408; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:03 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:34:03 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:04 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:34:04 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:04 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:34:04 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:04 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:34:04 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 473760264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:34:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 473760264; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:05 MarkDuplicates Marking 20000 records as duplicates. INFO 2024-07-02 11:34:05 MarkDuplicates Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:05 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:34:05 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:05 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:34:05 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:08 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:34:08 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:08 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:34:08 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:08 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:34:08 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:09 MarkDuplicates Before output close freeMemory: 743102016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:34:09 MarkDuplicates Before output close freeMemory: 743102016; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:09 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:34:09 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:09 MarkDuplicates After output close freeMemory: 743241984; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:34:09 MarkDuplicates After output close freeMemory: 743241984; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:34:09 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.20 minutes. [Tue Jul 02 11:34:09 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.20 minutes. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:11 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testBulkPairsNoDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:34:11 MarkDuplicates Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.6609565198642878960.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.6609565198642878960.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.6609565198642878960.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.6609565198642878960.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.6609565198642878960.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.6609565198642878960.tmp/output.sam Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:34:11.547 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:34:11.547 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:34:11.547 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:34:11.547 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:34:11.548 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:34:11.548 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:34:11.548 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:34:11.548 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:34:11 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.6609565198642878960.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.6609565198642878960.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.6609565198642878960.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:34:11 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.6609565198642878960.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.6609565198642878960.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.6609565198642878960.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:34:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:34:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:12 MarkDuplicates Start of doWork freeMemory: 1012215064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:34:12 MarkDuplicates Start of doWork freeMemory: 1012215064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:12 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:34:12 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:12 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:34:12 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:34:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:34:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:14 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2024-07-02 11:34:14 MarkDuplicates Read 20200 records. 0 pairs never matched. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:15 MarkDuplicates After buildSortedReadEndLists freeMemory: 947113360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:34:15 MarkDuplicates After buildSortedReadEndLists freeMemory: 947113360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:34:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:17 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:34:17 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:17 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:34:17 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:17 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:34:17 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 473241480; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:34:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 473241480; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:17 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:34:17 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:17 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:34:17 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:17 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:34:17 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:18 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:34:18 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:18 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:34:18 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:18 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:34:18 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:19 MarkDuplicates Before output close freeMemory: 742585120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:34:19 MarkDuplicates Before output close freeMemory: 742585120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:19 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:34:19 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:19 MarkDuplicates After output close freeMemory: 742725328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:34:19 MarkDuplicates After output close freeMemory: 742725328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:34:19 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.14 minutes. [Tue Jul 02 11:34:19 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.14 minutes. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:22 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testBulkPairsNoDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:34:22 MarkDuplicates Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.13172241193393658311.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.13172241193393658311.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesTester.13172241193393658311.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.13172241193393658311.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.13172241193393658311.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesTester.13172241193393658311.tmp/output.sam Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:34:22.847 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:34:22.847 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:34:22.847 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:34:22.847 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:34:22.848 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:34:22.848 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:34:22.848 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:34:22.848 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:34:22 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.13172241193393658311.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesTester.13172241193393658311.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.13172241193393658311.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:34:22 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.13172241193393658311.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesTester.13172241193393658311.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.13172241193393658311.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:34:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:34:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:23 MarkDuplicates Start of doWork freeMemory: 1012148728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:34:23 MarkDuplicates Start of doWork freeMemory: 1012148728; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:23 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:34:23 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:23 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:34:23 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:34:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:34:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:24 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2024-07-02 11:34:24 MarkDuplicates Read 20200 records. 0 pairs never matched. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 946980968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:34:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 946980968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:34:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:34:27 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:34:27 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:27 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:34:27 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 473240032; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:34:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 473240032; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:27 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:34:27 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:27 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:34:27 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:27 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:34:27 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:28 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:34:28 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:28 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:34:28 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:28 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:34:28 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:29 MarkDuplicates Before output close freeMemory: 742451696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:34:29 MarkDuplicates Before output close freeMemory: 742451696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:29 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:34:29 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:29 MarkDuplicates After output close freeMemory: 742592128; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:34:29 MarkDuplicates After output close freeMemory: 742592128; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:34:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.12 minutes. [Tue Jul 02 11:34:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.12 minutes. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:37 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testBulkPairsNoDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:34:37 MarkDuplicates Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.16539746435367598035.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.16539746435367598035.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesTester.16539746435367598035.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester9786691455444278636/input.fasta ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.16539746435367598035.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.16539746435367598035.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesTester.16539746435367598035.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester9786691455444278636/input.fasta Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:34:37.956 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:34:37.956 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:34:37.956 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:34:37.956 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:34:37.956 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:34:37.956 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:34:37.956 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:34:37.956 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:34:37 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.16539746435367598035.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesTester.16539746435367598035.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.16539746435367598035.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester9786691455444278636/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:34:37 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.16539746435367598035.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesTester.16539746435367598035.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.16539746435367598035.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester9786691455444278636/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:34:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:34:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:38 MarkDuplicates Start of doWork freeMemory: 1012209696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:34:38 MarkDuplicates Start of doWork freeMemory: 1012209696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:38 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:34:38 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:38 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:34:38 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:34:39 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:34:39 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:43 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2024-07-02 11:34:43 MarkDuplicates Read 20200 records. 0 pairs never matched. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 947109104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:34:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 947109104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:34:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:34:44 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:44 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:34:44 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:44 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:34:44 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 473237608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:34:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 473237608; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:45 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:34:45 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:45 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:34:45 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:45 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:34:45 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:49 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:34:49 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:49 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:34:49 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:49 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:34:49 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:49 MarkDuplicates Before output close freeMemory: 742581320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:34:49 MarkDuplicates Before output close freeMemory: 742581320; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:49 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:34:49 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:50 MarkDuplicates After output close freeMemory: 742721376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:34:50 MarkDuplicates After output close freeMemory: 742721376; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:34:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.21 minutes. [Tue Jul 02 11:34:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.21 minutes. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:51 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testBulkPairsWithDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:34:51 MarkDuplicates Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.41114909195016082.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.41114909195016082.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.41114909195016082.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.41114909195016082.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.41114909195016082.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.41114909195016082.tmp/output.sam Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:34:51.581 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:34:51.581 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:34:51.582 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:34:51.582 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:34:51.582 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:34:51.582 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:34:51.582 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:34:51.582 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:34:51 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.41114909195016082.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.41114909195016082.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.41114909195016082.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:34:51 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.41114909195016082.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.41114909195016082.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.41114909195016082.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:34:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:34:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:52 MarkDuplicates Start of doWork freeMemory: 1022730456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:34:52 MarkDuplicates Start of doWork freeMemory: 1022730456; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:52 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:34:52 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:52 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:34:52 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:34:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:34:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:53 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2024-07-02 11:34:53 MarkDuplicates Read 6820 records. 0 pairs never matched. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 959073792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:34:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 959073792; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:54 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:34:54 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:34:55 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:55 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:34:55 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:55 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:34:55 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 753240904; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:34:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 753240904; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:56 MarkDuplicates Marking 6200 records as duplicates. INFO 2024-07-02 11:34:56 MarkDuplicates Marking 6200 records as duplicates. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:56 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:34:56 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:56 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:34:56 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:56 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:34:56 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:56 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:34:56 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:56 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:34:56 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:57 MarkDuplicates Before output close freeMemory: 763585616; totalMemory: 1084227584; maxMemory: 2147483648 INFO 2024-07-02 11:34:57 MarkDuplicates Before output close freeMemory: 763585616; totalMemory: 1084227584; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:57 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:34:57 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:57 MarkDuplicates After output close freeMemory: 759532248; totalMemory: 1080033280; maxMemory: 2147483648 INFO 2024-07-02 11:34:57 MarkDuplicates After output close freeMemory: 759532248; totalMemory: 1080033280; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:34:57 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.10 minutes. [Tue Jul 02 11:34:57 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.10 minutes. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1080033280 Runtime.totalMemory()=1080033280 Running Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:58 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testBulkPairsWithDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:34:58 MarkDuplicates Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.10947552103432917785.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.10947552103432917785.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesTester.10947552103432917785.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.10947552103432917785.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.10947552103432917785.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesTester.10947552103432917785.tmp/output.sam Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:34:58.391 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:34:58.391 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:34:58.391 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:34:58.391 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:34:58.391 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:34:58.391 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:34:58.391 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:34:58.391 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:34:58 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.10947552103432917785.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesTester.10947552103432917785.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.10947552103432917785.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:34:58 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.10947552103432917785.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesTester.10947552103432917785.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.10947552103432917785.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:34:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:34:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:58 MarkDuplicates Start of doWork freeMemory: 1022664120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:34:58 MarkDuplicates Start of doWork freeMemory: 1022664120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:58 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:34:58 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:58 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:34:58 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:34:59 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:34:59 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:34:59 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2024-07-02 11:34:59 MarkDuplicates Read 6820 records. 0 pairs never matched. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 958941176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 958941176; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:35:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:01 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:35:01 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:01 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:35:01 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:01 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:35:01 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 483755832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 483755832; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:01 MarkDuplicates Marking 6200 records as duplicates. INFO 2024-07-02 11:35:01 MarkDuplicates Marking 6200 records as duplicates. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:01 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:35:01 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:01 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:35:01 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:01 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:35:01 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:01 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:35:01 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:01 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:35:01 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:02 MarkDuplicates Before output close freeMemory: 752966840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:02 MarkDuplicates Before output close freeMemory: 752966840; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:02 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:35:02 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:02 MarkDuplicates After output close freeMemory: 753107928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:02 MarkDuplicates After output close freeMemory: 753107928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:02 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:35:02 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:04 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testBulkPairsWithDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:35:04 MarkDuplicates Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.15754621481924884932.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.15754621481924884932.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesTester.15754621481924884932.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester2328775928232818430/input.fasta ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.15754621481924884932.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.15754621481924884932.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesTester.15754621481924884932.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester2328775928232818430/input.fasta Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:04.583 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:35:04.583 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:04.583 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:35:04.583 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:04.583 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:35:04.583 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:04.583 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:35:04.583 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:04 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.15754621481924884932.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesTester.15754621481924884932.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.15754621481924884932.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester2328775928232818430/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:35:04 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.15754621481924884932.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesTester.15754621481924884932.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.15754621481924884932.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester2328775928232818430/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:35:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:05 MarkDuplicates Start of doWork freeMemory: 1022726944; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:05 MarkDuplicates Start of doWork freeMemory: 1022726944; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:05 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:35:05 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:05 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:35:05 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:35:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:35:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:07 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2024-07-02 11:35:07 MarkDuplicates Read 6820 records. 0 pairs never matched. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 959069688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 959069688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:35:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:35:11 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:35:11 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:12 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:35:12 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 483752456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 483752456; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:12 MarkDuplicates Marking 6200 records as duplicates. INFO 2024-07-02 11:35:12 MarkDuplicates Marking 6200 records as duplicates. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:12 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:35:12 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:12 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:35:12 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:14 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:35:14 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:14 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:35:14 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:14 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:35:14 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:15 MarkDuplicates Before output close freeMemory: 753096840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:15 MarkDuplicates Before output close freeMemory: 753096840; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:15 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:35:15 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:15 MarkDuplicates After output close freeMemory: 753237024; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:15 MarkDuplicates After output close freeMemory: 753237024; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.18 minutes. [Tue Jul 02 11:35:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.18 minutes. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:16 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testDifferentChromosomesInOppositeOrder STANDARD_ERROR INFO 2024-07-02 11:35:16 MarkDuplicates Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.12657038452434319907.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.12657038452434319907.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.12657038452434319907.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.12657038452434319907.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.12657038452434319907.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.12657038452434319907.tmp/output.sam Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:16.244 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:35:16.244 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:16.261 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:35:16.261 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:16.261 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:35:16.261 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:16.261 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:35:16.261 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:16 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.12657038452434319907.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.12657038452434319907.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.12657038452434319907.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:35:16 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.12657038452434319907.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.12657038452434319907.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.12657038452434319907.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:35:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:16 MarkDuplicates Start of doWork freeMemory: 1027845960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:16 MarkDuplicates Start of doWork freeMemory: 1027845960; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:16 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:35:16 MarkDuplicates Reading input file and constructing read end information. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:16 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:35:16 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:16 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:35:16 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 964927992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 964927992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:35:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:35:19 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:19 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:35:19 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:19 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:35:19 MarkDuplicates Sorting list of duplicate records. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 488874792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 488874792; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:19 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:35:19 MarkDuplicates Marking 2 records as duplicates. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:19 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:35:19 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:19 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:35:19 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:19 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:35:19 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:19 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:35:19 MarkDuplicates Duplicate Index cleanup. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:19 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:35:19 MarkDuplicates Getting Memory Stats. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:20 MarkDuplicates Before output close freeMemory: 758218368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:20 MarkDuplicates Before output close freeMemory: 758218368; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:20 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:35:20 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:20 MarkDuplicates After output close freeMemory: 758358640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:20 MarkDuplicates After output close freeMemory: 758358640; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:20 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. [Tue Jul 02 11:35:20 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:21 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:35:21 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.7581049202869110209.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.7581049202869110209.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.7581049202869110209.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.7581049202869110209.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.7581049202869110209.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.7581049202869110209.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:21.043 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:35:21.043 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:21.043 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:35:21.043 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:21.044 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:35:21.044 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:21.044 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:35:21.044 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:21 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.7581049202869110209.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.7581049202869110209.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.7581049202869110209.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:35:21 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.7581049202869110209.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.7581049202869110209.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.7581049202869110209.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:35:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:21 MarkDuplicates Start of doWork freeMemory: 1027841208; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:21 MarkDuplicates Start of doWork freeMemory: 1027841208; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:21 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:35:21 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:21 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:35:21 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:22 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:35:22 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 964919856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 964919856; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:35:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:24 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:35:24 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:24 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:35:24 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:24 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:35:24 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 488867304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 488867304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:24 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:35:24 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:24 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:35:24 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:24 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:35:24 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:24 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:35:24 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:24 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:35:24 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:24 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:35:24 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:25 MarkDuplicates Before output close freeMemory: 758210904; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:25 MarkDuplicates Before output close freeMemory: 758210904; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:25 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:35:25 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:26 MarkDuplicates After output close freeMemory: 758351152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:26 MarkDuplicates After output close freeMemory: 758351152; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:26 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.09 minutes. [Tue Jul 02 11:35:26 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.09 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:26 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:35:26 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.7397706854118077639.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.7397706854118077639.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.7397706854118077639.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.7397706854118077639.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.7397706854118077639.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.7397706854118077639.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:26.471 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:35:26.471 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:26.471 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:35:26.471 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:26.472 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:35:26.472 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:26.472 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:35:26.472 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:26 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.7397706854118077639.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.7397706854118077639.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.7397706854118077639.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:35:26 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.7397706854118077639.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.7397706854118077639.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.7397706854118077639.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:35:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:27 MarkDuplicates Start of doWork freeMemory: 1027840544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:27 MarkDuplicates Start of doWork freeMemory: 1027840544; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:27 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:35:27 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:27 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:35:27 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:27 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:35:27 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 964919192; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 964919192; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:35:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:30 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:35:30 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:30 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:35:30 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:30 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:35:30 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 488866640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 488866640; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:30 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:35:30 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:30 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:35:30 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:30 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:35:30 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:30 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:35:30 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:30 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:35:30 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:30 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:35:30 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:31 MarkDuplicates Before output close freeMemory: 758210240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:31 MarkDuplicates Before output close freeMemory: 758210240; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:31 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:35:31 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:32 MarkDuplicates After output close freeMemory: 758350488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:32 MarkDuplicates After output close freeMemory: 758350488; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.10 minutes. [Tue Jul 02 11:35:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.10 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:32 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:35:32 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.18361031859892340304.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.18361031859892340304.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.18361031859892340304.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.18361031859892340304.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.18361031859892340304.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.18361031859892340304.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:32.462 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:35:32.462 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:32.463 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:35:32.463 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:32.463 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:35:32.463 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:32.463 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:35:32.463 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:32 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.18361031859892340304.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.18361031859892340304.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.18361031859892340304.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:35:32 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.18361031859892340304.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.18361031859892340304.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.18361031859892340304.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:35:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:33 MarkDuplicates Start of doWork freeMemory: 1027837168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:33 MarkDuplicates Start of doWork freeMemory: 1027837168; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:33 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:35:33 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:33 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:35:33 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:33 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:35:33 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:34 MarkDuplicates After buildSortedReadEndLists freeMemory: 964918568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:34 MarkDuplicates After buildSortedReadEndLists freeMemory: 964918568; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:34 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:35:34 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:35 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:35:35 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:35 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:35:35 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:35 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:35:35 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 488866016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 488866016; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:36 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:35:36 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:36 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:35:36 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:36 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:35:36 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:36 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:35:36 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:36 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:35:36 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:36 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:35:36 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:36 MarkDuplicates Before output close freeMemory: 758209616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:36 MarkDuplicates Before output close freeMemory: 758209616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:36 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:35:36 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:37 MarkDuplicates After output close freeMemory: 758349864; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:37 MarkDuplicates After output close freeMemory: 758349864; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. [Tue Jul 02 11:35:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:37 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:35:37 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.5801468268940644962.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.5801468268940644962.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.5801468268940644962.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.5801468268940644962.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.5801468268940644962.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.5801468268940644962.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:37.790 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:35:37.790 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:37.791 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:35:37.791 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:37.791 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:35:37.791 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:37.791 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:35:37.791 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:37 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.5801468268940644962.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.5801468268940644962.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.5801468268940644962.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:35:37 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.5801468268940644962.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.5801468268940644962.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.5801468268940644962.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:35:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:38 MarkDuplicates Start of doWork freeMemory: 1027839312; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:38 MarkDuplicates Start of doWork freeMemory: 1027839312; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:38 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:35:38 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:38 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:35:38 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:38 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:35:38 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 964917960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 964917960; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:35:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:40 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:35:40 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:35:40 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:40 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:35:40 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 488865408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 488865408; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:41 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:35:41 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:41 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:35:41 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:35:41 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:41 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:35:41 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:41 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:35:41 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:41 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:35:41 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:41 MarkDuplicates Before output close freeMemory: 758209008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:41 MarkDuplicates Before output close freeMemory: 758209008; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:41 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:35:41 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:42 MarkDuplicates After output close freeMemory: 758349256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:42 MarkDuplicates After output close freeMemory: 758349256; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:35:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:42 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:35:42 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.1970319334477044764.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.1970319334477044764.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.1970319334477044764.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.1970319334477044764.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.1970319334477044764.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.1970319334477044764.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:42.095 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:35:42.095 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:42.095 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:35:42.095 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:42.095 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:35:42.095 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:42.095 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:35:42.095 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:42 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.1970319334477044764.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.1970319334477044764.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.1970319334477044764.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:35:42 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.1970319334477044764.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.1970319334477044764.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.1970319334477044764.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:35:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:42 MarkDuplicates Start of doWork freeMemory: 1027838696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:42 MarkDuplicates Start of doWork freeMemory: 1027838696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:42 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:35:42 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:42 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:35:42 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:42 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:35:42 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 964917344; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 964917344; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:35:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:43 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:35:43 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:43 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:35:43 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:43 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:35:43 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 488864792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 488864792; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:44 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:35:44 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:44 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:35:44 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:44 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:35:44 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:44 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:35:44 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:44 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:35:44 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:44 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:35:44 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:45 MarkDuplicates Before output close freeMemory: 758208392; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:45 MarkDuplicates Before output close freeMemory: 758208392; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:45 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:35:45 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:45 MarkDuplicates After output close freeMemory: 758382344; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:45 MarkDuplicates After output close freeMemory: 758382344; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:35:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:45 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:35:45 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.9939956130855186807.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.9939956130855186807.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.9939956130855186807.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.9939956130855186807.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.9939956130855186807.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.9939956130855186807.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:45.548 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:35:45.548 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:45.548 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:35:45.548 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:45.548 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:35:45.548 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:45.548 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:35:45.548 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:45 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.9939956130855186807.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.9939956130855186807.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.9939956130855186807.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:35:45 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.9939956130855186807.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.9939956130855186807.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.9939956130855186807.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:35:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:45 MarkDuplicates Start of doWork freeMemory: 1027871776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:45 MarkDuplicates Start of doWork freeMemory: 1027871776; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:45 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:35:45 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:45 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:35:45 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:46 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:35:46 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 964950424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 964950424; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:35:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:47 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:35:47 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:47 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:35:47 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:47 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:35:47 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 488897872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 488897872; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:48 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:35:48 MarkDuplicates Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:48 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:35:48 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:35:48 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:48 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:35:48 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:48 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:35:48 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:48 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:35:48 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:48 MarkDuplicates Before output close freeMemory: 758241472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:48 MarkDuplicates Before output close freeMemory: 758241472; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:48 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:35:48 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:49 MarkDuplicates After output close freeMemory: 758381720; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:49 MarkDuplicates After output close freeMemory: 758381720; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:35:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:49 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testMappedFragmentAndMappedPairFirstOfPairNonPrimary STANDARD_ERROR INFO 2024-07-02 11:35:49 MarkDuplicates Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.902181302660625659.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.902181302660625659.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.902181302660625659.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.902181302660625659.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.902181302660625659.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.902181302660625659.tmp/output.sam Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:49.188 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:35:49.188 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:49.188 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:35:49.188 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:49.201 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:35:49.201 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:49.201 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:35:49.201 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:49 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.902181302660625659.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.902181302660625659.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.902181302660625659.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:35:49 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.902181302660625659.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.902181302660625659.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.902181302660625659.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:35:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:49 MarkDuplicates Start of doWork freeMemory: 1027877768; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:49 MarkDuplicates Start of doWork freeMemory: 1027877768; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:49 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:35:49 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:35:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:35:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:35:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:50 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:35:50 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 964957608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 964957608; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:51 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:35:51 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:53 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:35:53 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:53 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:35:53 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:53 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:35:53 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 531895992; totalMemory: 1116733440; maxMemory: 2147483648 INFO 2024-07-02 11:35:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 531895992; totalMemory: 1116733440; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:53 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:35:53 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:53 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:35:53 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:53 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:35:53 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:53 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:35:53 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:53 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:35:53 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:53 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:35:53 MarkDuplicates Getting Memory Stats. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:54 MarkDuplicates Before output close freeMemory: 758147400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:54 MarkDuplicates Before output close freeMemory: 758147400; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:54 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:35:54 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:54 MarkDuplicates After output close freeMemory: 758388296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:54 MarkDuplicates After output close freeMemory: 758388296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:54 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.09 minutes. [Tue Jul 02 11:35:54 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.09 minutes. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:54 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testMappedFragmentAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:35:54 MarkDuplicates Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.13020694754669756018.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.13020694754669756018.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.13020694754669756018.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.13020694754669756018.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.13020694754669756018.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.13020694754669756018.tmp/output.sam Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:54.653 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:35:54.653 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:54.657 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:35:54.657 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:54.657 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:35:54.657 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:54.657 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:35:54.657 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:54 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.13020694754669756018.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.13020694754669756018.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.13020694754669756018.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:35:54 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.13020694754669756018.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.13020694754669756018.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.13020694754669756018.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:35:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:55 MarkDuplicates Start of doWork freeMemory: 1027874096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:55 MarkDuplicates Start of doWork freeMemory: 1027874096; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:55 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:35:55 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:55 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:35:55 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:35:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:35:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:55 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2024-07-02 11:35:55 MarkDuplicates Read 3 records. 0 pairs never matched. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 964956616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 964956616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:35:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:56 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:35:56 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:56 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:35:56 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:56 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:35:56 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 488903456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 488903456; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:57 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:35:57 MarkDuplicates Marking 1 records as duplicates. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:57 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:35:57 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:57 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:35:57 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:57 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:35:57 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:57 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:35:57 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:57 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:35:57 MarkDuplicates Getting Memory Stats. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:57 MarkDuplicates Before output close freeMemory: 758247336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:57 MarkDuplicates Before output close freeMemory: 758247336; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:57 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:35:57 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:58 MarkDuplicates After output close freeMemory: 758387376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:58 MarkDuplicates After output close freeMemory: 758387376; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:35:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:58 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testMappedFragmentAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:35:58 MarkDuplicates Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.4249503652887152106.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.4249503652887152106.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.4249503652887152106.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.4249503652887152106.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.4249503652887152106.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.4249503652887152106.tmp/output.sam Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:58.163 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:35:58.163 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:58.163 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:35:58.163 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:58.163 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:35:58.163 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:35:58.163 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:35:58.163 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:58 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.4249503652887152106.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.4249503652887152106.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.4249503652887152106.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:35:58 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.4249503652887152106.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.4249503652887152106.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.4249503652887152106.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:35:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:35:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:58 MarkDuplicates Start of doWork freeMemory: 1027876328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:58 MarkDuplicates Start of doWork freeMemory: 1027876328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:58 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:35:58 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:58 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:35:58 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:35:58 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:35:58 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:58 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2024-07-02 11:35:58 MarkDuplicates Read 3 records. 0 pairs never matched. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 964956096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:35:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 964956096; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:59 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:35:59 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:59 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:35:59 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:59 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:35:59 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:35:59 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:35:59 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 488902936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 488902936; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:00 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:36:00 MarkDuplicates Marking 1 records as duplicates. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:00 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:36:00 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:00 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:36:00 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:00 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:36:00 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:00 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:36:00 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:00 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:36:00 MarkDuplicates Getting Memory Stats. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:00 MarkDuplicates Before output close freeMemory: 758246816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:00 MarkDuplicates Before output close freeMemory: 758246816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:00 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:36:00 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:01 MarkDuplicates After output close freeMemory: 758386784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:01 MarkDuplicates After output close freeMemory: 758386784; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:01 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:36:01 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:01 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testMappedPairAndMappedFragmentAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:36:01 MarkDuplicates Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.18426743279760126317.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.18426743279760126317.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.18426743279760126317.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.18426743279760126317.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.18426743279760126317.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.18426743279760126317.tmp/output.sam Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:01.103 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:01.103 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:01.104 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:01.104 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:01.104 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:01.104 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:01.104 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:01.104 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:01 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.18426743279760126317.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.18426743279760126317.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.18426743279760126317.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:36:01 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.18426743279760126317.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.18426743279760126317.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.18426743279760126317.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:36:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:01 MarkDuplicates Start of doWork freeMemory: 1027874304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:01 MarkDuplicates Start of doWork freeMemory: 1027874304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:01 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:36:01 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:01 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:36:01 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:36:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:36:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:01 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:36:01 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 964953744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 964953744; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:02 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:36:02 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:03 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:36:03 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:03 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:36:03 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:03 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:36:03 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 488900624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 488900624; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:03 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:36:03 MarkDuplicates Marking 2 records as duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:03 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:36:03 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:03 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:36:03 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:03 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:36:03 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:03 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:36:03 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:03 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:36:03 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:04 MarkDuplicates Before output close freeMemory: 758244288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:04 MarkDuplicates Before output close freeMemory: 758244288; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:04 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:36:04 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:04 MarkDuplicates After output close freeMemory: 758384472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:04 MarkDuplicates After output close freeMemory: 758384472; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:04 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:36:04 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:04 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testMappedPairAndMappedFragmentAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:36:04 MarkDuplicates Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.18414557179942128323.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.18414557179942128323.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.18414557179942128323.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.18414557179942128323.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.18414557179942128323.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.18414557179942128323.tmp/output.sam Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:04.571 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:04.571 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:04.571 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:04.571 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:04.571 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:04.571 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:04.571 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:04.571 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:04 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.18414557179942128323.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.18414557179942128323.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.18414557179942128323.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:36:04 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.18414557179942128323.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.18414557179942128323.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.18414557179942128323.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:36:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:04 MarkDuplicates Start of doWork freeMemory: 1027873488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:04 MarkDuplicates Start of doWork freeMemory: 1027873488; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:04 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:36:04 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:04 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:36:04 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:36:05 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:36:05 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:05 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:36:05 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 964952920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 964952920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:36:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:06 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:36:06 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:06 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:36:06 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:06 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:36:06 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 609486040; totalMemory: 1194328064; maxMemory: 2147483648 INFO 2024-07-02 11:36:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 609486040; totalMemory: 1194328064; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:06 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:36:06 MarkDuplicates Marking 2 records as duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:06 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:36:06 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:06 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:36:06 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:06 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:36:06 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:06 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:36:06 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:06 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:36:06 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:07 MarkDuplicates Before output close freeMemory: 758243464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:07 MarkDuplicates Before output close freeMemory: 758243464; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:07 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:36:07 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:07 MarkDuplicates After output close freeMemory: 758383648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:07 MarkDuplicates After output close freeMemory: 758383648; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:07 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:36:07 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:07 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:36:07 MarkDuplicates Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.11593185080538469220.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.11593185080538469220.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.11593185080538469220.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.11593185080538469220.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.11593185080538469220.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.11593185080538469220.tmp/output.sam Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:07.428 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:07.428 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:07.428 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:07.428 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:07.428 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:07.428 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:07.428 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:07.428 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:07 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.11593185080538469220.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.11593185080538469220.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.11593185080538469220.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:36:07 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.11593185080538469220.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.11593185080538469220.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.11593185080538469220.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:36:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:07 MarkDuplicates Start of doWork freeMemory: 1027873232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:07 MarkDuplicates Start of doWork freeMemory: 1027873232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:07 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:36:07 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:07 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:36:07 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:36:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:36:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:08 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:36:08 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 964952736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 964952736; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:36:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:09 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:36:09 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:09 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:36:09 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:09 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:36:09 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 488899544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 488899544; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:09 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:36:09 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:09 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:36:09 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:09 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:36:09 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:09 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:36:09 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:09 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:36:09 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:09 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:36:09 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:10 MarkDuplicates Before output close freeMemory: 758243160; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:10 MarkDuplicates Before output close freeMemory: 758243160; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:10 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:36:10 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:10 MarkDuplicates After output close freeMemory: 758383392; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:10 MarkDuplicates After output close freeMemory: 758383392; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:10 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:36:10 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:10 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testMappedPairAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:36:10 MarkDuplicates Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.17233994770037103465.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.17233994770037103465.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.17233994770037103465.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.17233994770037103465.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.17233994770037103465.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.17233994770037103465.tmp/output.sam Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:10.557 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:10.557 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:10.557 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:10.557 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:10.557 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:10.557 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:10.557 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:10.557 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:10 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.17233994770037103465.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.17233994770037103465.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.17233994770037103465.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:36:10 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.17233994770037103465.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.17233994770037103465.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.17233994770037103465.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:36:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:10 MarkDuplicates Start of doWork freeMemory: 1027872680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:10 MarkDuplicates Start of doWork freeMemory: 1027872680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:10 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:36:10 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:10 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:36:10 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:36:11 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:36:11 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:11 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:36:11 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 964952184; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 964952184; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:36:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:12 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:36:12 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:12 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:36:12 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:12 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:36:12 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 488898992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 488898992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:12 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:36:12 MarkDuplicates Marking 1 records as duplicates. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:12 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:36:12 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:12 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:36:12 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:12 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:36:12 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:12 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:36:12 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:12 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:36:12 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:13 MarkDuplicates Before output close freeMemory: 758241088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:13 MarkDuplicates Before output close freeMemory: 758241088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:13 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:36:13 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:13 MarkDuplicates After output close freeMemory: 758382912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:13 MarkDuplicates After output close freeMemory: 758382912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:13 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:36:13 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:13 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testMappedPairAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:36:13 MarkDuplicates Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.16988266411416306603.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.16988266411416306603.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.16988266411416306603.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.16988266411416306603.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.16988266411416306603.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.16988266411416306603.tmp/output.sam Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:13.577 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:13.577 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:13.589 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:13.589 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:13.589 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:13.589 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:13.590 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:13.590 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:13 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.16988266411416306603.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.16988266411416306603.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.16988266411416306603.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:36:13 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.16988266411416306603.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.16988266411416306603.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.16988266411416306603.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:36:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:13 MarkDuplicates Start of doWork freeMemory: 1027872008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:13 MarkDuplicates Start of doWork freeMemory: 1027872008; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:13 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:36:13 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:13 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:36:13 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:36:14 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:36:14 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:14 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:36:14 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 964951512; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 964951512; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:14 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:36:14 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:15 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:36:15 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:15 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:36:15 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:15 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:36:15 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 488898320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 488898320; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:15 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:36:15 MarkDuplicates Marking 1 records as duplicates. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:15 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:36:15 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:15 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:36:15 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:15 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:36:15 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:15 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:36:15 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:15 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:36:15 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:16 MarkDuplicates Before output close freeMemory: 758240416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:16 MarkDuplicates Before output close freeMemory: 758240416; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:16 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:36:16 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:16 MarkDuplicates After output close freeMemory: 758279648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:16 MarkDuplicates After output close freeMemory: 758279648; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:16 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:36:16 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:16 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testMappedPairWithFirstEndSamePositionAndOther STANDARD_ERROR INFO 2024-07-02 11:36:16 MarkDuplicates Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.15127283794829643572.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.15127283794829643572.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.15127283794829643572.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.15127283794829643572.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.15127283794829643572.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.15127283794829643572.tmp/output.sam Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:16.446 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:16.446 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:16.447 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:16.447 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:16.447 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:16.447 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:16.447 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:16.447 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:16 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.15127283794829643572.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.15127283794829643572.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.15127283794829643572.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:36:16 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.15127283794829643572.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.15127283794829643572.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.15127283794829643572.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:36:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:16 MarkDuplicates Start of doWork freeMemory: 1027871096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:16 MarkDuplicates Start of doWork freeMemory: 1027871096; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:16 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:36:16 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:16 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:36:16 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:36:16 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:36:16 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:16 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:36:16 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 964950456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 964950456; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:17 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:36:17 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:18 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:36:18 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:18 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:36:18 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:18 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:36:18 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 624163712; totalMemory: 1209008128; maxMemory: 2147483648 INFO 2024-07-02 11:36:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 624163712; totalMemory: 1209008128; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:18 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:36:18 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:18 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:36:18 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:18 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:36:18 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:18 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:36:18 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:18 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:36:18 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:18 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:36:18 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:18 MarkDuplicates Before output close freeMemory: 758241072; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:18 MarkDuplicates Before output close freeMemory: 758241072; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:18 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:36:18 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:18 MarkDuplicates After output close freeMemory: 758381256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:18 MarkDuplicates After output close freeMemory: 758381256; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:18 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:36:18 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:18 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testMappedPairWithSamePosition STANDARD_ERROR INFO 2024-07-02 11:36:18 MarkDuplicates Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.3039534029959813451.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.3039534029959813451.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.3039534029959813451.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.3039534029959813451.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.3039534029959813451.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.3039534029959813451.tmp/output.sam Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:18.951 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:18.951 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:18.951 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:18.951 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:18.952 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:18.952 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:18.952 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:18.952 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:18 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.3039534029959813451.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.3039534029959813451.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.3039534029959813451.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:36:18 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.3039534029959813451.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.3039534029959813451.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.3039534029959813451.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:36:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:19 MarkDuplicates Start of doWork freeMemory: 1027871760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:19 MarkDuplicates Start of doWork freeMemory: 1027871760; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:19 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:36:19 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:19 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:36:19 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:36:19 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:36:19 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:19 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:36:19 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 964951336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 964951336; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:19 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:36:19 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:20 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:36:20 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:20 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:36:20 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:20 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:36:20 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 488898072; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 488898072; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:20 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:36:20 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:20 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:36:20 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:20 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:36:20 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:20 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:36:20 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:20 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:36:20 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:20 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:36:20 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:21 MarkDuplicates Before output close freeMemory: 758241736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:21 MarkDuplicates Before output close freeMemory: 758241736; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:21 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:36:21 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:21 MarkDuplicates After output close freeMemory: 758381424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:21 MarkDuplicates After output close freeMemory: 758381424; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:21 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:36:21 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:21 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testMappedPairWithSamePositionSameCigar STANDARD_ERROR INFO 2024-07-02 11:36:21 MarkDuplicates Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.9051378537590194793.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.9051378537590194793.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.9051378537590194793.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.9051378537590194793.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.9051378537590194793.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.9051378537590194793.tmp/output.sam Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:21.374 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:21.374 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:21.375 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:21.375 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:21.375 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:21.375 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:21.375 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:21.375 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:21 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.9051378537590194793.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.9051378537590194793.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.9051378537590194793.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:36:21 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.9051378537590194793.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.9051378537590194793.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.9051378537590194793.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:36:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:21 MarkDuplicates Start of doWork freeMemory: 1027871048; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:21 MarkDuplicates Start of doWork freeMemory: 1027871048; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:21 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:36:21 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:21 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:36:21 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:36:21 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:36:21 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:21 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:36:21 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 964950624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 964950624; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:36:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:22 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:36:22 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:22 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:36:22 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:22 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:36:22 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 488897360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 488897360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:22 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:36:22 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:22 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:36:22 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:22 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:36:22 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:22 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:36:22 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:22 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:36:22 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:22 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:36:22 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:23 MarkDuplicates Before output close freeMemory: 758241024; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:23 MarkDuplicates Before output close freeMemory: 758241024; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:23 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:36:23 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:23 MarkDuplicates After output close freeMemory: 758381208; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:23 MarkDuplicates After output close freeMemory: 758381208; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:23 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:36:23 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:23 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:36:23 MarkDuplicates Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.7713715434122366086.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.7713715434122366086.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.7713715434122366086.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.7713715434122366086.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.7713715434122366086.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.7713715434122366086.tmp/output.sam Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:23.451 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:23.451 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:23.452 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:23.452 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:23.452 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:23.452 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:23.452 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:23.452 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:23 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.7713715434122366086.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.7713715434122366086.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.7713715434122366086.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:36:23 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.7713715434122366086.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.7713715434122366086.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.7713715434122366086.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:36:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:23 MarkDuplicates Start of doWork freeMemory: 1027870496; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:23 MarkDuplicates Start of doWork freeMemory: 1027870496; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:23 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:36:23 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:23 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:36:23 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:36:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:36:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:23 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:36:23 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 964950336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 964950336; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:24 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:36:24 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:24 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:36:24 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:24 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:36:24 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:24 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:36:24 MarkDuplicates Sorting list of duplicate records. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 488897104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 488897104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:25 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:36:25 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:25 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:36:25 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:25 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:36:25 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:25 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:36:25 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:25 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:36:25 MarkDuplicates Duplicate Index cleanup. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:25 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:36:25 MarkDuplicates Getting Memory Stats. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:25 MarkDuplicates Before output close freeMemory: 758239312; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:25 MarkDuplicates Before output close freeMemory: 758239312; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:25 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:36:25 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:25 MarkDuplicates After output close freeMemory: 758380528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:25 MarkDuplicates After output close freeMemory: 758380528; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:25 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:36:25 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:25 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:36:25 MarkDuplicates Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.6078051230824367143.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.6078051230824367143.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.6078051230824367143.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.6078051230824367143.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.6078051230824367143.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.6078051230824367143.tmp/output.sam Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:25.747 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:25.747 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:25.747 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:25.747 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:25.747 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:25.747 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:25.747 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:25.747 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:25 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.6078051230824367143.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.6078051230824367143.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.6078051230824367143.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:36:25 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.6078051230824367143.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.6078051230824367143.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.6078051230824367143.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:36:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:25 MarkDuplicates Start of doWork freeMemory: 1027869896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:25 MarkDuplicates Start of doWork freeMemory: 1027869896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:25 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:36:25 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:25 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:36:25 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:36:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:36:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:26 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:36:26 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 964949736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 964949736; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:36:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:36:27 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:36:27 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:27 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:36:27 MarkDuplicates Sorting list of duplicate records. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 673445880; totalMemory: 1258291200; maxMemory: 2147483648 INFO 2024-07-02 11:36:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 673445880; totalMemory: 1258291200; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:27 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:36:27 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:27 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:36:27 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:27 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:36:27 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:27 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:36:27 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:27 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:36:27 MarkDuplicates Duplicate Index cleanup. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:27 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:36:27 MarkDuplicates Getting Memory Stats. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:27 MarkDuplicates Before output close freeMemory: 758238840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:27 MarkDuplicates Before output close freeMemory: 758238840; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:27 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:36:27 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:28 MarkDuplicates After output close freeMemory: 758378320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:28 MarkDuplicates After output close freeMemory: 758378320; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:28 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:36:28 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:28 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testOpticalDuplicateBehaviorNullRegex STANDARD_ERROR INFO 2024-07-02 11:36:28 MarkDuplicates Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.2532777617166004862.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_NAME_REGEX null -INPUT /tmp/MarkDuplicatesTester.2532777617166004862.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.2532777617166004862.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.2532777617166004862.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -READ_NAME_REGEX null -INPUT /tmp/MarkDuplicatesTester.2532777617166004862.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.2532777617166004862.tmp/output.sam Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:28.117 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:28.117 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:28.118 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:28.118 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:28.118 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:28.118 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:28.118 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:28.118 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:28 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.2532777617166004862.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.2532777617166004862.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.2532777617166004862.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH READ_NAME_REGEX=null MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:36:28 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.2532777617166004862.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.2532777617166004862.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.2532777617166004862.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH READ_NAME_REGEX=null MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:36:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:28 MarkDuplicates Start of doWork freeMemory: 1027867880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:28 MarkDuplicates Start of doWork freeMemory: 1027867880; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:28 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:36:28 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:28 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:36:28 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:28 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:36:28 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 964947240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 964947240; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:36:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:29 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:36:29 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:29 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:36:29 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:29 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:36:29 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 488894368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 488894368; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:29 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:36:29 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:36:29 MarkDuplicates Skipped optical duplicate cluster discovery; library size estimation may be inaccurate! WARNING 2024-07-02 11:36:29 MarkDuplicates Skipped optical duplicate cluster discovery; library size estimation may be inaccurate! Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:29 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:36:29 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:29 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:36:29 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:29 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:36:29 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:29 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:36:29 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:29 MarkDuplicates Before output close freeMemory: 758238048; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:29 MarkDuplicates Before output close freeMemory: 758238048; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:29 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:36:29 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:30 MarkDuplicates After output close freeMemory: 758378232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:30 MarkDuplicates After output close freeMemory: 758378232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:30 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:36:30 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:30 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testOpticalDuplicateClusterOneEndSamePositionOneCluster STANDARD_ERROR INFO 2024-07-02 11:36:30 MarkDuplicates Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.18082355168245111192.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.18082355168245111192.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.18082355168245111192.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.18082355168245111192.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.18082355168245111192.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.18082355168245111192.tmp/output.sam Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:30.259 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:30.259 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:30.259 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:30.259 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:30.260 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:30.260 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:30.260 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:30.260 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:30 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.18082355168245111192.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.18082355168245111192.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.18082355168245111192.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:36:30 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.18082355168245111192.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.18082355168245111192.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.18082355168245111192.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:36:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:30 MarkDuplicates Start of doWork freeMemory: 1027866816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:30 MarkDuplicates Start of doWork freeMemory: 1027866816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:30 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:36:30 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:30 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:36:30 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:30 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:36:30 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 964946112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 964946112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:36:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:31 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:36:31 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:31 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:36:31 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:31 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:36:31 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 488892912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 488892912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:31 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:36:31 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:31 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:36:31 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:32 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:36:32 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:32 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:36:32 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:32 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:36:32 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:32 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:36:32 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:32 MarkDuplicates Before output close freeMemory: 758236488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:32 MarkDuplicates Before output close freeMemory: 758236488; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:32 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:36:32 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:32 MarkDuplicates After output close freeMemory: 758376264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:32 MarkDuplicates After output close freeMemory: 758376264; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:36:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:32 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:36:32 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.11657894083968355249.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.11657894083968355249.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.11657894083968355249.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.11657894083968355249.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.11657894083968355249.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.11657894083968355249.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:32.603 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:32.603 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:32.603 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:32.603 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:32.603 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:32.603 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:32.603 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:32.603 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:32 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.11657894083968355249.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.11657894083968355249.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.11657894083968355249.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:36:32 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.11657894083968355249.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.11657894083968355249.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.11657894083968355249.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:36:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:32 MarkDuplicates Start of doWork freeMemory: 1027865320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:32 MarkDuplicates Start of doWork freeMemory: 1027865320; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:32 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:36:32 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:32 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:36:32 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:33 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:36:33 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 964944616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 964944616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:36:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:36:33 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:36:33 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:33 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:36:33 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 488891568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 488891568; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:34 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:36:34 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:34 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:36:34 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:34 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:36:34 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:34 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:36:34 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:34 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:36:34 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:34 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:36:34 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:34 MarkDuplicates Before output close freeMemory: 758132888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:34 MarkDuplicates Before output close freeMemory: 758132888; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:34 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:36:34 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:34 MarkDuplicates After output close freeMemory: 758274280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:34 MarkDuplicates After output close freeMemory: 758274280; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:36:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:34 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:36:34 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.8947744818972493055.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.8947744818972493055.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.8947744818972493055.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.8947744818972493055.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.8947744818972493055.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.8947744818972493055.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:34.722 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:34.722 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:34.722 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:34.722 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:34.723 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:34.723 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:34.723 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:34.723 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:34 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.8947744818972493055.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.8947744818972493055.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.8947744818972493055.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:36:34 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.8947744818972493055.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.8947744818972493055.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.8947744818972493055.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:36:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:34 MarkDuplicates Start of doWork freeMemory: 1027864664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:34 MarkDuplicates Start of doWork freeMemory: 1027864664; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:34 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:36:34 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:34 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:36:34 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:35 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:36:35 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 964943960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 964943960; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:36:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:36 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:36:36 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:36 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:36:36 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:36 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:36:36 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 703848992; totalMemory: 1288699904; maxMemory: 2147483648 INFO 2024-07-02 11:36:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 703848992; totalMemory: 1288699904; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:36 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:36:36 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:36 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:36:36 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:36 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:36:36 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:36 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:36:36 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:36 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:36:36 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:36 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:36:36 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:36 MarkDuplicates Before output close freeMemory: 758232944; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:36 MarkDuplicates Before output close freeMemory: 758232944; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:36 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:36:36 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:36 MarkDuplicates After output close freeMemory: 758372696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:36 MarkDuplicates After output close freeMemory: 758372696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:36 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:36:36 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:36 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:36:36 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.1115310772440965090.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.1115310772440965090.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.1115310772440965090.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.1115310772440965090.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.1115310772440965090.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.1115310772440965090.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:36.998 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:36.998 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:36.998 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:36.998 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:36.998 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:36.998 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:36.998 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:36.998 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:36 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.1115310772440965090.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.1115310772440965090.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.1115310772440965090.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:36:36 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.1115310772440965090.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.1115310772440965090.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.1115310772440965090.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:36:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:37 MarkDuplicates Start of doWork freeMemory: 1027864056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:37 MarkDuplicates Start of doWork freeMemory: 1027864056; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:37 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:36:37 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:37 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:36:37 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:37 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:36:37 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 964943352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 964943352; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:36:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:38 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:36:38 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:38 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:36:38 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:38 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:36:38 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 488890304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 488890304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:38 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:36:38 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:38 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:36:38 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:38 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:36:38 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:38 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:36:38 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:38 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:36:38 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:38 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:36:38 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:38 MarkDuplicates Before output close freeMemory: 758233904; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:38 MarkDuplicates Before output close freeMemory: 758233904; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:38 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:36:38 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:39 MarkDuplicates After output close freeMemory: 758374152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:39 MarkDuplicates After output close freeMemory: 758374152; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:36:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:39 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:36:39 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.1168408201260513932.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.1168408201260513932.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.1168408201260513932.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.1168408201260513932.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.1168408201260513932.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.1168408201260513932.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:39.206 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:39.206 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:39.206 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:39.206 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:39.206 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:39.206 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:39.206 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:39.206 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:39 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.1168408201260513932.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.1168408201260513932.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.1168408201260513932.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:36:39 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.1168408201260513932.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.1168408201260513932.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.1168408201260513932.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:36:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:39 MarkDuplicates Start of doWork freeMemory: 1027863448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:39 MarkDuplicates Start of doWork freeMemory: 1027863448; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:39 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:36:39 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:39 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:36:39 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:39 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:36:39 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 964942744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 964942744; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:36:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:40 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:36:40 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:36:40 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:40 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:36:40 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 488889696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 488889696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:41 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:36:41 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:41 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:36:41 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:36:41 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:41 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:36:41 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:41 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:36:41 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:41 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:36:41 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:41 MarkDuplicates Before output close freeMemory: 758233296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:41 MarkDuplicates Before output close freeMemory: 758233296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:41 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:36:41 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:41 MarkDuplicates After output close freeMemory: 758373544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:41 MarkDuplicates After output close freeMemory: 758373544; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:41 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:36:41 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:41 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:36:41 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.7619799642549134993.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.7619799642549134993.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.7619799642549134993.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.7619799642549134993.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.7619799642549134993.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.7619799642549134993.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:41.703 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:41.703 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:41.703 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:41.703 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:41.703 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:41.703 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:41.703 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:41.703 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:41 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.7619799642549134993.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.7619799642549134993.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.7619799642549134993.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:36:41 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.7619799642549134993.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.7619799642549134993.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.7619799642549134993.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:36:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:41 MarkDuplicates Start of doWork freeMemory: 1027862840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:41 MarkDuplicates Start of doWork freeMemory: 1027862840; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:41 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:36:41 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:41 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:36:41 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:42 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:36:42 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 964942136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 964942136; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:36:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:43 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:36:43 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:43 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:36:43 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:43 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:36:43 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 488889088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 488889088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:43 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:36:43 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:43 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:36:43 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:43 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:36:43 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:43 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:36:43 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:43 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:36:43 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:43 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:36:43 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:43 MarkDuplicates Before output close freeMemory: 758232688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:43 MarkDuplicates Before output close freeMemory: 758232688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:43 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:36:43 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:44 MarkDuplicates After output close freeMemory: 758372936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:44 MarkDuplicates After output close freeMemory: 758372936; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:44 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:36:44 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:44 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:36:44 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.12242783238493697686.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.12242783238493697686.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.12242783238493697686.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.12242783238493697686.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.12242783238493697686.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.12242783238493697686.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:44.107 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:44.107 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:44.107 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:44.107 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:44.107 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:44.107 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:44.107 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:44.107 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:44 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.12242783238493697686.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.12242783238493697686.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.12242783238493697686.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:36:44 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.12242783238493697686.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.12242783238493697686.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.12242783238493697686.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:36:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:44 MarkDuplicates Start of doWork freeMemory: 1027862232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:44 MarkDuplicates Start of doWork freeMemory: 1027862232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:44 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:36:44 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:44 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:36:44 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:44 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:36:44 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 964941528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 964941528; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:36:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:45 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:36:45 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:45 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:36:45 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:45 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:36:45 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 703880264; totalMemory: 1288699904; maxMemory: 2147483648 INFO 2024-07-02 11:36:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 703880264; totalMemory: 1288699904; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:46 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:36:46 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:46 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:36:46 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:46 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:36:46 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:46 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:36:46 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:46 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:36:46 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:46 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:36:46 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:46 MarkDuplicates Before output close freeMemory: 758264216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:46 MarkDuplicates Before output close freeMemory: 758264216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:46 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:36:46 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:46 MarkDuplicates After output close freeMemory: 758405608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:46 MarkDuplicates After output close freeMemory: 758405608; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:36:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:46 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:36:46 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.10732451888187380583.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.10732451888187380583.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.10732451888187380583.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.10732451888187380583.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.10732451888187380583.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.10732451888187380583.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:46.823 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:46.823 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:46.823 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:46.823 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:46.823 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:46.823 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:46.823 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:46.823 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:46 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.10732451888187380583.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.10732451888187380583.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.10732451888187380583.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:36:46 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.10732451888187380583.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.10732451888187380583.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.10732451888187380583.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:36:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:47 MarkDuplicates Start of doWork freeMemory: 1027895328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:47 MarkDuplicates Start of doWork freeMemory: 1027895328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:47 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:36:47 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:47 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:36:47 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:47 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:36:47 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 964974624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 964974624; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:36:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:47 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:36:47 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:47 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:36:47 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:47 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:36:47 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 488921576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 488921576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:48 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:36:48 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:48 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:36:48 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:36:48 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:48 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:36:48 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:48 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:36:48 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:48 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:36:48 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:48 MarkDuplicates Before output close freeMemory: 758264544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:48 MarkDuplicates Before output close freeMemory: 758264544; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:48 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:36:48 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:48 MarkDuplicates After output close freeMemory: 758405000; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:48 MarkDuplicates After output close freeMemory: 758405000; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:48 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:36:48 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:48 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:36:48 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.12718776502403280784.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.12718776502403280784.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.12718776502403280784.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.12718776502403280784.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.12718776502403280784.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.12718776502403280784.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:48.957 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:48.957 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:48.957 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:48.957 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:48.957 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:48.957 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:48.957 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:48.957 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:48 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.12718776502403280784.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.12718776502403280784.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.12718776502403280784.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:36:48 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.12718776502403280784.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.12718776502403280784.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.12718776502403280784.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:36:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:49 MarkDuplicates Start of doWork freeMemory: 1027894720; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:49 MarkDuplicates Start of doWork freeMemory: 1027894720; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:49 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:36:49 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:36:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:49 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:36:49 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 964974024; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 964974024; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:49 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:36:49 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:50 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:36:50 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:50 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:36:50 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:50 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:36:50 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 488920280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:50 MarkDuplicates After generateDuplicateIndexes freeMemory: 488920280; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:50 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:36:50 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:50 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:36:50 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:50 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:36:50 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:50 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:36:50 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:50 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:36:50 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:50 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:36:50 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:50 MarkDuplicates Before output close freeMemory: 758264576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:50 MarkDuplicates Before output close freeMemory: 758264576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:50 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:36:50 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:51 MarkDuplicates After output close freeMemory: 758404328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:51 MarkDuplicates After output close freeMemory: 758404328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:36:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:51 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:36:51 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.8326260160804655723.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.8326260160804655723.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.8326260160804655723.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.8326260160804655723.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.8326260160804655723.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.8326260160804655723.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:51.238 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:51.238 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:51.238 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:51.238 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:51.238 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:51.238 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:51.238 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:51.238 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:51 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.8326260160804655723.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.8326260160804655723.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.8326260160804655723.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:36:51 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.8326260160804655723.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.8326260160804655723.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.8326260160804655723.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:36:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:51 MarkDuplicates Start of doWork freeMemory: 1027894120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:51 MarkDuplicates Start of doWork freeMemory: 1027894120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:51 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:36:51 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:51 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:36:51 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:51 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:36:51 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 964973416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 964973416; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:36:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:52 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:36:52 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:52 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:36:52 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:52 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:36:52 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:52 MarkDuplicates After generateDuplicateIndexes freeMemory: 488920368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:52 MarkDuplicates After generateDuplicateIndexes freeMemory: 488920368; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:52 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:36:52 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:52 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:36:52 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:52 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:36:52 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:52 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:36:52 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:52 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:36:52 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:52 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:36:52 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:53 MarkDuplicates Before output close freeMemory: 758263968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:53 MarkDuplicates Before output close freeMemory: 758263968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:53 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:36:53 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:53 MarkDuplicates After output close freeMemory: 758404288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:53 MarkDuplicates After output close freeMemory: 758404288; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:36:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:53 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:36:53 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.3378728163046923817.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.3378728163046923817.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.3378728163046923817.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.3378728163046923817.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.3378728163046923817.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.3378728163046923817.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:53.755 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:53.755 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:53.755 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:53.755 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:53.755 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:53.755 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:53.755 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:53.755 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:53 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.3378728163046923817.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.3378728163046923817.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.3378728163046923817.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:36:53 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.3378728163046923817.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.3378728163046923817.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.3378728163046923817.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:36:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:54 MarkDuplicates Start of doWork freeMemory: 1027893512; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:54 MarkDuplicates Start of doWork freeMemory: 1027893512; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:54 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:36:54 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:54 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:36:54 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:54 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:36:54 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 964972808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:54 MarkDuplicates After buildSortedReadEndLists freeMemory: 964972808; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:36:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:36:55 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:55 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:36:55 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:55 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:36:55 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 688149200; totalMemory: 1272971264; maxMemory: 2147483648 INFO 2024-07-02 11:36:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 688149200; totalMemory: 1272971264; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:56 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:36:56 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:56 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:36:56 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:56 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:36:56 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:56 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:36:56 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:56 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:36:56 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:56 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:36:56 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:56 MarkDuplicates Before output close freeMemory: 758263360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:56 MarkDuplicates Before output close freeMemory: 758263360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:56 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:36:56 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:56 MarkDuplicates After output close freeMemory: 758403680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:56 MarkDuplicates After output close freeMemory: 758403680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:56 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:36:56 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:56 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756) STANDARD_ERROR INFO 2024-07-02 11:36:56 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.15232840377206479593.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.15232840377206479593.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.15232840377206479593.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.15232840377206479593.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.15232840377206479593.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.15232840377206479593.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:56.739 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:56.739 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:56.739 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:56.739 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:56.739 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:56.739 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:56.739 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:56.739 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:56 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.15232840377206479593.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.15232840377206479593.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.15232840377206479593.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:36:56 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.15232840377206479593.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.15232840377206479593.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.15232840377206479593.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:36:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:57 MarkDuplicates Start of doWork freeMemory: 1027892904; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:57 MarkDuplicates Start of doWork freeMemory: 1027892904; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:57 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:36:57 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:57 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:36:57 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:57 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:36:57 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 964972200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 964972200; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:36:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:58 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:36:58 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:58 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:36:58 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:58 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:36:58 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 488919152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 488919152; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:59 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:36:59 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:59 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:36:59 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:59 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:36:59 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:59 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:36:59 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:59 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:36:59 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:59 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:36:59 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:59 MarkDuplicates Before output close freeMemory: 758262752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:59 MarkDuplicates Before output close freeMemory: 758262752; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:59 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:36:59 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:59 MarkDuplicates After output close freeMemory: 758403000; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:36:59 MarkDuplicates After output close freeMemory: 758403000; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:59 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:36:59 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:36:59 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756) STANDARD_ERROR INFO 2024-07-02 11:36:59 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.5707907609016631909.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.5707907609016631909.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.5707907609016631909.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.5707907609016631909.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.5707907609016631909.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.5707907609016631909.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:59.947 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:59.947 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:59.947 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:59.947 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:59.947 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:36:59.947 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:36:59.947 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:36:59.947 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:59 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.5707907609016631909.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.5707907609016631909.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.5707907609016631909.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:36:59 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.5707907609016631909.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.5707907609016631909.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.5707907609016631909.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:36:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:36:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:00 MarkDuplicates Start of doWork freeMemory: 1027892272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:00 MarkDuplicates Start of doWork freeMemory: 1027892272; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:00 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:37:00 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:00 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:37:00 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:00 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:37:00 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 964971568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 964971568; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:37:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:01 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:37:01 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:01 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:37:01 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:01 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:37:01 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 488918520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 488918520; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:02 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:37:02 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:02 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:37:02 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:02 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:37:02 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:02 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:37:02 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:02 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:37:02 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:02 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:37:02 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:02 MarkDuplicates Before output close freeMemory: 758262120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:02 MarkDuplicates Before output close freeMemory: 758262120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:02 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:37:02 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:03 MarkDuplicates After output close freeMemory: 758402368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:03 MarkDuplicates After output close freeMemory: 758402368; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:03 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:37:03 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:03 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756) STANDARD_ERROR INFO 2024-07-02 11:37:03 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.17557557050978554454.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.17557557050978554454.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.17557557050978554454.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.17557557050978554454.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.17557557050978554454.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.17557557050978554454.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:03.143 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:03.143 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:03.143 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:03.143 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:03.144 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:03.144 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:03.144 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:03.144 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:03 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.17557557050978554454.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.17557557050978554454.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.17557557050978554454.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:37:03 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.17557557050978554454.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.17557557050978554454.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.17557557050978554454.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:37:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:03 MarkDuplicates Start of doWork freeMemory: 1027886376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:03 MarkDuplicates Start of doWork freeMemory: 1027886376; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:03 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:37:03 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:03 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:37:03 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:03 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:37:03 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 964970960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 964970960; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:04 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:37:04 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:05 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:37:05 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:05 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:37:05 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:05 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:37:05 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 488917912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 488917912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:05 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:37:05 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:05 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:37:05 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:05 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:37:05 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:05 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:37:05 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:05 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:37:05 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:05 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:37:05 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:06 MarkDuplicates Before output close freeMemory: 758261512; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:06 MarkDuplicates Before output close freeMemory: 758261512; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:06 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:37:06 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:06 MarkDuplicates After output close freeMemory: 758401760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:06 MarkDuplicates After output close freeMemory: 758401760; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:06 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:37:06 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:06 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756) STANDARD_ERROR INFO 2024-07-02 11:37:06 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.5864756659437312222.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.5864756659437312222.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.5864756659437312222.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.5864756659437312222.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.5864756659437312222.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.5864756659437312222.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:06.636 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:06.636 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:06.636 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:06.636 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:06.636 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:06.636 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:06.636 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:06.636 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:06 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.5864756659437312222.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.5864756659437312222.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.5864756659437312222.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:37:06 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.5864756659437312222.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.5864756659437312222.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.5864756659437312222.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:37:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:07 MarkDuplicates Start of doWork freeMemory: 1027891056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:07 MarkDuplicates Start of doWork freeMemory: 1027891056; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:07 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:37:07 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:07 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:37:07 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:07 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:37:07 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 964970352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 964970352; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:37:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:09 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:37:09 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:09 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:37:09 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:09 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:37:09 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 682903864; totalMemory: 1267728384; maxMemory: 2147483648 INFO 2024-07-02 11:37:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 682903864; totalMemory: 1267728384; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:09 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:37:09 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:09 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:37:09 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:09 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:37:09 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:09 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:37:09 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:09 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:37:09 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:09 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:37:09 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:09 MarkDuplicates Before output close freeMemory: 758260048; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:09 MarkDuplicates Before output close freeMemory: 758260048; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:09 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:37:09 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:10 MarkDuplicates After output close freeMemory: 758400728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:10 MarkDuplicates After output close freeMemory: 758400728; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:10 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:37:10 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:10 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance STANDARD_ERROR INFO 2024-07-02 11:37:10 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.11866461337391034218.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.11866461337391034218.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.11866461337391034218.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.11866461337391034218.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.11866461337391034218.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.11866461337391034218.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:10.352 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:10.352 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:10.352 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:10.352 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:10.352 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:10.352 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:10.352 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:10.352 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:10 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.11866461337391034218.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.11866461337391034218.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.11866461337391034218.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:37:10 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.11866461337391034218.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.11866461337391034218.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.11866461337391034218.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:37:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:10 MarkDuplicates Start of doWork freeMemory: 1027888848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:10 MarkDuplicates Start of doWork freeMemory: 1027888848; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:10 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:37:10 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:10 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:37:10 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:10 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:37:10 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 964969776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 964969776; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:37:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:12 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:37:12 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:12 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:37:12 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:12 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:37:12 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 488916728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 488916728; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:12 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:37:12 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:12 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:37:12 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:12 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:37:12 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:12 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:37:12 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:12 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:37:12 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:12 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:37:12 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:13 MarkDuplicates Before output close freeMemory: 758260328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:13 MarkDuplicates Before output close freeMemory: 758260328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:13 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:37:13 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:13 MarkDuplicates After output close freeMemory: 758400648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:13 MarkDuplicates After output close freeMemory: 758400648; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:13 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:37:13 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:13 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance STANDARD_ERROR INFO 2024-07-02 11:37:13 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.18390052139488118381.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.18390052139488118381.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.18390052139488118381.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.18390052139488118381.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.18390052139488118381.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.18390052139488118381.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:13.712 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:13.712 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:13.712 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:13.712 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:13.712 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:13.712 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:13.713 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:13.713 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:13 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.18390052139488118381.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.18390052139488118381.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.18390052139488118381.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:37:13 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.18390052139488118381.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.18390052139488118381.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.18390052139488118381.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:37:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:14 MarkDuplicates Start of doWork freeMemory: 1027890280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:14 MarkDuplicates Start of doWork freeMemory: 1027890280; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:14 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:37:14 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:14 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:37:14 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:14 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:37:14 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 964969576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 964969576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:15 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:37:15 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:15 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:37:15 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:15 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:37:15 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:15 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:37:15 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 488915680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 488915680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:15 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:37:15 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:15 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:37:15 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:15 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:37:15 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:15 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:37:15 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:15 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:37:15 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:15 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:37:15 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:16 MarkDuplicates Before output close freeMemory: 758260088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:16 MarkDuplicates Before output close freeMemory: 758260088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:16 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:37:16 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:16 MarkDuplicates After output close freeMemory: 758400224; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:16 MarkDuplicates After output close freeMemory: 758400224; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:16 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:37:16 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:16 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate STANDARD_ERROR INFO 2024-07-02 11:37:16 MarkDuplicates Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.1996951270952531248.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.1996951270952531248.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.1996951270952531248.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.1996951270952531248.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.1996951270952531248.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.1996951270952531248.tmp/output.sam Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:16.611 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:16.611 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:16.611 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:16.611 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:16.611 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:16.611 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:16.611 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:16.611 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:16 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.1996951270952531248.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.1996951270952531248.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.1996951270952531248.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:37:16 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.1996951270952531248.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.1996951270952531248.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.1996951270952531248.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:37:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:16 MarkDuplicates Start of doWork freeMemory: 1027785912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:16 MarkDuplicates Start of doWork freeMemory: 1027785912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:16 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:37:16 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:16 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:37:16 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:17 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:37:17 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 964968680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 964968680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:17 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:37:17 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:18 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:37:18 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:18 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:37:18 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:18 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:37:18 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 488915480; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 488915480; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:18 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:37:18 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:18 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:37:18 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:18 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:37:18 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:18 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:37:18 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:18 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:37:18 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:18 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:37:18 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:19 MarkDuplicates Before output close freeMemory: 758259120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:19 MarkDuplicates Before output close freeMemory: 758259120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:19 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:37:19 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:19 MarkDuplicates After output close freeMemory: 758399328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:19 MarkDuplicates After output close freeMemory: 758399328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:19 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:37:19 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:19 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testOpticalDuplicateFinding STANDARD_ERROR INFO 2024-07-02 11:37:19 MarkDuplicates Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.17865477777824905085.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.17865477777824905085.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.17865477777824905085.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.17865477777824905085.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.17865477777824905085.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.17865477777824905085.tmp/output.sam Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:19.740 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:19.740 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:19.740 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:19.740 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:19.740 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:19.740 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:19.740 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:19.740 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:19 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.17865477777824905085.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.17865477777824905085.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.17865477777824905085.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:37:19 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.17865477777824905085.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.17865477777824905085.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.17865477777824905085.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:37:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:20 MarkDuplicates Start of doWork freeMemory: 1027882416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:20 MarkDuplicates Start of doWork freeMemory: 1027882416; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:20 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:37:20 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:20 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:37:20 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:20 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:37:20 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 964966792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 964966792; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:21 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:37:21 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:21 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:37:21 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:21 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:37:21 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:21 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:37:21 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 657733848; totalMemory: 1242562560; maxMemory: 2147483648 INFO 2024-07-02 11:37:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 657733848; totalMemory: 1242562560; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:21 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:37:21 MarkDuplicates Marking 4 records as duplicates. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:21 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:37:21 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:21 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:37:21 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:21 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:37:21 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:21 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:37:21 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:21 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:37:21 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:22 MarkDuplicates Before output close freeMemory: 758256656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:22 MarkDuplicates Before output close freeMemory: 758256656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:22 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:37:22 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:22 MarkDuplicates After output close freeMemory: 758397656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:22 MarkDuplicates After output close freeMemory: 758397656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:22 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:37:22 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:22 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testPathologicalOrderingAtTheSamePosition STANDARD_ERROR INFO 2024-07-02 11:37:22 MarkDuplicates Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.15373062153549439831.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.15373062153549439831.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.15373062153549439831.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.15373062153549439831.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.15373062153549439831.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.15373062153549439831.tmp/output.sam Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:22.654 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:22.654 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:22.655 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:22.655 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:22.655 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:22.655 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:22.655 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:22.655 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:22 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.15373062153549439831.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.15373062153549439831.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.15373062153549439831.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:37:22 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.15373062153549439831.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.15373062153549439831.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.15373062153549439831.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:37:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:23 MarkDuplicates Start of doWork freeMemory: 1027885784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:23 MarkDuplicates Start of doWork freeMemory: 1027885784; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:23 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:37:23 MarkDuplicates Reading input file and constructing read end information. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:23 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:37:23 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:23 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:37:23 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 964967272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 964967272; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:37:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:24 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:37:24 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:24 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:37:24 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:24 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:37:24 MarkDuplicates Sorting list of duplicate records. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 488914072; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 488914072; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:24 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:37:24 MarkDuplicates Marking 2 records as duplicates. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:24 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:37:24 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:24 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:37:24 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:24 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:37:24 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:24 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:37:24 MarkDuplicates Duplicate Index cleanup. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:24 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:37:24 MarkDuplicates Getting Memory Stats. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:24 MarkDuplicates Before output close freeMemory: 758257736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:24 MarkDuplicates Before output close freeMemory: 758257736; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:24 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:37:24 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:25 MarkDuplicates After output close freeMemory: 758296712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:25 MarkDuplicates After output close freeMemory: 758296712; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:25 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:37:25 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:25 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testSecondEndIsBeforeFirstInCoordinate STANDARD_ERROR INFO 2024-07-02 11:37:25 MarkDuplicates Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.14650670821024919334.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.14650670821024919334.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.14650670821024919334.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.14650670821024919334.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.14650670821024919334.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.14650670821024919334.tmp/output.sam Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:25.325 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:25.325 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:25.326 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:25.326 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:25.326 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:25.326 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:25.326 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:25.326 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:25 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.14650670821024919334.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.14650670821024919334.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.14650670821024919334.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:37:25 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.14650670821024919334.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.14650670821024919334.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.14650670821024919334.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:37:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:25 MarkDuplicates Start of doWork freeMemory: 1027888536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:25 MarkDuplicates Start of doWork freeMemory: 1027888536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:25 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:37:25 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:25 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:37:25 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:37:25 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:37:25 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:25 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:37:25 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 964968112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 964968112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:37:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:37:27 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:37:27 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:27 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:37:27 MarkDuplicates Sorting list of duplicate records. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 488914848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 488914848; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:27 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:37:27 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:27 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:37:27 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:27 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:37:27 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:27 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:37:27 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:27 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:37:27 MarkDuplicates Duplicate Index cleanup. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:27 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:37:27 MarkDuplicates Getting Memory Stats. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:27 MarkDuplicates Before output close freeMemory: 758258528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:27 MarkDuplicates Before output close freeMemory: 758258528; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:27 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:37:27 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:28 MarkDuplicates After output close freeMemory: 758398696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:28 MarkDuplicates After output close freeMemory: 758398696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:28 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:37:28 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:28 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testSingleMappedFragment STANDARD_ERROR INFO 2024-07-02 11:37:28 MarkDuplicates Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.6610910138948294362.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.6610910138948294362.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.6610910138948294362.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.6610910138948294362.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.6610910138948294362.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.6610910138948294362.tmp/output.sam Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:28.286 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:28.286 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:28.286 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:28.286 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:28.286 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:28.286 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:28.286 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:28.286 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:28 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.6610910138948294362.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.6610910138948294362.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.6610910138948294362.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:37:28 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.6610910138948294362.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.6610910138948294362.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.6610910138948294362.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:37:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:28 MarkDuplicates Start of doWork freeMemory: 1027881744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:28 MarkDuplicates Start of doWork freeMemory: 1027881744; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:28 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:37:28 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:28 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:37:28 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:37:28 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:37:28 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:28 MarkDuplicates Read 1 records. 0 pairs never matched. INFO 2024-07-02 11:37:28 MarkDuplicates Read 1 records. 0 pairs never matched. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 964964336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 964964336; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:37:29 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:30 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:37:30 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:30 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:37:30 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:30 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:37:30 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 488911104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 488911104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:30 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:37:30 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:30 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:37:30 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:30 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:37:30 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:30 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:37:30 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:30 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:37:30 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:30 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:37:30 MarkDuplicates Getting Memory Stats. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:30 MarkDuplicates Before output close freeMemory: 758152656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:30 MarkDuplicates Before output close freeMemory: 758152656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:30 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:37:30 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:31 MarkDuplicates After output close freeMemory: 758394952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:31 MarkDuplicates After output close freeMemory: 758394952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:31 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:37:31 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:31 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testSingleMappedFragmentAndSingleMappedPair STANDARD_ERROR INFO 2024-07-02 11:37:31 MarkDuplicates Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.3918154867302775716.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.3918154867302775716.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.3918154867302775716.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.3918154867302775716.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.3918154867302775716.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.3918154867302775716.tmp/output.sam Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:31.169 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:31.169 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:31.169 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:31.169 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:31.169 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:31.169 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:31.169 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:31.169 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:31 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.3918154867302775716.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.3918154867302775716.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.3918154867302775716.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:37:31 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.3918154867302775716.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.3918154867302775716.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.3918154867302775716.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:37:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:31 MarkDuplicates Start of doWork freeMemory: 1027882608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:31 MarkDuplicates Start of doWork freeMemory: 1027882608; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:31 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:37:31 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:31 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:37:31 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:37:31 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:37:31 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:31 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2024-07-02 11:37:31 MarkDuplicates Read 3 records. 0 pairs never matched. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 964962112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 964962112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:37:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:37:33 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:37:33 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:33 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:37:33 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 673458296; totalMemory: 1258291200; maxMemory: 2147483648 INFO 2024-07-02 11:37:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 673458296; totalMemory: 1258291200; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:33 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:37:33 MarkDuplicates Marking 1 records as duplicates. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:33 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:37:33 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:33 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:37:33 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:33 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:37:33 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:33 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:37:33 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:33 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:37:33 MarkDuplicates Getting Memory Stats. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:33 MarkDuplicates Before output close freeMemory: 758252656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:33 MarkDuplicates Before output close freeMemory: 758252656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:33 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:37:33 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:34 MarkDuplicates After output close freeMemory: 758392768; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:34 MarkDuplicates After output close freeMemory: 758392768; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:37:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:34 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testSingleMappedFragmentAndTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:37:34 MarkDuplicates Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.13202179321398254745.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.13202179321398254745.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.13202179321398254745.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.13202179321398254745.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.13202179321398254745.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.13202179321398254745.tmp/output.sam Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:34.135 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:34.135 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:34.136 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:34.136 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:34.136 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:34.136 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:34.136 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:34.136 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:34 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.13202179321398254745.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.13202179321398254745.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.13202179321398254745.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:37:34 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.13202179321398254745.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.13202179321398254745.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.13202179321398254745.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:37:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:34 MarkDuplicates Start of doWork freeMemory: 1027880520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:34 MarkDuplicates Start of doWork freeMemory: 1027880520; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:34 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:37:34 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:34 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:37:34 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:37:34 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:37:34 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:34 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:37:34 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:34 MarkDuplicates After buildSortedReadEndLists freeMemory: 964959808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:34 MarkDuplicates After buildSortedReadEndLists freeMemory: 964959808; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:37:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:35 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:37:35 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:35 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:37:35 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:35 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:37:35 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 488906832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:35 MarkDuplicates After generateDuplicateIndexes freeMemory: 488906832; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:35 MarkDuplicates Marking 3 records as duplicates. INFO 2024-07-02 11:37:35 MarkDuplicates Marking 3 records as duplicates. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:35 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:37:35 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:35 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:37:35 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:35 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:37:35 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:35 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:37:35 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:35 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:37:35 MarkDuplicates Getting Memory Stats. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:36 MarkDuplicates Before output close freeMemory: 758250568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:36 MarkDuplicates Before output close freeMemory: 758250568; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:36 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:37:36 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:36 MarkDuplicates After output close freeMemory: 758390680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:36 MarkDuplicates After output close freeMemory: 758390680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:36 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:37:36 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:36 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testSingleMappedPair STANDARD_ERROR INFO 2024-07-02 11:37:36 MarkDuplicates Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.17743967274632452561.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.17743967274632452561.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.17743967274632452561.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.17743967274632452561.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.17743967274632452561.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.17743967274632452561.tmp/output.sam Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:36.467 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:36.467 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:36.467 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:36.467 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:36.467 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:36.467 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:36.467 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:36.467 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:36 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.17743967274632452561.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.17743967274632452561.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.17743967274632452561.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:37:36 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.17743967274632452561.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.17743967274632452561.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.17743967274632452561.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:37:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:36 MarkDuplicates Start of doWork freeMemory: 1027881800; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:36 MarkDuplicates Start of doWork freeMemory: 1027881800; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:36 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:37:36 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:36 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:37:36 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:37:36 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:37:36 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:36 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:37:36 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 964961376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 964961376; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:37:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:38 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:37:38 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:38 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:37:38 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:38 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:37:38 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 488908112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 488908112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:38 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:37:38 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:38 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:37:38 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:38 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:37:38 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:38 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:37:38 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:38 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:37:38 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:38 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:37:38 MarkDuplicates Getting Memory Stats. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:38 MarkDuplicates Before output close freeMemory: 758251848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:38 MarkDuplicates Before output close freeMemory: 758251848; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:38 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:37:38 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:38 MarkDuplicates After output close freeMemory: 758391960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:38 MarkDuplicates After output close freeMemory: 758391960; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:38 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:37:38 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:38 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testSingleUnmappedFragment STANDARD_ERROR INFO 2024-07-02 11:37:38 MarkDuplicates Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.1252900114780122367.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.1252900114780122367.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.1252900114780122367.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.1252900114780122367.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.1252900114780122367.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.1252900114780122367.tmp/output.sam Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:38.939 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:38.939 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:38.939 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:38.939 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:38.940 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:38.940 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:38.940 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:38.940 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:38 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.1252900114780122367.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.1252900114780122367.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.1252900114780122367.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:37:38 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.1252900114780122367.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.1252900114780122367.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.1252900114780122367.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:37:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:39 MarkDuplicates Start of doWork freeMemory: 1027879176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:39 MarkDuplicates Start of doWork freeMemory: 1027879176; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:39 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:37:39 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:39 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:37:39 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:39 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2024-07-02 11:37:39 MarkDuplicates Read 0 records. 0 pairs never matched. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 964961952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 964961952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:37:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:40 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:37:40 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:37:40 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:40 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:37:40 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 488908648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 488908648; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:40 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:37:40 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:40 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:37:40 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:40 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:37:40 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:40 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:37:40 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:40 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:37:40 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:40 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:37:40 MarkDuplicates Getting Memory Stats. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:41 MarkDuplicates Before output close freeMemory: 758251136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:41 MarkDuplicates Before output close freeMemory: 758251136; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:41 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:37:41 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:41 MarkDuplicates After output close freeMemory: 758291520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:41 MarkDuplicates After output close freeMemory: 758291520; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:41 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:37:41 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:41 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testSingleUnmappedPair STANDARD_ERROR INFO 2024-07-02 11:37:41 MarkDuplicates Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.9178557041912019411.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.9178557041912019411.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.9178557041912019411.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.9178557041912019411.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.9178557041912019411.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.9178557041912019411.tmp/output.sam Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:41.449 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:41.449 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:41.449 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:41.449 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:41.449 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:41.449 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:41.449 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:41.449 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:41 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.9178557041912019411.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.9178557041912019411.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.9178557041912019411.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:37:41 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.9178557041912019411.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.9178557041912019411.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.9178557041912019411.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:37:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:41 MarkDuplicates Start of doWork freeMemory: 1027880904; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:41 MarkDuplicates Start of doWork freeMemory: 1027880904; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:41 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:37:41 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:41 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:37:41 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:41 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2024-07-02 11:37:41 MarkDuplicates Read 0 records. 0 pairs never matched. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 964960928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 964960928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:37:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:42 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:37:42 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:42 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:37:42 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:42 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:37:42 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 660874088; totalMemory: 1245708288; maxMemory: 2147483648 INFO 2024-07-02 11:37:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 660874088; totalMemory: 1245708288; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:43 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:37:43 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:43 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:37:43 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:43 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:37:43 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:43 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:37:43 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:43 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:37:43 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:43 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:37:43 MarkDuplicates Getting Memory Stats. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:43 MarkDuplicates Before output close freeMemory: 758251680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:43 MarkDuplicates Before output close freeMemory: 758251680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:43 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:37:43 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:43 MarkDuplicates After output close freeMemory: 758391472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:43 MarkDuplicates After output close freeMemory: 758391472; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:43 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:37:43 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:43 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testStackOverFlowPairSetSwap STANDARD_ERROR INFO 2024-07-02 11:37:43 MarkDuplicates Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.371923206195119280.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.371923206195119280.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.371923206195119280.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.371923206195119280.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.371923206195119280.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.371923206195119280.tmp/output.sam Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:43.734 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:43.734 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:43.735 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:43.735 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:43.735 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:43.735 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:43.735 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:43.735 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:43 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.371923206195119280.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.371923206195119280.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.371923206195119280.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:37:43 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.371923206195119280.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.371923206195119280.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.371923206195119280.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:37:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:43 MarkDuplicates Start of doWork freeMemory: 1027771264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:43 MarkDuplicates Start of doWork freeMemory: 1027771264; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:43 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:37:43 MarkDuplicates Reading input file and constructing read end information. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:43 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:37:43 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:44 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:37:44 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 964822248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 964822248; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:37:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:45 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:37:45 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:45 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:37:45 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:45 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:37:45 MarkDuplicates Sorting list of duplicate records. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 488802752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 488802752; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:45 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:37:45 MarkDuplicates Marking 2 records as duplicates. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:45 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:37:45 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:45 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:37:45 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:45 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:37:45 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:45 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:37:45 MarkDuplicates Duplicate Index cleanup. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:45 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:37:45 MarkDuplicates Getting Memory Stats. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:46 MarkDuplicates Before output close freeMemory: 758117920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:46 MarkDuplicates Before output close freeMemory: 758117920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:46 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:37:46 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:46 MarkDuplicates After output close freeMemory: 758286600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:46 MarkDuplicates After output close freeMemory: 758286600; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:37:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:46 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:37:46 MarkDuplicates Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.7822291626017513441.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.7822291626017513441.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.7822291626017513441.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.7822291626017513441.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.7822291626017513441.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.7822291626017513441.tmp/output.sam Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:46.512 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:46.512 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:46.512 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:46.512 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:46.521 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:46.521 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:46.521 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:46.521 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:46 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.7822291626017513441.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.7822291626017513441.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.7822291626017513441.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:37:46 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.7822291626017513441.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.7822291626017513441.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.7822291626017513441.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:37:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:47 MarkDuplicates Start of doWork freeMemory: 1027901952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:47 MarkDuplicates Start of doWork freeMemory: 1027901952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:47 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:37:47 MarkDuplicates Reading input file and constructing read end information. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:47 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:37:47 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:37:47 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:37:47 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:47 MarkDuplicates Read 18 records. 0 pairs never matched. INFO 2024-07-02 11:37:47 MarkDuplicates Read 18 records. 0 pairs never matched. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 964979560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 964979560; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:48 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:37:48 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:49 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:37:49 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:49 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:37:49 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:49 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:37:49 MarkDuplicates Sorting list of duplicate records. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 488928024; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 488928024; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:49 MarkDuplicates Marking 12 records as duplicates. INFO 2024-07-02 11:37:49 MarkDuplicates Marking 12 records as duplicates. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:49 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:37:49 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:49 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:37:49 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:49 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:37:49 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:49 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:37:49 MarkDuplicates Duplicate Index cleanup. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:49 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:37:49 MarkDuplicates Getting Memory Stats. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:50 MarkDuplicates Before output close freeMemory: 758271760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:50 MarkDuplicates Before output close freeMemory: 758271760; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:50 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:37:50 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:50 MarkDuplicates After output close freeMemory: 758411872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:50 MarkDuplicates After output close freeMemory: 758411872; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:37:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:50 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:37:50 MarkDuplicates Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.1787987255642571499.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.1787987255642571499.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.1787987255642571499.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.1787987255642571499.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.1787987255642571499.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.1787987255642571499.tmp/output.sam Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:50.863 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:50.863 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:50.863 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:50.863 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:50.863 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:50.863 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:50.863 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:50.863 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:50 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.1787987255642571499.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.1787987255642571499.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.1787987255642571499.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:37:50 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.1787987255642571499.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.1787987255642571499.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.1787987255642571499.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:37:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:51 MarkDuplicates Start of doWork freeMemory: 1027904144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:51 MarkDuplicates Start of doWork freeMemory: 1027904144; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:51 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:37:51 MarkDuplicates Reading input file and constructing read end information. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:51 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:37:51 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:37:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:37:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:51 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:37:51 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 964988376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 964988376; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:37:52 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:52 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:37:52 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:52 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:37:52 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:52 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:37:52 MarkDuplicates Sorting list of duplicate records. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 488935544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 488935544; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:53 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:37:53 MarkDuplicates Marking 4 records as duplicates. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:53 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:37:53 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:53 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:37:53 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:53 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:37:53 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:53 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:37:53 MarkDuplicates Duplicate Index cleanup. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:53 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:37:53 MarkDuplicates Getting Memory Stats. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:53 MarkDuplicates Before output close freeMemory: 758279280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:53 MarkDuplicates Before output close freeMemory: 758279280; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:53 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:37:53 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:54 MarkDuplicates After output close freeMemory: 758419464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:54 MarkDuplicates After output close freeMemory: 758419464; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:54 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:37:54 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:54 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testThreeMappedPairsWithMatchingSecondMate STANDARD_ERROR INFO 2024-07-02 11:37:54 MarkDuplicates Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.15800048921222228416.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.15800048921222228416.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.15800048921222228416.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.15800048921222228416.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.15800048921222228416.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.15800048921222228416.tmp/output.sam Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:54.353 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:54.353 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:54.353 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:54.353 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:54.353 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:54.353 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:54.353 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:54.353 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:54 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.15800048921222228416.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.15800048921222228416.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.15800048921222228416.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:37:54 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.15800048921222228416.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.15800048921222228416.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.15800048921222228416.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:37:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:54 MarkDuplicates Start of doWork freeMemory: 1027908368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:54 MarkDuplicates Start of doWork freeMemory: 1027908368; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:54 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:37:54 MarkDuplicates Reading input file and constructing read end information. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:54 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:37:54 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:37:54 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:37:54 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:54 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:37:54 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 964987520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 964987520; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:37:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:56 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:37:56 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:56 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:37:56 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:56 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:37:56 MarkDuplicates Sorting list of duplicate records. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 660900976; totalMemory: 1245708288; maxMemory: 2147483648 INFO 2024-07-02 11:37:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 660900976; totalMemory: 1245708288; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:57 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:37:57 MarkDuplicates Marking 2 records as duplicates. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:57 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:37:57 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:57 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:37:57 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:57 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:37:57 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:57 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:37:57 MarkDuplicates Duplicate Index cleanup. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:57 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:37:57 MarkDuplicates Getting Memory Stats. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:57 MarkDuplicates Before output close freeMemory: 758278176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:57 MarkDuplicates Before output close freeMemory: 758278176; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:57 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:37:57 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:58 MarkDuplicates After output close freeMemory: 758418360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:58 MarkDuplicates After output close freeMemory: 758418360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:37:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:58 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:37:58 MarkDuplicates Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.11695822748080894445.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.11695822748080894445.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.11695822748080894445.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.11695822748080894445.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.11695822748080894445.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.11695822748080894445.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:58.238 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:58.238 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:58.238 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:58.238 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:58.238 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:37:58.238 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:37:58.238 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:37:58.238 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:58 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.11695822748080894445.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.11695822748080894445.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.11695822748080894445.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:37:58 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.11695822748080894445.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.11695822748080894445.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.11695822748080894445.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:37:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:37:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:58 MarkDuplicates Start of doWork freeMemory: 1027903704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:58 MarkDuplicates Start of doWork freeMemory: 1027903704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:58 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:37:58 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:58 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:37:58 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:37:58 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:37:58 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:58 MarkDuplicates Read 12 records. 0 pairs never matched. INFO 2024-07-02 11:37:58 MarkDuplicates Read 12 records. 0 pairs never matched. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:37:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 964982080; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:37:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 964982080; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:38:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:01 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:38:01 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:01 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:38:01 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:01 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:38:01 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 488929896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 488929896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:01 MarkDuplicates Marking 8 records as duplicates. INFO 2024-07-02 11:38:01 MarkDuplicates Marking 8 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:01 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:38:01 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:01 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:38:01 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:01 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:38:01 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:01 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:38:01 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:01 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:38:01 MarkDuplicates Getting Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:02 MarkDuplicates Before output close freeMemory: 758272344; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:02 MarkDuplicates Before output close freeMemory: 758272344; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:02 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:38:02 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:02 MarkDuplicates After output close freeMemory: 758413816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:02 MarkDuplicates After output close freeMemory: 758413816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:02 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:38:02 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:02 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoGroupsOnDifferentChromosomesOfTwoFragments STANDARD_ERROR INFO 2024-07-02 11:38:02 MarkDuplicates Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.12640443908596564952.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.12640443908596564952.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.12640443908596564952.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.12640443908596564952.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.12640443908596564952.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.12640443908596564952.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:02.810 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:02.810 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:02.811 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:02.811 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:02.811 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:02.811 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:02.811 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:02.811 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:02 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.12640443908596564952.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.12640443908596564952.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.12640443908596564952.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:38:02 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.12640443908596564952.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.12640443908596564952.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.12640443908596564952.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:38:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:03 MarkDuplicates Start of doWork freeMemory: 1027908464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:03 MarkDuplicates Start of doWork freeMemory: 1027908464; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:03 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:38:03 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:03 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:38:03 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:38:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:38:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:03 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:38:03 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 964988088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 964988088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:38:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:06 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:38:06 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:06 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:38:06 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:06 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:38:06 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 488935072; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 488935072; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:07 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:38:07 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:07 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:38:07 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:07 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:38:07 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:07 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:38:07 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:07 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:38:07 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:07 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:38:07 MarkDuplicates Getting Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:07 MarkDuplicates Before output close freeMemory: 758278920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:07 MarkDuplicates Before output close freeMemory: 758278920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:07 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:38:07 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:08 MarkDuplicates After output close freeMemory: 758418920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:08 MarkDuplicates After output close freeMemory: 758418920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:08 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.09 minutes. [Tue Jul 02 11:38:08 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.09 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:08 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:38:08 MarkDuplicates Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.3104975181425609937.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.3104975181425609937.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.3104975181425609937.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.3104975181425609937.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.3104975181425609937.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.3104975181425609937.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:08.400 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:08.400 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:08.429 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:08.429 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:08.429 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:08.429 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:08.429 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:08.429 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:08 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.3104975181425609937.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.3104975181425609937.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.3104975181425609937.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:38:08 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.3104975181425609937.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.3104975181425609937.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.3104975181425609937.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:38:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:08 MarkDuplicates Start of doWork freeMemory: 1027905032; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:08 MarkDuplicates Start of doWork freeMemory: 1027905032; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:08 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:38:08 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:08 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:38:08 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:38:09 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:38:09 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:09 MarkDuplicates Read 8 records. 0 pairs never matched. INFO 2024-07-02 11:38:09 MarkDuplicates Read 8 records. 0 pairs never matched. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 964983840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 964983840; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:38:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:38:11 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:38:11 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:11 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:38:11 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 488931224; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 488931224; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:11 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:38:11 MarkDuplicates Marking 4 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:11 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:38:11 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:11 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:38:11 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:11 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:38:11 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:11 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:38:11 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:11 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:38:11 MarkDuplicates Getting Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:12 MarkDuplicates Before output close freeMemory: 758274960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:12 MarkDuplicates Before output close freeMemory: 758274960; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:12 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:38:12 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:13 MarkDuplicates After output close freeMemory: 758415072; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:13 MarkDuplicates After output close freeMemory: 758415072; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:13 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. [Tue Jul 02 11:38:13 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:13 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoMappedFragments STANDARD_ERROR INFO 2024-07-02 11:38:13 MarkDuplicates Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.1246051214174232466.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.1246051214174232466.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.1246051214174232466.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.1246051214174232466.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.1246051214174232466.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.1246051214174232466.tmp/output.sam Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:13.278 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:13.278 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:13.278 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:13.278 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:13.278 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:13.278 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:13.278 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:13.278 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:13 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.1246051214174232466.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.1246051214174232466.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.1246051214174232466.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:38:13 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.1246051214174232466.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.1246051214174232466.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.1246051214174232466.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:38:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:13 MarkDuplicates Start of doWork freeMemory: 1027908288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:13 MarkDuplicates Start of doWork freeMemory: 1027908288; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:13 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:38:13 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:13 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:38:13 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:38:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:38:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:13 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:38:13 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 964988056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 964988056; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:14 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:38:14 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:15 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:38:15 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:15 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:38:15 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:15 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:38:15 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 633638384; totalMemory: 1218445312; maxMemory: 2147483648 INFO 2024-07-02 11:38:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 633638384; totalMemory: 1218445312; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:15 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:38:15 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:15 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:38:15 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:15 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:38:15 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:15 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:38:15 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:15 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:38:15 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:15 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:38:15 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:16 MarkDuplicates Before output close freeMemory: 758278744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:16 MarkDuplicates Before output close freeMemory: 758278744; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:16 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:38:16 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:16 MarkDuplicates After output close freeMemory: 758418816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:16 MarkDuplicates After output close freeMemory: 758418816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:16 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:38:16 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:16 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoMappedPairWithSamePosition STANDARD_ERROR INFO 2024-07-02 11:38:16 MarkDuplicates Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.3166637450521754074.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.3166637450521754074.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.3166637450521754074.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.3166637450521754074.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.3166637450521754074.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.3166637450521754074.tmp/output.sam Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:16.650 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:16.650 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:16.650 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:16.650 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:16.650 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:16.650 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:16.650 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:16.650 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:16 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.3166637450521754074.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.3166637450521754074.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.3166637450521754074.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:38:16 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.3166637450521754074.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.3166637450521754074.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.3166637450521754074.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:38:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:16 MarkDuplicates Start of doWork freeMemory: 1027903440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:16 MarkDuplicates Start of doWork freeMemory: 1027903440; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:16 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:38:16 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:16 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:38:16 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:38:17 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:38:17 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:17 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:38:17 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 964985544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 964985544; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:38:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:18 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:38:18 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:18 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:38:18 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:18 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:38:18 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 488932496; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 488932496; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:19 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:38:19 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:19 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:38:19 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:19 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:38:19 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:19 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:38:19 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:19 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:38:19 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:19 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:38:19 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:19 MarkDuplicates Before output close freeMemory: 758276160; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:19 MarkDuplicates Before output close freeMemory: 758276160; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:19 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:38:19 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:19 MarkDuplicates After output close freeMemory: 758416344; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:19 MarkDuplicates After output close freeMemory: 758416344; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:19 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:38:19 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:19 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoMappedPairWithSamePositionDifferentStrands STANDARD_ERROR INFO 2024-07-02 11:38:19 MarkDuplicates Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.2017677582590955624.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.2017677582590955624.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.2017677582590955624.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.2017677582590955624.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.2017677582590955624.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.2017677582590955624.tmp/output.sam Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:19.975 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:19.975 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:19.975 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:19.975 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:19.975 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:19.975 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:19.975 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:19.975 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:19 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.2017677582590955624.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.2017677582590955624.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.2017677582590955624.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:38:19 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.2017677582590955624.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.2017677582590955624.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.2017677582590955624.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:38:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:20 MarkDuplicates Start of doWork freeMemory: 1027905664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:20 MarkDuplicates Start of doWork freeMemory: 1027905664; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:20 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:38:20 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:20 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:38:20 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:38:20 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:38:20 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:20 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:38:20 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 964985024; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 964985024; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:21 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:38:21 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:22 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:38:22 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:22 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:38:22 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:22 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:38:22 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 488931976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 488931976; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:22 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:38:22 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:22 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:38:22 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:22 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:38:22 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:22 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:38:22 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:22 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:38:22 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:22 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:38:22 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:22 MarkDuplicates Before output close freeMemory: 758275712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:22 MarkDuplicates Before output close freeMemory: 758275712; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:22 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:38:22 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:23 MarkDuplicates After output close freeMemory: 758415824; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:23 MarkDuplicates After output close freeMemory: 758415824; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:23 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:38:23 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:23 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoMappedPairWithSamePositionDifferentStrands2 STANDARD_ERROR INFO 2024-07-02 11:38:23 MarkDuplicates Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.14673799769760557483.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.14673799769760557483.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.14673799769760557483.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.14673799769760557483.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.14673799769760557483.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.14673799769760557483.tmp/output.sam Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:23.304 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:23.304 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:23.304 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:23.304 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:23.304 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:23.304 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:23.304 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:23.304 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:23 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.14673799769760557483.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.14673799769760557483.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.14673799769760557483.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:38:23 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.14673799769760557483.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.14673799769760557483.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.14673799769760557483.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:38:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:23 MarkDuplicates Start of doWork freeMemory: 1027904904; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:23 MarkDuplicates Start of doWork freeMemory: 1027904904; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:23 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:38:23 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:23 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:38:23 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:38:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:38:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:23 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:38:23 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 964984264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 964984264; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:24 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:38:24 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:25 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:38:25 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:25 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:38:25 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:25 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:38:25 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 488931216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 488931216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:25 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:38:25 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:25 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:38:25 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:25 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:38:25 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:25 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:38:25 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:25 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:38:25 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:25 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:38:25 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:26 MarkDuplicates Before output close freeMemory: 758274952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:26 MarkDuplicates Before output close freeMemory: 758274952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:26 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:38:26 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:26 MarkDuplicates After output close freeMemory: 758415064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:26 MarkDuplicates After output close freeMemory: 758415064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:26 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:38:26 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:26 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:38:26 MarkDuplicates Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.14537523030747806705.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.14537523030747806705.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.14537523030747806705.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.14537523030747806705.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.14537523030747806705.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.14537523030747806705.tmp/output.sam Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:26.783 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:26.783 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:26.783 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:26.783 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:26.784 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:26.784 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:26.784 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:26.784 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:26 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.14537523030747806705.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.14537523030747806705.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.14537523030747806705.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:38:26 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.14537523030747806705.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.14537523030747806705.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.14537523030747806705.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:38:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:27 MarkDuplicates Start of doWork freeMemory: 1027901248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:27 MarkDuplicates Start of doWork freeMemory: 1027901248; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:27 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:38:27 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:27 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:38:27 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:38:27 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:38:27 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:27 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:38:27 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 964983360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 964983360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:38:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:28 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:38:28 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:28 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:38:28 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:28 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:38:28 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 599030792; totalMemory: 1183842304; maxMemory: 2147483648 INFO 2024-07-02 11:38:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 599030792; totalMemory: 1183842304; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:28 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:38:28 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:28 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:38:28 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:28 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:38:28 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:28 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:38:28 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:28 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:38:28 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:28 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:38:28 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:29 MarkDuplicates Before output close freeMemory: 758273448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:29 MarkDuplicates Before output close freeMemory: 758273448; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:29 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:38:29 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:29 MarkDuplicates After output close freeMemory: 758413736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:29 MarkDuplicates After output close freeMemory: 758413736; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:38:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:29 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoMappedPairsAndMappedSecondaryFragment STANDARD_ERROR INFO 2024-07-02 11:38:29 MarkDuplicates Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.14331605014639040979.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.14331605014639040979.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.14331605014639040979.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.14331605014639040979.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.14331605014639040979.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.14331605014639040979.tmp/output.sam Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:29.682 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:29.682 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:29.683 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:29.683 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:29.683 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:29.683 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:29.683 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:29.683 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:29 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.14331605014639040979.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.14331605014639040979.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.14331605014639040979.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:38:29 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.14331605014639040979.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.14331605014639040979.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.14331605014639040979.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:38:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:29 MarkDuplicates Start of doWork freeMemory: 1027799288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:29 MarkDuplicates Start of doWork freeMemory: 1027799288; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:29 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:38:29 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:29 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:38:29 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:38:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:38:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:30 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:38:30 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 964982112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 964982112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:38:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:31 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:38:31 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:31 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:38:31 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:31 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:38:31 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 488929064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 488929064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:31 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:38:31 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:31 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:38:31 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:31 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:38:31 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:31 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:38:31 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:31 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:38:31 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:31 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:38:31 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:31 MarkDuplicates Before output close freeMemory: 758272912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:31 MarkDuplicates Before output close freeMemory: 758272912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:31 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:38:31 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:32 MarkDuplicates After output close freeMemory: 758412912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:32 MarkDuplicates After output close freeMemory: 758412912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:38:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:32 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoMappedPairsAndTerminalUnmappedFragment STANDARD_ERROR INFO 2024-07-02 11:38:32 MarkDuplicates Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.4498046268312795009.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.4498046268312795009.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.4498046268312795009.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.4498046268312795009.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.4498046268312795009.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.4498046268312795009.tmp/output.sam Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:32.387 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:32.387 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:32.387 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:32.387 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:32.387 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:32.387 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:32.387 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:32.387 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:32 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.4498046268312795009.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.4498046268312795009.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.4498046268312795009.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:38:32 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.4498046268312795009.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.4498046268312795009.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.4498046268312795009.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:38:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:32 MarkDuplicates Start of doWork freeMemory: 1027899432; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:32 MarkDuplicates Start of doWork freeMemory: 1027899432; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:32 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:38:32 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:32 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:38:32 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:38:32 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:38:32 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:32 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:38:32 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 964981536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 964981536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:38:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:38:34 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:34 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:38:34 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:34 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:38:34 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 488928488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 488928488; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:34 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:38:34 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:34 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:38:34 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:34 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:38:34 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:34 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:38:34 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:34 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:38:34 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:34 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:38:34 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:35 MarkDuplicates Before output close freeMemory: 758272544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:35 MarkDuplicates Before output close freeMemory: 758272544; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:35 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:38:35 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:35 MarkDuplicates After output close freeMemory: 758412336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:35 MarkDuplicates After output close freeMemory: 758412336; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:35 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:38:35 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:35 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoMappedPairsAndTerminalUnmappedPair STANDARD_ERROR INFO 2024-07-02 11:38:35 MarkDuplicates Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.5915621511198979097.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.5915621511198979097.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.5915621511198979097.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.5915621511198979097.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.5915621511198979097.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.5915621511198979097.tmp/output.sam Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:35.645 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:35.645 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:35.645 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:35.645 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:35.645 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:35.645 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:35.645 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:35.645 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:35 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.5915621511198979097.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.5915621511198979097.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.5915621511198979097.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:38:35 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.5915621511198979097.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.5915621511198979097.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.5915621511198979097.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:38:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:35 MarkDuplicates Start of doWork freeMemory: 1027898272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:35 MarkDuplicates Start of doWork freeMemory: 1027898272; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:35 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:38:35 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:35 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:38:35 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:38:36 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:38:36 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:36 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:38:36 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 964980376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 964980376; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:38:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:38:37 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:38:37 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:37 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:38:37 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 488927328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 488927328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:37 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:38:37 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:37 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:38:37 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:37 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:38:37 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:37 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:38:37 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:37 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:38:37 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:37 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:38:37 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:38 MarkDuplicates Before output close freeMemory: 758271384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:38 MarkDuplicates Before output close freeMemory: 758271384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:38 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:38:38 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:38 MarkDuplicates After output close freeMemory: 758411176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:38 MarkDuplicates After output close freeMemory: 758411176; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:38 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:38:38 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:38 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoMappedPairsMatesSoftClipped STANDARD_ERROR INFO 2024-07-02 11:38:38 MarkDuplicates Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.16414843586541190513.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.16414843586541190513.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.16414843586541190513.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.16414843586541190513.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.16414843586541190513.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.16414843586541190513.tmp/output.sam Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:38.572 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:38.572 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:38.573 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:38.573 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:38.589 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:38.589 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:38.589 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:38.589 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:38 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.16414843586541190513.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.16414843586541190513.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.16414843586541190513.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:38:38 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.16414843586541190513.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.16414843586541190513.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.16414843586541190513.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:38:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:38 MarkDuplicates Start of doWork freeMemory: 1027901200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:38 MarkDuplicates Start of doWork freeMemory: 1027901200; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:38 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:38:38 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:38 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:38:38 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:38:39 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:38:39 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:39 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:38:39 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 964980560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:39 MarkDuplicates After buildSortedReadEndLists freeMemory: 964980560; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:38:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:40 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:38:40 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:38:40 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:40 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:38:40 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 646213912; totalMemory: 1231028224; maxMemory: 2147483648 INFO 2024-07-02 11:38:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 646213912; totalMemory: 1231028224; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:41 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:38:41 MarkDuplicates Marking 0 records as duplicates. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:41 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:38:41 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:38:41 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:41 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:38:41 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:41 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:38:41 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:41 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:38:41 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:41 MarkDuplicates Before output close freeMemory: 758271176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:41 MarkDuplicates Before output close freeMemory: 758271176; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:41 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:38:41 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:42 MarkDuplicates After output close freeMemory: 758411360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:42 MarkDuplicates After output close freeMemory: 758411360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:38:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:42 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoMappedPairsWithOppositeOrientations STANDARD_ERROR INFO 2024-07-02 11:38:42 MarkDuplicates Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.13841847451701534718.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.13841847451701534718.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.13841847451701534718.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.13841847451701534718.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.13841847451701534718.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.13841847451701534718.tmp/output.sam Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:42.177 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:42.177 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:42.177 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:42.177 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:42.177 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:42.177 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:42.177 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:42.177 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:42 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.13841847451701534718.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.13841847451701534718.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.13841847451701534718.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:38:42 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.13841847451701534718.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.13841847451701534718.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.13841847451701534718.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:38:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:42 MarkDuplicates Start of doWork freeMemory: 1027897592; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:42 MarkDuplicates Start of doWork freeMemory: 1027897592; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:42 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:38:42 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:42 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:38:42 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:38:42 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:38:42 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:42 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:38:42 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 964979704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 964979704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:38:43 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:38:44 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:44 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:38:44 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:44 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:38:44 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 488926656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 488926656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:44 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:38:44 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:44 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:38:44 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:44 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:38:44 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:44 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:38:44 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:44 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:38:44 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:44 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:38:44 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:44 MarkDuplicates Before output close freeMemory: 758270320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:44 MarkDuplicates Before output close freeMemory: 758270320; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:44 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:38:44 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:45 MarkDuplicates After output close freeMemory: 758410504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:45 MarkDuplicates After output close freeMemory: 758410504; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:38:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:45 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoMappedPairsWithOppositeOrientationsNumberTwo STANDARD_ERROR INFO 2024-07-02 11:38:45 MarkDuplicates Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.10257968699955677781.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.10257968699955677781.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.10257968699955677781.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.10257968699955677781.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.10257968699955677781.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.10257968699955677781.tmp/output.sam Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:45.420 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:45.420 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:45.420 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:45.420 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:45.433 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:45.433 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:45.433 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:45.433 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:45 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.10257968699955677781.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.10257968699955677781.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.10257968699955677781.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:38:45 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.10257968699955677781.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.10257968699955677781.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.10257968699955677781.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:38:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:45 MarkDuplicates Start of doWork freeMemory: 1027933328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:45 MarkDuplicates Start of doWork freeMemory: 1027933328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:45 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:38:45 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:45 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:38:45 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:38:45 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:38:45 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:45 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:38:45 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 965012688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 965012688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:38:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:47 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:38:47 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:47 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:38:47 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:47 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:38:47 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 488959640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 488959640; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:47 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:38:47 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:47 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:38:47 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:47 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:38:47 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:47 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:38:47 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:47 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:38:47 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:47 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:38:47 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:48 MarkDuplicates Before output close freeMemory: 758303304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:48 MarkDuplicates Before output close freeMemory: 758303304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:48 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:38:48 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:48 MarkDuplicates After output close freeMemory: 758443488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:48 MarkDuplicates After output close freeMemory: 758443488; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:48 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:38:48 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:48 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoMappedPairsWithSoftClipping STANDARD_ERROR INFO 2024-07-02 11:38:48 MarkDuplicates Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.760304774934693167.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.760304774934693167.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.760304774934693167.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.760304774934693167.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.760304774934693167.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.760304774934693167.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:48.803 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:48.803 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:48.803 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:48.803 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:48.803 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:48.803 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:48.804 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:48.804 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:48 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.760304774934693167.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.760304774934693167.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.760304774934693167.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:38:48 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.760304774934693167.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.760304774934693167.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.760304774934693167.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:38:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:49 MarkDuplicates Start of doWork freeMemory: 1027932536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:49 MarkDuplicates Start of doWork freeMemory: 1027932536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:49 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:38:49 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:38:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:38:49 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:38:49 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:49 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:38:49 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 965011896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 965011896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:38:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:50 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:38:50 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:50 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:38:50 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:50 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:38:50 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 488958848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 488958848; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:51 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:38:51 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:51 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:38:51 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:51 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:38:51 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:51 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:38:51 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:51 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:38:51 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:51 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:38:51 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:51 MarkDuplicates Before output close freeMemory: 758302512; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:51 MarkDuplicates Before output close freeMemory: 758302512; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:51 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:38:51 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:52 MarkDuplicates After output close freeMemory: 758442696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:52 MarkDuplicates After output close freeMemory: 758442696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:38:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:52 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoMappedPairsWithSoftClippingBoth STANDARD_ERROR INFO 2024-07-02 11:38:52 MarkDuplicates Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.10666588912767486137.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.10666588912767486137.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.10666588912767486137.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.10666588912767486137.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.10666588912767486137.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.10666588912767486137.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:52.160 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:52.160 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:52.160 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:52.160 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:52.160 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:52.160 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:52.160 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:52.160 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:52 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.10666588912767486137.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.10666588912767486137.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.10666588912767486137.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:38:52 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.10666588912767486137.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.10666588912767486137.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.10666588912767486137.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:38:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:52 MarkDuplicates Start of doWork freeMemory: 1027931800; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:52 MarkDuplicates Start of doWork freeMemory: 1027931800; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:52 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:38:52 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:52 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:38:52 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:38:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:38:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:52 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:38:52 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 965011160; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 965011160; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:38:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:54 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:38:54 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:54 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:38:54 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:54 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:38:54 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 629467296; totalMemory: 1214251008; maxMemory: 2147483648 INFO 2024-07-02 11:38:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 629467296; totalMemory: 1214251008; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:54 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:38:54 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:54 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:38:54 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:54 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:38:54 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:54 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:38:54 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:54 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:38:54 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:54 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:38:54 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:55 MarkDuplicates Before output close freeMemory: 758301776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:55 MarkDuplicates Before output close freeMemory: 758301776; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:55 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:38:55 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:55 MarkDuplicates After output close freeMemory: 758441960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:55 MarkDuplicates After output close freeMemory: 758441960; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:55 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:38:55 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:55 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar STANDARD_ERROR INFO 2024-07-02 11:38:55 MarkDuplicates Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.3158530987749895003.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.3158530987749895003.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.3158530987749895003.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.3158530987749895003.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.3158530987749895003.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.3158530987749895003.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:55.693 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:55.693 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:55.693 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:55.693 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:55.693 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:55.693 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:55.694 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:55.694 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:55 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.3158530987749895003.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.3158530987749895003.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.3158530987749895003.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:38:55 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.3158530987749895003.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.3158530987749895003.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.3158530987749895003.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:38:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:56 MarkDuplicates Start of doWork freeMemory: 1027932296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:56 MarkDuplicates Start of doWork freeMemory: 1027932296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:56 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:38:56 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:56 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:38:56 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:38:56 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:38:56 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:56 MarkDuplicates Read 2 records. 2 pairs never matched. INFO 2024-07-02 11:38:56 MarkDuplicates Read 2 records. 2 pairs never matched. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 965011944; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 965011944; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:38:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:57 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:38:57 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:57 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:38:57 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:57 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:38:57 MarkDuplicates Sorting list of duplicate records. Gradle is still running, please be patient... Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 488958784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 488958784; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:58 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:38:58 MarkDuplicates Marking 0 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:58 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:38:58 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:58 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:38:58 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:58 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:38:58 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:58 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:38:58 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:58 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:38:58 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:58 MarkDuplicates Before output close freeMemory: 758200216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:58 MarkDuplicates Before output close freeMemory: 758200216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:58 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:38:58 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:58 MarkDuplicates After output close freeMemory: 758442408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:58 MarkDuplicates After output close freeMemory: 758442408; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:38:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:58 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoMappedPairsWithSupplementaryReads[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:38:58 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.7526199393367603075.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.7526199393367603075.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.7526199393367603075.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.7526199393367603075.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.7526199393367603075.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.7526199393367603075.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:58.993 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:58.993 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:58.993 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:58.993 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:58.994 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:38:58.994 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:38:58.994 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:38:58.994 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:58 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.7526199393367603075.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.7526199393367603075.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.7526199393367603075.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:38:58 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.7526199393367603075.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.7526199393367603075.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.7526199393367603075.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:38:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:38:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:59 MarkDuplicates Start of doWork freeMemory: 1027929216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:59 MarkDuplicates Start of doWork freeMemory: 1027929216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:59 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:38:59 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:59 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:38:59 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:59 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:38:59 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:38:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 965008512; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:38:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 965008512; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:39:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:00 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:39:00 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:00 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:39:00 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:00 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:39:00 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 488955312; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 488955312; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:01 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:39:01 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:01 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:39:01 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:01 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:39:01 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:01 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:39:01 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:01 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:39:01 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:01 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:39:01 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:01 MarkDuplicates Before output close freeMemory: 758297384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:01 MarkDuplicates Before output close freeMemory: 758297384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:01 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:39:01 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:02 MarkDuplicates After output close freeMemory: 758439232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:02 MarkDuplicates After output close freeMemory: 758439232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:02 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:39:02 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:02 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoMappedPairsWithSupplementaryReads[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:39:02 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.18220072033461154457.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.18220072033461154457.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.18220072033461154457.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.18220072033461154457.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.18220072033461154457.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.18220072033461154457.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:02.083 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:02.083 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:02.083 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:02.083 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:02.084 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:02.084 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:02.084 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:02.084 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:02 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.18220072033461154457.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.18220072033461154457.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.18220072033461154457.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:39:02 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.18220072033461154457.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.18220072033461154457.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.18220072033461154457.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:39:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:02 MarkDuplicates Start of doWork freeMemory: 1027928512; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:02 MarkDuplicates Start of doWork freeMemory: 1027928512; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:02 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:39:02 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:02 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:39:02 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:02 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:39:02 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 965007808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:02 MarkDuplicates After buildSortedReadEndLists freeMemory: 965007808; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:03 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:39:03 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:03 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:39:03 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:03 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:39:03 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:03 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:39:03 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 488954608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:03 MarkDuplicates After generateDuplicateIndexes freeMemory: 488954608; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:03 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:39:03 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:03 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:39:03 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:03 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:39:03 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:03 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:39:03 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:03 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:39:03 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:03 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:39:03 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:04 MarkDuplicates Before output close freeMemory: 758298248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:04 MarkDuplicates Before output close freeMemory: 758298248; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:04 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:39:04 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:04 MarkDuplicates After output close freeMemory: 758438456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:04 MarkDuplicates After output close freeMemory: 758438456; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:04 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:39:04 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:04 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoMappedPairsWithSupplementaryReads[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:39:04 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.2059332577334020911.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.2059332577334020911.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.2059332577334020911.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.2059332577334020911.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.2059332577334020911.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.2059332577334020911.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:04.828 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:04.828 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:04.828 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:04.828 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:04.828 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:04.828 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:04.828 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:04.828 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:04 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.2059332577334020911.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.2059332577334020911.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.2059332577334020911.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:39:04 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.2059332577334020911.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.2059332577334020911.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.2059332577334020911.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:39:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:05 MarkDuplicates Start of doWork freeMemory: 1027927896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:05 MarkDuplicates Start of doWork freeMemory: 1027927896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:05 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:39:05 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:05 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:39:05 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:05 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:39:05 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 965007192; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:05 MarkDuplicates After buildSortedReadEndLists freeMemory: 965007192; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:06 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:39:06 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:06 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:39:06 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:06 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:39:06 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:06 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:39:06 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 596957320; totalMemory: 1181745152; maxMemory: 2147483648 INFO 2024-07-02 11:39:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 596957320; totalMemory: 1181745152; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:07 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:39:07 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:07 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:39:07 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:07 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:39:07 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:07 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:39:07 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:07 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:39:07 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:07 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:39:07 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:07 MarkDuplicates Before output close freeMemory: 758297632; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:07 MarkDuplicates Before output close freeMemory: 758297632; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:07 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:39:07 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:07 MarkDuplicates After output close freeMemory: 758437344; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:07 MarkDuplicates After output close freeMemory: 758437344; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:07 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:39:07 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:07 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoMappedPairsWithSupplementaryReads[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:39:07 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.705315962422344059.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.705315962422344059.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.705315962422344059.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.705315962422344059.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.705315962422344059.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.705315962422344059.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:07.910 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:07.910 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:07.910 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:07.910 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:07.910 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:07.910 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:07.910 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:07.910 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:07 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.705315962422344059.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.705315962422344059.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.705315962422344059.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:39:07 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.705315962422344059.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.705315962422344059.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.705315962422344059.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:39:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:08 MarkDuplicates Start of doWork freeMemory: 1027924536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:08 MarkDuplicates Start of doWork freeMemory: 1027924536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:08 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:39:08 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:08 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:39:08 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:08 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:39:08 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 965006576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 965006576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:39:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:10 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:39:10 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:10 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:39:10 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:10 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:39:10 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 488953376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 488953376; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:10 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:39:10 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:10 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:39:10 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:10 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:39:10 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:10 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:39:10 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:10 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:39:10 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:10 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:39:10 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:10 MarkDuplicates Before output close freeMemory: 758295448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:10 MarkDuplicates Before output close freeMemory: 758295448; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:10 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:39:10 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:11 MarkDuplicates After output close freeMemory: 758334448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:11 MarkDuplicates After output close freeMemory: 758334448; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:11 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:39:11 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:11 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoMappedPairsWithSupplementaryReads[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:39:11 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.14843457766469931174.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.14843457766469931174.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.14843457766469931174.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.14843457766469931174.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.14843457766469931174.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.14843457766469931174.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:11.239 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:11.239 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:11.239 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:11.239 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:11.239 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:11.239 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:11.239 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:11.239 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:11 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.14843457766469931174.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.14843457766469931174.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.14843457766469931174.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:39:11 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.14843457766469931174.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.14843457766469931174.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.14843457766469931174.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:39:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:11 MarkDuplicates Start of doWork freeMemory: 1027923896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:11 MarkDuplicates Start of doWork freeMemory: 1027923896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:11 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:39:11 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:11 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:39:11 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:11 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:39:11 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 965005944; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 965005944; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:12 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:39:12 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:13 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:39:13 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:13 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:39:13 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:13 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:39:13 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 488952744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 488952744; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:13 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:39:13 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:13 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:39:13 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:13 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:39:13 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:13 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:39:13 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:13 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:39:13 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:13 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:39:13 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:14 MarkDuplicates Before output close freeMemory: 758294816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:14 MarkDuplicates Before output close freeMemory: 758294816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:14 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:39:14 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:14 MarkDuplicates After output close freeMemory: 758436168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:14 MarkDuplicates After output close freeMemory: 758436168; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:14 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:39:14 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:14 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoMappedPairsWithSupplementaryReads[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:39:14 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.8340609565650044537.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.8340609565650044537.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.8340609565650044537.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.8340609565650044537.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.8340609565650044537.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.8340609565650044537.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:14.657 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:14.657 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:14.657 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:14.657 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:14.658 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:14.658 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:14.658 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:14.658 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:14 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.8340609565650044537.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.8340609565650044537.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.8340609565650044537.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:39:14 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.8340609565650044537.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.8340609565650044537.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.8340609565650044537.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:39:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:15 MarkDuplicates Start of doWork freeMemory: 1027822600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:15 MarkDuplicates Start of doWork freeMemory: 1027822600; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:15 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:39:15 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:15 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:39:15 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:15 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:39:15 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:15 MarkDuplicates After buildSortedReadEndLists freeMemory: 965005352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:15 MarkDuplicates After buildSortedReadEndLists freeMemory: 965005352; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:39:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:17 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:39:17 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:17 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:39:17 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:17 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:39:17 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 488952152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 488952152; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:17 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:39:17 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:17 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:39:17 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:17 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:39:17 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:17 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:39:17 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:17 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:39:17 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:17 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:39:17 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:17 MarkDuplicates Before output close freeMemory: 758295792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:17 MarkDuplicates Before output close freeMemory: 758295792; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:17 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:39:17 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:18 MarkDuplicates After output close freeMemory: 758436072; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:18 MarkDuplicates After output close freeMemory: 758436072; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:18 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:39:18 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:18 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:39:18 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.12230741004556838519.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.12230741004556838519.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.12230741004556838519.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.12230741004556838519.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.12230741004556838519.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.12230741004556838519.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:18.538 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:18.538 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:18.538 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:18.538 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:18.539 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:18.539 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:18.539 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:18.539 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:18 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.12230741004556838519.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.12230741004556838519.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.12230741004556838519.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:39:18 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.12230741004556838519.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.12230741004556838519.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.12230741004556838519.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:39:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:18 MarkDuplicates Start of doWork freeMemory: 1027921656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:18 MarkDuplicates Start of doWork freeMemory: 1027921656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:18 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:39:18 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:18 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:39:18 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:19 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:39:19 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 965000952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 965000952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:39:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:20 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:39:20 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:20 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:39:20 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:20 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:39:20 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 668254248; totalMemory: 1253048320; maxMemory: 2147483648 INFO 2024-07-02 11:39:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 668254248; totalMemory: 1253048320; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:21 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:39:21 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:21 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:39:21 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:21 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:39:21 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:21 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:39:21 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:21 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:39:21 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:21 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:39:21 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:21 MarkDuplicates Before output close freeMemory: 758291552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:21 MarkDuplicates Before output close freeMemory: 758291552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:21 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:39:21 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:22 MarkDuplicates After output close freeMemory: 758431600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:22 MarkDuplicates After output close freeMemory: 758431600; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:22 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:39:22 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:22 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:39:22 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.756672368709223032.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.756672368709223032.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.756672368709223032.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.756672368709223032.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.756672368709223032.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.756672368709223032.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:22.316 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:22.316 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:22.316 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:22.316 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:22.316 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:22.316 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:22.316 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:22.316 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:22 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.756672368709223032.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.756672368709223032.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.756672368709223032.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:39:22 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.756672368709223032.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.756672368709223032.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.756672368709223032.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:39:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:22 MarkDuplicates Start of doWork freeMemory: 1027921056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:22 MarkDuplicates Start of doWork freeMemory: 1027921056; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:22 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:39:22 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:22 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:39:22 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:22 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:39:22 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 965000352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 965000352; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:39:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:24 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:39:24 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:24 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:39:24 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:24 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:39:24 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 488947152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 488947152; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:24 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:39:24 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:24 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:39:24 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:24 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:39:24 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:24 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:39:24 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:24 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:39:24 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:24 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:39:24 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:25 MarkDuplicates Before output close freeMemory: 758290952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:25 MarkDuplicates Before output close freeMemory: 758290952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:25 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:39:25 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:25 MarkDuplicates After output close freeMemory: 758431072; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:25 MarkDuplicates After output close freeMemory: 758431072; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:25 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:39:25 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:25 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:39:25 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.16780191023195522546.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.16780191023195522546.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.16780191023195522546.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.16780191023195522546.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.16780191023195522546.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.16780191023195522546.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:25.647 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:25.647 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:25.648 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:25.648 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:25.648 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:25.648 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:25.648 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:25.648 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:25 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.16780191023195522546.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.16780191023195522546.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.16780191023195522546.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:39:25 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.16780191023195522546.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.16780191023195522546.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.16780191023195522546.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:39:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:26 MarkDuplicates Start of doWork freeMemory: 1027917672; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:26 MarkDuplicates Start of doWork freeMemory: 1027917672; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:26 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:39:26 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:26 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:39:26 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:26 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:39:26 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 964999720; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 964999720; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:39:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:39:27 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:39:27 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:27 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:39:27 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 488946520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 488946520; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:28 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:39:28 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:28 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:39:28 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:28 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:39:28 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:28 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:39:28 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:28 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:39:28 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:28 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:39:28 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:28 MarkDuplicates Before output close freeMemory: 758188064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:28 MarkDuplicates Before output close freeMemory: 758188064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:28 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:39:28 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:29 MarkDuplicates After output close freeMemory: 758430368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:29 MarkDuplicates After output close freeMemory: 758430368; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:39:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:29 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:39:29 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.4408091861163258296.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.4408091861163258296.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.4408091861163258296.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.4408091861163258296.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.4408091861163258296.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.4408091861163258296.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:29.398 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:29.398 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:29.398 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:29.398 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:29.398 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:29.398 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:29.398 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:29.398 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:29 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.4408091861163258296.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.4408091861163258296.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.4408091861163258296.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:39:29 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.4408091861163258296.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.4408091861163258296.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.4408091861163258296.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:39:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:29 MarkDuplicates Start of doWork freeMemory: 1027919808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:29 MarkDuplicates Start of doWork freeMemory: 1027919808; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:29 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:39:29 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:29 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:39:29 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:30 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:39:30 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 964999104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 964999104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:39:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:31 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:39:31 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:31 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:39:31 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:31 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:39:31 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 488945904; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 488945904; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:31 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:39:31 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:31 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:39:31 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:31 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:39:31 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:31 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:39:31 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:31 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:39:31 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:31 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:39:31 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:32 MarkDuplicates Before output close freeMemory: 758289704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:32 MarkDuplicates Before output close freeMemory: 758289704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:32 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:39:32 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:32 MarkDuplicates After output close freeMemory: 758429256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:32 MarkDuplicates After output close freeMemory: 758429256; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:39:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:32 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:39:32 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.14334310311801724178.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.14334310311801724178.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.14334310311801724178.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.14334310311801724178.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.14334310311801724178.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.14334310311801724178.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:32.495 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:32.495 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:32.495 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:32.495 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:32.495 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:32.495 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:32.495 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:32.495 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:32 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.14334310311801724178.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.14334310311801724178.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.14334310311801724178.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:39:32 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.14334310311801724178.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.14334310311801724178.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.14334310311801724178.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:39:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:32 MarkDuplicates Start of doWork freeMemory: 1027913936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:32 MarkDuplicates Start of doWork freeMemory: 1027913936; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:32 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:39:32 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:32 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:39:32 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:33 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:39:33 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 964897560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 964897560; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:34 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:39:34 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:39:34 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:34 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:39:34 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:34 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:39:34 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 591705736; totalMemory: 1176502272; maxMemory: 2147483648 INFO 2024-07-02 11:39:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 591705736; totalMemory: 1176502272; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:34 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:39:34 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:34 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:39:34 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:34 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:39:34 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:34 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:39:34 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:34 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:39:34 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:34 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:39:34 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:35 MarkDuplicates Before output close freeMemory: 758289088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:35 MarkDuplicates Before output close freeMemory: 758289088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:35 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:39:35 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:35 MarkDuplicates After output close freeMemory: 758429208; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:35 MarkDuplicates After output close freeMemory: 758429208; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:35 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:39:35 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:35 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:39:35 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.18375714590554382271.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.18375714590554382271.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.18375714590554382271.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.18375714590554382271.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.18375714590554382271.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.18375714590554382271.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:35.787 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:35.787 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:35.787 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:35.787 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:35.787 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:35.787 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:35.787 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:35.787 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:35 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.18375714590554382271.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.18375714590554382271.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.18375714590554382271.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:39:35 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.18375714590554382271.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.18375714590554382271.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.18375714590554382271.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:39:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:36 MarkDuplicates Start of doWork freeMemory: 1027918576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:36 MarkDuplicates Start of doWork freeMemory: 1027918576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:36 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:39:36 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:36 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:39:36 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:36 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:39:36 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 964997872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 964997872; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:39:37 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:39:37 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:39:37 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:37 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:39:37 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 488944672; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 488944672; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:38 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:39:38 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:38 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:39:38 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:38 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:39:38 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:38 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:39:38 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:38 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:39:38 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:38 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:39:38 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:38 MarkDuplicates Before output close freeMemory: 758288472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:38 MarkDuplicates Before output close freeMemory: 758288472; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:38 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:39:38 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:39 MarkDuplicates After output close freeMemory: 758428520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:39 MarkDuplicates After output close freeMemory: 758428520; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:39:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:39 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoUnmappedFragments STANDARD_ERROR INFO 2024-07-02 11:39:39 MarkDuplicates Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.10216287236531348731.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.10216287236531348731.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.10216287236531348731.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.10216287236531348731.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.10216287236531348731.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.10216287236531348731.tmp/output.sam Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:39.112 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:39.112 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:39.112 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:39.112 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:39.112 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:39.112 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:39.112 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:39.112 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:39 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.10216287236531348731.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.10216287236531348731.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.10216287236531348731.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:39:39 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.10216287236531348731.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.10216287236531348731.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.10216287236531348731.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:39:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:39 MarkDuplicates Start of doWork freeMemory: 1027920192; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:39 MarkDuplicates Start of doWork freeMemory: 1027920192; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:39 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:39:39 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:39 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:39:39 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:39 MarkDuplicates Read 0 records. 0 pairs never matched. INFO 2024-07-02 11:39:39 MarkDuplicates Read 0 records. 0 pairs never matched. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 965000216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 965000216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:39:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:40 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:39:40 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:39:40 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:40 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:39:40 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 488946912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 488946912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:41 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:39:41 MarkDuplicates Marking 0 records as duplicates. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:41 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:39:41 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:41 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:39:41 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:41 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:39:41 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:41 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:39:41 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:41 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:39:41 MarkDuplicates Getting Memory Stats. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:41 MarkDuplicates Before output close freeMemory: 758290968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:41 MarkDuplicates Before output close freeMemory: 758290968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:41 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:39:41 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:42 MarkDuplicates After output close freeMemory: 758430760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:42 MarkDuplicates After output close freeMemory: 758430760; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:39:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:42 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]}) STANDARD_ERROR INFO 2024-07-02 11:39:42 MarkDuplicates Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam -OUTPUT /tmp/MarkDuplicates.12172053845188830693.tmp/MarkDuplicates.sam -METRICS_FILE /tmp/MarkDuplicates.12172053845188830693.tmp/MarkDuplicates.duplicate_metrics -ADD_PG_TAG_TO_READS true ********** MarkDuplicates -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam -OUTPUT /tmp/MarkDuplicates.12172053845188830693.tmp/MarkDuplicates.sam -METRICS_FILE /tmp/MarkDuplicates.12172053845188830693.tmp/MarkDuplicates.duplicate_metrics -ADD_PG_TAG_TO_READS true Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:42.288 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:42.288 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:42.288 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:42.288 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:42.288 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:42.288 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:42.288 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:42.288 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:42 GMT+14:00 2024] MarkDuplicates ADD_PG_TAG_TO_READS=true INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.12172053845188830693.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.12172053845188830693.tmp/MarkDuplicates.duplicate_metrics MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:39:42 GMT+14:00 2024] MarkDuplicates ADD_PG_TAG_TO_READS=true INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.12172053845188830693.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.12172053845188830693.tmp/MarkDuplicates.duplicate_metrics MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:39:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:42 MarkDuplicates Start of doWork freeMemory: 1027924216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:42 MarkDuplicates Start of doWork freeMemory: 1027924216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:42 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:39:42 MarkDuplicates Reading input file and constructing read end information. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:42 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:39:42 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:39:42 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name '1AAXX.1.1'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. WARNING 2024-07-02 11:39:42 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name '1AAXX.1.1'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:42 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:39:42 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 965001184; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 965001184; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:43 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2024-07-02 11:39:43 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:39:44 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:44 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:39:44 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:44 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:39:44 MarkDuplicates Sorting list of duplicate records. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 489997168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 489997168; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:44 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:39:44 MarkDuplicates Marking 4 records as duplicates. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:44 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:39:44 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:44 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:39:44 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:44 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:39:44 MarkDuplicates Writing complete. Closing input iterator. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:44 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:39:44 MarkDuplicates Duplicate Index cleanup. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:44 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:39:44 MarkDuplicates Getting Memory Stats. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:45 MarkDuplicates Before output close freeMemory: 1027772976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:45 MarkDuplicates Before output close freeMemory: 1027772976; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:45 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:39:45 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:45 MarkDuplicates After output close freeMemory: 1027916360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:45 MarkDuplicates After output close freeMemory: 1027916360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:39:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@188aa126, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5fd11059, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@43f5317], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@51bd7ac, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4855c5b8], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1f515733]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:45 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]}) STANDARD_ERROR INFO 2024-07-02 11:39:45 MarkDuplicates Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam -OUTPUT /tmp/MarkDuplicates.8006017720431530375.tmp/MarkDuplicates.sam -METRICS_FILE /tmp/MarkDuplicates.8006017720431530375.tmp/MarkDuplicates.duplicate_metrics -ADD_PG_TAG_TO_READS true -PROGRAM_RECORD_ID null ********** MarkDuplicates -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam -OUTPUT /tmp/MarkDuplicates.8006017720431530375.tmp/MarkDuplicates.sam -METRICS_FILE /tmp/MarkDuplicates.8006017720431530375.tmp/MarkDuplicates.duplicate_metrics -ADD_PG_TAG_TO_READS true -PROGRAM_RECORD_ID null Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:45.623 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:45.623 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:45.623 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:45.623 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:45.623 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:45.623 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:45.623 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:45.623 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:45 GMT+14:00 2024] MarkDuplicates ADD_PG_TAG_TO_READS=true INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.8006017720431530375.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.8006017720431530375.tmp/MarkDuplicates.duplicate_metrics PROGRAM_RECORD_ID=null MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:39:45 GMT+14:00 2024] MarkDuplicates ADD_PG_TAG_TO_READS=true INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.8006017720431530375.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.8006017720431530375.tmp/MarkDuplicates.duplicate_metrics PROGRAM_RECORD_ID=null MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:39:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:45 MarkDuplicates Start of doWork freeMemory: 1027853560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:45 MarkDuplicates Start of doWork freeMemory: 1027853560; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:45 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:39:45 MarkDuplicates Reading input file and constructing read end information. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:45 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:39:45 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:39:46 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name '1AAXX.1.1'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. WARNING 2024-07-02 11:39:46 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name '1AAXX.1.1'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:46 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:39:46 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 965034392; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 965034392; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:46 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2024-07-02 11:39:46 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:48 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:39:48 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:48 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:39:48 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:48 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:39:48 MarkDuplicates Sorting list of duplicate records. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 685065512; totalMemory: 1268776960; maxMemory: 2147483648 INFO 2024-07-02 11:39:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 685065512; totalMemory: 1268776960; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:48 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:39:48 MarkDuplicates Marking 4 records as duplicates. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:48 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:39:48 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:48 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:39:48 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:48 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:39:48 MarkDuplicates Writing complete. Closing input iterator. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:48 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:39:48 MarkDuplicates Duplicate Index cleanup. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:48 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:39:48 MarkDuplicates Getting Memory Stats. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:48 MarkDuplicates Before output close freeMemory: 1027807336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:48 MarkDuplicates Before output close freeMemory: 1027807336; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:48 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:39:48 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:49 MarkDuplicates After output close freeMemory: 1027949304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:49 MarkDuplicates After output close freeMemory: 1027949304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:39:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@4733f0cf, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@231f04f5], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@5051ac5d], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:49 MarkDuplicates Start of doWork freeMemory: 1027972360; totalMemory: 1073741824; maxMemory: 2147483648 Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1) STANDARD_ERROR INFO 2024-07-02 11:39:49 MarkDuplicates Start of doWork freeMemory: 1027972360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:49 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:39:49 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:39:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:49 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:39:49 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 965051832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 965051832; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:50 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2024-07-02 11:39:50 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:51 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:39:51 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:51 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:39:51 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:51 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:39:51 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:52 MarkDuplicates After generateDuplicateIndexes freeMemory: 490047304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:52 MarkDuplicates After generateDuplicateIndexes freeMemory: 490047304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:52 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:39:52 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:52 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:39:52 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:52 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:39:52 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:52 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:39:52 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:52 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:39:52 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:52 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:39:52 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:52 MarkDuplicates Before output close freeMemory: 1027827728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:52 MarkDuplicates Before output close freeMemory: 1027827728; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:52 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:39:52 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:52 MarkDuplicates After output close freeMemory: 1027966720; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:52 MarkDuplicates After output close freeMemory: 1027966720; totalMemory: 1073741824; maxMemory: 2147483648 Running Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:53 MarkDuplicates Start of doWork freeMemory: 1027971416; totalMemory: 1073741824; maxMemory: 2147483648 Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1) STANDARD_ERROR INFO 2024-07-02 11:39:53 MarkDuplicates Start of doWork freeMemory: 1027971416; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:53 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:39:53 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:53 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:39:53 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:53 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:39:53 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 965050800; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 965050800; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:53 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2024-07-02 11:39:53 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:54 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:39:54 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:54 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:39:54 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:54 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:39:54 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 490046272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 490046272; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:54 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:39:54 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:54 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:39:54 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:54 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:39:54 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:54 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:39:54 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:54 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:39:54 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:54 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:39:54 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:55 MarkDuplicates Before output close freeMemory: 1027826728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:55 MarkDuplicates Before output close freeMemory: 1027826728; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:55 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:39:55 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:55 MarkDuplicates After output close freeMemory: 1027965664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:55 MarkDuplicates After output close freeMemory: 1027965664; totalMemory: 1073741824; maxMemory: 2147483648 Running Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:55 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testTwoMappedPairsWithSoftClippingFirstOfPairOnly STANDARD_ERROR INFO 2024-07-02 11:39:55 MarkDuplicates Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.5998897154626126711.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.5998897154626126711.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.5998897154626126711.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.5998897154626126711.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -INPUT /tmp/MarkDuplicatesTester.5998897154626126711.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.5998897154626126711.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:55.691 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:55.691 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:55.691 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:55.691 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:55.691 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:55.691 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:55.691 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:55.691 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:55 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.5998897154626126711.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.5998897154626126711.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.5998897154626126711.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:39:55 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.5998897154626126711.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.5998897154626126711.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.5998897154626126711.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:39:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:56 MarkDuplicates Start of doWork freeMemory: 1027947688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:56 MarkDuplicates Start of doWork freeMemory: 1027947688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:56 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:39:56 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:56 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:39:56 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:39:56 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:39:56 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:56 MarkDuplicates Read 2 records. 2 pairs never matched. INFO 2024-07-02 11:39:56 MarkDuplicates Read 2 records. 2 pairs never matched. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 965027264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 965027264; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:39:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:57 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:39:57 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:57 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:39:57 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:57 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:39:57 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 488974104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 488974104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:57 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:39:57 MarkDuplicates Marking 0 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:57 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:39:57 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:57 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:39:57 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:57 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:39:57 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:57 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:39:57 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:57 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:39:57 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:58 MarkDuplicates Before output close freeMemory: 758317744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:58 MarkDuplicates Before output close freeMemory: 758317744; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:58 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:39:58 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:58 MarkDuplicates After output close freeMemory: 758457952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:58 MarkDuplicates After output close freeMemory: 758457952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:39:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:58 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testWithBarcodeComplex STANDARD_ERROR INFO 2024-07-02 11:39:58 MarkDuplicates Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.9784753516473152253.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesTester.9784753516473152253.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.9784753516473152253.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.9784753516473152253.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesTester.9784753516473152253.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.9784753516473152253.tmp/output.sam Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:58.684 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:58.684 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:58.684 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:58.684 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:58.684 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:39:58.684 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:39:58.684 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:39:58.684 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:58 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.9784753516473152253.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.9784753516473152253.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.9784753516473152253.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:39:58 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.9784753516473152253.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.9784753516473152253.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.9784753516473152253.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:39:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:39:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:59 MarkDuplicates Start of doWork freeMemory: 1027944176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:59 MarkDuplicates Start of doWork freeMemory: 1027944176; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:59 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:39:59 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:59 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:39:59 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:59 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:39:59 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:39:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 973411720; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:39:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 973411720; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:40:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:00 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:40:00 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:00 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:40:00 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:00 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:40:00 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 703928328; totalMemory: 1288699904; maxMemory: 2147483648 INFO 2024-07-02 11:40:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 703928328; totalMemory: 1288699904; maxMemory: 2147483648 Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:01 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:40:01 MarkDuplicates Marking 2 records as duplicates. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:01 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:40:01 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:01 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:40:01 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:01 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:40:01 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:01 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:40:01 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:01 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:40:01 MarkDuplicates Getting Memory Stats. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:01 MarkDuplicates Before output close freeMemory: 758313840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:01 MarkDuplicates Before output close freeMemory: 758313840; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:01 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:40:01 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:02 MarkDuplicates After output close freeMemory: 758454096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:02 MarkDuplicates After output close freeMemory: 758454096; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:40:02 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:40:02 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:02 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testWithBarcodeDuplicate STANDARD_ERROR INFO 2024-07-02 11:40:02 MarkDuplicates Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.12727079611969470234.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesTester.12727079611969470234.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.12727079611969470234.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.12727079611969470234.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesTester.12727079611969470234.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.12727079611969470234.tmp/output.sam Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:40:02.417 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:40:02.417 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:40:02.417 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:40:02.417 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:40:02.418 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:40:02.418 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:40:02.418 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:40:02.418 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:40:02 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.12727079611969470234.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.12727079611969470234.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.12727079611969470234.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:40:02 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.12727079611969470234.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.12727079611969470234.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.12727079611969470234.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:40:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:40:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:02 MarkDuplicates Start of doWork freeMemory: 1027944816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:02 MarkDuplicates Start of doWork freeMemory: 1027944816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:02 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:40:02 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:02 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:40:02 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:02 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:40:02 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 973412624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 973412624; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:03 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:40:03 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:04 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:40:04 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:04 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:40:04 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:04 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:40:04 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 488971064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:04 MarkDuplicates After generateDuplicateIndexes freeMemory: 488971064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:04 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:40:04 MarkDuplicates Marking 2 records as duplicates. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:04 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:40:04 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:04 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:40:04 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:04 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:40:04 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:04 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:40:04 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:04 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:40:04 MarkDuplicates Getting Memory Stats. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:05 MarkDuplicates Before output close freeMemory: 758314656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:05 MarkDuplicates Before output close freeMemory: 758314656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:05 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:40:05 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:05 MarkDuplicates After output close freeMemory: 758454912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:05 MarkDuplicates After output close freeMemory: 758454912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:40:05 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:40:05 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:05 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testWithBarcodeFragmentDuplicate STANDARD_ERROR INFO 2024-07-02 11:40:05 MarkDuplicates Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.11366517199000655509.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesTester.11366517199000655509.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.11366517199000655509.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.11366517199000655509.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -INPUT /tmp/MarkDuplicatesTester.11366517199000655509.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.11366517199000655509.tmp/output.sam Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:40:05.615 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:40:05.615 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:40:05.615 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:40:05.615 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:40:05.615 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:40:05.615 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:40:05.615 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:40:05.615 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:40:05 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.11366517199000655509.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.11366517199000655509.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.11366517199000655509.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:40:05 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.11366517199000655509.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.11366517199000655509.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.11366517199000655509.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:40:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:40:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:06 MarkDuplicates Start of doWork freeMemory: 1027945680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:06 MarkDuplicates Start of doWork freeMemory: 1027945680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:06 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:40:06 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:06 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:40:06 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:40:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:40:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:06 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:40:06 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 973414024; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 973414024; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:06 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:40:06 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:07 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:40:07 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:07 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:40:07 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:07 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:40:07 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 488972288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 488972288; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:08 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:40:08 MarkDuplicates Marking 1 records as duplicates. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:08 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:40:08 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:08 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:40:08 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:08 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:40:08 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:08 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:40:08 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:08 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:40:08 MarkDuplicates Getting Memory Stats. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:08 MarkDuplicates Before output close freeMemory: 758316064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:08 MarkDuplicates Before output close freeMemory: 758316064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:08 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:40:08 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:08 MarkDuplicates After output close freeMemory: 758456136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:08 MarkDuplicates After output close freeMemory: 758456136; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:40:08 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:40:08 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:09 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testWithIndividualReadBarcodes STANDARD_ERROR INFO 2024-07-02 11:40:09 MarkDuplicates Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.9027415610405489161.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -READ_ONE_BARCODE_TAG BX -READ_TWO_BARCODE_TAG BX -INPUT /tmp/MarkDuplicatesTester.9027415610405489161.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.9027415610405489161.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.9027415610405489161.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG BC -READ_ONE_BARCODE_TAG BX -READ_TWO_BARCODE_TAG BX -INPUT /tmp/MarkDuplicatesTester.9027415610405489161.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.9027415610405489161.tmp/output.sam Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:40:09.044 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:40:09.044 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:40:09.044 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:40:09.044 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:40:09.044 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:40:09.044 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:40:09.044 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:40:09.044 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:40:09 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC READ_ONE_BARCODE_TAG=BX READ_TWO_BARCODE_TAG=BX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.9027415610405489161.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.9027415610405489161.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.9027415610405489161.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:40:09 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC READ_ONE_BARCODE_TAG=BX READ_TWO_BARCODE_TAG=BX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/MarkDuplicatesTester.9027415610405489161.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.9027415610405489161.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.9027415610405489161.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:40:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:40:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:09 MarkDuplicates Start of doWork freeMemory: 1027941896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:09 MarkDuplicates Start of doWork freeMemory: 1027941896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:09 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:40:09 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:09 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:40:09 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:09 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:40:09 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 973409440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 973409440; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:40:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:40:11 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:40:11 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:11 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:40:11 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 488967968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 488967968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:11 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:40:11 MarkDuplicates Marking 2 records as duplicates. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:11 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:40:11 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:11 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:40:11 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:11 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:40:11 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:11 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:40:11 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:11 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:40:11 MarkDuplicates Getting Memory Stats. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:12 MarkDuplicates Before output close freeMemory: 758311488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:12 MarkDuplicates Before output close freeMemory: 758311488; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:12 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:40:12 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:12 MarkDuplicates After output close freeMemory: 758451816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:12 MarkDuplicates After output close freeMemory: 758451816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:40:12 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:40:12 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:12 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true]) STANDARD_ERROR INFO 2024-07-02 11:40:12 MarkDuplicates Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.7468741292863444525.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI false -INPUT /tmp/MarkDuplicatesTester.7468741292863444525.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.7468741292863444525.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.7468741292863444525.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI false -INPUT /tmp/MarkDuplicatesTester.7468741292863444525.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.7468741292863444525.tmp/output.sam Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:40:12.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:40:12.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:40:12.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:40:12.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:40:12.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:40:12.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:40:12.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:40:12.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:40:12 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=false INPUT=[/tmp/MarkDuplicatesTester.7468741292863444525.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.7468741292863444525.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.7468741292863444525.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:40:12 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=false INPUT=[/tmp/MarkDuplicatesTester.7468741292863444525.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.7468741292863444525.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.7468741292863444525.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:40:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:40:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:12 MarkDuplicates Start of doWork freeMemory: 1027941776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:12 MarkDuplicates Start of doWork freeMemory: 1027941776; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:12 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:40:12 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:12 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:40:12 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:40:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. WARNING 2024-07-02 11:40:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:13 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:40:13 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 973409648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 973409648; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:13 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:40:13 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:40:14 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:14 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:40:14 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:14 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:40:14 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 651497368; totalMemory: 1236271104; maxMemory: 2147483648 INFO 2024-07-02 11:40:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 651497368; totalMemory: 1236271104; maxMemory: 2147483648 Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:14 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:40:14 MarkDuplicates Marking 2 records as duplicates. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:14 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:40:14 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:14 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:40:14 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:14 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:40:14 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:14 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:40:14 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:14 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:40:14 MarkDuplicates Getting Memory Stats. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:15 MarkDuplicates Before output close freeMemory: 758311832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:15 MarkDuplicates Before output close freeMemory: 758311832; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:15 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:40:15 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:15 MarkDuplicates After output close freeMemory: 758451936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:15 MarkDuplicates After output close freeMemory: 758451936; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:40:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:40:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:15 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true]) STANDARD_ERROR INFO 2024-07-02 11:40:15 MarkDuplicates Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.16883649619201567732.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI false -INPUT /tmp/MarkDuplicatesTester.16883649619201567732.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.16883649619201567732.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.16883649619201567732.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI false -INPUT /tmp/MarkDuplicatesTester.16883649619201567732.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.16883649619201567732.tmp/output.sam Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:40:15.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:40:15.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:40:15.743 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:40:15.743 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:40:15.744 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:40:15.744 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:40:15.744 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:40:15.744 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:40:15 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=false INPUT=[/tmp/MarkDuplicatesTester.16883649619201567732.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.16883649619201567732.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.16883649619201567732.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:40:15 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=false INPUT=[/tmp/MarkDuplicatesTester.16883649619201567732.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.16883649619201567732.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.16883649619201567732.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:40:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:40:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:16 MarkDuplicates Start of doWork freeMemory: 1027941224; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:16 MarkDuplicates Start of doWork freeMemory: 1027941224; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:16 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:40:16 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:16 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:40:16 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:40:16 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. WARNING 2024-07-02 11:40:16 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:16 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:40:16 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 973409096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 973409096; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:40:16 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:17 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:40:17 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:17 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:40:17 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:17 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:40:17 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 488967536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 488967536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:17 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:40:17 MarkDuplicates Marking 0 records as duplicates. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:17 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:40:17 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:17 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:40:17 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:17 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:40:17 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:17 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:40:17 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:17 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:40:17 MarkDuplicates Getting Memory Stats. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:18 MarkDuplicates Before output close freeMemory: 758311280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:18 MarkDuplicates Before output close freeMemory: 758311280; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:18 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:40:18 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:18 MarkDuplicates After output close freeMemory: 758451384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:18 MarkDuplicates After output close freeMemory: 758451384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:40:18 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:40:18 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:18 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false]) STANDARD_ERROR INFO 2024-07-02 11:40:18 MarkDuplicates Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.2035141581022650273.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI true -INPUT /tmp/MarkDuplicatesTester.2035141581022650273.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.2035141581022650273.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.2035141581022650273.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI true -INPUT /tmp/MarkDuplicatesTester.2035141581022650273.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.2035141581022650273.tmp/output.sam Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:40:18.535 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:40:18.535 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:40:18.535 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:40:18.535 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:40:18.536 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:40:18.536 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:40:18.536 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:40:18.536 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:40:18 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=true INPUT=[/tmp/MarkDuplicatesTester.2035141581022650273.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.2035141581022650273.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.2035141581022650273.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:40:18 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=true INPUT=[/tmp/MarkDuplicatesTester.2035141581022650273.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.2035141581022650273.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.2035141581022650273.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:40:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:40:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:18 MarkDuplicates Start of doWork freeMemory: 1027940600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:18 MarkDuplicates Start of doWork freeMemory: 1027940600; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:18 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:40:18 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:18 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:40:18 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:40:18 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. WARNING 2024-07-02 11:40:18 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:18 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:40:18 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 973408472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 973408472; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:19 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:40:19 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:20 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:40:20 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:20 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:40:20 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:20 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:40:20 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 488966912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 488966912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:20 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:40:20 MarkDuplicates Marking 2 records as duplicates. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:20 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:40:20 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:20 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:40:20 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:20 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:40:20 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:20 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:40:20 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:20 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:40:20 MarkDuplicates Getting Memory Stats. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:20 MarkDuplicates Before output close freeMemory: 758310656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:20 MarkDuplicates Before output close freeMemory: 758310656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:20 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:40:20 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:21 MarkDuplicates After output close freeMemory: 758450760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:21 MarkDuplicates After output close freeMemory: 758450760; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:40:21 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:40:21 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:21 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTest.testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false]) STANDARD_ERROR INFO 2024-07-02 11:40:21 MarkDuplicates Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.2051505753860813447.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI true -INPUT /tmp/MarkDuplicatesTester.2051505753860813447.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.2051505753860813447.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/MarkDuplicatesTester.2051505753860813447.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -BARCODE_TAG RX -DUPLEX_UMI true -INPUT /tmp/MarkDuplicatesTester.2051505753860813447.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesTester.2051505753860813447.tmp/output.sam Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:40:21.398 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:40:21.398 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:40:21.398 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:40:21.398 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:40:21.399 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:40:21.399 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: 11:40:21.399 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:40:21.399 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:40:21 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=true INPUT=[/tmp/MarkDuplicatesTester.2051505753860813447.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.2051505753860813447.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.2051505753860813447.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:40:21 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=true INPUT=[/tmp/MarkDuplicatesTester.2051505753860813447.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesTester.2051505753860813447.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesTester.2051505753860813447.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:40:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:40:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:21 MarkDuplicates Start of doWork freeMemory: 1027938632; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:21 MarkDuplicates Start of doWork freeMemory: 1027938632; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:21 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:40:21 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:21 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:40:21 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: WARNING 2024-07-02 11:40:21 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. WARNING 2024-07-02 11:40:21 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:21 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:40:21 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 973406504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 973406504; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:40:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:23 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:40:23 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:23 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:40:23 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:23 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:40:23 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 488964944; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 488964944; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:23 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:40:23 MarkDuplicates Marking 0 records as duplicates. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:23 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:40:23 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:23 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:40:23 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:23 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:40:23 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:23 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:40:23 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:23 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:40:23 MarkDuplicates Getting Memory Stats. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:24 MarkDuplicates Before output close freeMemory: 758308688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:24 MarkDuplicates Before output close freeMemory: 758308688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:24 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:40:24 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:40:24 MarkDuplicates After output close freeMemory: 758448296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:24 MarkDuplicates After output close freeMemory: 758448296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:40:24 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:40:24 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:24 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testBulkFragmentsNoDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:40:24 MarkDuplicates Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.9397931286478399625.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.9397931286478399625.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.9397931286478399625.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.9397931286478399625.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.9397931286478399625.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.9397931286478399625.tmp/output.sam Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:40:24.930 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:40:24.930 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:40:24.930 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:40:24.930 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:40:24.930 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:40:24.930 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:40:24.930 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:40:24.930 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:40:24 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.9397931286478399625.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.9397931286478399625.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.9397931286478399625.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:40:24 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.9397931286478399625.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.9397931286478399625.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.9397931286478399625.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:40:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:40:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:25 MarkDuplicates Start of doWork freeMemory: 1021001032; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:25 MarkDuplicates Start of doWork freeMemory: 1021001032; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:25 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:40:25 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:25 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:40:25 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:40:25 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:40:25 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:26 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2024-07-02 11:40:26 MarkDuplicates Read 10000 records. 0 pairs never matched. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 957360912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 957360912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:40:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:40:27 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:40:27 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:27 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:40:27 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 674965592; totalMemory: 1266679808; maxMemory: 2147483648 INFO 2024-07-02 11:40:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 674965592; totalMemory: 1266679808; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:28 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:40:28 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:28 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:40:28 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:28 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:40:28 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:28 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:40:28 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:28 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:40:28 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:28 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:40:28 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:28 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:40:28 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:28 MarkDuplicates Before output close freeMemory: 765002904; totalMemory: 1087373312; maxMemory: 2147483648 INFO 2024-07-02 11:40:28 MarkDuplicates Before output close freeMemory: 765002904; totalMemory: 1087373312; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:29 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:40:29 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:29 MarkDuplicates After output close freeMemory: 765142952; totalMemory: 1087373312; maxMemory: 2147483648 INFO 2024-07-02 11:40:29 MarkDuplicates After output close freeMemory: 765142952; totalMemory: 1087373312; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:40:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:40:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1087373312 Runtime.totalMemory()=1087373312 Running Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:30 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testBulkFragmentsNoDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:40:30 MarkDuplicates Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.11943107439077336235.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.11943107439077336235.tmp/input.bam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.11943107439077336235.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.11943107439077336235.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.11943107439077336235.tmp/input.bam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.11943107439077336235.tmp/output.sam Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:40:30.352 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:40:30.352 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:40:30.352 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:40:30.352 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:40:30.352 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:40:30.352 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:40:30.352 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:40:30.352 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:40:30 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.11943107439077336235.tmp/input.bam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.11943107439077336235.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.11943107439077336235.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:40:30 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.11943107439077336235.tmp/input.bam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.11943107439077336235.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.11943107439077336235.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:40:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:40:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:30 MarkDuplicates Start of doWork freeMemory: 1020934664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:30 MarkDuplicates Start of doWork freeMemory: 1020934664; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:30 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:40:30 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:30 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:40:30 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:40:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:40:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:31 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2024-07-02 11:40:31 MarkDuplicates Read 10000 records. 0 pairs never matched. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 957228504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 957228504; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:40:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:40:33 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:40:33 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:33 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:40:33 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 482026552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 482026552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:33 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:40:33 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:33 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:40:33 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:33 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:40:33 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:33 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:40:33 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:34 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:40:34 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:34 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:40:34 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:34 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:40:34 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:34 MarkDuplicates Before output close freeMemory: 751239296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:34 MarkDuplicates Before output close freeMemory: 751239296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:34 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:40:34 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:34 MarkDuplicates After output close freeMemory: 751378640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:34 MarkDuplicates After output close freeMemory: 751378640; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:40:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. [Tue Jul 02 11:40:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:37 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testBulkFragmentsNoDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:40:37 MarkDuplicates Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.12386333945730103604.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.12386333945730103604.tmp/input.cram -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.12386333945730103604.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester13300543679882813506/input.fasta ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.12386333945730103604.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.12386333945730103604.tmp/input.cram -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.12386333945730103604.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester13300543679882813506/input.fasta Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:40:37.718 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:40:37.718 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:40:37.718 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:40:37.718 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:40:37.718 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:40:37.718 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:40:37.718 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:40:37.718 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:40:37 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.12386333945730103604.tmp/input.cram] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.12386333945730103604.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.12386333945730103604.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester13300543679882813506/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:40:37 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.12386333945730103604.tmp/input.cram] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.12386333945730103604.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.12386333945730103604.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester13300543679882813506/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:40:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:40:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:38 MarkDuplicates Start of doWork freeMemory: 1020997448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:38 MarkDuplicates Start of doWork freeMemory: 1020997448; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:38 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:40:38 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:38 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:40:38 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:40:38 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:40:38 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:39 MarkDuplicates Read 10000 records. 0 pairs never matched. INFO 2024-07-02 11:40:39 MarkDuplicates Read 10000 records. 0 pairs never matched. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 957356768; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 957356768; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:40:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:40:41 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:40:41 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:41 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:40:41 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 482023848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 482023848; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:41 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:40:41 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:41 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:40:41 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:41 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:40:41 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:41 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:40:41 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:42 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:40:42 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:42 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:40:42 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:42 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:40:42 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:43 MarkDuplicates Before output close freeMemory: 751367664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:43 MarkDuplicates Before output close freeMemory: 751367664; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:43 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:40:43 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:43 MarkDuplicates After output close freeMemory: 751507712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:43 MarkDuplicates After output close freeMemory: 751507712; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:40:43 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.10 minutes. [Tue Jul 02 11:40:43 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.10 minutes. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:44 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testBulkFragmentsWithDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:40:44 MarkDuplicates Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.7068185384931694323.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.7068185384931694323.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.7068185384931694323.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.7068185384931694323.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.7068185384931694323.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.7068185384931694323.tmp/output.sam Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:40:44.645 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:40:44.645 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:40:44.645 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:40:44.645 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:40:44.646 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:40:44.646 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:40:44.646 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:40:44.646 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:40:44 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.7068185384931694323.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.7068185384931694323.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.7068185384931694323.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:40:44 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.7068185384931694323.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.7068185384931694323.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.7068185384931694323.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:40:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:40:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:45 MarkDuplicates Start of doWork freeMemory: 1012798144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:45 MarkDuplicates Start of doWork freeMemory: 1012798144; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:45 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:40:45 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:45 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:40:45 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:40:45 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:40:45 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:46 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. INFO 2024-07-02 11:40:46 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:46 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2024-07-02 11:40:46 MarkDuplicates Read 21000 records. 0 pairs never matched. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 948368920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 948368920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:40:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:48 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:40:48 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:48 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:40:48 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:48 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:40:48 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 473827616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 473827616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:49 MarkDuplicates Marking 20000 records as duplicates. INFO 2024-07-02 11:40:49 MarkDuplicates Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:49 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:40:49 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:49 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:40:49 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:49 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:40:49 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:49 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. INFO 2024-07-02 11:40:49 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:50 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:40:50 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:50 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:40:50 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:50 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:40:50 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:50 MarkDuplicates Before output close freeMemory: 743172056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:50 MarkDuplicates Before output close freeMemory: 743172056; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:50 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:40:50 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:50 MarkDuplicates After output close freeMemory: 743311400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:50 MarkDuplicates After output close freeMemory: 743311400; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:40:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.10 minutes. [Tue Jul 02 11:40:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.10 minutes. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:53 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testBulkFragmentsWithDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:40:53 MarkDuplicates Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.17865764399987223051.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.17865764399987223051.tmp/input.bam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.17865764399987223051.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.17865764399987223051.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.17865764399987223051.tmp/input.bam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.17865764399987223051.tmp/output.sam Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:40:53.486 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:40:53.486 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:40:53.487 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:40:53.487 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:40:53.487 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:40:53.487 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:40:53.487 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:40:53.487 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:40:53 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.17865764399987223051.tmp/input.bam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.17865764399987223051.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.17865764399987223051.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:40:53 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.17865764399987223051.tmp/input.bam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.17865764399987223051.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.17865764399987223051.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:40:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:40:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:53 MarkDuplicates Start of doWork freeMemory: 1012732064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:53 MarkDuplicates Start of doWork freeMemory: 1012732064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:53 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:40:53 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:53 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:40:53 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:40:54 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:40:54 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:54 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. INFO 2024-07-02 11:40:54 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:55 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2024-07-02 11:40:55 MarkDuplicates Read 21000 records. 0 pairs never matched. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 948236712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 948236712; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:40:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:57 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:40:57 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:57 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:40:57 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:57 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:40:57 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 473826760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 473826760; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:57 MarkDuplicates Marking 20000 records as duplicates. INFO 2024-07-02 11:40:57 MarkDuplicates Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:57 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:40:57 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:57 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:40:57 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:57 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:40:57 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:58 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. INFO 2024-07-02 11:40:58 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:58 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:40:58 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:58 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:40:58 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:58 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:40:58 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:58 MarkDuplicates Before output close freeMemory: 743031896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:58 MarkDuplicates Before output close freeMemory: 743031896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:58 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:40:58 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:40:59 MarkDuplicates After output close freeMemory: 743031896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:40:59 MarkDuplicates After output close freeMemory: 743031896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:40:59 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.10 minutes. [Tue Jul 02 11:40:59 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.10 minutes. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:05 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testBulkFragmentsWithDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:41:05 MarkDuplicates Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.5718706122767128182.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.5718706122767128182.tmp/input.cram -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.5718706122767128182.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester16894285681702160253/input.fasta ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.5718706122767128182.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.5718706122767128182.tmp/input.cram -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.5718706122767128182.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester16894285681702160253/input.fasta Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:41:05.075 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:41:05.075 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:41:05.075 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:41:05.075 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:41:05.075 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:41:05.075 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:41:05.075 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:41:05.075 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:41:05 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.5718706122767128182.tmp/input.cram] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.5718706122767128182.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.5718706122767128182.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester16894285681702160253/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:41:05 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.5718706122767128182.tmp/input.cram] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.5718706122767128182.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.5718706122767128182.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester16894285681702160253/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:41:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:41:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:05 MarkDuplicates Start of doWork freeMemory: 1012626168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:41:05 MarkDuplicates Start of doWork freeMemory: 1012626168; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:05 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:41:05 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:05 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:41:05 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:41:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:41:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:07 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. INFO 2024-07-02 11:41:07 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:07 MarkDuplicates Read 21000 records. 0 pairs never matched. INFO 2024-07-02 11:41:07 MarkDuplicates Read 21000 records. 0 pairs never matched. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 948365656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:41:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 948365656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:41:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:09 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:41:09 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:09 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:41:09 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:09 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:41:09 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 1012792576; totalMemory: 1612709888; maxMemory: 2147483648 INFO 2024-07-02 11:41:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 1012792576; totalMemory: 1612709888; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:10 MarkDuplicates Marking 20000 records as duplicates. INFO 2024-07-02 11:41:10 MarkDuplicates Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:10 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:41:10 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:10 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:41:10 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:10 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:41:10 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:11 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. INFO 2024-07-02 11:41:11 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:12 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:41:12 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:12 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:41:12 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:12 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:41:12 MarkDuplicates Getting Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:12 MarkDuplicates Before output close freeMemory: 788257384; totalMemory: 1118830592; maxMemory: 2147483648 INFO 2024-07-02 11:41:12 MarkDuplicates Before output close freeMemory: 788257384; totalMemory: 1118830592; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:12 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:41:12 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:13 MarkDuplicates After output close freeMemory: 777911200; totalMemory: 1108344832; maxMemory: 2147483648 INFO 2024-07-02 11:41:13 MarkDuplicates After output close freeMemory: 777911200; totalMemory: 1108344832; maxMemory: 2147483648 Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:41:13 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.13 minutes. [Tue Jul 02 11:41:13 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.13 minutes. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1108344832 Runtime.totalMemory()=1108344832 Running Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:14 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testBulkPairsNoDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:41:14 MarkDuplicates Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.14551051159817734231.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.14551051159817734231.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.14551051159817734231.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.14551051159817734231.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.14551051159817734231.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.14551051159817734231.tmp/output.sam Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:41:14.960 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:41:14.960 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:41:14.960 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:41:14.960 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:41:14.960 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:41:14.960 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:41:14.960 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:41:14.960 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:41:14 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.14551051159817734231.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.14551051159817734231.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.14551051159817734231.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:41:14 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.14551051159817734231.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.14551051159817734231.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.14551051159817734231.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:41:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:41:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:15 MarkDuplicates Start of doWork freeMemory: 1012282552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:41:15 MarkDuplicates Start of doWork freeMemory: 1012282552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:15 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:41:15 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:15 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:41:15 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:41:15 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:41:15 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:15 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. INFO 2024-07-02 11:41:15 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:17 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2024-07-02 11:41:17 MarkDuplicates Read 20200 records. 0 pairs never matched. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 947180920; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:41:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 947180920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:41:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:41:19 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:19 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:41:19 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:19 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:41:19 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 742793072; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:41:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 742793072; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:19 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:41:19 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:19 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:41:19 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:19 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:41:19 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:19 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:41:19 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:19 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. INFO 2024-07-02 11:41:19 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:20 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:41:20 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:20 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:41:20 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:20 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:41:20 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:21 MarkDuplicates Before output close freeMemory: 787742248; totalMemory: 1118830592; maxMemory: 2147483648 INFO 2024-07-02 11:41:21 MarkDuplicates Before output close freeMemory: 787742248; totalMemory: 1118830592; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:21 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:41:21 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:21 MarkDuplicates After output close freeMemory: 787881592; totalMemory: 1118830592; maxMemory: 2147483648 INFO 2024-07-02 11:41:21 MarkDuplicates After output close freeMemory: 787881592; totalMemory: 1118830592; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:41:21 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.12 minutes. [Tue Jul 02 11:41:21 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.12 minutes. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1118830592 Runtime.totalMemory()=1118830592 Running Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:24 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testBulkPairsNoDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:41:24 MarkDuplicates Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.7228178139995236389.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.7228178139995236389.tmp/input.bam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.7228178139995236389.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.7228178139995236389.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.7228178139995236389.tmp/input.bam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.7228178139995236389.tmp/output.sam Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:41:24.623 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:41:24.623 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:41:24.623 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:41:24.623 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:41:24.629 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:41:24.629 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:41:24.629 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:41:24.629 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:41:24 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.7228178139995236389.tmp/input.bam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.7228178139995236389.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.7228178139995236389.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:41:24 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.7228178139995236389.tmp/input.bam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.7228178139995236389.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.7228178139995236389.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:41:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:41:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:25 MarkDuplicates Start of doWork freeMemory: 1012216448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:41:25 MarkDuplicates Start of doWork freeMemory: 1012216448; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:25 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:41:25 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:25 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:41:25 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:41:25 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:41:25 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:25 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. INFO 2024-07-02 11:41:25 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:27 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2024-07-02 11:41:27 MarkDuplicates Read 20200 records. 0 pairs never matched. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 947048688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:41:28 MarkDuplicates After buildSortedReadEndLists freeMemory: 947048688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:41:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:29 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:41:29 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:29 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:41:29 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:29 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:41:29 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 473308160; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:41:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 473308160; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:30 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:41:30 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:30 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:41:30 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:30 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:41:30 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:30 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:41:30 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:30 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. INFO 2024-07-02 11:41:30 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:31 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:41:31 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:31 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:41:31 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:31 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:41:31 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:31 MarkDuplicates Before output close freeMemory: 742520904; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:41:31 MarkDuplicates Before output close freeMemory: 742520904; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:31 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:41:31 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:32 MarkDuplicates After output close freeMemory: 742660248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:41:32 MarkDuplicates After output close freeMemory: 742660248; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:41:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.12 minutes. [Tue Jul 02 11:41:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.12 minutes. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:38 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testBulkPairsNoDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:41:38 MarkDuplicates Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.16576965906549274140.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.16576965906549274140.tmp/input.cram -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.16576965906549274140.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester9517554689468515682/input.fasta ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.16576965906549274140.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.16576965906549274140.tmp/input.cram -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.16576965906549274140.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester9517554689468515682/input.fasta Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:41:38.423 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:41:38.423 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:41:38.423 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:41:38.423 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:41:38.423 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:41:38.423 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:41:38.424 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:41:38.424 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:41:38 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.16576965906549274140.tmp/input.cram] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.16576965906549274140.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.16576965906549274140.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester9517554689468515682/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:41:38 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.16576965906549274140.tmp/input.cram] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.16576965906549274140.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.16576965906549274140.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester9517554689468515682/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:41:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:41:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:39 MarkDuplicates Start of doWork freeMemory: 1012279712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:41:39 MarkDuplicates Start of doWork freeMemory: 1012279712; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:39 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:41:39 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:39 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:41:39 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:41:40 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:41:40 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:40 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. INFO 2024-07-02 11:41:40 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:43 MarkDuplicates Read 20200 records. 0 pairs never matched. INFO 2024-07-02 11:41:43 MarkDuplicates Read 20200 records. 0 pairs never matched. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 947177552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:41:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 947177552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:41:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:46 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:41:46 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:46 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:41:46 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:46 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:41:46 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 742789864; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:41:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 742789864; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:47 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:41:47 MarkDuplicates Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:47 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:41:47 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:47 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:41:47 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:47 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:41:47 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:48 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. INFO 2024-07-02 11:41:48 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:50 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:41:50 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:50 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:41:50 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:50 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:41:50 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:51 MarkDuplicates Before output close freeMemory: 795079048; totalMemory: 1126170624; maxMemory: 2147483648 INFO 2024-07-02 11:41:51 MarkDuplicates Before output close freeMemory: 795079048; totalMemory: 1126170624; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:51 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:41:51 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:52 MarkDuplicates After output close freeMemory: 787878360; totalMemory: 1118830592; maxMemory: 2147483648 INFO 2024-07-02 11:41:52 MarkDuplicates After output close freeMemory: 787878360; totalMemory: 1118830592; maxMemory: 2147483648 Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:41:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.23 minutes. [Tue Jul 02 11:41:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.23 minutes. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1118830592 Runtime.totalMemory()=1118830592 Running Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:54 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testBulkPairsWithDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:41:54 MarkDuplicates Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.11326689649808033326.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.11326689649808033326.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.11326689649808033326.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.11326689649808033326.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.11326689649808033326.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.11326689649808033326.tmp/output.sam Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:41:54.131 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:41:54.131 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:41:54.131 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:41:54.131 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:41:54.132 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:41:54.132 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:41:54.132 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:41:54.132 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:41:54 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.11326689649808033326.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.11326689649808033326.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.11326689649808033326.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:41:54 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.11326689649808033326.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.11326689649808033326.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.11326689649808033326.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:41:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:41:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:54 MarkDuplicates Start of doWork freeMemory: 1022800016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:41:54 MarkDuplicates Start of doWork freeMemory: 1022800016; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:54 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:41:54 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:54 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:41:54 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:41:54 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:41:54 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:55 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. INFO 2024-07-02 11:41:55 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:55 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2024-07-02 11:41:55 MarkDuplicates Read 6820 records. 0 pairs never matched. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 959143424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:41:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 959143424; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:41:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:58 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:41:58 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:58 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:41:58 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:58 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:41:58 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 483826504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:41:58 MarkDuplicates After generateDuplicateIndexes freeMemory: 483826504; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:58 MarkDuplicates Marking 3100 records as duplicates. INFO 2024-07-02 11:41:58 MarkDuplicates Marking 3100 records as duplicates. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:58 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:41:58 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:58 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:41:58 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:58 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:41:58 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:59 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. INFO 2024-07-02 11:41:59 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:59 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:41:59 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:59 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:41:59 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:59 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:41:59 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:59 MarkDuplicates Before output close freeMemory: 753170944; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:41:59 MarkDuplicates Before output close freeMemory: 753170944; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:41:59 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:41:59 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:00 MarkDuplicates After output close freeMemory: 753310288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:00 MarkDuplicates After output close freeMemory: 753310288; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.10 minutes. [Tue Jul 02 11:42:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.10 minutes. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:01 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testBulkPairsWithDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:42:01 MarkDuplicates Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.3882671844650924225.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.3882671844650924225.tmp/input.bam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.3882671844650924225.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.3882671844650924225.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.3882671844650924225.tmp/input.bam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.3882671844650924225.tmp/output.sam Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:01.650 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:42:01.650 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:01.650 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:42:01.650 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:01.651 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:42:01.651 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:01.651 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:42:01.651 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:01 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.3882671844650924225.tmp/input.bam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.3882671844650924225.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.3882671844650924225.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:42:01 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.3882671844650924225.tmp/input.bam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.3882671844650924225.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.3882671844650924225.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:42:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:02 MarkDuplicates Start of doWork freeMemory: 1022733984; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:02 MarkDuplicates Start of doWork freeMemory: 1022733984; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:02 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:42:02 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:02 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:42:02 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:42:02 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:42:02 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:02 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. INFO 2024-07-02 11:42:02 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:03 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2024-07-02 11:42:03 MarkDuplicates Read 6820 records. 0 pairs never matched. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 959011264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 959011264; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:04 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:42:04 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:06 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:42:06 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:06 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:42:06 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:06 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:42:06 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 483825696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 483825696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:07 MarkDuplicates Marking 3100 records as duplicates. INFO 2024-07-02 11:42:07 MarkDuplicates Marking 3100 records as duplicates. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:07 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:42:07 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:07 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:42:07 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:07 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:42:07 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:07 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. INFO 2024-07-02 11:42:07 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:08 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:42:08 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:08 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:42:08 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:08 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:42:08 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:08 MarkDuplicates Before output close freeMemory: 753037808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:08 MarkDuplicates Before output close freeMemory: 753037808; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:08 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:42:08 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:09 MarkDuplicates After output close freeMemory: 753177784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:09 MarkDuplicates After output close freeMemory: 753177784; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:09 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.13 minutes. [Tue Jul 02 11:42:09 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.13 minutes. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:14 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testBulkPairsWithDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:42:14 MarkDuplicates Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.16731902355299767811.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.16731902355299767811.tmp/input.cram -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.16731902355299767811.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester852550070914960105/input.fasta ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.16731902355299767811.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.16731902355299767811.tmp/input.cram -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.16731902355299767811.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester852550070914960105/input.fasta Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:14.177 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:42:14.177 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:14.177 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:42:14.177 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:14.177 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:42:14.177 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:14.177 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:42:14.177 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:14 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.16731902355299767811.tmp/input.cram] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.16731902355299767811.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.16731902355299767811.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester852550070914960105/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:42:14 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.16731902355299767811.tmp/input.cram] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.16731902355299767811.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.16731902355299767811.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester852550070914960105/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:42:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:14 MarkDuplicates Start of doWork freeMemory: 1022797272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:14 MarkDuplicates Start of doWork freeMemory: 1022797272; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:14 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:42:14 MarkDuplicates Reading input file and constructing read end information. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:14 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:42:14 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:42:16 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:42:16 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:16 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. INFO 2024-07-02 11:42:16 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:17 MarkDuplicates Read 6820 records. 0 pairs never matched. INFO 2024-07-02 11:42:17 MarkDuplicates Read 6820 records. 0 pairs never matched. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 959140272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 959140272; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:42:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:42:19 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:19 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:42:19 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:19 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:42:19 MarkDuplicates Sorting list of duplicate records. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 483823512; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 483823512; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:20 MarkDuplicates Marking 3100 records as duplicates. INFO 2024-07-02 11:42:20 MarkDuplicates Marking 3100 records as duplicates. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:20 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:42:20 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:20 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:42:20 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:20 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:42:20 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:22 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. INFO 2024-07-02 11:42:22 MarkDuplicates Seen many non-increasing record positions. Printing Read-names as well. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:22 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:42:22 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:22 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:42:22 MarkDuplicates Duplicate Index cleanup. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:22 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:42:22 MarkDuplicates Getting Memory Stats. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:22 MarkDuplicates Before output close freeMemory: 753167928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:22 MarkDuplicates Before output close freeMemory: 753167928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:22 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:42:22 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:23 MarkDuplicates After output close freeMemory: 753307272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:23 MarkDuplicates After output close freeMemory: 753307272; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:23 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.16 minutes. [Tue Jul 02 11:42:23 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.16 minutes. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:24 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testDifferentChromosomesInOppositeOrder STANDARD_ERROR INFO 2024-07-02 11:42:24 MarkDuplicates Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.16739490902442988045.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.16739490902442988045.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.16739490902442988045.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.16739490902442988045.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.16739490902442988045.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.16739490902442988045.tmp/output.sam Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:24.932 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:42:24.932 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:24.945 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:42:24.945 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:24.959 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:42:24.959 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:24.969 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:42:24.969 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:24 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.16739490902442988045.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.16739490902442988045.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.16739490902442988045.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:42:24 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.16739490902442988045.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.16739490902442988045.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.16739490902442988045.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:42:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:25 MarkDuplicates Start of doWork freeMemory: 1027919264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:25 MarkDuplicates Start of doWork freeMemory: 1027919264; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:25 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:42:25 MarkDuplicates Reading input file and constructing read end information. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:25 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:42:25 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:25 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:42:25 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 964998736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 964998736; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:42:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:42:27 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:42:27 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:27 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:42:27 MarkDuplicates Sorting list of duplicate records. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 488945536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 488945536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:28 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:42:28 MarkDuplicates Marking 1 records as duplicates. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:28 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:42:28 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:28 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:42:28 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:28 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:42:28 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:28 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:42:28 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:28 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:42:28 MarkDuplicates Duplicate Index cleanup. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:28 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:42:28 MarkDuplicates Getting Memory Stats. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:28 MarkDuplicates Before output close freeMemory: 758289976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:28 MarkDuplicates Before output close freeMemory: 758289976; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:28 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:42:28 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:29 MarkDuplicates After output close freeMemory: 758429320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:29 MarkDuplicates After output close freeMemory: 758429320; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. [Tue Jul 02 11:42:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:29 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:42:29 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.7479207067597679676.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.7479207067597679676.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.7479207067597679676.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.7479207067597679676.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.7479207067597679676.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.7479207067597679676.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:29.670 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:42:29.670 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:29.670 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:42:29.670 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:29.671 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:42:29.671 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:29.671 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:42:29.671 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:29 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.7479207067597679676.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.7479207067597679676.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.7479207067597679676.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:42:29 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.7479207067597679676.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.7479207067597679676.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.7479207067597679676.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:42:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:30 MarkDuplicates Start of doWork freeMemory: 1027913288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:30 MarkDuplicates Start of doWork freeMemory: 1027913288; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:30 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:42:30 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:30 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:42:30 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:30 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:42:30 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 964992008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 964992008; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:42:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:32 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:42:32 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:32 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:42:32 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:32 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:42:32 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 488939456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 488939456; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:32 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:42:32 MarkDuplicates Marking 4 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:32 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:42:32 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:32 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:42:32 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:32 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:42:32 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:32 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:42:32 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:32 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:42:32 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:32 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:42:32 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:33 MarkDuplicates Before output close freeMemory: 758283896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:33 MarkDuplicates Before output close freeMemory: 758283896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:33 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:42:33 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:34 MarkDuplicates After output close freeMemory: 758423240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:34 MarkDuplicates After output close freeMemory: 758423240; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:42:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:34 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:42:34 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.9141561084354278862.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.9141561084354278862.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.9141561084354278862.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.9141561084354278862.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.9141561084354278862.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.9141561084354278862.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:34.208 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:42:34.208 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:34.208 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:42:34.208 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:34.208 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:42:34.208 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:34.208 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:42:34.208 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:34 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.9141561084354278862.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.9141561084354278862.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.9141561084354278862.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:42:34 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.9141561084354278862.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.9141561084354278862.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.9141561084354278862.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:42:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:34 MarkDuplicates Start of doWork freeMemory: 1027912760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:34 MarkDuplicates Start of doWork freeMemory: 1027912760; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:34 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:42:34 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:34 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:42:34 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:34 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:42:34 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 964991480; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 964991480; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:42:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:42:37 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:42:37 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:37 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:42:37 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 488938928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 488938928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:38 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:42:38 MarkDuplicates Marking 4 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:38 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:42:38 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:38 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:42:38 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:38 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:42:38 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:38 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:42:38 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:38 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:42:38 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:38 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:42:38 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:38 MarkDuplicates Before output close freeMemory: 758283368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:38 MarkDuplicates Before output close freeMemory: 758283368; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:38 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:42:38 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:38 MarkDuplicates After output close freeMemory: 758422712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:38 MarkDuplicates After output close freeMemory: 758422712; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:38 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. [Tue Jul 02 11:42:38 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:39 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:42:39 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.9671005232331087225.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.9671005232331087225.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.9671005232331087225.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.9671005232331087225.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.9671005232331087225.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.9671005232331087225.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:39.012 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:42:39.012 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:39.025 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:42:39.025 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:39.025 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:42:39.025 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:39.025 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:42:39.025 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:39 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.9671005232331087225.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.9671005232331087225.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.9671005232331087225.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:42:39 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.9671005232331087225.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.9671005232331087225.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.9671005232331087225.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:42:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:39 MarkDuplicates Start of doWork freeMemory: 1027912368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:39 MarkDuplicates Start of doWork freeMemory: 1027912368; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:39 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:42:39 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:39 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:42:39 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:39 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:42:39 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 964991088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 964991088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:42:40 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:41 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:42:41 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:41 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:42:41 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:41 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:42:41 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 488938536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:41 MarkDuplicates After generateDuplicateIndexes freeMemory: 488938536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:41 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:42:41 MarkDuplicates Marking 4 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:41 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:42:41 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:41 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:42:41 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:41 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:42:41 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:41 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:42:41 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:41 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:42:41 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:41 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:42:41 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:42 MarkDuplicates Before output close freeMemory: 758281152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:42 MarkDuplicates Before output close freeMemory: 758281152; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:42 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:42:42 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:42 MarkDuplicates After output close freeMemory: 758422392; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:42 MarkDuplicates After output close freeMemory: 758422392; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:42:42 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:42 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:42:42 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.976009579515604641.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.976009579515604641.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.976009579515604641.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.976009579515604641.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.976009579515604641.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.976009579515604641.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:42.643 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:42:42.643 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:42.643 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:42:42.643 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:42.644 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:42:42.644 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:42.644 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:42:42.644 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:42 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.976009579515604641.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.976009579515604641.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.976009579515604641.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:42:42 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.976009579515604641.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.976009579515604641.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.976009579515604641.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:42:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:42 MarkDuplicates Start of doWork freeMemory: 1027912088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:42 MarkDuplicates Start of doWork freeMemory: 1027912088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:42 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:42:42 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:42 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:42:42 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:43 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:42:43 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 964990808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 964990808; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:42:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:42:44 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:44 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:42:44 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:44 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:42:44 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 488938256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 488938256; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:45 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:42:45 MarkDuplicates Marking 4 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:45 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:42:45 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:45 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:42:45 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:45 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:42:45 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:45 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:42:45 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:45 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:42:45 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:45 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:42:45 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:45 MarkDuplicates Before output close freeMemory: 758282696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:45 MarkDuplicates Before output close freeMemory: 758282696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:45 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:42:45 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:45 MarkDuplicates After output close freeMemory: 758422040; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:45 MarkDuplicates After output close freeMemory: 758422040; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:42:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:46 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:42:46 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.18211152359516430528.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.18211152359516430528.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.18211152359516430528.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.18211152359516430528.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.18211152359516430528.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.18211152359516430528.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:46.028 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:42:46.028 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:46.028 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:42:46.028 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:46.028 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:42:46.028 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:46.028 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:42:46.028 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:46 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.18211152359516430528.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.18211152359516430528.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.18211152359516430528.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:42:46 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.18211152359516430528.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.18211152359516430528.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.18211152359516430528.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:42:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:46 MarkDuplicates Start of doWork freeMemory: 1027911680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:46 MarkDuplicates Start of doWork freeMemory: 1027911680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:46 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:42:46 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:46 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:42:46 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:46 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:42:46 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 964990400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 964990400; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:42:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:47 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:42:47 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:47 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:42:47 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:47 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:42:47 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 488971552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 488971552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:48 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:42:48 MarkDuplicates Marking 4 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:48 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:42:48 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:48 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:42:48 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:48 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:42:48 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:48 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:42:48 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:48 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:42:48 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:48 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:42:48 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:48 MarkDuplicates Before output close freeMemory: 758315992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:48 MarkDuplicates Before output close freeMemory: 758315992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:48 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:42:48 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:49 MarkDuplicates After output close freeMemory: 758454840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:49 MarkDuplicates After output close freeMemory: 758454840; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:42:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:49 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:42:49 MarkDuplicates Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.11074490666597865140.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.11074490666597865140.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.11074490666597865140.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.11074490666597865140.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.11074490666597865140.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.11074490666597865140.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:49.222 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:42:49.222 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:49.222 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:42:49.222 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:49.222 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:42:49.222 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:49.223 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:42:49.223 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:49 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.11074490666597865140.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.11074490666597865140.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.11074490666597865140.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:42:49 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.11074490666597865140.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.11074490666597865140.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.11074490666597865140.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:42:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:49 MarkDuplicates Start of doWork freeMemory: 1027942136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:49 MarkDuplicates Start of doWork freeMemory: 1027942136; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:49 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:42:49 MarkDuplicates Reading input file and constructing read end information. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:42:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:49 MarkDuplicates Read 11 records. 0 pairs never matched. INFO 2024-07-02 11:42:49 MarkDuplicates Read 11 records. 0 pairs never matched. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 965023664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 965023664; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:42:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:51 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:42:51 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:51 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:42:51 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:51 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:42:51 MarkDuplicates Sorting list of duplicate records. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 620043112; totalMemory: 1204813824; maxMemory: 2147483648 INFO 2024-07-02 11:42:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 620043112; totalMemory: 1204813824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:51 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:42:51 MarkDuplicates Marking 4 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:51 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:42:51 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:51 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:42:51 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:51 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:42:51 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:51 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:42:51 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:51 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:42:51 MarkDuplicates Duplicate Index cleanup. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:51 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:42:51 MarkDuplicates Getting Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:51 MarkDuplicates Before output close freeMemory: 758315552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:51 MarkDuplicates Before output close freeMemory: 758315552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:51 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:42:51 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:52 MarkDuplicates After output close freeMemory: 758454400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:52 MarkDuplicates After output close freeMemory: 758454400; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:42:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:52 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testMappedFragmentAndMappedPairFirstOfPairNonPrimary STANDARD_ERROR INFO 2024-07-02 11:42:52 MarkDuplicates Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.15928997720438266854.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.15928997720438266854.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.15928997720438266854.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.15928997720438266854.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.15928997720438266854.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.15928997720438266854.tmp/output.sam Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:52.225 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:42:52.225 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:52.225 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:42:52.225 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:52.225 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:42:52.225 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:52.226 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:42:52.226 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:52 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.15928997720438266854.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.15928997720438266854.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.15928997720438266854.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:42:52 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.15928997720438266854.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.15928997720438266854.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.15928997720438266854.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:42:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:52 MarkDuplicates Start of doWork freeMemory: 1027951144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:52 MarkDuplicates Start of doWork freeMemory: 1027951144; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:52 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:42:52 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:52 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:42:52 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:42:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:42:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:52 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:42:52 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 964929624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 964929624; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:42:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:54 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:42:54 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:54 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:42:54 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:54 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:42:54 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 488977704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 488977704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:54 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:42:54 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:54 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:42:54 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:54 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:42:54 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:54 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:42:54 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:54 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:42:54 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:54 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:42:54 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:54 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:42:54 MarkDuplicates Getting Memory Stats. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:55 MarkDuplicates Before output close freeMemory: 758322144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:55 MarkDuplicates Before output close freeMemory: 758322144; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:55 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:42:55 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:55 MarkDuplicates After output close freeMemory: 758461488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:55 MarkDuplicates After output close freeMemory: 758461488; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:55 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:42:55 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:55 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testMappedFragmentAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:42:55 MarkDuplicates Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.13860134629295454004.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.13860134629295454004.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.13860134629295454004.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.13860134629295454004.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.13860134629295454004.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.13860134629295454004.tmp/output.sam Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:55.990 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:42:55.990 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:55.990 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:42:55.990 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:55.990 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:42:55.990 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:42:55.990 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:42:55.990 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:55 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.13860134629295454004.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.13860134629295454004.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.13860134629295454004.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:42:55 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.13860134629295454004.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.13860134629295454004.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.13860134629295454004.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:42:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:56 MarkDuplicates Start of doWork freeMemory: 1027950352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:56 MarkDuplicates Start of doWork freeMemory: 1027950352; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:56 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:42:56 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:56 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:42:56 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:42:56 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:42:56 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:56 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2024-07-02 11:42:56 MarkDuplicates Read 3 records. 0 pairs never matched. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 964928760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 964928760; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:42:57 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:58 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:42:58 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:58 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:42:58 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:58 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:42:58 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 488976248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 488976248; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:59 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:42:59 MarkDuplicates Marking 1 records as duplicates. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:59 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:42:59 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:59 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:42:59 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:59 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:42:59 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:59 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:42:59 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:59 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:42:59 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:59 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:42:59 MarkDuplicates Getting Memory Stats. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:59 MarkDuplicates Before output close freeMemory: 758319528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:59 MarkDuplicates Before output close freeMemory: 758319528; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:59 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:42:59 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:42:59 MarkDuplicates After output close freeMemory: 758460696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:42:59 MarkDuplicates After output close freeMemory: 758460696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:42:59 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:42:59 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:00 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testMappedFragmentAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:43:00 MarkDuplicates Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.9466093831691373965.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.9466093831691373965.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.9466093831691373965.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.9466093831691373965.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.9466093831691373965.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.9466093831691373965.tmp/output.sam Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:00.126 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:43:00.126 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:00.126 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:43:00.126 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:00.127 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:43:00.127 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:00.127 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:43:00.127 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:00 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.9466093831691373965.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.9466093831691373965.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.9466093831691373965.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:43:00 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.9466093831691373965.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.9466093831691373965.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.9466093831691373965.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:43:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:00 MarkDuplicates Start of doWork freeMemory: 1027949968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:00 MarkDuplicates Start of doWork freeMemory: 1027949968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:00 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:43:00 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:00 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:43:00 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:43:00 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:43:00 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:00 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2024-07-02 11:43:00 MarkDuplicates Read 3 records. 0 pairs never matched. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 965029088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 965029088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:43:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:02 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:43:02 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:02 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:43:02 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:02 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:43:02 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 488976528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 488976528; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:02 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:43:02 MarkDuplicates Marking 1 records as duplicates. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:02 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:43:02 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:02 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:43:02 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:02 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:43:02 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:02 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:43:02 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:02 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:43:02 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:02 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:43:02 MarkDuplicates Getting Memory Stats. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:03 MarkDuplicates Before output close freeMemory: 758319144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:03 MarkDuplicates Before output close freeMemory: 758319144; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:03 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:43:03 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:03 MarkDuplicates After output close freeMemory: 758460312; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:03 MarkDuplicates After output close freeMemory: 758460312; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:03 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:43:03 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:03 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testMappedPairAndMappedFragmentAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:43:03 MarkDuplicates Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.13846000401594938610.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.13846000401594938610.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.13846000401594938610.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.13846000401594938610.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.13846000401594938610.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.13846000401594938610.tmp/output.sam Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:03.726 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:43:03.726 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:03.726 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:43:03.726 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:03.726 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:43:03.726 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:03.726 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:43:03.726 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:03 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.13846000401594938610.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.13846000401594938610.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.13846000401594938610.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:43:03 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.13846000401594938610.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.13846000401594938610.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.13846000401594938610.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:43:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:04 MarkDuplicates Start of doWork freeMemory: 1027844560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:04 MarkDuplicates Start of doWork freeMemory: 1027844560; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:04 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:43:04 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:04 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:43:04 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:43:04 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:43:04 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:04 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:43:04 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 964926272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 964926272; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:43:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:06 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:43:06 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:06 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:43:06 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:06 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:43:06 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 603269248; totalMemory: 1188036608; maxMemory: 2147483648 INFO 2024-07-02 11:43:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 603269248; totalMemory: 1188036608; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:06 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:43:06 MarkDuplicates Marking 2 records as duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:06 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:43:06 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:06 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:43:06 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:06 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:43:06 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:06 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:43:06 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:06 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:43:06 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:06 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:43:06 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:07 MarkDuplicates Before output close freeMemory: 758318904; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:07 MarkDuplicates Before output close freeMemory: 758318904; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:07 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:43:07 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:07 MarkDuplicates After output close freeMemory: 758458248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:07 MarkDuplicates After output close freeMemory: 758458248; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:07 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:43:07 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:07 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testMappedPairAndMappedFragmentAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:43:07 MarkDuplicates Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.12079420379469132801.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.12079420379469132801.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.12079420379469132801.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.12079420379469132801.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.12079420379469132801.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.12079420379469132801.tmp/output.sam Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:07.959 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:43:07.959 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:07.960 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:43:07.960 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:07.960 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:43:07.960 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:07.960 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:43:07.960 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:07 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.12079420379469132801.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.12079420379469132801.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.12079420379469132801.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:43:07 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.12079420379469132801.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.12079420379469132801.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.12079420379469132801.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:43:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:08 MarkDuplicates Start of doWork freeMemory: 1027942296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:08 MarkDuplicates Start of doWork freeMemory: 1027942296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:08 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:43:08 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:08 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:43:08 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:43:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:43:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:08 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:43:08 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 965027016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 965027016; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:43:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:10 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:43:10 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:10 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:43:10 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:10 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:43:10 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 491358320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 491358320; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:10 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:43:10 MarkDuplicates Marking 2 records as duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:10 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:43:10 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:10 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:43:10 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:10 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:43:10 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:10 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:43:10 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:10 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:43:10 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:10 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:43:10 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:11 MarkDuplicates Before output close freeMemory: 760702760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:11 MarkDuplicates Before output close freeMemory: 760702760; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:11 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:43:11 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:11 MarkDuplicates After output close freeMemory: 760842104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:11 MarkDuplicates After output close freeMemory: 760842104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:11 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:43:11 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:11 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:43:11 MarkDuplicates Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.12959448946198899774.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.12959448946198899774.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.12959448946198899774.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.12959448946198899774.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.12959448946198899774.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.12959448946198899774.tmp/output.sam Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:11.944 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:43:11.944 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:11.944 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:43:11.944 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:11.944 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:43:11.944 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:11.944 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:43:11.944 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:11 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.12959448946198899774.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.12959448946198899774.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.12959448946198899774.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:43:11 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.12959448946198899774.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.12959448946198899774.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.12959448946198899774.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:43:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:12 MarkDuplicates Start of doWork freeMemory: 1030331888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:12 MarkDuplicates Start of doWork freeMemory: 1030331888; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:12 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:43:12 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:12 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:43:12 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:43:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:43:12 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:12 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:43:12 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 967411464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 967411464; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:13 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:43:13 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:43:14 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:14 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:43:14 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:14 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:43:14 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 491391576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 491391576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:15 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:43:15 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:15 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:43:15 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:15 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:43:15 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:15 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:43:15 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:15 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:43:15 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:15 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:43:15 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:15 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:43:15 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:15 MarkDuplicates Before output close freeMemory: 760736016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:15 MarkDuplicates Before output close freeMemory: 760736016; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:15 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:43:15 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:15 MarkDuplicates After output close freeMemory: 760875360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:15 MarkDuplicates After output close freeMemory: 760875360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:43:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:16 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testMappedPairAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:43:16 MarkDuplicates Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.3266483998809847703.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.3266483998809847703.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.3266483998809847703.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.3266483998809847703.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.3266483998809847703.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.3266483998809847703.tmp/output.sam Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:16.067 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:43:16.067 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:16.068 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:43:16.068 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:16.068 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:43:16.068 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:16.068 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:43:16.068 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:16 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.3266483998809847703.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.3266483998809847703.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.3266483998809847703.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:43:16 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.3266483998809847703.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.3266483998809847703.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.3266483998809847703.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:43:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:16 MarkDuplicates Start of doWork freeMemory: 1030364864; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:16 MarkDuplicates Start of doWork freeMemory: 1030364864; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:16 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:43:16 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:16 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:43:16 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:43:16 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:43:16 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:16 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:43:16 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 967444440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 967444440; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:17 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:43:17 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:43:19 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:19 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:43:19 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:19 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:43:19 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 491435024; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 491435024; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:19 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:43:19 MarkDuplicates Marking 1 records as duplicates. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:19 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:43:19 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:19 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:43:19 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:19 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:43:19 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:19 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:43:19 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:19 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:43:19 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:19 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:43:19 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:20 MarkDuplicates Before output close freeMemory: 760779464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:20 MarkDuplicates Before output close freeMemory: 760779464; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:20 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:43:20 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:20 MarkDuplicates After output close freeMemory: 760918880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:20 MarkDuplicates After output close freeMemory: 760918880; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:20 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. [Tue Jul 02 11:43:20 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:20 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testMappedPairAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:43:20 MarkDuplicates Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.15932523123035080955.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.15932523123035080955.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.15932523123035080955.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.15932523123035080955.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.15932523123035080955.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.15932523123035080955.tmp/output.sam Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:20.806 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:43:20.806 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:20.806 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:43:20.806 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:20.807 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:43:20.807 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:20.807 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:43:20.807 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:20 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.15932523123035080955.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.15932523123035080955.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.15932523123035080955.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:43:20 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.15932523123035080955.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.15932523123035080955.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.15932523123035080955.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:43:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:21 MarkDuplicates Start of doWork freeMemory: 1030408208; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:21 MarkDuplicates Start of doWork freeMemory: 1030408208; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:21 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:43:21 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:21 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:43:21 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:43:21 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:43:21 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:21 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:43:21 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 967487784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 967487784; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:43:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:23 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:43:23 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:23 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:43:23 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:23 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:43:23 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 648725912; totalMemory: 1231028224; maxMemory: 2147483648 INFO 2024-07-02 11:43:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 648725912; totalMemory: 1231028224; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:24 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:43:24 MarkDuplicates Marking 1 records as duplicates. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:24 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:43:24 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:24 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:43:24 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:24 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:43:24 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:24 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:43:24 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:24 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:43:24 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:24 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:43:24 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:24 MarkDuplicates Before output close freeMemory: 760783952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:24 MarkDuplicates Before output close freeMemory: 760783952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:24 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:43:24 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:25 MarkDuplicates After output close freeMemory: 760923296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:25 MarkDuplicates After output close freeMemory: 760923296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:25 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:43:25 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:25 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testMappedPairWithFirstEndSamePositionAndOther STANDARD_ERROR INFO 2024-07-02 11:43:25 MarkDuplicates Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.13064800887908855724.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.13064800887908855724.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.13064800887908855724.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.13064800887908855724.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.13064800887908855724.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.13064800887908855724.tmp/output.sam Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:25.377 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:43:25.377 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:25.389 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:43:25.389 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:25.389 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:43:25.389 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:25.389 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:43:25.389 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:25 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.13064800887908855724.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.13064800887908855724.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.13064800887908855724.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:43:25 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.13064800887908855724.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.13064800887908855724.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.13064800887908855724.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:43:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:25 MarkDuplicates Start of doWork freeMemory: 1030412448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:25 MarkDuplicates Start of doWork freeMemory: 1030412448; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:25 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:43:25 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:25 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:43:25 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:43:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:43:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:26 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:43:26 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 967491880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 967491880; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:43:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:28 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:43:28 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:28 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:43:28 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:28 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:43:28 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 491439344; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 491439344; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:29 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:43:29 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:29 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:43:29 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:29 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:43:29 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:29 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:43:29 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:29 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:43:29 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:29 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:43:29 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:29 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:43:29 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:29 MarkDuplicates Before output close freeMemory: 760783784; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:29 MarkDuplicates Before output close freeMemory: 760783784; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:29 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:43:29 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:30 MarkDuplicates After output close freeMemory: 760923200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:30 MarkDuplicates After output close freeMemory: 760923200; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:30 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. [Tue Jul 02 11:43:30 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:30 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testMappedPairWithSamePosition STANDARD_ERROR INFO 2024-07-02 11:43:30 MarkDuplicates Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.12024508341871929617.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.12024508341871929617.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.12024508341871929617.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.12024508341871929617.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.12024508341871929617.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.12024508341871929617.tmp/output.sam Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:30.330 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:43:30.330 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:30.330 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:43:30.330 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:30.330 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:43:30.330 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:30.330 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:43:30.330 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:30 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.12024508341871929617.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.12024508341871929617.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.12024508341871929617.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:43:30 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.12024508341871929617.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.12024508341871929617.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.12024508341871929617.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:43:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:30 MarkDuplicates Start of doWork freeMemory: 1030413864; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:30 MarkDuplicates Start of doWork freeMemory: 1030413864; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:30 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:43:30 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:30 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:43:30 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:43:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:43:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:30 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:43:30 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 967493512; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:31 MarkDuplicates After buildSortedReadEndLists freeMemory: 967493512; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:43:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:32 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:43:32 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:32 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:43:32 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:32 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:43:32 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 491440248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 491440248; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:33 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:43:33 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:33 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:43:33 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:33 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:43:33 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:33 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:43:33 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:33 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:43:33 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:33 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:43:33 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:33 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:43:33 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:33 MarkDuplicates Before output close freeMemory: 760784688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:33 MarkDuplicates Before output close freeMemory: 760784688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:33 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:43:33 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:34 MarkDuplicates After output close freeMemory: 760924104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:34 MarkDuplicates After output close freeMemory: 760924104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:43:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:34 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testMappedPairWithSamePositionSameCigar STANDARD_ERROR INFO 2024-07-02 11:43:34 MarkDuplicates Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.10852076582809313761.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.10852076582809313761.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.10852076582809313761.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.10852076582809313761.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.10852076582809313761.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.10852076582809313761.tmp/output.sam Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:34.662 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:43:34.662 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:34.662 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:43:34.662 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:34.662 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:43:34.662 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:34.662 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:43:34.662 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:34 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.10852076582809313761.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.10852076582809313761.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.10852076582809313761.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:43:34 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.10852076582809313761.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.10852076582809313761.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.10852076582809313761.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:43:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:35 MarkDuplicates Start of doWork freeMemory: 1030413376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:35 MarkDuplicates Start of doWork freeMemory: 1030413376; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:35 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:43:35 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:35 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:43:35 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:43:35 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:43:35 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:35 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:43:35 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 967493024; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 967493024; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:43:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:37 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:43:37 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:37 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:43:37 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:37 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:43:37 MarkDuplicates Sorting list of duplicate records. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 491439760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:38 MarkDuplicates After generateDuplicateIndexes freeMemory: 491439760; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:38 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:43:38 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:38 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:43:38 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:38 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:43:38 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:38 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:43:38 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:38 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:43:38 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:38 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:43:38 MarkDuplicates Duplicate Index cleanup. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:38 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:43:38 MarkDuplicates Getting Memory Stats. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:38 MarkDuplicates Before output close freeMemory: 760784200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:38 MarkDuplicates Before output close freeMemory: 760784200; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:38 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:43:38 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:39 MarkDuplicates After output close freeMemory: 760923616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:39 MarkDuplicates After output close freeMemory: 760923616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:43:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:39 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:43:39 MarkDuplicates Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.4255584955246371897.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.4255584955246371897.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.4255584955246371897.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.4255584955246371897.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.4255584955246371897.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.4255584955246371897.tmp/output.sam Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:39.141 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:43:39.141 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:39.141 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:43:39.141 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:39.141 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:43:39.141 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:39.141 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:43:39.141 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:39 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.4255584955246371897.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.4255584955246371897.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.4255584955246371897.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:43:39 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.4255584955246371897.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.4255584955246371897.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.4255584955246371897.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:43:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:39 MarkDuplicates Start of doWork freeMemory: 1030413080; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:39 MarkDuplicates Start of doWork freeMemory: 1030413080; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:39 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:43:39 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:39 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:43:39 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:43:39 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:43:39 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:39 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:43:39 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 967492872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:40 MarkDuplicates After buildSortedReadEndLists freeMemory: 967492872; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:43:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:42 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:43:42 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:42 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:43:42 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:42 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:43:42 MarkDuplicates Sorting list of duplicate records. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 600492720; totalMemory: 1182793728; maxMemory: 2147483648 INFO 2024-07-02 11:43:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 600492720; totalMemory: 1182793728; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:42 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:43:42 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:42 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:43:42 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:42 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:43:42 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:42 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:43:42 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:42 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:43:42 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:42 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:43:42 MarkDuplicates Duplicate Index cleanup. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:42 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:43:42 MarkDuplicates Getting Memory Stats. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:43 MarkDuplicates Before output close freeMemory: 760785256; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:43 MarkDuplicates Before output close freeMemory: 760785256; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:43 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:43:43 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:43 MarkDuplicates After output close freeMemory: 760924600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:43 MarkDuplicates After output close freeMemory: 760924600; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:43 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. [Tue Jul 02 11:43:43 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:43 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:43:43 MarkDuplicates Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.10250070325142098179.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.10250070325142098179.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.10250070325142098179.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.10250070325142098179.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.10250070325142098179.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.10250070325142098179.tmp/output.sam Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:43.908 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:43:43.908 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:43.929 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:43:43.929 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:43.929 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:43:43.929 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:43.929 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:43:43.929 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:43 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.10250070325142098179.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.10250070325142098179.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.10250070325142098179.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:43:43 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.10250070325142098179.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.10250070325142098179.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.10250070325142098179.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:43:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:44 MarkDuplicates Start of doWork freeMemory: 1030413744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:44 MarkDuplicates Start of doWork freeMemory: 1030413744; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:44 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:43:44 MarkDuplicates Reading input file and constructing read end information. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:44 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:43:44 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:43:44 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:43:44 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:44 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:43:44 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 967493536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:45 MarkDuplicates After buildSortedReadEndLists freeMemory: 967493536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:43:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:47 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:43:47 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:47 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:43:47 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:47 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:43:47 MarkDuplicates Sorting list of duplicate records. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 491474560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 491474560; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:48 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:43:48 MarkDuplicates Marking 0 records as duplicates. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:48 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:43:48 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:48 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:43:48 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:48 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:43:48 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:48 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:43:48 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:48 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:43:48 MarkDuplicates Duplicate Index cleanup. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:48 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:43:48 MarkDuplicates Getting Memory Stats. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:48 MarkDuplicates Before output close freeMemory: 760817176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:48 MarkDuplicates Before output close freeMemory: 760817176; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:48 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:43:48 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:49 MarkDuplicates After output close freeMemory: 760958416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:49 MarkDuplicates After output close freeMemory: 760958416; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.09 minutes. [Tue Jul 02 11:43:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.09 minutes. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:49 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testOpticalDuplicateBehaviorNullRegex STANDARD_ERROR INFO 2024-07-02 11:43:49 MarkDuplicates Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.7689845068398545998.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -READ_NAME_REGEX null -INPUT /tmp/QuerySortedMarkDuplicatesTester.7689845068398545998.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.7689845068398545998.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.7689845068398545998.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -READ_NAME_REGEX null -INPUT /tmp/QuerySortedMarkDuplicatesTester.7689845068398545998.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.7689845068398545998.tmp/output.sam Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:49.435 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:43:49.435 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:49.435 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:43:49.435 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:49.435 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:43:49.435 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:49.435 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:43:49.435 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:49 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.7689845068398545998.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.7689845068398545998.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.7689845068398545998.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH READ_NAME_REGEX=null MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:43:49 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.7689845068398545998.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.7689845068398545998.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.7689845068398545998.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH READ_NAME_REGEX=null MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:43:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:49 MarkDuplicates Start of doWork freeMemory: 1030446104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:49 MarkDuplicates Start of doWork freeMemory: 1030446104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:49 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:43:49 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:43:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:50 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:43:50 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 967525536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 967525536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:51 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:43:51 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:52 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:43:52 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:52 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:43:52 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:52 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:43:52 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 491472840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 491472840; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:53 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:43:53 MarkDuplicates Marking 1 records as duplicates. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:43:53 MarkDuplicates Skipped optical duplicate cluster discovery; library size estimation may be inaccurate! WARNING 2024-07-02 11:43:53 MarkDuplicates Skipped optical duplicate cluster discovery; library size estimation may be inaccurate! Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:53 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:43:53 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:53 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:43:53 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:53 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:43:53 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:53 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:43:53 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:53 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:43:53 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:53 MarkDuplicates Before output close freeMemory: 760817296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:53 MarkDuplicates Before output close freeMemory: 760817296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:53 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:43:53 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:53 MarkDuplicates After output close freeMemory: 760956640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:53 MarkDuplicates After output close freeMemory: 760956640; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. [Tue Jul 02 11:43:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:54 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testOpticalDuplicateClusterOneEndSamePositionOneCluster STANDARD_ERROR INFO 2024-07-02 11:43:54 MarkDuplicates Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.584054417060769144.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.584054417060769144.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.584054417060769144.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.584054417060769144.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.584054417060769144.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.584054417060769144.tmp/output.sam Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:54.071 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:43:54.071 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:54.071 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:43:54.071 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:54.071 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:43:54.071 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:54.071 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:43:54.071 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:54 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.584054417060769144.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.584054417060769144.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.584054417060769144.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:43:54 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.584054417060769144.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.584054417060769144.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.584054417060769144.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:43:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:54 MarkDuplicates Start of doWork freeMemory: 1030440064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:54 MarkDuplicates Start of doWork freeMemory: 1030440064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:54 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:43:54 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:54 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:43:54 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:54 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:43:54 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 967524832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 967524832; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:43:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:57 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:43:57 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:57 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:43:57 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:57 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:43:57 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 491471632; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 491471632; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:57 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:43:57 MarkDuplicates Marking 1 records as duplicates. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:57 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:43:57 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:57 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:43:57 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:57 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:43:57 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:57 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:43:57 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:57 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:43:57 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:57 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:43:57 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:58 MarkDuplicates Before output close freeMemory: 760816072; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:58 MarkDuplicates Before output close freeMemory: 760816072; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:58 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:43:58 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:58 MarkDuplicates After output close freeMemory: 760955416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:58 MarkDuplicates After output close freeMemory: 760955416; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. [Tue Jul 02 11:43:58 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:58 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:43:58 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.9427396264004290906.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.9427396264004290906.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.9427396264004290906.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.9427396264004290906.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.9427396264004290906.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.9427396264004290906.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:58.778 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:43:58.778 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:58.778 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:43:58.778 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:58.779 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:43:58.779 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:43:58.779 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:43:58.779 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:58 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.9427396264004290906.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.9427396264004290906.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.9427396264004290906.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:43:58 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.9427396264004290906.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.9427396264004290906.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.9427396264004290906.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:43:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:43:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:59 MarkDuplicates Start of doWork freeMemory: 1030444200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:59 MarkDuplicates Start of doWork freeMemory: 1030444200; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:59 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:43:59 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:59 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:43:59 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:59 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:43:59 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:43:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 967523568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:43:59 MarkDuplicates After buildSortedReadEndLists freeMemory: 967523568; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:00 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:01 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:01 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:01 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:01 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:01 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:01 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 556482232; totalMemory: 1138753536; maxMemory: 2147483648 INFO 2024-07-02 11:44:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 556482232; totalMemory: 1138753536; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:01 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:44:01 MarkDuplicates Marking 1 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:01 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:44:01 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:01 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:01 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:01 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:01 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:01 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:01 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:01 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:01 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:01 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:01 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:02 MarkDuplicates Before output close freeMemory: 760813136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:02 MarkDuplicates Before output close freeMemory: 760813136; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:02 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:02 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:02 MarkDuplicates After output close freeMemory: 760954376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:02 MarkDuplicates After output close freeMemory: 760954376; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:02 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:44:02 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[0](RUNID:7:1203:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:03 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:44:03 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.4590365598518262425.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.4590365598518262425.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.4590365598518262425.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.4590365598518262425.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.4590365598518262425.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.4590365598518262425.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:03.043 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:03.043 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:03.043 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:03.043 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:03.043 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:03.043 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:03.043 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:03.043 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:03 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.4590365598518262425.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.4590365598518262425.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.4590365598518262425.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:03 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.4590365598518262425.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.4590365598518262425.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.4590365598518262425.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:03 MarkDuplicates Start of doWork freeMemory: 1030443776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:03 MarkDuplicates Start of doWork freeMemory: 1030443776; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:03 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:03 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:03 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:03 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:03 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:44:03 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 967523144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 967523144; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:05 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:05 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:05 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:05 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:05 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:05 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:05 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 491470096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 491470096; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:06 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:44:06 MarkDuplicates Marking 1 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:06 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:44:06 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:06 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:06 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:06 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:06 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:06 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:06 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:06 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:06 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:06 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:06 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:06 MarkDuplicates Before output close freeMemory: 760814536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:06 MarkDuplicates Before output close freeMemory: 760814536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:06 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:06 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:07 MarkDuplicates After output close freeMemory: 760953880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:07 MarkDuplicates After output close freeMemory: 760953880; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:07 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:44:07 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[1](RUNID:7:1204:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:07 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:44:07 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.15606651414163060541.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.15606651414163060541.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.15606651414163060541.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.15606651414163060541.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.15606651414163060541.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.15606651414163060541.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:07.191 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:07.191 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:07.191 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:07.191 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:07.191 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:07.191 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:07.191 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:07.191 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:07 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.15606651414163060541.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.15606651414163060541.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.15606651414163060541.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:07 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.15606651414163060541.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.15606651414163060541.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.15606651414163060541.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:07 MarkDuplicates Start of doWork freeMemory: 1030443376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:07 MarkDuplicates Start of doWork freeMemory: 1030443376; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:07 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:07 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:07 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:07 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:07 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:44:07 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 967522744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 967522744; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:08 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:09 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:09 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:09 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:09 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:09 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:09 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 491469696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 491469696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:09 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:44:09 MarkDuplicates Marking 1 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:09 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:44:09 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:09 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:09 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:09 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:09 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:09 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:09 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:09 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:09 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:09 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:09 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:09 MarkDuplicates Before output close freeMemory: 760814136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:09 MarkDuplicates Before output close freeMemory: 760814136; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:09 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:09 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:10 MarkDuplicates After output close freeMemory: 760953480; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:10 MarkDuplicates After output close freeMemory: 760953480; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:10 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:44:10 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[2](RUNID:7:1205:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:10 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:44:10 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.10430059799459817166.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.10430059799459817166.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.10430059799459817166.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.10430059799459817166.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.10430059799459817166.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.10430059799459817166.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:10.212 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:10.212 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:10.212 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:10.212 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:10.212 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:10.212 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:10.212 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:10.212 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:10 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.10430059799459817166.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.10430059799459817166.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.10430059799459817166.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:10 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.10430059799459817166.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.10430059799459817166.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.10430059799459817166.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:10 MarkDuplicates Start of doWork freeMemory: 1030443000; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:10 MarkDuplicates Start of doWork freeMemory: 1030443000; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:10 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:10 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:10 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:10 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:10 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:44:10 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 967522368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 967522368; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:11 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:11 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:11 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:11 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 491469320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 491469320; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:11 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:44:11 MarkDuplicates Marking 1 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:11 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:44:11 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:11 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:11 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:11 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:11 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:11 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:11 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:11 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:11 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:11 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:11 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:11 MarkDuplicates Before output close freeMemory: 760812216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:11 MarkDuplicates Before output close freeMemory: 760812216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:11 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:11 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:12 MarkDuplicates After output close freeMemory: 760953176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:12 MarkDuplicates After output close freeMemory: 760953176; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:12 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:44:12 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[3](RUNID:7:1206:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:12 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756) STANDARD_ERROR INFO 2024-07-02 11:44:12 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.3631323484612831660.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.3631323484612831660.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.3631323484612831660.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.3631323484612831660.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.3631323484612831660.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.3631323484612831660.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:12.132 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:12.132 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:12.133 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:12.133 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:12.133 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:12.133 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:12.133 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:12.133 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:12 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.3631323484612831660.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.3631323484612831660.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.3631323484612831660.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:12 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.3631323484612831660.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.3631323484612831660.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.3631323484612831660.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:12 MarkDuplicates Start of doWork freeMemory: 1030442648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:12 MarkDuplicates Start of doWork freeMemory: 1030442648; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:12 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:12 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:12 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:12 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:12 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:44:12 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 967521800; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:12 MarkDuplicates After buildSortedReadEndLists freeMemory: 967521800; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:12 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:12 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:13 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:13 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:13 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:13 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:13 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:13 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 541800616; totalMemory: 1124073472; maxMemory: 2147483648 INFO 2024-07-02 11:44:13 MarkDuplicates After generateDuplicateIndexes freeMemory: 541800616; totalMemory: 1124073472; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:13 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:44:13 MarkDuplicates Marking 1 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:13 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:44:13 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:13 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:13 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:13 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:13 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:13 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:13 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:13 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:13 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:13 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:13 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:13 MarkDuplicates Before output close freeMemory: 760813408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:13 MarkDuplicates Before output close freeMemory: 760813408; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:13 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:13 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:13 MarkDuplicates After output close freeMemory: 760952752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:13 MarkDuplicates After output close freeMemory: 760952752; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:13 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:44:13 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[4](RUNID:7:1207:2886:16756, RUNID:7:1205:3886:16756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:14 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:44:14 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.16176952804945456356.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.16176952804945456356.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.16176952804945456356.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.16176952804945456356.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.16176952804945456356.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.16176952804945456356.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:14.018 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:14.018 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:14.018 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:14.018 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:14.019 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:14.019 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:14.019 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:14.019 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:14 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.16176952804945456356.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.16176952804945456356.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.16176952804945456356.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:14 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.16176952804945456356.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.16176952804945456356.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.16176952804945456356.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:14 MarkDuplicates Start of doWork freeMemory: 1030442248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:14 MarkDuplicates Start of doWork freeMemory: 1030442248; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:14 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:14 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:14 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:14 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:14 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:44:14 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 967521616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:14 MarkDuplicates After buildSortedReadEndLists freeMemory: 967521616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:14 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:14 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:14 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:14 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:14 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:14 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:14 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 491468568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 491468568; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:14 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:44:14 MarkDuplicates Marking 1 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:14 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:44:14 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:14 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:14 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:14 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:14 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:14 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:14 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:14 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:14 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:14 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:14 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:15 MarkDuplicates Before output close freeMemory: 760813008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:15 MarkDuplicates Before output close freeMemory: 760813008; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:15 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:15 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:15 MarkDuplicates After output close freeMemory: 760951856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:15 MarkDuplicates After output close freeMemory: 760951856; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:44:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[5](RUNID:7:1203:2886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:15 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:44:15 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.7813979615752388357.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.7813979615752388357.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.7813979615752388357.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.7813979615752388357.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.7813979615752388357.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.7813979615752388357.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:15.326 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:15.326 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:15.326 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:15.326 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:15.326 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:15.326 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:15.326 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:15.326 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:15 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.7813979615752388357.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.7813979615752388357.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.7813979615752388357.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:15 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.7813979615752388357.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.7813979615752388357.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.7813979615752388357.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:15 MarkDuplicates Start of doWork freeMemory: 1030441896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:15 MarkDuplicates Start of doWork freeMemory: 1030441896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:15 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:15 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:15 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:15 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:15 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:44:15 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:15 MarkDuplicates After buildSortedReadEndLists freeMemory: 967521264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:15 MarkDuplicates After buildSortedReadEndLists freeMemory: 967521264; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:15 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:15 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:16 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:16 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:16 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:16 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:16 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:16 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 491468216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:16 MarkDuplicates After generateDuplicateIndexes freeMemory: 491468216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:16 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:44:16 MarkDuplicates Marking 1 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:16 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:44:16 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:16 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:16 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:16 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:16 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:16 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:16 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:16 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:16 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:16 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:16 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:16 MarkDuplicates Before output close freeMemory: 760812656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:16 MarkDuplicates Before output close freeMemory: 760812656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:16 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:16 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:16 MarkDuplicates After output close freeMemory: 760850864; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:16 MarkDuplicates After output close freeMemory: 760850864; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:16 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:44:16 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[6](RUNID:7:1203:3886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:16 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:44:16 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.9485715066158078701.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.9485715066158078701.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.9485715066158078701.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.9485715066158078701.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.9485715066158078701.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.9485715066158078701.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:16.742 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:16.742 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:16.742 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:16.742 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:16.742 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:16.742 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:16.742 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:16.742 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:16 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.9485715066158078701.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.9485715066158078701.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.9485715066158078701.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:16 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.9485715066158078701.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.9485715066158078701.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.9485715066158078701.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:16 MarkDuplicates Start of doWork freeMemory: 1030441520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:16 MarkDuplicates Start of doWork freeMemory: 1030441520; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:16 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:16 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:16 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:16 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:16 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:44:16 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 967520888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:17 MarkDuplicates After buildSortedReadEndLists freeMemory: 967520888; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:17 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:17 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:17 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:17 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:17 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:17 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:17 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:17 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 491467840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:17 MarkDuplicates After generateDuplicateIndexes freeMemory: 491467840; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:17 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:44:17 MarkDuplicates Marking 1 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:17 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:44:17 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:17 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:17 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:17 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:17 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:17 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:17 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:17 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:17 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:17 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:17 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:17 MarkDuplicates Before output close freeMemory: 760810456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:17 MarkDuplicates Before output close freeMemory: 760810456; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:17 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:17 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:17 MarkDuplicates After output close freeMemory: 760951472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:17 MarkDuplicates After output close freeMemory: 760951472; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:17 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:44:17 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[7](RUNID:7:1203:4886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:17 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:44:17 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.5305379996439678722.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.5305379996439678722.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.5305379996439678722.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.5305379996439678722.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.5305379996439678722.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.5305379996439678722.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:17.982 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:17.982 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:17.982 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:17.982 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:17.982 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:17.982 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:17.982 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:17.982 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:17 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.5305379996439678722.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.5305379996439678722.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.5305379996439678722.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:17 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.5305379996439678722.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.5305379996439678722.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.5305379996439678722.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:18 MarkDuplicates Start of doWork freeMemory: 1030441144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:18 MarkDuplicates Start of doWork freeMemory: 1030441144; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:18 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:18 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:18 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:18 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:18 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:44:18 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 967520512; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 967520512; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:18 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:18 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:18 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:18 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:18 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:18 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:18 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 670773960; totalMemory: 1253048320; maxMemory: 2147483648 INFO 2024-07-02 11:44:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 670773960; totalMemory: 1253048320; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:18 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:44:18 MarkDuplicates Marking 1 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:18 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:44:18 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:18 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:18 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:18 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:18 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:18 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:18 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:18 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:18 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:18 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:18 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:18 MarkDuplicates Before output close freeMemory: 760811904; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:18 MarkDuplicates Before output close freeMemory: 760811904; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:18 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:18 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:18 MarkDuplicates After output close freeMemory: 760850112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:18 MarkDuplicates After output close freeMemory: 760850112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:18 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:44:18 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[8](RUNID:7:1203:5886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:18 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756) STANDARD_ERROR INFO 2024-07-02 11:44:18 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.10491185140632482696.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.10491185140632482696.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.10491185140632482696.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.10491185140632482696.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.10491185140632482696.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.10491185140632482696.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:18.975 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:18.975 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:18.975 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:18.975 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:18.976 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:18.976 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:18.976 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:18.976 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:18 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.10491185140632482696.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.10491185140632482696.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.10491185140632482696.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:18 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.10491185140632482696.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.10491185140632482696.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.10491185140632482696.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:19 MarkDuplicates Start of doWork freeMemory: 1030440744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:19 MarkDuplicates Start of doWork freeMemory: 1030440744; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:19 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:19 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:19 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:19 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:19 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:44:19 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 967419176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 967419176; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:19 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:19 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:19 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:19 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:19 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:19 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:19 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 491467064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:19 MarkDuplicates After generateDuplicateIndexes freeMemory: 491467064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:19 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:44:19 MarkDuplicates Marking 1 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:19 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:44:19 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:19 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:19 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:19 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:19 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:19 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:19 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:19 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:19 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:19 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:19 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:19 MarkDuplicates Before output close freeMemory: 760811504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:19 MarkDuplicates Before output close freeMemory: 760811504; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:19 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:19 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:19 MarkDuplicates After output close freeMemory: 760849712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:19 MarkDuplicates After output close freeMemory: 760849712; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:19 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:44:19 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[9](RUNID:7:1203:6886:16756, RUNID:7:1203:4886:26756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:19 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756) STANDARD_ERROR INFO 2024-07-02 11:44:19 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.14563954307996275673.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.14563954307996275673.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.14563954307996275673.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.14563954307996275673.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.14563954307996275673.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.14563954307996275673.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:19.769 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:19.769 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:19.769 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:19.769 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:19.769 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:19.769 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:19.769 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:19.769 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:19 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.14563954307996275673.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.14563954307996275673.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.14563954307996275673.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:19 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.14563954307996275673.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.14563954307996275673.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.14563954307996275673.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:19 MarkDuplicates Start of doWork freeMemory: 1030339240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:19 MarkDuplicates Start of doWork freeMemory: 1030339240; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:19 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:19 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:19 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:19 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:19 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:44:19 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 967418776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 967418776; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:20 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:20 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:20 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:20 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:20 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:20 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 491466664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 491466664; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:20 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:44:20 MarkDuplicates Marking 1 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:20 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:44:20 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:20 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:20 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:20 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:20 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:20 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:20 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:20 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:20 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:20 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:20 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:20 MarkDuplicates Before output close freeMemory: 760811104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:20 MarkDuplicates Before output close freeMemory: 760811104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:20 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:20 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:20 MarkDuplicates After output close freeMemory: 760950024; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:20 MarkDuplicates After output close freeMemory: 760950024; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:20 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:44:20 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[10](RUNID:7:1203:2886:34756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:20 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756) STANDARD_ERROR INFO 2024-07-02 11:44:20 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.4144062716009876252.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.4144062716009876252.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.4144062716009876252.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.4144062716009876252.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.4144062716009876252.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.4144062716009876252.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:20.587 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:20.587 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:20.587 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:20.587 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:20.587 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:20.587 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:20.587 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:20.587 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:20 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.4144062716009876252.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.4144062716009876252.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.4144062716009876252.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:20 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.4144062716009876252.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.4144062716009876252.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.4144062716009876252.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:20 MarkDuplicates Start of doWork freeMemory: 1030439968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:20 MarkDuplicates Start of doWork freeMemory: 1030439968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:20 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:20 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:20 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:20 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:20 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:44:20 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 967519120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:20 MarkDuplicates After buildSortedReadEndLists freeMemory: 967519120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:21 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:21 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:21 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 491466288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 491466288; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:44:21 MarkDuplicates Marking 1 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:44:21 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:21 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:21 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:21 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:21 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:21 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates Before output close freeMemory: 760810728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:21 MarkDuplicates Before output close freeMemory: 760810728; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:21 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates After output close freeMemory: 760848936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:21 MarkDuplicates After output close freeMemory: 760848936; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:21 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:44:21 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[11](RUNID:7:1203:2886:35756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756) STANDARD_ERROR INFO 2024-07-02 11:44:21 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.1322349355529656009.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.1322349355529656009.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.1322349355529656009.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.1322349355529656009.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.1322349355529656009.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.1322349355529656009.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:21.390 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:21.390 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:21.390 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:21.390 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:21.390 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:21.390 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:21.390 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:21.390 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:21 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.1322349355529656009.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.1322349355529656009.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.1322349355529656009.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:21 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.1322349355529656009.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.1322349355529656009.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.1322349355529656009.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates Start of doWork freeMemory: 1030439200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:21 MarkDuplicates Start of doWork freeMemory: 1030439200; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:21 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:21 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:44:21 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 967518744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:21 MarkDuplicates After buildSortedReadEndLists freeMemory: 967518744; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:21 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:21 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:21 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:21 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 491465912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 491465912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:44:21 MarkDuplicates Marking 1 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:44:21 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:21 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:21 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:21 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:21 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:21 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:21 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:22 MarkDuplicates Before output close freeMemory: 760809720; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:22 MarkDuplicates Before output close freeMemory: 760809720; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:22 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:22 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:22 MarkDuplicates After output close freeMemory: 760949768; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:22 MarkDuplicates After output close freeMemory: 760949768; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:22 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:44:22 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[12](RUNID:7:1203:2886:37756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:22 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756) STANDARD_ERROR INFO 2024-07-02 11:44:22 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.8623750910197599918.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.8623750910197599918.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.8623750910197599918.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.8623750910197599918.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.8623750910197599918.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.8623750910197599918.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:22.384 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:22.384 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:22.385 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:22.385 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:22.385 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:22.385 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:22.385 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:22.385 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:22 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.8623750910197599918.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.8623750910197599918.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.8623750910197599918.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:22 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.8623750910197599918.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.8623750910197599918.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.8623750910197599918.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:22 MarkDuplicates Start of doWork freeMemory: 1030335696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:22 MarkDuplicates Start of doWork freeMemory: 1030335696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:22 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:22 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:22 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:22 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:22 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:44:22 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 967518368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 967518368; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:22 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:22 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:22 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:22 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:22 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:22 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:22 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 491465536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:22 MarkDuplicates After generateDuplicateIndexes freeMemory: 491465536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:22 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:44:22 MarkDuplicates Marking 1 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:22 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:44:22 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:22 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:22 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:22 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:22 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:22 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:22 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:22 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:22 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:22 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:22 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:23 MarkDuplicates Before output close freeMemory: 760708632; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:23 MarkDuplicates Before output close freeMemory: 760708632; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:23 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:23 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:23 MarkDuplicates After output close freeMemory: 760848456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:23 MarkDuplicates After output close freeMemory: 760848456; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:23 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:44:23 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicates[13](RUNID:7:1203:2886:38756, RUNID:7:1203:2886:36756)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:23 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance STANDARD_ERROR INFO 2024-07-02 11:44:23 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.4076728519547769021.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.4076728519547769021.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.4076728519547769021.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.4076728519547769021.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.4076728519547769021.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.4076728519547769021.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:23.353 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:23.353 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:23.353 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:23.353 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:23.354 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:23.354 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:23.354 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:23.354 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:23 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.4076728519547769021.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.4076728519547769021.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.4076728519547769021.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:23 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.4076728519547769021.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.4076728519547769021.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.4076728519547769021.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:23 MarkDuplicates Start of doWork freeMemory: 1030436624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:23 MarkDuplicates Start of doWork freeMemory: 1030436624; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:23 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:23 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:23 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:23 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:23 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:44:23 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 967417304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 967417304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:23 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:23 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:23 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:23 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:23 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:23 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 491465192; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 491465192; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:23 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:44:23 MarkDuplicates Marking 1 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:23 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:44:23 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:23 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:23 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:23 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:23 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:23 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:23 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:23 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:23 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:23 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:23 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:23 MarkDuplicates Before output close freeMemory: 760809632; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:23 MarkDuplicates Before output close freeMemory: 760809632; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:23 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:23 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:24 MarkDuplicates After output close freeMemory: 760949048; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:24 MarkDuplicates After output close freeMemory: 760949048; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:24 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:44:24 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:24 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance STANDARD_ERROR INFO 2024-07-02 11:44:24 MarkDuplicates Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.16375063463644418460.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.16375063463644418460.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.16375063463644418460.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.16375063463644418460.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.16375063463644418460.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.16375063463644418460.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:24.098 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:24.098 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:24.098 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:24.098 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:24.098 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:24.098 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:24.099 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:24.099 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:24 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.16375063463644418460.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.16375063463644418460.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.16375063463644418460.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:24 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.16375063463644418460.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.16375063463644418460.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.16375063463644418460.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:24 MarkDuplicates Start of doWork freeMemory: 1030438904; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:24 MarkDuplicates Start of doWork freeMemory: 1030438904; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:24 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:24 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:24 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:24 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:24 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:44:24 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 967417368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:24 MarkDuplicates After buildSortedReadEndLists freeMemory: 967417368; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:24 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:24 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:24 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:24 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:24 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:24 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:24 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:24 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 760949104; totalMemory: 1343225856; maxMemory: 2147483648 INFO 2024-07-02 11:44:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 760949104; totalMemory: 1343225856; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:24 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:44:24 MarkDuplicates Marking 1 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:24 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:44:24 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:24 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:24 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:24 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:24 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:24 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:24 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:24 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:24 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:24 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:24 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:24 MarkDuplicates Before output close freeMemory: 760809512; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:24 MarkDuplicates Before output close freeMemory: 760809512; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:24 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:24 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:24 MarkDuplicates After output close freeMemory: 760948360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:24 MarkDuplicates After output close freeMemory: 760948360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:24 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:44:24 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:24 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate STANDARD_ERROR INFO 2024-07-02 11:44:24 MarkDuplicates Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.4875245150210196787.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.4875245150210196787.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.4875245150210196787.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.4875245150210196787.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.4875245150210196787.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.4875245150210196787.tmp/output.sam Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:24.861 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:24.861 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:24.861 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:24.861 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:24.862 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:24.862 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:24.862 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:24.862 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:24 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.4875245150210196787.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.4875245150210196787.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.4875245150210196787.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:24 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.4875245150210196787.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.4875245150210196787.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.4875245150210196787.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:24 MarkDuplicates Start of doWork freeMemory: 1030337160; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:24 MarkDuplicates Start of doWork freeMemory: 1030337160; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:24 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:24 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:24 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:24 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:25 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:44:25 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 967517632; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:25 MarkDuplicates After buildSortedReadEndLists freeMemory: 967517632; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:25 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:25 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:25 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:25 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:25 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:25 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:25 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:25 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 491464432; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 491464432; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:25 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:44:25 MarkDuplicates Marking 1 records as duplicates. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:25 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:44:25 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:25 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:25 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:25 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:25 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:25 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:25 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:25 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:25 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:25 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:25 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:25 MarkDuplicates Before output close freeMemory: 760707528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:25 MarkDuplicates Before output close freeMemory: 760707528; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:25 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:25 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:25 MarkDuplicates After output close freeMemory: 760948064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:25 MarkDuplicates After output close freeMemory: 760948064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:25 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:44:25 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:25 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testPathologicalOrderingAtTheSamePosition STANDARD_ERROR INFO 2024-07-02 11:44:25 MarkDuplicates Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.3198494268787254864.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.3198494268787254864.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.3198494268787254864.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.3198494268787254864.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.3198494268787254864.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.3198494268787254864.tmp/output.sam Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:25.819 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:25.819 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:25.819 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:25.819 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:25.820 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:25.820 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:25.820 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:25.820 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:25 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.3198494268787254864.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.3198494268787254864.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.3198494268787254864.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:25 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.3198494268787254864.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.3198494268787254864.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.3198494268787254864.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:25 MarkDuplicates Start of doWork freeMemory: 1030437728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:25 MarkDuplicates Start of doWork freeMemory: 1030437728; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:25 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:25 MarkDuplicates Reading input file and constructing read end information. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:25 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:25 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:25 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:44:25 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 967416160; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 967416160; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:26 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:26 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:26 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:26 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:26 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:26 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:26 MarkDuplicates Sorting list of duplicate records. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 491404144; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:26 MarkDuplicates After generateDuplicateIndexes freeMemory: 491404144; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:26 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:44:26 MarkDuplicates Marking 1 records as duplicates. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:26 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:44:26 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:26 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:26 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:26 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:26 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:26 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:26 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:26 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:26 MarkDuplicates Duplicate Index cleanup. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:26 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:26 MarkDuplicates Getting Memory Stats. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:26 MarkDuplicates Before output close freeMemory: 760808336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:26 MarkDuplicates Before output close freeMemory: 760808336; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:26 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:26 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:26 MarkDuplicates After output close freeMemory: 760947680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:26 MarkDuplicates After output close freeMemory: 760947680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:26 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:44:26 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:26 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testSecondEndIsBeforeFirstInCoordinate STANDARD_ERROR INFO 2024-07-02 11:44:26 MarkDuplicates Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.15647189625297949474.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.15647189625297949474.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.15647189625297949474.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.15647189625297949474.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.15647189625297949474.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.15647189625297949474.tmp/output.sam Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:26.732 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:26.732 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:26.732 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:26.732 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:26.732 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:26.732 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:26.732 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:26.732 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:26 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.15647189625297949474.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.15647189625297949474.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.15647189625297949474.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:26 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.15647189625297949474.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.15647189625297949474.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.15647189625297949474.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:26 MarkDuplicates Start of doWork freeMemory: 1030438552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:26 MarkDuplicates Start of doWork freeMemory: 1030438552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:26 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:26 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:26 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:26 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:44:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:44:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:26 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:44:26 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 967518200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 967518200; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:27 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:27 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:27 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:27 MarkDuplicates Sorting list of duplicate records. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 491464936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:27 MarkDuplicates After generateDuplicateIndexes freeMemory: 491464936; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:27 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:44:27 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:27 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:44:27 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:27 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:27 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:27 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:27 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:27 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:27 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:27 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:27 MarkDuplicates Duplicate Index cleanup. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:27 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:27 MarkDuplicates Getting Memory Stats. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:27 MarkDuplicates Before output close freeMemory: 760809376; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:27 MarkDuplicates Before output close freeMemory: 760809376; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:27 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:27 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:27 MarkDuplicates After output close freeMemory: 760948792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:27 MarkDuplicates After output close freeMemory: 760948792; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:27 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:44:27 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:27 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testSingleMappedFragment STANDARD_ERROR INFO 2024-07-02 11:44:27 MarkDuplicates Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.10650678122545823271.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.10650678122545823271.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.10650678122545823271.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.10650678122545823271.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.10650678122545823271.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.10650678122545823271.tmp/output.sam Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:27.580 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:27.580 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:27.580 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:27.580 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:27.580 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:27.580 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:27.580 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:27.580 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:27 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.10650678122545823271.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.10650678122545823271.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.10650678122545823271.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:27 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.10650678122545823271.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.10650678122545823271.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.10650678122545823271.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:27 MarkDuplicates Start of doWork freeMemory: 1030438832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:27 MarkDuplicates Start of doWork freeMemory: 1030438832; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:27 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:27 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:27 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:27 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:44:27 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:44:27 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:27 MarkDuplicates Read 1 records. 0 pairs never matched. INFO 2024-07-02 11:44:27 MarkDuplicates Read 1 records. 0 pairs never matched. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 967518624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 967518624; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:28 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:28 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:28 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:28 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:28 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:28 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 921381552; totalMemory: 1503657984; maxMemory: 2147483648 INFO 2024-07-02 11:44:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 921381552; totalMemory: 1503657984; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:28 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:44:28 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:28 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:44:28 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:28 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:28 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:28 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:28 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:28 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:28 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:28 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:28 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:28 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:28 MarkDuplicates Getting Memory Stats. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:28 MarkDuplicates Before output close freeMemory: 760809832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:28 MarkDuplicates Before output close freeMemory: 760809832; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:28 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:28 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:29 MarkDuplicates After output close freeMemory: 760949176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:29 MarkDuplicates After output close freeMemory: 760949176; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:44:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:29 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testSingleMappedFragmentAndSingleMappedPair STANDARD_ERROR INFO 2024-07-02 11:44:29 MarkDuplicates Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.7288931089299818908.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.7288931089299818908.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.7288931089299818908.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.7288931089299818908.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.7288931089299818908.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.7288931089299818908.tmp/output.sam Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:29.066 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:29.066 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:29.066 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:29.066 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:29.066 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:29.066 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:29.066 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:29.066 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:29 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.7288931089299818908.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.7288931089299818908.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.7288931089299818908.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:29 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.7288931089299818908.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.7288931089299818908.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.7288931089299818908.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:29 MarkDuplicates Start of doWork freeMemory: 1030437104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:29 MarkDuplicates Start of doWork freeMemory: 1030437104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:29 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:29 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:29 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:29 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:44:29 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:44:29 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:29 MarkDuplicates Read 3 records. 0 pairs never matched. INFO 2024-07-02 11:44:29 MarkDuplicates Read 3 records. 0 pairs never matched. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 967516680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 967516680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:30 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:30 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:30 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:30 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:30 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:30 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 491463488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 491463488; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:30 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:44:30 MarkDuplicates Marking 1 records as duplicates. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:30 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:44:30 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:30 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:30 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:30 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:30 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:30 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:30 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:30 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:30 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:30 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:30 MarkDuplicates Getting Memory Stats. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:31 MarkDuplicates Before output close freeMemory: 760807928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:31 MarkDuplicates Before output close freeMemory: 760807928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:31 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:31 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:31 MarkDuplicates After output close freeMemory: 760846408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:31 MarkDuplicates After output close freeMemory: 760846408; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:31 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:44:31 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:31 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testSingleMappedFragmentAndTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:44:31 MarkDuplicates Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.14015077814943862807.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.14015077814943862807.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.14015077814943862807.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.14015077814943862807.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.14015077814943862807.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.14015077814943862807.tmp/output.sam Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:31.921 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:31.921 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:31.921 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:31.921 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:31.921 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:31.921 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:31.921 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:31.921 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:31 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.14015077814943862807.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.14015077814943862807.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.14015077814943862807.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:31 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.14015077814943862807.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.14015077814943862807.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.14015077814943862807.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:32 MarkDuplicates Start of doWork freeMemory: 1030435248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:32 MarkDuplicates Start of doWork freeMemory: 1030435248; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:32 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:32 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:32 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:32 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:44:32 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:44:32 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:32 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:44:32 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 967514608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 967514608; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:32 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:33 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:33 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:33 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:33 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 491461632; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:33 MarkDuplicates After generateDuplicateIndexes freeMemory: 491461632; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:33 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:44:33 MarkDuplicates Marking 2 records as duplicates. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:33 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:44:33 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:33 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:33 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:33 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:33 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:33 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:33 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:33 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:33 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:33 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:33 MarkDuplicates Getting Memory Stats. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:34 MarkDuplicates Before output close freeMemory: 760806072; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:34 MarkDuplicates Before output close freeMemory: 760806072; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:34 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:34 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:34 MarkDuplicates After output close freeMemory: 760945416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:34 MarkDuplicates After output close freeMemory: 760945416; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:44:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:34 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testSingleMappedPair STANDARD_ERROR INFO 2024-07-02 11:44:34 MarkDuplicates Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.14059035680933997723.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.14059035680933997723.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.14059035680933997723.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.14059035680933997723.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.14059035680933997723.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.14059035680933997723.tmp/output.sam Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:34.410 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:34.410 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:34.410 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:34.410 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:34.411 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:34.411 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:34.411 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:34.411 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:34 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.14059035680933997723.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.14059035680933997723.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.14059035680933997723.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:34 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.14059035680933997723.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.14059035680933997723.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.14059035680933997723.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:34 MarkDuplicates Start of doWork freeMemory: 1030436736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:34 MarkDuplicates Start of doWork freeMemory: 1030436736; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:34 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:34 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:34 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:34 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:44:34 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:44:34 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:34 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:44:34 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 967516384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 967516384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:35 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:36 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:36 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:36 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:36 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:36 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:36 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 491463120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:36 MarkDuplicates After generateDuplicateIndexes freeMemory: 491463120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:36 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:44:36 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:36 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:44:36 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:36 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:36 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:36 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:36 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:36 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:36 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:36 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:36 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:36 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:36 MarkDuplicates Getting Memory Stats. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:37 MarkDuplicates Before output close freeMemory: 760807560; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:37 MarkDuplicates Before output close freeMemory: 760807560; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:37 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:37 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:37 MarkDuplicates After output close freeMemory: 760946976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:37 MarkDuplicates After output close freeMemory: 760946976; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:44:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:37 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testSingleUnmappedFragment STANDARD_ERROR INFO 2024-07-02 11:44:37 MarkDuplicates Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.12063339091158268802.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.12063339091158268802.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.12063339091158268802.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.12063339091158268802.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.12063339091158268802.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.12063339091158268802.tmp/output.sam Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:37.762 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:37.762 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:37.762 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:37.762 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:37.762 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:37.762 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:37.762 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:37.762 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:37 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.12063339091158268802.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.12063339091158268802.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.12063339091158268802.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:37 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.12063339091158268802.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.12063339091158268802.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.12063339091158268802.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:38 MarkDuplicates Start of doWork freeMemory: 1030437088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:38 MarkDuplicates Start of doWork freeMemory: 1030437088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:38 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:38 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:38 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:38 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:38 MarkDuplicates Read 1 records. 0 pairs never matched. INFO 2024-07-02 11:44:38 MarkDuplicates Read 1 records. 0 pairs never matched. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 967517064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 967517064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:39 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:39 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:39 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:39 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:39 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:39 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 706421840; totalMemory: 1288699904; maxMemory: 2147483648 INFO 2024-07-02 11:44:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 706421840; totalMemory: 1288699904; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:39 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:44:39 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:39 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:44:39 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:39 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:39 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:39 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:39 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:39 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:39 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:39 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:39 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:39 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:39 MarkDuplicates Getting Memory Stats. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:40 MarkDuplicates Before output close freeMemory: 760808200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:40 MarkDuplicates Before output close freeMemory: 760808200; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:40 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:40 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:40 MarkDuplicates After output close freeMemory: 760947544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:40 MarkDuplicates After output close freeMemory: 760947544; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:40 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:44:40 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:40 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testSingleUnmappedPair STANDARD_ERROR INFO 2024-07-02 11:44:40 MarkDuplicates Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.12609771480951901566.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.12609771480951901566.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.12609771480951901566.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.12609771480951901566.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.12609771480951901566.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.12609771480951901566.tmp/output.sam Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:40.727 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:40.727 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:40.727 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:40.727 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:40.727 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:40.727 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:40.727 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:40.727 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:40 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.12609771480951901566.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.12609771480951901566.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.12609771480951901566.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:40 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.12609771480951901566.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.12609771480951901566.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.12609771480951901566.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:41 MarkDuplicates Start of doWork freeMemory: 1030436176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:41 MarkDuplicates Start of doWork freeMemory: 1030436176; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:41 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:41 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:41 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:41 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:41 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:44:41 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 967516152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 967516152; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:42 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:42 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:42 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:42 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:42 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:42 MarkDuplicates Sorting list of duplicate records. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 491462848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 491462848; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:43 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:44:43 MarkDuplicates Marking 0 records as duplicates. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:43 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:44:43 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:43 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:43 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:43 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:43 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:43 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:43 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:43 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:43 MarkDuplicates Duplicate Index cleanup. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:43 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:43 MarkDuplicates Getting Memory Stats. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:43 MarkDuplicates Before output close freeMemory: 760807288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:43 MarkDuplicates Before output close freeMemory: 760807288; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:43 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:43 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:43 MarkDuplicates After output close freeMemory: 760946632; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:43 MarkDuplicates After output close freeMemory: 760946632; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:43 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:44:43 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:43 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testStackOverFlowPairSetSwap STANDARD_ERROR INFO 2024-07-02 11:44:43 MarkDuplicates Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.13251834126477235048.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.13251834126477235048.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.13251834126477235048.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.13251834126477235048.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.13251834126477235048.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.13251834126477235048.tmp/output.sam Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:43.883 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:43.883 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:43.883 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:43.883 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:43.884 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:43.884 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:43.884 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:43.884 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:43 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.13251834126477235048.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.13251834126477235048.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.13251834126477235048.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:43 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.13251834126477235048.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.13251834126477235048.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.13251834126477235048.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:44 MarkDuplicates Start of doWork freeMemory: 1030326624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:44 MarkDuplicates Start of doWork freeMemory: 1030326624; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:44 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:44 MarkDuplicates Reading input file and constructing read end information. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:44 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:44 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:44 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:44:44 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 967377680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 967377680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:45 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:45 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:45 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:45 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:45 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:45 MarkDuplicates Sorting list of duplicate records. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 491324480; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 491324480; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:45 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:44:45 MarkDuplicates Marking 1 records as duplicates. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:45 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:44:45 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:45 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:45 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:45 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:45 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:45 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:45 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:45 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:45 MarkDuplicates Duplicate Index cleanup. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:45 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:45 MarkDuplicates Getting Memory Stats. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:46 MarkDuplicates Before output close freeMemory: 760638728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:46 MarkDuplicates Before output close freeMemory: 760638728; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:46 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:46 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:46 MarkDuplicates After output close freeMemory: 760805976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:46 MarkDuplicates After output close freeMemory: 760805976; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:44:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:46 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:44:46 MarkDuplicates Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.9373235478492578095.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.9373235478492578095.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.9373235478492578095.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.9373235478492578095.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.9373235478492578095.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.9373235478492578095.tmp/output.sam Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:46.533 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:46.533 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:46.541 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:46.541 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:46.541 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:46.541 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:46.541 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:46.541 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:46 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.9373235478492578095.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.9373235478492578095.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.9373235478492578095.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:46 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.9373235478492578095.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.9373235478492578095.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.9373235478492578095.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:46 MarkDuplicates Start of doWork freeMemory: 1030421072; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:46 MarkDuplicates Start of doWork freeMemory: 1030421072; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:46 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:46 MarkDuplicates Reading input file and constructing read end information. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:46 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:46 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:44:46 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:44:46 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:46 MarkDuplicates Read 18 records. 0 pairs never matched. INFO 2024-07-02 11:44:46 MarkDuplicates Read 18 records. 0 pairs never matched. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 967501800; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 967501800; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:47 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:48 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:48 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:48 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:48 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:48 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:48 MarkDuplicates Sorting list of duplicate records. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 491483968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 491483968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:48 MarkDuplicates Marking 6 records as duplicates. INFO 2024-07-02 11:44:48 MarkDuplicates Marking 6 records as duplicates. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:48 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:44:48 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:48 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:48 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:48 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:48 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:48 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:48 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:48 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:48 MarkDuplicates Duplicate Index cleanup. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:48 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:48 MarkDuplicates Getting Memory Stats. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:48 MarkDuplicates Before output close freeMemory: 760826584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:48 MarkDuplicates Before output close freeMemory: 760826584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:48 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:48 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:49 MarkDuplicates After output close freeMemory: 760864688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:49 MarkDuplicates After output close freeMemory: 760864688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:44:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:49 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:44:49 MarkDuplicates Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.15998485162446133785.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.15998485162446133785.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.15998485162446133785.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.15998485162446133785.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.15998485162446133785.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.15998485162446133785.tmp/output.sam Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:49.088 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:49.088 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:49.088 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:49.088 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:49.088 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:49.088 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:49.088 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:49.088 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:49 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.15998485162446133785.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.15998485162446133785.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.15998485162446133785.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:49 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.15998485162446133785.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.15998485162446133785.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.15998485162446133785.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:49 MarkDuplicates Start of doWork freeMemory: 1030465312; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:49 MarkDuplicates Start of doWork freeMemory: 1030465312; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:49 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:49 MarkDuplicates Reading input file and constructing read end information. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:44:49 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:44:49 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:49 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:44:49 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 967543928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:49 MarkDuplicates After buildSortedReadEndLists freeMemory: 967543928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:50 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:50 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:50 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:50 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:50 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:50 MarkDuplicates Sorting list of duplicate records. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 659263856; totalMemory: 1241513984; maxMemory: 2147483648 INFO 2024-07-02 11:44:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 659263856; totalMemory: 1241513984; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:51 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:44:51 MarkDuplicates Marking 2 records as duplicates. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:51 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:44:51 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:51 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:51 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:51 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:51 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:51 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:51 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:51 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:51 MarkDuplicates Duplicate Index cleanup. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:51 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:51 MarkDuplicates Getting Memory Stats. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:51 MarkDuplicates Before output close freeMemory: 760836136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:51 MarkDuplicates Before output close freeMemory: 760836136; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:51 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:51 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:51 MarkDuplicates After output close freeMemory: 760975480; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:51 MarkDuplicates After output close freeMemory: 760975480; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:44:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:51 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testThreeMappedPairsWithMatchingSecondMate STANDARD_ERROR INFO 2024-07-02 11:44:51 MarkDuplicates Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.17931857847075810942.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.17931857847075810942.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.17931857847075810942.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.17931857847075810942.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.17931857847075810942.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.17931857847075810942.tmp/output.sam Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:51.838 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:51.838 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:51.838 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:51.838 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:51.838 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:51.838 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:51.838 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:51.838 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:51 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.17931857847075810942.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.17931857847075810942.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.17931857847075810942.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:51 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.17931857847075810942.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.17931857847075810942.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.17931857847075810942.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:52 MarkDuplicates Start of doWork freeMemory: 1030361160; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:52 MarkDuplicates Start of doWork freeMemory: 1030361160; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:52 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:52 MarkDuplicates Reading input file and constructing read end information. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:52 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:52 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:44:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:44:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:52 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:44:52 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 967543296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 967543296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:53 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:53 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:53 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:53 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:53 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:53 MarkDuplicates Sorting list of duplicate records. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 491491232; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:54 MarkDuplicates After generateDuplicateIndexes freeMemory: 491491232; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:54 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:44:54 MarkDuplicates Marking 1 records as duplicates. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:54 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:44:54 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:54 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:54 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:54 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:54 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:54 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:54 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:54 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:54 MarkDuplicates Duplicate Index cleanup. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:54 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:54 MarkDuplicates Getting Memory Stats. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:54 MarkDuplicates Before output close freeMemory: 760833848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:54 MarkDuplicates Before output close freeMemory: 760833848; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:54 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:54 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:54 MarkDuplicates After output close freeMemory: 760974592; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:54 MarkDuplicates After output close freeMemory: 760974592; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:54 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:44:54 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:54 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:44:54 MarkDuplicates Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.16782094182834846693.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.16782094182834846693.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.16782094182834846693.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.16782094182834846693.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.16782094182834846693.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.16782094182834846693.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:54.773 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:54.773 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:54.773 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:54.773 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:54.773 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:54.773 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:54.773 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:54.773 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:54 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.16782094182834846693.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.16782094182834846693.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.16782094182834846693.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:54 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.16782094182834846693.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.16782094182834846693.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.16782094182834846693.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:55 MarkDuplicates Start of doWork freeMemory: 1030457680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:55 MarkDuplicates Start of doWork freeMemory: 1030457680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:55 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:55 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:55 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:55 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:44:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:44:55 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:55 MarkDuplicates Read 12 records. 0 pairs never matched. INFO 2024-07-02 11:44:55 MarkDuplicates Read 12 records. 0 pairs never matched. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 967538456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 967538456; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:56 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:56 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:56 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:56 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:56 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:56 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:56 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 491488576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:57 MarkDuplicates After generateDuplicateIndexes freeMemory: 491488576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:57 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:44:57 MarkDuplicates Marking 4 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:57 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:44:57 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:57 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:44:57 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:57 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:44:57 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:57 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:44:57 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:57 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:44:57 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:57 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:44:57 MarkDuplicates Getting Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:57 MarkDuplicates Before output close freeMemory: 760831192; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:57 MarkDuplicates Before output close freeMemory: 760831192; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:57 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:44:57 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:57 MarkDuplicates After output close freeMemory: 760972360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:57 MarkDuplicates After output close freeMemory: 760972360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:57 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:44:57 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:57 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoGroupsOnDifferentChromosomesOfTwoFragments STANDARD_ERROR INFO 2024-07-02 11:44:57 MarkDuplicates Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.12980473220282411630.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.12980473220282411630.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.12980473220282411630.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.12980473220282411630.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.12980473220282411630.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.12980473220282411630.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:57.685 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:57.685 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:57.685 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:57.685 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:57.686 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:44:57.686 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:44:57.686 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:44:57.686 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:57 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.12980473220282411630.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.12980473220282411630.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.12980473220282411630.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:44:57 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.12980473220282411630.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.12980473220282411630.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.12980473220282411630.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:44:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:44:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:58 MarkDuplicates Start of doWork freeMemory: 1030464496; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:58 MarkDuplicates Start of doWork freeMemory: 1030464496; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:58 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:44:58 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:58 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:44:58 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:44:58 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:44:58 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:58 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:44:58 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 967546880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:44:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 967546880; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:59 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:44:59 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:59 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:44:59 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:59 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:44:59 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:44:59 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:44:59 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 491493864; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:00 MarkDuplicates After generateDuplicateIndexes freeMemory: 491493864; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:00 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:45:00 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:00 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:45:00 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:00 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:45:00 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:00 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:45:00 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:00 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:45:00 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:00 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:45:00 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:00 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:45:00 MarkDuplicates Getting Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:00 MarkDuplicates Before output close freeMemory: 760838304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:00 MarkDuplicates Before output close freeMemory: 760838304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:00 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:45:00 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:00 MarkDuplicates After output close freeMemory: 760977648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:00 MarkDuplicates After output close freeMemory: 760977648; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:45:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:00 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:45:00 MarkDuplicates Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.7917449202050705768.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.7917449202050705768.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.7917449202050705768.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.7917449202050705768.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.7917449202050705768.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.7917449202050705768.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:00.678 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:00.678 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:00.678 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:00.678 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:00.678 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:00.678 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:00.678 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:00.678 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:00 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.7917449202050705768.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.7917449202050705768.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.7917449202050705768.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:45:00 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.7917449202050705768.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.7917449202050705768.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.7917449202050705768.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:45:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:00 MarkDuplicates Start of doWork freeMemory: 1030464104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:00 MarkDuplicates Start of doWork freeMemory: 1030464104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:00 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:45:00 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:00 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:45:00 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:45:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:45:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:01 MarkDuplicates Read 8 records. 0 pairs never matched. INFO 2024-07-02 11:45:01 MarkDuplicates Read 8 records. 0 pairs never matched. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 967543104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 967543104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:45:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:02 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:45:02 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:02 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:45:02 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:02 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:45:02 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 695963640; totalMemory: 1278214144; maxMemory: 2147483648 INFO 2024-07-02 11:45:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 695963640; totalMemory: 1278214144; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:02 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:45:02 MarkDuplicates Marking 2 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:02 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:45:02 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:02 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:45:02 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:02 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:45:02 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:02 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:45:02 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:02 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:45:02 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:02 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:45:02 MarkDuplicates Getting Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:02 MarkDuplicates Before output close freeMemory: 760835760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:02 MarkDuplicates Before output close freeMemory: 760835760; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:02 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:45:02 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:03 MarkDuplicates After output close freeMemory: 760975104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:03 MarkDuplicates After output close freeMemory: 760975104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:03 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:45:03 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:03 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoMappedFragments STANDARD_ERROR INFO 2024-07-02 11:45:03 MarkDuplicates Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.7409286164060350073.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.7409286164060350073.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.7409286164060350073.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.7409286164060350073.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.7409286164060350073.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.7409286164060350073.tmp/output.sam Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:03.297 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:03.297 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:03.297 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:03.297 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:03.297 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:03.297 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:03.297 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:03.297 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:03 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.7409286164060350073.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.7409286164060350073.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.7409286164060350073.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:45:03 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.7409286164060350073.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.7409286164060350073.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.7409286164060350073.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:45:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:03 MarkDuplicates Start of doWork freeMemory: 1030468544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:03 MarkDuplicates Start of doWork freeMemory: 1030468544; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:03 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:45:03 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:03 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:45:03 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:45:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:45:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:03 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:45:03 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 967547696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 967547696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:04 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:45:04 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:04 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:45:04 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:04 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:45:04 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:04 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:45:04 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 491495104; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 491495104; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:05 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:45:05 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:05 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:45:05 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:05 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:45:05 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:05 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:45:05 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:05 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:45:05 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:05 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:45:05 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:05 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:45:05 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:05 MarkDuplicates Before output close freeMemory: 760838912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:05 MarkDuplicates Before output close freeMemory: 760838912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:05 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:45:05 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:05 MarkDuplicates After output close freeMemory: 760978736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:05 MarkDuplicates After output close freeMemory: 760978736; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:05 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:45:05 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:05 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoMappedPairWithSamePosition STANDARD_ERROR INFO 2024-07-02 11:45:05 MarkDuplicates Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.6687533061344432913.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.6687533061344432913.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.6687533061344432913.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.6687533061344432913.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.6687533061344432913.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.6687533061344432913.tmp/output.sam Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:05.978 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:05.978 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:05.978 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:05.978 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:05.978 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:05.978 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:05.978 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:05.978 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:05 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.6687533061344432913.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.6687533061344432913.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.6687533061344432913.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:45:05 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.6687533061344432913.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.6687533061344432913.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.6687533061344432913.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:45:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:06 MarkDuplicates Start of doWork freeMemory: 1030466552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:06 MarkDuplicates Start of doWork freeMemory: 1030466552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:06 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:45:06 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:06 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:45:06 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:45:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:45:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:06 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:45:06 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 967545384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 967545384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:06 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:45:06 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:07 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:45:07 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:07 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:45:07 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:07 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:45:07 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 491492936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 491492936; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:07 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:45:07 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:07 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:45:07 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:07 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:45:07 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:07 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:45:07 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:07 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:45:07 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:07 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:45:07 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:07 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:45:07 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:07 MarkDuplicates Before output close freeMemory: 760734864; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:07 MarkDuplicates Before output close freeMemory: 760734864; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:07 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:45:07 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:08 MarkDuplicates After output close freeMemory: 760976720; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:08 MarkDuplicates After output close freeMemory: 760976720; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:08 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:45:08 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:08 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoMappedPairWithSamePositionDifferentStrands STANDARD_ERROR INFO 2024-07-02 11:45:08 MarkDuplicates Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.18433632354102765019.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.18433632354102765019.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.18433632354102765019.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.18433632354102765019.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.18433632354102765019.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.18433632354102765019.tmp/output.sam Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:08.384 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:08.384 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:08.384 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:08.384 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:08.384 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:08.384 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:08.384 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:08.384 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:08 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.18433632354102765019.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.18433632354102765019.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.18433632354102765019.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:45:08 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.18433632354102765019.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.18433632354102765019.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.18433632354102765019.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:45:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:08 MarkDuplicates Start of doWork freeMemory: 1030466240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:08 MarkDuplicates Start of doWork freeMemory: 1030466240; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:08 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:45:08 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:08 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:45:08 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:45:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:45:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:08 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:45:08 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 967545072; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 967545072; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:45:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:09 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:45:09 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:09 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:45:09 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:09 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:45:09 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 491492624; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 491492624; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:09 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:45:09 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:09 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:45:09 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:09 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:45:09 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:09 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:45:09 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:09 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:45:09 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:09 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:45:09 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:09 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:45:09 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:10 MarkDuplicates Before output close freeMemory: 760837064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:10 MarkDuplicates Before output close freeMemory: 760837064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:10 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:45:10 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:10 MarkDuplicates After output close freeMemory: 760975912; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:10 MarkDuplicates After output close freeMemory: 760975912; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:10 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:45:10 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:10 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoMappedPairWithSamePositionDifferentStrands2 STANDARD_ERROR INFO 2024-07-02 11:45:10 MarkDuplicates Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.13367442254659986157.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.13367442254659986157.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.13367442254659986157.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.13367442254659986157.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.13367442254659986157.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.13367442254659986157.tmp/output.sam Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:10.505 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:10.505 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:10.505 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:10.505 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:10.505 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:10.505 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:10.505 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:10.505 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:10 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.13367442254659986157.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.13367442254659986157.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.13367442254659986157.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:45:10 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.13367442254659986157.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.13367442254659986157.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.13367442254659986157.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:45:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:10 MarkDuplicates Start of doWork freeMemory: 1030465808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:10 MarkDuplicates Start of doWork freeMemory: 1030465808; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:10 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:45:10 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:10 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:45:10 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:45:10 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:45:10 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:10 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:45:10 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 967544640; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 967544640; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:45:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:45:11 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:45:11 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:11 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:45:11 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 705401696; totalMemory: 1287651328; maxMemory: 2147483648 INFO 2024-07-02 11:45:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 705401696; totalMemory: 1287651328; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:12 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:45:12 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:12 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:45:12 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:12 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:45:12 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:12 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:45:12 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:12 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:45:12 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:12 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:45:12 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:12 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:45:12 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:12 MarkDuplicates Before output close freeMemory: 760836632; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:12 MarkDuplicates Before output close freeMemory: 760836632; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:12 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:45:12 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:12 MarkDuplicates After output close freeMemory: 760975552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:12 MarkDuplicates After output close freeMemory: 760975552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:12 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:45:12 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:12 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:45:12 MarkDuplicates Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.896075084210142863.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.896075084210142863.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.896075084210142863.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.896075084210142863.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.896075084210142863.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.896075084210142863.tmp/output.sam Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:12.919 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:12.919 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:12.919 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:12.919 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:12.919 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:12.919 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:12.919 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:12.919 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:12 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.896075084210142863.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.896075084210142863.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.896075084210142863.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:45:12 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.896075084210142863.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.896075084210142863.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.896075084210142863.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:45:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:13 MarkDuplicates Start of doWork freeMemory: 1030459752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:13 MarkDuplicates Start of doWork freeMemory: 1030459752; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:13 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:45:13 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:13 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:45:13 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:45:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:45:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:13 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:45:13 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 967544584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 967544584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:13 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:45:13 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:45:14 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:14 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:45:14 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:14 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:45:14 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 491491536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 491491536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:14 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:45:14 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:14 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:45:14 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:14 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:45:14 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:14 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:45:14 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:14 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:45:14 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:14 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:45:14 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:14 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:45:14 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:15 MarkDuplicates Before output close freeMemory: 760835976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:15 MarkDuplicates Before output close freeMemory: 760835976; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:15 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:45:15 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:15 MarkDuplicates After output close freeMemory: 760975320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:15 MarkDuplicates After output close freeMemory: 760975320; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:45:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:15 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoMappedPairsAndMappedSecondaryFragment STANDARD_ERROR INFO 2024-07-02 11:45:15 MarkDuplicates Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.1810254521477621411.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.1810254521477621411.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.1810254521477621411.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.1810254521477621411.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.1810254521477621411.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.1810254521477621411.tmp/output.sam Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:15.727 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:15.727 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:15.727 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:15.727 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:15.727 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:15.727 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:15.728 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:15.728 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:15 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.1810254521477621411.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.1810254521477621411.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.1810254521477621411.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:45:15 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.1810254521477621411.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.1810254521477621411.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.1810254521477621411.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:45:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:16 MarkDuplicates Start of doWork freeMemory: 1030461240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:16 MarkDuplicates Start of doWork freeMemory: 1030461240; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:16 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:45:16 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:16 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:45:16 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:45:16 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:45:16 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:16 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:45:16 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 967442168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:16 MarkDuplicates After buildSortedReadEndLists freeMemory: 967442168; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:17 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:45:17 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:17 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:45:17 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:17 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:45:17 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:17 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:45:17 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 491490432; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:18 MarkDuplicates After generateDuplicateIndexes freeMemory: 491490432; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:18 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:45:18 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:18 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:45:18 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:18 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:45:18 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:18 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:45:18 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:18 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:45:18 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:18 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:45:18 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:18 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:45:18 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:18 MarkDuplicates Before output close freeMemory: 760834872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:18 MarkDuplicates Before output close freeMemory: 760834872; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:18 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:45:18 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:18 MarkDuplicates After output close freeMemory: 760873008; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:18 MarkDuplicates After output close freeMemory: 760873008; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:18 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:45:18 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:19 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoMappedPairsAndTerminalUnmappedFragment STANDARD_ERROR INFO 2024-07-02 11:45:19 MarkDuplicates Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.18130931492917092631.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.18130931492917092631.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.18130931492917092631.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.18130931492917092631.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.18130931492917092631.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.18130931492917092631.tmp/output.sam Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:19.063 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:19.063 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:19.063 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:19.063 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:19.063 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:19.063 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:19.063 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:19.063 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:19 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.18130931492917092631.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.18130931492917092631.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.18130931492917092631.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:45:19 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.18130931492917092631.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.18130931492917092631.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.18130931492917092631.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:45:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:19 MarkDuplicates Start of doWork freeMemory: 1030460848; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:19 MarkDuplicates Start of doWork freeMemory: 1030460848; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:19 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:45:19 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:19 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:45:19 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:45:19 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:45:19 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:19 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:45:19 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 967543088; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:19 MarkDuplicates After buildSortedReadEndLists freeMemory: 967543088; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:45:20 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:21 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:45:21 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:21 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:45:21 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:21 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:45:21 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 491490040; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:21 MarkDuplicates After generateDuplicateIndexes freeMemory: 491490040; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:21 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:45:21 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:21 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:45:21 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:21 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:45:21 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:21 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:45:21 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:21 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:45:21 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:21 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:45:21 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:21 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:45:21 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:21 MarkDuplicates Before output close freeMemory: 760834480; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:21 MarkDuplicates Before output close freeMemory: 760834480; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:21 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:45:21 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:22 MarkDuplicates After output close freeMemory: 760973824; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:22 MarkDuplicates After output close freeMemory: 760973824; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:22 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:45:22 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:22 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoMappedPairsAndTerminalUnmappedPair STANDARD_ERROR INFO 2024-07-02 11:45:22 MarkDuplicates Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.2722426246053721795.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.2722426246053721795.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.2722426246053721795.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.2722426246053721795.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.2722426246053721795.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.2722426246053721795.tmp/output.sam Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:22.205 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:22.205 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:22.206 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:22.206 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:22.206 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:22.206 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:22.206 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:22.206 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:22 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.2722426246053721795.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.2722426246053721795.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.2722426246053721795.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:45:22 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.2722426246053721795.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.2722426246053721795.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.2722426246053721795.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:45:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:22 MarkDuplicates Start of doWork freeMemory: 1030462752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:22 MarkDuplicates Start of doWork freeMemory: 1030462752; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:22 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:45:22 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:22 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:45:22 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:45:22 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:45:22 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:22 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:45:22 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 967542184; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:23 MarkDuplicates After buildSortedReadEndLists freeMemory: 967542184; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:45:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:24 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:45:24 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:24 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:45:24 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:24 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:45:24 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 706447216; totalMemory: 1288699904; maxMemory: 2147483648 INFO 2024-07-02 11:45:24 MarkDuplicates After generateDuplicateIndexes freeMemory: 706447216; totalMemory: 1288699904; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:24 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:45:24 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:24 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:45:24 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:24 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:45:24 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:24 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:45:24 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:24 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:45:24 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:24 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:45:24 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:24 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:45:24 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:25 MarkDuplicates Before output close freeMemory: 760833576; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:25 MarkDuplicates Before output close freeMemory: 760833576; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:25 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:45:25 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:25 MarkDuplicates After output close freeMemory: 760972992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:25 MarkDuplicates After output close freeMemory: 760972992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:25 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:45:25 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:25 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoMappedPairsMatesSoftClipped STANDARD_ERROR INFO 2024-07-02 11:45:25 MarkDuplicates Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.15045132753669383968.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.15045132753669383968.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.15045132753669383968.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.15045132753669383968.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.15045132753669383968.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.15045132753669383968.tmp/output.sam Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:25.707 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:25.707 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:25.708 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:25.708 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:25.708 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:25.708 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:25.708 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:25.708 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:25 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.15045132753669383968.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.15045132753669383968.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.15045132753669383968.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:45:25 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.15045132753669383968.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.15045132753669383968.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.15045132753669383968.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:45:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:26 MarkDuplicates Start of doWork freeMemory: 1030463168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:26 MarkDuplicates Start of doWork freeMemory: 1030463168; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:26 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:45:26 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:26 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:45:26 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:45:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:45:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:26 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:45:26 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 967542600; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:26 MarkDuplicates After buildSortedReadEndLists freeMemory: 967542600; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:45:27 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:27 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:45:27 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:27 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:45:27 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:27 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:45:27 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 491489552; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:28 MarkDuplicates After generateDuplicateIndexes freeMemory: 491489552; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:28 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:45:28 MarkDuplicates Marking 0 records as duplicates. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:28 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:45:28 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:28 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:45:28 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:28 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:45:28 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:28 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:45:28 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:28 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:45:28 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:28 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:45:28 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:28 MarkDuplicates Before output close freeMemory: 760833992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:28 MarkDuplicates Before output close freeMemory: 760833992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:28 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:45:28 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:28 MarkDuplicates After output close freeMemory: 760973408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:28 MarkDuplicates After output close freeMemory: 760973408; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:28 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:45:28 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:28 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoMappedPairsWithOppositeOrientations STANDARD_ERROR INFO 2024-07-02 11:45:28 MarkDuplicates Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.11215037829568317434.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.11215037829568317434.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.11215037829568317434.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.11215037829568317434.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.11215037829568317434.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.11215037829568317434.tmp/output.sam Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:28.822 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:28.822 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:28.822 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:28.822 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:28.823 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:28.823 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:28.823 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:28.823 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:28 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.11215037829568317434.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.11215037829568317434.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.11215037829568317434.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:45:28 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.11215037829568317434.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.11215037829568317434.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.11215037829568317434.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:45:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:29 MarkDuplicates Start of doWork freeMemory: 1030462544; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:29 MarkDuplicates Start of doWork freeMemory: 1030462544; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:29 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:45:29 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:29 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:45:29 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:45:29 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:45:29 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:29 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:45:29 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 967541976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 967541976; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:45:30 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:30 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:45:30 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:30 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:45:30 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:30 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:45:30 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 491488928; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:31 MarkDuplicates After generateDuplicateIndexes freeMemory: 491488928; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:31 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:45:31 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:31 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:45:31 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:31 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:45:31 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:31 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:45:31 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:31 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:45:31 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:31 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:45:31 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:31 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:45:31 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:31 MarkDuplicates Before output close freeMemory: 760833368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:31 MarkDuplicates Before output close freeMemory: 760833368; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:31 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:45:31 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:31 MarkDuplicates After output close freeMemory: 760972712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:31 MarkDuplicates After output close freeMemory: 760972712; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:31 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:45:31 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:31 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoMappedPairsWithOppositeOrientationsNumberTwo STANDARD_ERROR INFO 2024-07-02 11:45:31 MarkDuplicates Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.14361003176340933998.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.14361003176340933998.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.14361003176340933998.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.14361003176340933998.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.14361003176340933998.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.14361003176340933998.tmp/output.sam Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:31.991 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:31.991 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:31.991 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:31.991 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:31.992 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:31.992 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:31.992 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:31.992 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:31 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.14361003176340933998.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.14361003176340933998.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.14361003176340933998.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:45:31 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.14361003176340933998.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.14361003176340933998.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.14361003176340933998.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:45:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:32 MarkDuplicates Start of doWork freeMemory: 1030459248; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:32 MarkDuplicates Start of doWork freeMemory: 1030459248; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:32 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:45:32 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:32 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:45:32 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:45:32 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:45:32 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:32 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:45:32 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 967540888; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 967540888; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:45:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:33 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:45:33 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:33 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:45:33 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:33 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:45:33 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 491488440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 491488440; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:34 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:45:34 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:34 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:45:34 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:34 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:45:34 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:34 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:45:34 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:34 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:45:34 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:34 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:45:34 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:34 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:45:34 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:34 MarkDuplicates Before output close freeMemory: 760731056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:34 MarkDuplicates Before output close freeMemory: 760731056; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:34 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:45:34 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:34 MarkDuplicates After output close freeMemory: 760972224; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:34 MarkDuplicates After output close freeMemory: 760972224; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:45:34 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:34 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoMappedPairsWithSoftClipping STANDARD_ERROR INFO 2024-07-02 11:45:34 MarkDuplicates Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.14163718014044504099.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.14163718014044504099.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.14163718014044504099.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.14163718014044504099.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.14163718014044504099.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.14163718014044504099.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:34.876 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:34.876 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:34.876 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:34.876 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:34.887 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:34.887 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:34.887 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:34.887 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:34 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.14163718014044504099.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.14163718014044504099.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.14163718014044504099.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:45:34 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.14163718014044504099.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.14163718014044504099.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.14163718014044504099.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:45:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:35 MarkDuplicates Start of doWork freeMemory: 1030459272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:35 MarkDuplicates Start of doWork freeMemory: 1030459272; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:35 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:45:35 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:35 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:45:35 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:45:35 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:45:35 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:35 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:45:35 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 967540352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:35 MarkDuplicates After buildSortedReadEndLists freeMemory: 967540352; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:45:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:36 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:45:36 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:36 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:45:36 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:36 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:45:36 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 668697248; totalMemory: 1250951168; maxMemory: 2147483648 INFO 2024-07-02 11:45:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 668697248; totalMemory: 1250951168; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:37 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:45:37 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:37 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:45:37 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:37 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:45:37 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:37 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:45:37 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:37 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:45:37 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:37 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:45:37 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:37 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:45:37 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:37 MarkDuplicates Before output close freeMemory: 760730520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:37 MarkDuplicates Before output close freeMemory: 760730520; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:37 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:45:37 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:37 MarkDuplicates After output close freeMemory: 760971688; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:37 MarkDuplicates After output close freeMemory: 760971688; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:45:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:38 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoMappedPairsWithSoftClippingBoth STANDARD_ERROR INFO 2024-07-02 11:45:38 MarkDuplicates Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.10328368012819141426.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.10328368012819141426.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.10328368012819141426.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.10328368012819141426.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.10328368012819141426.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.10328368012819141426.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:38.019 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:38.019 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:38.019 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:38.019 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:38.020 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:38.020 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:38.020 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:38.020 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:38 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.10328368012819141426.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.10328368012819141426.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.10328368012819141426.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:45:38 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.10328368012819141426.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.10328368012819141426.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.10328368012819141426.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:45:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:38 MarkDuplicates Start of doWork freeMemory: 1030458224; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:38 MarkDuplicates Start of doWork freeMemory: 1030458224; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:38 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:45:38 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:38 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:45:38 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:45:38 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:45:38 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:38 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:45:38 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 967539864; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 967539864; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:45:39 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:40 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:45:40 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:40 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:45:40 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:40 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:45:40 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 491487416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 491487416; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:40 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:45:40 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:40 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:45:40 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:40 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:45:40 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:40 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:45:40 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:40 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:45:40 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:40 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:45:40 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:40 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:45:40 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:41 MarkDuplicates Before output close freeMemory: 760831856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:41 MarkDuplicates Before output close freeMemory: 760831856; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:41 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:45:41 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:41 MarkDuplicates After output close freeMemory: 760869992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:41 MarkDuplicates After output close freeMemory: 760869992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:41 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:45:41 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:41 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar STANDARD_ERROR INFO 2024-07-02 11:45:41 MarkDuplicates Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.2567552845388045576.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.2567552845388045576.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.2567552845388045576.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.2567552845388045576.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.2567552845388045576.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.2567552845388045576.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:41.399 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:41.399 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:41.399 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:41.399 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:41.400 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:41.400 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:41.400 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:41.400 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:41 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.2567552845388045576.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.2567552845388045576.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.2567552845388045576.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:45:41 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.2567552845388045576.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.2567552845388045576.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.2567552845388045576.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:45:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:41 MarkDuplicates Start of doWork freeMemory: 1030461736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:41 MarkDuplicates Start of doWork freeMemory: 1030461736; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:41 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:45:41 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:41 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:45:41 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:45:41 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:45:41 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:41 MarkDuplicates Read 2 records. 2 pairs never matched. INFO 2024-07-02 11:45:41 MarkDuplicates Read 2 records. 2 pairs never matched. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 967541456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:42 MarkDuplicates After buildSortedReadEndLists freeMemory: 967541456; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:45:42 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:43 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:45:43 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:43 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:45:43 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:43 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:45:43 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 491488296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 491488296; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:43 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:45:43 MarkDuplicates Marking 0 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:43 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:45:43 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:43 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:45:43 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:43 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:45:43 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:43 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:45:43 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:43 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:45:43 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:43 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:45:43 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:43 MarkDuplicates Before output close freeMemory: 760832736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:43 MarkDuplicates Before output close freeMemory: 760832736; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:43 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:45:43 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:44 MarkDuplicates After output close freeMemory: 760971584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:44 MarkDuplicates After output close freeMemory: 760971584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:44 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:45:44 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:44 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoMappedPairsWithSupplementaryReads[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:45:44 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.10840725313048245401.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.10840725313048245401.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.10840725313048245401.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.10840725313048245401.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.10840725313048245401.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.10840725313048245401.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:44.138 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:44.138 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:44.138 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:44.138 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:44.138 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:44.138 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:44.138 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:44.138 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:44 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.10840725313048245401.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.10840725313048245401.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.10840725313048245401.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:45:44 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.10840725313048245401.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.10840725313048245401.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.10840725313048245401.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:45:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:44 MarkDuplicates Start of doWork freeMemory: 1030459160; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:44 MarkDuplicates Start of doWork freeMemory: 1030459160; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:44 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:45:44 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:44 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:45:44 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:44 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:45:44 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 967538528; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 967538528; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:45:45 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:45 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:45:45 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:45 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:45:45 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:45 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:45:45 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 491485416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 491485416; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:45 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:45:45 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:45 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:45:45 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:45 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:45:45 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:45 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:45:45 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:45 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:45:45 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:45 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:45:45 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:45 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:45:45 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:46 MarkDuplicates Before output close freeMemory: 760829856; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:46 MarkDuplicates Before output close freeMemory: 760829856; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:46 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:45:46 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:46 MarkDuplicates After output close freeMemory: 760969200; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:46 MarkDuplicates After output close freeMemory: 760969200; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:45:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:46 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoMappedPairsWithSupplementaryReads[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:45:46 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.9244866346585324816.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.9244866346585324816.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.9244866346585324816.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.9244866346585324816.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.9244866346585324816.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.9244866346585324816.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:46.751 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:46.751 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:46.752 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:46.752 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:46.752 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:46.752 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:46.752 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:46.752 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:46 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.9244866346585324816.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.9244866346585324816.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.9244866346585324816.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:45:46 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.9244866346585324816.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.9244866346585324816.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.9244866346585324816.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:45:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:47 MarkDuplicates Start of doWork freeMemory: 1030453400; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:47 MarkDuplicates Start of doWork freeMemory: 1030453400; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:47 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:45:47 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:47 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:45:47 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:47 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:45:47 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 967538168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 967538168; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:48 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:45:48 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:48 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:45:48 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:48 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:45:48 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:48 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:45:48 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 662436560; totalMemory: 1244659712; maxMemory: 2147483648 INFO 2024-07-02 11:45:48 MarkDuplicates After generateDuplicateIndexes freeMemory: 662436560; totalMemory: 1244659712; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:48 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:45:48 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:48 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:45:48 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:48 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:45:48 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:48 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:45:48 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:48 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:45:48 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:48 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:45:48 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:48 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:45:48 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:49 MarkDuplicates Before output close freeMemory: 760863112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:49 MarkDuplicates Before output close freeMemory: 760863112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:49 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:45:49 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:49 MarkDuplicates After output close freeMemory: 761002456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:49 MarkDuplicates After output close freeMemory: 761002456; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:45:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:49 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoMappedPairsWithSupplementaryReads[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:45:49 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.10243096291853188264.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.10243096291853188264.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.10243096291853188264.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.10243096291853188264.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.10243096291853188264.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.10243096291853188264.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:49.474 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:49.474 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:49.474 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:49.474 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:49.474 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:49.474 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:49.474 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:49.474 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:49 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.10243096291853188264.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.10243096291853188264.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.10243096291853188264.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:45:49 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.10243096291853188264.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.10243096291853188264.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.10243096291853188264.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:45:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:49 MarkDuplicates Start of doWork freeMemory: 1030492096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:49 MarkDuplicates Start of doWork freeMemory: 1030492096; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:49 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:45:49 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:45:49 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:49 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:45:49 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 967571464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 967571464; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:45:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:51 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:45:51 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:51 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:45:51 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:51 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:45:51 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 491518264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 491518264; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:51 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:45:51 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:51 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:45:51 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:51 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:45:51 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:51 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:45:51 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:51 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:45:51 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:51 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:45:51 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:51 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:45:51 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:52 MarkDuplicates Before output close freeMemory: 760860880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:52 MarkDuplicates Before output close freeMemory: 760860880; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:52 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:45:52 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:52 MarkDuplicates After output close freeMemory: 761002120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:52 MarkDuplicates After output close freeMemory: 761002120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:45:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:52 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoMappedPairsWithSupplementaryReads[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:45:52 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.12449073690713194741.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.12449073690713194741.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.12449073690713194741.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.12449073690713194741.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.12449073690713194741.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.12449073690713194741.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:52.375 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:52.375 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:52.375 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:52.375 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:52.375 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:52.375 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:52.375 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:52.375 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:52 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.12449073690713194741.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.12449073690713194741.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.12449073690713194741.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:45:52 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.12449073690713194741.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.12449073690713194741.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.12449073690713194741.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:45:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:52 MarkDuplicates Start of doWork freeMemory: 1030491712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:52 MarkDuplicates Start of doWork freeMemory: 1030491712; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:52 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:45:52 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:52 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:45:52 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:52 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:45:52 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 967571080; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:53 MarkDuplicates After buildSortedReadEndLists freeMemory: 967571080; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:54 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:45:54 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:55 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:45:55 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:55 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:45:55 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:55 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:45:55 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 491517880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:55 MarkDuplicates After generateDuplicateIndexes freeMemory: 491517880; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:55 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:45:55 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:55 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:45:55 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:55 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:45:55 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:55 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:45:55 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:55 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:45:55 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:55 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:45:55 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:55 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:45:55 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:56 MarkDuplicates Before output close freeMemory: 760861208; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:56 MarkDuplicates Before output close freeMemory: 760861208; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:56 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:45:56 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:56 MarkDuplicates After output close freeMemory: 761001736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:56 MarkDuplicates After output close freeMemory: 761001736; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:56 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:45:56 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:56 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoMappedPairsWithSupplementaryReads[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:45:56 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.13909063062389861743.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.13909063062389861743.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.13909063062389861743.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.13909063062389861743.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.13909063062389861743.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.13909063062389861743.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:56.783 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:56.783 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:56.783 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:56.783 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:56.784 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:45:56.784 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:45:56.784 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:45:56.784 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:56 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.13909063062389861743.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.13909063062389861743.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.13909063062389861743.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:45:56 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.13909063062389861743.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.13909063062389861743.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.13909063062389861743.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:45:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:45:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:57 MarkDuplicates Start of doWork freeMemory: 1030491368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:57 MarkDuplicates Start of doWork freeMemory: 1030491368; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:57 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:45:57 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:57 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:45:57 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:57 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:45:57 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 967570736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:57 MarkDuplicates After buildSortedReadEndLists freeMemory: 967570736; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:45:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:59 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:45:59 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:59 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:45:59 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:59 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:45:59 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 491517536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 491517536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:59 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:45:59 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:59 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:45:59 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:59 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:45:59 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:59 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:45:59 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:59 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:45:59 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:59 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:45:59 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:59 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:45:59 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:59 MarkDuplicates Before output close freeMemory: 760861976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:45:59 MarkDuplicates Before output close freeMemory: 760861976; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:45:59 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:45:59 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:00 MarkDuplicates After output close freeMemory: 761001320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:00 MarkDuplicates After output close freeMemory: 761001320; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:46:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:00 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoMappedPairsWithSupplementaryReads[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:46:00 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.6627698625966289064.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.6627698625966289064.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.6627698625966289064.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.6627698625966289064.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.6627698625966289064.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.6627698625966289064.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:00.238 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:46:00.238 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:00.238 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:46:00.238 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:00.238 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:46:00.238 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:00.239 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:46:00.239 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:00 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.6627698625966289064.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.6627698625966289064.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.6627698625966289064.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:46:00 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.6627698625966289064.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.6627698625966289064.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.6627698625966289064.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:46:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:00 MarkDuplicates Start of doWork freeMemory: 1030489216; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:00 MarkDuplicates Start of doWork freeMemory: 1030489216; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:00 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:46:00 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:00 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:46:00 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:00 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:46:00 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 967568584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:01 MarkDuplicates After buildSortedReadEndLists freeMemory: 967568584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:46:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:02 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:46:02 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:02 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:46:02 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:02 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:46:02 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 705424888; totalMemory: 1287651328; maxMemory: 2147483648 INFO 2024-07-02 11:46:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 705424888; totalMemory: 1287651328; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:02 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:46:02 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:02 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:46:02 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:02 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:46:02 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:02 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:46:02 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:02 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:46:02 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:02 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:46:02 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:02 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:46:02 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:02 MarkDuplicates Before output close freeMemory: 760859824; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:02 MarkDuplicates Before output close freeMemory: 760859824; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:02 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:46:02 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:03 MarkDuplicates After output close freeMemory: 760999168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:03 MarkDuplicates After output close freeMemory: 760999168; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:03 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:46:03 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:03 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:46:03 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.2869850709815431737.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.2869850709815431737.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.2869850709815431737.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.2869850709815431737.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.2869850709815431737.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.2869850709815431737.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:03.644 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:46:03.644 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:03.644 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:46:03.644 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:03.645 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:46:03.645 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:03.661 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:46:03.661 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:03 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.2869850709815431737.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.2869850709815431737.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.2869850709815431737.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:46:03 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.2869850709815431737.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.2869850709815431737.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.2869850709815431737.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:46:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:04 MarkDuplicates Start of doWork freeMemory: 1030488328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:04 MarkDuplicates Start of doWork freeMemory: 1030488328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:04 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:46:04 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:04 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:46:04 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:04 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:46:04 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 967567696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:04 MarkDuplicates After buildSortedReadEndLists freeMemory: 967567696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:06 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:46:06 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:07 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:46:07 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:07 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:46:07 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:07 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:46:07 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 491514496; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 491514496; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:07 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:46:07 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:07 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:46:07 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:07 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:46:07 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:07 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:46:07 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:07 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:46:07 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:07 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:46:07 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:07 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:46:07 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:08 MarkDuplicates Before output close freeMemory: 760858936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:08 MarkDuplicates Before output close freeMemory: 760858936; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:08 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:46:08 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:08 MarkDuplicates After output close freeMemory: 760998280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:08 MarkDuplicates After output close freeMemory: 760998280; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:08 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. [Tue Jul 02 11:46:08 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:08 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:46:08 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.15846861908332855354.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.15846861908332855354.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.15846861908332855354.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.15846861908332855354.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.15846861908332855354.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.15846861908332855354.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:08.805 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:46:08.805 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:08.806 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:46:08.806 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:08.806 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:46:08.806 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:08.806 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:46:08.806 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:08 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.15846861908332855354.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.15846861908332855354.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.15846861908332855354.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:46:08 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.15846861908332855354.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.15846861908332855354.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.15846861908332855354.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:46:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:09 MarkDuplicates Start of doWork freeMemory: 1030487728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:09 MarkDuplicates Start of doWork freeMemory: 1030487728; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:09 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:46:09 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:09 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:46:09 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:09 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:46:09 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 967567096; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 967567096; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:46:10 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:11 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:46:11 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:11 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:46:11 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:11 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:46:11 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 491513896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 491513896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:11 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:46:11 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:11 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:46:11 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:11 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:46:11 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:11 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:46:11 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:11 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:46:11 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:11 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:46:11 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:11 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:46:11 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:12 MarkDuplicates Before output close freeMemory: 760858336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:12 MarkDuplicates Before output close freeMemory: 760858336; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:12 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:46:12 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:12 MarkDuplicates After output close freeMemory: 760997680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:12 MarkDuplicates After output close freeMemory: 760997680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:12 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:46:12 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:12 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:46:12 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.5601752979048532296.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.5601752979048532296.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.5601752979048532296.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.5601752979048532296.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.5601752979048532296.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.5601752979048532296.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:12.729 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:46:12.729 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:12.730 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:46:12.730 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:12.730 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:46:12.730 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:12.730 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:46:12.730 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:12 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.5601752979048532296.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.5601752979048532296.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.5601752979048532296.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:46:12 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.5601752979048532296.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.5601752979048532296.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.5601752979048532296.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:46:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:13 MarkDuplicates Start of doWork freeMemory: 1030487368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:13 MarkDuplicates Start of doWork freeMemory: 1030487368; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:13 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:46:13 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:13 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:46:13 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:13 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:46:13 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 967566736; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 967566736; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:14 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:46:14 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:15 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:46:15 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:15 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:46:15 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:15 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:46:15 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 491513536; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:15 MarkDuplicates After generateDuplicateIndexes freeMemory: 491513536; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:15 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:46:15 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:15 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:46:15 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:15 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:46:15 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:15 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:46:15 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:15 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:46:15 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:15 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:46:15 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:15 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:46:15 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:16 MarkDuplicates Before output close freeMemory: 760857976; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:16 MarkDuplicates Before output close freeMemory: 760857976; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:16 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:46:16 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:16 MarkDuplicates After output close freeMemory: 760997320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:16 MarkDuplicates After output close freeMemory: 760997320; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:16 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:46:16 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.06 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:16 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:46:16 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.12377918068415636875.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.12377918068415636875.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.12377918068415636875.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.12377918068415636875.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.12377918068415636875.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.12377918068415636875.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:16.712 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:46:16.712 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:16.712 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:46:16.712 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:16.712 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:46:16.712 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:16.712 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:46:16.712 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:16 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.12377918068415636875.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.12377918068415636875.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.12377918068415636875.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:46:16 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.12377918068415636875.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.12377918068415636875.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.12377918068415636875.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:46:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:17 MarkDuplicates Start of doWork freeMemory: 1030487056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:17 MarkDuplicates Start of doWork freeMemory: 1030487056; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:17 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:46:17 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:17 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:46:17 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:17 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:46:17 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 967566424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:18 MarkDuplicates After buildSortedReadEndLists freeMemory: 967566424; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:19 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:46:19 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:19 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:46:19 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:19 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:46:19 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:19 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:46:19 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 654042504; totalMemory: 1236271104; maxMemory: 2147483648 INFO 2024-07-02 11:46:20 MarkDuplicates After generateDuplicateIndexes freeMemory: 654042504; totalMemory: 1236271104; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:20 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:46:20 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:20 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:46:20 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:20 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:46:20 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:20 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:46:20 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:20 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:46:20 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:20 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:46:20 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:20 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:46:20 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:20 MarkDuplicates Before output close freeMemory: 760755840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:20 MarkDuplicates Before output close freeMemory: 760755840; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:20 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:46:20 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:21 MarkDuplicates After output close freeMemory: 760997080; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:21 MarkDuplicates After output close freeMemory: 760997080; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:21 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. [Tue Jul 02 11:46:21 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:21 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:46:21 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.13276751637043649270.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.13276751637043649270.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.13276751637043649270.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.13276751637043649270.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.13276751637043649270.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.13276751637043649270.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:21.588 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:46:21.588 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:21.588 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:46:21.588 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:21.588 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:46:21.588 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:21.588 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:46:21.588 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:21 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.13276751637043649270.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.13276751637043649270.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.13276751637043649270.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:46:21 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.13276751637043649270.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.13276751637043649270.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.13276751637043649270.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:46:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:22 MarkDuplicates Start of doWork freeMemory: 1030486712; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:22 MarkDuplicates Start of doWork freeMemory: 1030486712; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:22 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:46:22 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:22 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:46:22 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:22 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:46:22 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 967566080; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:22 MarkDuplicates After buildSortedReadEndLists freeMemory: 967566080; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:46:23 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:25 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:46:25 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:25 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:46:25 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:25 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:46:25 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 491512880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:25 MarkDuplicates After generateDuplicateIndexes freeMemory: 491512880; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:25 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:46:25 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:25 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:46:25 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:25 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:46:25 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:25 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:46:25 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:25 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:46:25 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:25 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:46:25 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:25 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:46:25 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:26 MarkDuplicates Before output close freeMemory: 760857320; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:26 MarkDuplicates Before output close freeMemory: 760857320; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:26 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:46:26 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:26 MarkDuplicates After output close freeMemory: 760996664; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:26 MarkDuplicates After output close freeMemory: 760996664; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:26 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. [Tue Jul 02 11:46:26 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:26 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:46:26 MarkDuplicates Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.9675665841450996028.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.9675665841450996028.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.9675665841450996028.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.9675665841450996028.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.9675665841450996028.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.9675665841450996028.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:26.683 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:46:26.683 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:26.683 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:46:26.683 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:26.684 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:46:26.684 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:26.684 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:46:26.684 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:26 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.9675665841450996028.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.9675665841450996028.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.9675665841450996028.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:46:26 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.9675665841450996028.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.9675665841450996028.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.9675665841450996028.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:46:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:27 MarkDuplicates Start of doWork freeMemory: 1030486328; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:27 MarkDuplicates Start of doWork freeMemory: 1030486328; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:27 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:46:27 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:27 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:46:27 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:27 MarkDuplicates Read 5 records. 0 pairs never matched. INFO 2024-07-02 11:46:27 MarkDuplicates Read 5 records. 0 pairs never matched. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 967565696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 967565696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:46:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:30 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:46:30 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:30 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:46:30 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:30 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:46:30 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 491512496; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:30 MarkDuplicates After generateDuplicateIndexes freeMemory: 491512496; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:30 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:46:30 MarkDuplicates Marking 1 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:30 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:46:30 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:30 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:46:30 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:30 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:46:30 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:30 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:46:30 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:30 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:46:30 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:30 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:46:30 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:30 MarkDuplicates Before output close freeMemory: 760856936; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:30 MarkDuplicates Before output close freeMemory: 760856936; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:30 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:46:30 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:31 MarkDuplicates After output close freeMemory: 760996280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:31 MarkDuplicates After output close freeMemory: 760996280; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:31 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. [Tue Jul 02 11:46:31 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.08 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:31 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoUnmappedFragments STANDARD_ERROR INFO 2024-07-02 11:46:31 MarkDuplicates Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.14699662179147132597.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.14699662179147132597.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.14699662179147132597.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.14699662179147132597.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.14699662179147132597.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.14699662179147132597.tmp/output.sam Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:31.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:46:31.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:31.477 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:46:31.477 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:31.478 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:46:31.478 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:31.478 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:46:31.478 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:31 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.14699662179147132597.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.14699662179147132597.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.14699662179147132597.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:46:31 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.14699662179147132597.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.14699662179147132597.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.14699662179147132597.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:46:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:31 MarkDuplicates Start of doWork freeMemory: 1030488152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:31 MarkDuplicates Start of doWork freeMemory: 1030488152; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:31 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:46:31 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:31 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:46:31 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:32 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:46:32 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 967568128; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 967568128; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:46:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:46:34 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:34 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:46:34 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:34 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:46:34 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 491514824; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 491514824; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:34 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:46:34 MarkDuplicates Marking 0 records as duplicates. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:34 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:46:34 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:34 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:46:34 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:34 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:46:34 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:34 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:46:34 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:34 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:46:34 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:34 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:46:34 MarkDuplicates Getting Memory Stats. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:35 MarkDuplicates Before output close freeMemory: 760859264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:35 MarkDuplicates Before output close freeMemory: 760859264; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:35 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:46:35 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:35 MarkDuplicates After output close freeMemory: 760998608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:35 MarkDuplicates After output close freeMemory: 760998608; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:35 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:46:35 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.07 minutes. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:35 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]}) STANDARD_ERROR INFO 2024-07-02 11:46:35 MarkDuplicates Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam -OUTPUT /tmp/MarkDuplicates.14904704416030065084.tmp/MarkDuplicates.sam -METRICS_FILE /tmp/MarkDuplicates.14904704416030065084.tmp/MarkDuplicates.duplicate_metrics -ADD_PG_TAG_TO_READS true ********** MarkDuplicates -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam -OUTPUT /tmp/MarkDuplicates.14904704416030065084.tmp/MarkDuplicates.sam -METRICS_FILE /tmp/MarkDuplicates.14904704416030065084.tmp/MarkDuplicates.duplicate_metrics -ADD_PG_TAG_TO_READS true Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:35.676 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:46:35.676 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:35.676 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:46:35.676 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:35.676 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:46:35.676 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:35.676 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:46:35.676 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:35 GMT+14:00 2024] MarkDuplicates ADD_PG_TAG_TO_READS=true INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.14904704416030065084.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.14904704416030065084.tmp/MarkDuplicates.duplicate_metrics MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:46:35 GMT+14:00 2024] MarkDuplicates ADD_PG_TAG_TO_READS=true INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.14904704416030065084.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.14904704416030065084.tmp/MarkDuplicates.duplicate_metrics MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:46:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:36 MarkDuplicates Start of doWork freeMemory: 1030492384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:36 MarkDuplicates Start of doWork freeMemory: 1030492384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:36 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:46:36 MarkDuplicates Reading input file and constructing read end information. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:36 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:46:36 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:46:36 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name '1AAXX.1.1'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. WARNING 2024-07-02 11:46:36 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name '1AAXX.1.1'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:36 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:46:36 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 967569352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 967569352; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:36 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2024-07-02 11:46:36 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:39 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:46:39 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:39 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:46:39 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:39 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:46:39 MarkDuplicates Sorting list of duplicate records. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 1111225176; totalMemory: 1692401664; maxMemory: 2147483648 INFO 2024-07-02 11:46:40 MarkDuplicates After generateDuplicateIndexes freeMemory: 1111225176; totalMemory: 1692401664; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:40 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:46:40 MarkDuplicates Marking 4 records as duplicates. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:40 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:46:40 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:40 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:46:40 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:40 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:46:40 MarkDuplicates Writing complete. Closing input iterator. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:40 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:46:40 MarkDuplicates Duplicate Index cleanup. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:40 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:46:40 MarkDuplicates Getting Memory Stats. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:40 MarkDuplicates Before output close freeMemory: 1030341776; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:40 MarkDuplicates Before output close freeMemory: 1030341776; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:40 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:46:40 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:41 MarkDuplicates After output close freeMemory: 1030484744; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:41 MarkDuplicates After output close freeMemory: 1030484744; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:41 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.09 minutes. [Tue Jul 02 11:46:41 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.09 minutes. Test: Test method pgRecordChainingTest[0](false, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@412420c, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@60bde854, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7b37a3af], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@3ed99f3, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1579b9a0], 1AAXX.3.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@1a091c13]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:41 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]}) STANDARD_ERROR INFO 2024-07-02 11:46:41 MarkDuplicates Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam -OUTPUT /tmp/MarkDuplicates.1395518900119358432.tmp/MarkDuplicates.sam -METRICS_FILE /tmp/MarkDuplicates.1395518900119358432.tmp/MarkDuplicates.duplicate_metrics -ADD_PG_TAG_TO_READS true -PROGRAM_RECORD_ID null ********** MarkDuplicates -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam -OUTPUT /tmp/MarkDuplicates.1395518900119358432.tmp/MarkDuplicates.sam -METRICS_FILE /tmp/MarkDuplicates.1395518900119358432.tmp/MarkDuplicates.duplicate_metrics -ADD_PG_TAG_TO_READS true -PROGRAM_RECORD_ID null Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:41.044 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:46:41.044 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:41.044 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:46:41.044 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:41.044 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:46:41.044 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:41.045 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:46:41.045 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:41 GMT+14:00 2024] MarkDuplicates ADD_PG_TAG_TO_READS=true INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.1395518900119358432.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.1395518900119358432.tmp/MarkDuplicates.duplicate_metrics PROGRAM_RECORD_ID=null MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:46:41 GMT+14:00 2024] MarkDuplicates ADD_PG_TAG_TO_READS=true INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MarkDuplicates/merge3.sam] OUTPUT=/tmp/MarkDuplicates.1395518900119358432.tmp/MarkDuplicates.sam METRICS_FILE=/tmp/MarkDuplicates.1395518900119358432.tmp/MarkDuplicates.duplicate_metrics PROGRAM_RECORD_ID=null MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:46:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:41 MarkDuplicates Start of doWork freeMemory: 1030491808; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:41 MarkDuplicates Start of doWork freeMemory: 1030491808; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:41 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:46:41 MarkDuplicates Reading input file and constructing read end information. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:41 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:46:41 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:46:41 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name '1AAXX.1.1'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. WARNING 2024-07-02 11:46:41 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name '1AAXX.1.1'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:41 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:46:41 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 967568952; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 967568952; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:41 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2024-07-02 11:46:41 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:42 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:46:42 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:42 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:46:42 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:42 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:46:42 MarkDuplicates Sorting list of duplicate records. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 492564240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:43 MarkDuplicates After generateDuplicateIndexes freeMemory: 492564240; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:43 MarkDuplicates Marking 4 records as duplicates. INFO 2024-07-02 11:46:43 MarkDuplicates Marking 4 records as duplicates. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:43 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:46:43 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:43 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:46:43 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:43 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:46:43 MarkDuplicates Writing complete. Closing input iterator. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:43 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:46:43 MarkDuplicates Duplicate Index cleanup. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:43 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:46:43 MarkDuplicates Getting Memory Stats. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:43 MarkDuplicates Before output close freeMemory: 1030341672; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:43 MarkDuplicates Before output close freeMemory: 1030341672; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:43 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:46:43 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:44 MarkDuplicates After output close freeMemory: 1030482792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:44 MarkDuplicates After output close freeMemory: 1030482792; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:44 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:46:44 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method pgRecordChainingTest[1](true, {1AAXX.1.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@7657eed0, picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@d7d6f43], 1AAXX.2.1=[picard.sam.markduplicates.MarkDuplicatesTest$ExpectedPnAndVn@615b157e], 1AAXX.3.1=[]})(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:44 MarkDuplicates Start of doWork freeMemory: 1030506920; totalMemory: 1073741824; maxMemory: 2147483648 Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1) STANDARD_ERROR INFO 2024-07-02 11:46:44 MarkDuplicates Start of doWork freeMemory: 1030506920; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:44 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:46:44 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:44 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:46:44 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:44 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:46:44 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 967586176; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:44 MarkDuplicates After buildSortedReadEndLists freeMemory: 967586176; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:44 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2024-07-02 11:46:44 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:46 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:46:46 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:46 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:46:46 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:46 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:46:46 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 492581864; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:46 MarkDuplicates After generateDuplicateIndexes freeMemory: 492581864; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:46 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:46:46 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:46 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:46:46 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:46 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:46:46 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:46 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:46:46 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:46 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:46:46 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:46 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:46:46 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:46 MarkDuplicates Before output close freeMemory: 1030362288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:46 MarkDuplicates Before output close freeMemory: 1030362288; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:46 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:46:46 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateDetection[0](testdata/picard/sam/MarkDuplicates/optical_dupes.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:47 MarkDuplicates After output close freeMemory: 1030501280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:47 MarkDuplicates After output close freeMemory: 1030501280; totalMemory: 1073741824; maxMemory: 2147483648 Running Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:47 MarkDuplicates Start of doWork freeMemory: 1030505976; totalMemory: 1073741824; maxMemory: 2147483648 Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1) STANDARD_ERROR INFO 2024-07-02 11:46:47 MarkDuplicates Start of doWork freeMemory: 1030505976; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:47 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:46:47 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:47 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:46:47 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:47 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:46:47 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 967585360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:47 MarkDuplicates After buildSortedReadEndLists freeMemory: 967585360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:47 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. INFO 2024-07-02 11:46:47 MarkDuplicates Will retain up to 67108864 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:49 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:46:49 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:49 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:46:49 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:49 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:46:49 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 492580136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:49 MarkDuplicates After generateDuplicateIndexes freeMemory: 492580136; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:49 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:46:49 MarkDuplicates Marking 2 records as duplicates. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:49 MarkDuplicates Found 1 optical duplicate clusters. INFO 2024-07-02 11:46:49 MarkDuplicates Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:49 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:46:49 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:49 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:46:49 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:49 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:46:49 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:49 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:46:49 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:49 MarkDuplicates Before output close freeMemory: 1030360432; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:49 MarkDuplicates Before output close freeMemory: 1030360432; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:49 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:46:49 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateDetection[1](testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam, 1)(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:49 MarkDuplicates After output close freeMemory: 1030500296; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:49 MarkDuplicates After output close freeMemory: 1030500296; totalMemory: 1073741824; maxMemory: 2147483648 Running Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:49 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testTwoMappedPairsWithSoftClippingFirstOfPairOnly STANDARD_ERROR INFO 2024-07-02 11:46:49 MarkDuplicates Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.8237865983001422647.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.8237865983001422647.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.8237865983001422647.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.8237865983001422647.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.8237865983001422647.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.8237865983001422647.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:49.881 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:46:49.881 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:49.881 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:46:49.881 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:49.881 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:46:49.881 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:49.881 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:46:49.881 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:49 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.8237865983001422647.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.8237865983001422647.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.8237865983001422647.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:46:49 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.8237865983001422647.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.8237865983001422647.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.8237865983001422647.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:46:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:50 MarkDuplicates Start of doWork freeMemory: 1030482112; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:50 MarkDuplicates Start of doWork freeMemory: 1030482112; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:50 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:46:50 MarkDuplicates Reading input file and constructing read end information. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:50 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:46:50 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:46:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:46:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:50 MarkDuplicates Read 2 records. 2 pairs never matched. INFO 2024-07-02 11:46:50 MarkDuplicates Read 2 records. 2 pairs never matched. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 967561760; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:50 MarkDuplicates After buildSortedReadEndLists freeMemory: 967561760; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:46:50 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:51 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:46:51 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:51 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:46:51 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:51 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:46:51 MarkDuplicates Sorting list of duplicate records. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 638309240; totalMemory: 1220542464; maxMemory: 2147483648 INFO 2024-07-02 11:46:51 MarkDuplicates After generateDuplicateIndexes freeMemory: 638309240; totalMemory: 1220542464; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:51 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:46:51 MarkDuplicates Marking 0 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:51 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:46:51 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:51 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:46:51 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:51 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:46:51 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:51 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:46:51 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:51 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:46:51 MarkDuplicates Duplicate Index cleanup. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:51 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:46:51 MarkDuplicates Getting Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:51 MarkDuplicates Before output close freeMemory: 760853040; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:51 MarkDuplicates Before output close freeMemory: 760853040; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:51 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:46:51 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:52 MarkDuplicates After output close freeMemory: 760992384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:52 MarkDuplicates After output close freeMemory: 760992384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:46:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:52 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testWithBarcodeComplex STANDARD_ERROR INFO 2024-07-02 11:46:52 MarkDuplicates Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.2631267730940443455.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -BARCODE_TAG BC -INPUT /tmp/QuerySortedMarkDuplicatesTester.2631267730940443455.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.2631267730940443455.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.2631267730940443455.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -BARCODE_TAG BC -INPUT /tmp/QuerySortedMarkDuplicatesTester.2631267730940443455.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.2631267730940443455.tmp/output.sam Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:52.081 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:46:52.081 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:52.081 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:46:52.081 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:52.082 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:46:52.082 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:52.082 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:46:52.082 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:52 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.2631267730940443455.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.2631267730940443455.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.2631267730940443455.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:46:52 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.2631267730940443455.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.2631267730940443455.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.2631267730940443455.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:46:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:52 MarkDuplicates Start of doWork freeMemory: 1030478824; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:52 MarkDuplicates Start of doWork freeMemory: 1030478824; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:52 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:46:52 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:52 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:46:52 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:52 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:46:52 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 975946440; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:52 MarkDuplicates After buildSortedReadEndLists freeMemory: 975946440; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:46:53 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:53 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:46:53 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:53 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:46:53 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:53 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:46:53 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 491504968; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:53 MarkDuplicates After generateDuplicateIndexes freeMemory: 491504968; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:53 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:46:53 MarkDuplicates Marking 1 records as duplicates. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:53 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:46:53 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:53 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:46:53 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:53 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:46:53 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:53 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:46:53 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:53 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:46:53 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:53 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:46:53 MarkDuplicates Getting Memory Stats. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:54 MarkDuplicates Before output close freeMemory: 760849408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:54 MarkDuplicates Before output close freeMemory: 760849408; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:54 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:46:54 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:54 MarkDuplicates After output close freeMemory: 760988288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:54 MarkDuplicates After output close freeMemory: 760988288; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:54 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:46:54 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testWithBarcodeComplex(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:54 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testWithBarcodeDuplicate STANDARD_ERROR INFO 2024-07-02 11:46:54 MarkDuplicates Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.10097189316622385136.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -BARCODE_TAG BC -INPUT /tmp/QuerySortedMarkDuplicatesTester.10097189316622385136.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.10097189316622385136.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.10097189316622385136.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -BARCODE_TAG BC -INPUT /tmp/QuerySortedMarkDuplicatesTester.10097189316622385136.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.10097189316622385136.tmp/output.sam Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:54.678 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:46:54.678 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:54.678 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:46:54.678 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:54.679 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:46:54.679 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:54.679 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:46:54.679 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:54 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.10097189316622385136.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.10097189316622385136.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.10097189316622385136.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:46:54 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.10097189316622385136.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.10097189316622385136.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.10097189316622385136.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:46:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:54 MarkDuplicates Start of doWork freeMemory: 1030476872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:54 MarkDuplicates Start of doWork freeMemory: 1030476872; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:54 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:46:54 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:54 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:46:54 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:55 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:46:55 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 975947360; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:55 MarkDuplicates After buildSortedReadEndLists freeMemory: 975947360; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:46:55 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:56 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:46:56 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:56 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:46:56 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:56 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:46:56 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 491506016; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:56 MarkDuplicates After generateDuplicateIndexes freeMemory: 491506016; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:56 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:46:56 MarkDuplicates Marking 1 records as duplicates. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:56 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:46:56 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:56 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:46:56 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:56 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:46:56 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:56 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:46:56 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:56 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:46:56 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:56 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:46:56 MarkDuplicates Getting Memory Stats. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:56 MarkDuplicates Before output close freeMemory: 760850456; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:56 MarkDuplicates Before output close freeMemory: 760850456; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:56 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:46:56 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:57 MarkDuplicates After output close freeMemory: 760989872; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:57 MarkDuplicates After output close freeMemory: 760989872; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:57 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:46:57 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testWithBarcodeDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:57 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testWithBarcodeFragmentDuplicate STANDARD_ERROR INFO 2024-07-02 11:46:57 MarkDuplicates Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.17018093702116605681.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -BARCODE_TAG BC -INPUT /tmp/QuerySortedMarkDuplicatesTester.17018093702116605681.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.17018093702116605681.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.17018093702116605681.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -BARCODE_TAG BC -INPUT /tmp/QuerySortedMarkDuplicatesTester.17018093702116605681.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.17018093702116605681.tmp/output.sam Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:57.314 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:46:57.314 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:57.314 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:46:57.314 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:57.314 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:46:57.314 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:46:57.314 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:46:57.314 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:57 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.17018093702116605681.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.17018093702116605681.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.17018093702116605681.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:46:57 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.17018093702116605681.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.17018093702116605681.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.17018093702116605681.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:46:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:46:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:57 MarkDuplicates Start of doWork freeMemory: 1030377240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:57 MarkDuplicates Start of doWork freeMemory: 1030377240; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:57 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:46:57 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:57 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:46:57 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:46:57 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:46:57 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:57 MarkDuplicates Read 2 records. 0 pairs never matched. INFO 2024-07-02 11:46:57 MarkDuplicates Read 2 records. 0 pairs never matched. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 975848152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 975848152; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:46:58 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:59 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:46:59 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:59 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:46:59 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:59 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:46:59 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 491506656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:59 MarkDuplicates After generateDuplicateIndexes freeMemory: 491506656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:59 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:46:59 MarkDuplicates Marking 1 records as duplicates. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:59 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:46:59 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:59 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:46:59 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:59 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:46:59 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:59 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:46:59 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:59 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:46:59 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:59 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:46:59 MarkDuplicates Getting Memory Stats. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:59 MarkDuplicates Before output close freeMemory: 760851160; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:46:59 MarkDuplicates Before output close freeMemory: 760851160; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:46:59 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:46:59 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:00 MarkDuplicates After output close freeMemory: 760991208; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:00 MarkDuplicates After output close freeMemory: 760991208; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:47:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:47:00 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testWithBarcodeFragmentDuplicate(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:00 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testWithIndividualReadBarcodes STANDARD_ERROR INFO 2024-07-02 11:47:00 MarkDuplicates Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.6279936425167934564.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -BARCODE_TAG BC -READ_ONE_BARCODE_TAG BX -READ_TWO_BARCODE_TAG BX -INPUT /tmp/QuerySortedMarkDuplicatesTester.6279936425167934564.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.6279936425167934564.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.6279936425167934564.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -BARCODE_TAG BC -READ_ONE_BARCODE_TAG BX -READ_TWO_BARCODE_TAG BX -INPUT /tmp/QuerySortedMarkDuplicatesTester.6279936425167934564.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.6279936425167934564.tmp/output.sam Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:47:00.185 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:00.185 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:47:00.186 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:00.186 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:47:00.186 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:00.186 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:47:00.186 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:00.186 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:47:00 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC READ_ONE_BARCODE_TAG=BX READ_TWO_BARCODE_TAG=BX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.6279936425167934564.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.6279936425167934564.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.6279936425167934564.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:00 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=BC READ_ONE_BARCODE_TAG=BX READ_TWO_BARCODE_TAG=BX TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.6279936425167934564.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.6279936425167934564.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.6279936425167934564.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:47:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:00 MarkDuplicates Start of doWork freeMemory: 1030477120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:00 MarkDuplicates Start of doWork freeMemory: 1030477120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:00 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:47:00 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:00 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:47:00 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:00 MarkDuplicates Read 6 records. 0 pairs never matched. INFO 2024-07-02 11:47:00 MarkDuplicates Read 6 records. 0 pairs never matched. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 975944520; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:00 MarkDuplicates After buildSortedReadEndLists freeMemory: 975944520; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:47:01 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:02 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:47:02 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:02 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:47:02 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:02 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:47:02 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 644595360; totalMemory: 1226833920; maxMemory: 2147483648 INFO 2024-07-02 11:47:02 MarkDuplicates After generateDuplicateIndexes freeMemory: 644595360; totalMemory: 1226833920; maxMemory: 2147483648 Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:02 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:47:02 MarkDuplicates Marking 1 records as duplicates. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:02 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:02 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:02 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:47:02 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:02 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:47:02 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:02 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:47:02 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:02 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:47:02 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:02 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:47:02 MarkDuplicates Getting Memory Stats. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:02 MarkDuplicates Before output close freeMemory: 760847704; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:02 MarkDuplicates Before output close freeMemory: 760847704; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:02 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:47:02 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:03 MarkDuplicates After output close freeMemory: 760987120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:03 MarkDuplicates After output close freeMemory: 760987120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:47:03 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:47:03 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testWithIndividualReadBarcodes(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:03 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true]) STANDARD_ERROR INFO 2024-07-02 11:47:03 MarkDuplicates Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.12147368970933335016.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -BARCODE_TAG RX -DUPLEX_UMI false -INPUT /tmp/QuerySortedMarkDuplicatesTester.12147368970933335016.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.12147368970933335016.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.12147368970933335016.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -BARCODE_TAG RX -DUPLEX_UMI false -INPUT /tmp/QuerySortedMarkDuplicatesTester.12147368970933335016.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.12147368970933335016.tmp/output.sam Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:47:03.195 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:03.195 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:47:03.195 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:03.195 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:47:03.195 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:03.195 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:47:03.195 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:03.195 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:47:03 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=false INPUT=[/tmp/QuerySortedMarkDuplicatesTester.12147368970933335016.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.12147368970933335016.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.12147368970933335016.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:03 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=false INPUT=[/tmp/QuerySortedMarkDuplicatesTester.12147368970933335016.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.12147368970933335016.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.12147368970933335016.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:47:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:03 MarkDuplicates Start of doWork freeMemory: 1030477120; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:03 MarkDuplicates Start of doWork freeMemory: 1030477120; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:03 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:47:03 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:03 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:47:03 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:47:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. WARNING 2024-07-02 11:47:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:03 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:47:03 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 975843752; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:03 MarkDuplicates After buildSortedReadEndLists freeMemory: 975843752; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:04 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:47:04 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:04 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:47:04 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:04 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:47:04 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:04 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:47:04 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 491503504; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 491503504; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:05 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:47:05 MarkDuplicates Marking 1 records as duplicates. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:05 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:05 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:05 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:47:05 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:05 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:47:05 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:05 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:47:05 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:05 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:47:05 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:05 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:47:05 MarkDuplicates Getting Memory Stats. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:05 MarkDuplicates Before output close freeMemory: 760745408; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:05 MarkDuplicates Before output close freeMemory: 760745408; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:05 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:47:05 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:05 MarkDuplicates After output close freeMemory: 760986864; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:05 MarkDuplicates After output close freeMemory: 760986864; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:47:05 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:47:05 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testWithUMIs[0](false, [ATC, ATC], [4, 4], [10, 10], [false, true], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:05 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true]) STANDARD_ERROR INFO 2024-07-02 11:47:05 MarkDuplicates Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.15669227785556356273.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -BARCODE_TAG RX -DUPLEX_UMI false -INPUT /tmp/QuerySortedMarkDuplicatesTester.15669227785556356273.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.15669227785556356273.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.15669227785556356273.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -BARCODE_TAG RX -DUPLEX_UMI false -INPUT /tmp/QuerySortedMarkDuplicatesTester.15669227785556356273.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.15669227785556356273.tmp/output.sam Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:47:05.701 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:05.701 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:47:05.701 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:05.701 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:47:05.702 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:05.702 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:47:05.702 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:05.702 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:47:05 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=false INPUT=[/tmp/QuerySortedMarkDuplicatesTester.15669227785556356273.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.15669227785556356273.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.15669227785556356273.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:05 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=false INPUT=[/tmp/QuerySortedMarkDuplicatesTester.15669227785556356273.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.15669227785556356273.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.15669227785556356273.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:47:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:05 MarkDuplicates Start of doWork freeMemory: 1030476824; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:05 MarkDuplicates Start of doWork freeMemory: 1030476824; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:05 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:47:05 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:05 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:47:05 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:47:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. WARNING 2024-07-02 11:47:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:06 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:47:06 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 975944768; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 975944768; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:06 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:47:06 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:07 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:47:07 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:07 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:47:07 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:07 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:47:07 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 491503208; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 491503208; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:07 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:47:07 MarkDuplicates Marking 0 records as duplicates. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:07 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:07 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:07 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:47:07 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:07 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:47:07 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:07 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:47:07 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:07 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:47:07 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:07 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:47:07 MarkDuplicates Getting Memory Stats. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:07 MarkDuplicates Before output close freeMemory: 760847648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:07 MarkDuplicates Before output close freeMemory: 760847648; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:07 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:47:07 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:08 MarkDuplicates After output close freeMemory: 760986992; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:08 MarkDuplicates After output close freeMemory: 760986992; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:47:08 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:47:08 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testWithUMIs[1](false, [ATC, GCG], [4, 4], [10, 10], [false, false], [false, false], [true, true])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:08 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false]) STANDARD_ERROR INFO 2024-07-02 11:47:08 MarkDuplicates Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.3022012692353513321.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -BARCODE_TAG RX -DUPLEX_UMI true -INPUT /tmp/QuerySortedMarkDuplicatesTester.3022012692353513321.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.3022012692353513321.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.3022012692353513321.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -BARCODE_TAG RX -DUPLEX_UMI true -INPUT /tmp/QuerySortedMarkDuplicatesTester.3022012692353513321.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.3022012692353513321.tmp/output.sam Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:47:08.146 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:08.146 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:47:08.147 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:08.147 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:47:08.147 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:08.147 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:47:08.147 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:08.147 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:47:08 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=true INPUT=[/tmp/QuerySortedMarkDuplicatesTester.3022012692353513321.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.3022012692353513321.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.3022012692353513321.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:08 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=true INPUT=[/tmp/QuerySortedMarkDuplicatesTester.3022012692353513321.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.3022012692353513321.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.3022012692353513321.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:47:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:08 MarkDuplicates Start of doWork freeMemory: 1030476448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:08 MarkDuplicates Start of doWork freeMemory: 1030476448; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:08 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:47:08 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:08 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:47:08 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:47:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. WARNING 2024-07-02 11:47:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:08 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:47:08 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 975944392; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 975944392; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:47:09 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:09 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:47:09 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:09 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:47:09 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:09 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:47:09 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 491502832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 491502832; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:09 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:47:09 MarkDuplicates Marking 1 records as duplicates. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:09 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:09 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:09 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:47:09 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:09 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:47:09 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:09 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:47:09 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:09 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:47:09 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:09 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:47:09 MarkDuplicates Getting Memory Stats. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:10 MarkDuplicates Before output close freeMemory: 760845448; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:10 MarkDuplicates Before output close freeMemory: 760845448; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:10 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:47:10 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:10 MarkDuplicates After output close freeMemory: 760986616; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:10 MarkDuplicates After output close freeMemory: 760986616; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:47:10 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:47:10 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testWithUMIs[2](true, [AAA-GGG, GGG-AAA], [4, 10], [10, 4], [false, true], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:10 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false]) STANDARD_ERROR INFO 2024-07-02 11:47:10 MarkDuplicates Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.291574873170710624.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -BARCODE_TAG RX -DUPLEX_UMI true -INPUT /tmp/QuerySortedMarkDuplicatesTester.291574873170710624.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.291574873170710624.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.291574873170710624.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -BARCODE_TAG RX -DUPLEX_UMI true -INPUT /tmp/QuerySortedMarkDuplicatesTester.291574873170710624.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.291574873170710624.tmp/output.sam Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:47:10.467 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:10.467 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:47:10.467 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:10.467 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:47:10.467 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:10.467 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:47:10.467 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:10.467 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:47:10 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=true INPUT=[/tmp/QuerySortedMarkDuplicatesTester.291574873170710624.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.291574873170710624.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.291574873170710624.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:10 GMT+14:00 2024] MarkDuplicates BARCODE_TAG=RX TAGGING_POLICY=OpticalOnly DUPLEX_UMI=true INPUT=[/tmp/QuerySortedMarkDuplicatesTester.291574873170710624.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.291574873170710624.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.291574873170710624.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:47:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:10 MarkDuplicates Start of doWork freeMemory: 1030476136; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:10 MarkDuplicates Start of doWork freeMemory: 1030476136; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:10 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:47:10 MarkDuplicates Reading input file and constructing read end information. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:10 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. INFO 2024-07-02 11:47:10 MarkDuplicates Will retain up to 6628035 data points before spilling to disk. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: WARNING 2024-07-02 11:47:10 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. WARNING 2024-07-02 11:47:10 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: RUNID0. Cause: String 'RUNID0' did not start with a parsable number. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:10 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:47:10 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 975944080; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:11 MarkDuplicates After buildSortedReadEndLists freeMemory: 975944080; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:47:11 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:12 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:47:12 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:12 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:47:12 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:12 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:47:12 MarkDuplicates Sorting list of duplicate records. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 687586320; totalMemory: 1269825536; maxMemory: 2147483648 INFO 2024-07-02 11:47:12 MarkDuplicates After generateDuplicateIndexes freeMemory: 687586320; totalMemory: 1269825536; maxMemory: 2147483648 Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:12 MarkDuplicates Marking 0 records as duplicates. INFO 2024-07-02 11:47:12 MarkDuplicates Marking 0 records as duplicates. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:12 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:12 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:12 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:47:12 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:12 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:47:12 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:12 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:47:12 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:12 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:47:12 MarkDuplicates Duplicate Index cleanup. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:12 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:47:12 MarkDuplicates Getting Memory Stats. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:12 MarkDuplicates Before output close freeMemory: 760846416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:12 MarkDuplicates Before output close freeMemory: 760846416; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:12 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:47:12 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:13 MarkDuplicates After output close freeMemory: 760985264; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:13 MarkDuplicates After output close freeMemory: 760985264; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:47:13 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:47:13 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testWithUMIs[3](true, [AAA-GGG, AAA-GGG], [4, 10], [10, 4], [false, false], [false, true], [true, false])(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:13 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted.testOpticalDuplicateFinding STANDARD_ERROR INFO 2024-07-02 11:47:13 MarkDuplicates Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.375571531216218553.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.375571531216218553.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.375571531216218553.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/QuerySortedMarkDuplicatesTester.375571531216218553.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/QuerySortedMarkDuplicatesTester.375571531216218553.tmp/input.sam -OUTPUT /tmp/QuerySortedMarkDuplicatesTester.375571531216218553.tmp/output.sam Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:47:13.163 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:13.163 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:47:13.163 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:13.163 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:47:13.163 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:13.163 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: 11:47:13.163 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:13.163 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:47:13 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.375571531216218553.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.375571531216218553.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.375571531216218553.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:13 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/QuerySortedMarkDuplicatesTester.375571531216218553.tmp/input.sam] OUTPUT=/tmp/QuerySortedMarkDuplicatesTester.375571531216218553.tmp/output.sam METRICS_FILE=/tmp/QuerySortedMarkDuplicatesTester.375571531216218553.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:47:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:13 MarkDuplicates Start of doWork freeMemory: 1030470304; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:13 MarkDuplicates Start of doWork freeMemory: 1030470304; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:13 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:47:13 MarkDuplicates Reading input file and constructing read end information. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:13 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:47:13 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:13 MarkDuplicates Read 8 records. 0 pairs never matched. INFO 2024-07-02 11:47:13 MarkDuplicates Read 8 records. 0 pairs never matched. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 967551840; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:13 MarkDuplicates After buildSortedReadEndLists freeMemory: 967551840; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:13 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:47:13 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:14 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:47:14 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:14 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:47:14 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:14 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:47:14 MarkDuplicates Sorting list of duplicate records. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 491499288; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:14 MarkDuplicates After generateDuplicateIndexes freeMemory: 491499288; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:14 MarkDuplicates Marking 3 records as duplicates. INFO 2024-07-02 11:47:14 MarkDuplicates Marking 3 records as duplicates. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:14 MarkDuplicates Found 2 optical duplicate clusters. INFO 2024-07-02 11:47:14 MarkDuplicates Found 2 optical duplicate clusters. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:14 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:47:14 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:14 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:47:14 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:14 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:47:14 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:14 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:47:14 MarkDuplicates Duplicate Index cleanup. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:14 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:47:14 MarkDuplicates Getting Memory Stats. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:14 MarkDuplicates Before output close freeMemory: 760843728; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:14 MarkDuplicates Before output close freeMemory: 760843728; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:14 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:47:14 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: INFO 2024-07-02 11:47:15 MarkDuplicates After output close freeMemory: 760983072; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:47:15 MarkDuplicates After output close freeMemory: 760983072; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: [Tue Jul 02 11:47:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:47:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.03 minutes. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:15 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testBulkFragmentsNoDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:47:15 MarkDuplicatesWithMateCigar Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.14086872248356566229.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.14086872248356566229.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.14086872248356566229.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.14086872248356566229.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.14086872248356566229.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.14086872248356566229.tmp/output.sam Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:15.321 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:15.321 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:15.321 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:15.321 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:15.322 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:15.322 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:15.322 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:15.322 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:15 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.14086872248356566229.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.14086872248356566229.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.14086872248356566229.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:15 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.14086872248356566229.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.14086872248356566229.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.14086872248356566229.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:15 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:15 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:15 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 100b aligned to chr1:1-100. WARNING 2024-07-02 11:47:15 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 100b aligned to chr1:1-100. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:15 MarkDuplicatesWithMateCigar Processed 10000 records INFO 2024-07-02 11:47:15 MarkDuplicatesWithMateCigar Processed 10000 records Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:15 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:15 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:15 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:47:15 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:15 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:15 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:47:15 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:16 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testBulkFragmentsNoDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:47:16 MarkDuplicatesWithMateCigar Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.14510575572353127110.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.14510575572353127110.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.14510575572353127110.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.14510575572353127110.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.14510575572353127110.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.14510575572353127110.tmp/output.sam Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:16.312 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:16.312 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:16.312 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:16.312 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:16.312 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:16.312 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:16.312 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:16.312 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:16 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.14510575572353127110.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.14510575572353127110.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.14510575572353127110.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:16 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.14510575572353127110.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.14510575572353127110.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.14510575572353127110.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:16 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:16 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:16 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 100b aligned to chr1:1-100. WARNING 2024-07-02 11:47:16 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 100b aligned to chr1:1-100. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:17 MarkDuplicatesWithMateCigar Processed 10000 records INFO 2024-07-02 11:47:17 MarkDuplicatesWithMateCigar Processed 10000 records Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:17 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:17 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:17 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:47:17 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:17 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:17 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:17 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:47:17 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:18 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testBulkFragmentsNoDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:47:18 MarkDuplicatesWithMateCigar Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.15613662061970729949.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.15613662061970729949.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.15613662061970729949.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester12182521632135933113/input.fasta ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.15613662061970729949.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.15613662061970729949.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.15613662061970729949.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester12182521632135933113/input.fasta Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:18.843 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:18.843 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:18.843 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:18.843 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:18.843 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:18.843 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:18.843 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:18.843 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:18 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.15613662061970729949.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.15613662061970729949.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.15613662061970729949.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 REFERENCE_SEQUENCE=/tmp/SamFileTester12182521632135933113/input.fasta MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:18 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.15613662061970729949.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.15613662061970729949.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.15613662061970729949.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 REFERENCE_SEQUENCE=/tmp/SamFileTester12182521632135933113/input.fasta MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:19 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:19 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:19 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 100b aligned to chr1:1-100. WARNING 2024-07-02 11:47:19 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 100b aligned to chr1:1-100. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:20 MarkDuplicatesWithMateCigar Processed 10000 records INFO 2024-07-02 11:47:20 MarkDuplicatesWithMateCigar Processed 10000 records Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:20 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:20 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:20 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:47:20 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:20 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:20 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:20 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:47:20 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.02 minutes. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:20 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testBulkFragmentsWithDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:47:20 MarkDuplicatesWithMateCigar Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.11291547596357422214.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.11291547596357422214.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.11291547596357422214.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.11291547596357422214.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.11291547596357422214.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.11291547596357422214.tmp/output.sam Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:20.874 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:20.874 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:20.874 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:20.874 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:20.874 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:20.874 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:20.874 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:20.874 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:20 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.11291547596357422214.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.11291547596357422214.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.11291547596357422214.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:20 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.11291547596357422214.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.11291547596357422214.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.11291547596357422214.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:20 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:20 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:21 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 100b aligned to chr1:1-100. WARNING 2024-07-02 11:47:21 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 100b aligned to chr1:1-100. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:24 MarkDuplicatesWithMateCigar Processed 21000 records INFO 2024-07-02 11:47:24 MarkDuplicatesWithMateCigar Processed 21000 records Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:24 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:24 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:24 MarkDuplicatesWithMateCigar Marking 20000 records as duplicates. INFO 2024-07-02 11:47:24 MarkDuplicatesWithMateCigar Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:24 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:24 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:24 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:47:24 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.06 minutes. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:26 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testBulkFragmentsWithDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:47:26 MarkDuplicatesWithMateCigar Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.7335432140413283505.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.7335432140413283505.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.7335432140413283505.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.7335432140413283505.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.7335432140413283505.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.7335432140413283505.tmp/output.sam Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:26.029 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:26.029 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:26.029 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:26.029 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:26.030 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:26.030 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:26.030 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:26.030 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:26 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.7335432140413283505.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.7335432140413283505.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.7335432140413283505.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:26 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.7335432140413283505.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.7335432140413283505.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.7335432140413283505.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:26 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 100b aligned to chr1:1-100. WARNING 2024-07-02 11:47:26 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 100b aligned to chr1:1-100. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:27 MarkDuplicatesWithMateCigar Processed 21000 records INFO 2024-07-02 11:47:27 MarkDuplicatesWithMateCigar Processed 21000 records Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:27 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:27 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:27 MarkDuplicatesWithMateCigar Marking 20000 records as duplicates. INFO 2024-07-02 11:47:27 MarkDuplicatesWithMateCigar Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:27 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:27 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:27 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:47:27 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.03 minutes. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:30 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testBulkFragmentsWithDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:47:30 MarkDuplicatesWithMateCigar Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.3562092983721975736.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.3562092983721975736.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.3562092983721975736.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester13117319367797965712/input.fasta ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.3562092983721975736.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.3562092983721975736.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.3562092983721975736.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester13117319367797965712/input.fasta Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:30.180 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:30.180 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:30.182 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:30.182 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:30.182 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:30.182 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:30.182 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:30.182 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:30 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3562092983721975736.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3562092983721975736.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3562092983721975736.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 REFERENCE_SEQUENCE=/tmp/SamFileTester13117319367797965712/input.fasta MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:30 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3562092983721975736.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3562092983721975736.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3562092983721975736.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 REFERENCE_SEQUENCE=/tmp/SamFileTester13117319367797965712/input.fasta MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:30 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 100b aligned to chr1:1-100. WARNING 2024-07-02 11:47:30 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 100b aligned to chr1:1-100. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:33 MarkDuplicatesWithMateCigar Processed 21000 records INFO 2024-07-02 11:47:33 MarkDuplicatesWithMateCigar Processed 21000 records Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:33 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:33 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:33 MarkDuplicatesWithMateCigar Marking 20000 records as duplicates. INFO 2024-07-02 11:47:33 MarkDuplicatesWithMateCigar Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:33 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:33 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:33 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:47:33 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.05 minutes. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:34 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testBulkPairsNoDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:47:34 MarkDuplicatesWithMateCigar Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.2149910627989807972.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.2149910627989807972.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.2149910627989807972.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.2149910627989807972.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.2149910627989807972.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.2149910627989807972.tmp/output.sam Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:34.036 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:34.036 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:34.036 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:34.036 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:34.036 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:34.036 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:34.036 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:34.036 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:34 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2149910627989807972.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2149910627989807972.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2149910627989807972.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:34 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2149910627989807972.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2149910627989807972.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2149910627989807972.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:34 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:34 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:35 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 100b aligned to chr1:1-100. WARNING 2024-07-02 11:47:35 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 100b aligned to chr1:1-100. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:36 MarkDuplicatesWithMateCigar Processed 20200 records INFO 2024-07-02 11:47:36 MarkDuplicatesWithMateCigar Processed 20200 records Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:36 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:36 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:36 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:47:36 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:36 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:36 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:36 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:47:36 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.04 minutes. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:37 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testBulkPairsNoDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:47:37 MarkDuplicatesWithMateCigar Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.12666736348875551421.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.12666736348875551421.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.12666736348875551421.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.12666736348875551421.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.12666736348875551421.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.12666736348875551421.tmp/output.sam Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:37.345 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:37.345 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:37.345 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:37.345 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:37.346 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:37.346 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:37.346 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:37.346 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:37 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.12666736348875551421.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.12666736348875551421.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.12666736348875551421.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:37 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.12666736348875551421.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.12666736348875551421.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.12666736348875551421.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:37 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:37 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:38 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 100b aligned to chr1:1-100. WARNING 2024-07-02 11:47:38 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 100b aligned to chr1:1-100. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:39 MarkDuplicatesWithMateCigar Processed 20200 records INFO 2024-07-02 11:47:39 MarkDuplicatesWithMateCigar Processed 20200 records Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:39 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:39 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:39 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:47:39 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:39 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:39 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:47:39 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.03 minutes. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1221591040 Runtime.totalMemory()=1221591040 Running Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:41 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testBulkPairsNoDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:47:41 MarkDuplicatesWithMateCigar Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.5248252173915177062.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.5248252173915177062.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.5248252173915177062.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester18024086312341188706/input.fasta ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.5248252173915177062.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.5248252173915177062.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.5248252173915177062.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester18024086312341188706/input.fasta Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:41.974 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:41.974 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:41.974 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:41.974 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:41.975 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:41.975 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:41.975 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:41.975 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:41 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.5248252173915177062.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.5248252173915177062.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.5248252173915177062.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 REFERENCE_SEQUENCE=/tmp/SamFileTester18024086312341188706/input.fasta MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:41 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.5248252173915177062.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.5248252173915177062.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.5248252173915177062.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 REFERENCE_SEQUENCE=/tmp/SamFileTester18024086312341188706/input.fasta MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:42 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:42 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:43 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 100b aligned to chr1:1-100. WARNING 2024-07-02 11:47:43 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 100b aligned to chr1:1-100. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:44 MarkDuplicatesWithMateCigar Processed 20200 records INFO 2024-07-02 11:47:44 MarkDuplicatesWithMateCigar Processed 20200 records Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:44 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:44 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:44 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:47:44 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:44 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:44 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:44 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:47:44 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.05 minutes. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1221591040 Runtime.totalMemory()=1221591040 Running Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:45 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testBulkPairsWithDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:47:45 MarkDuplicatesWithMateCigar Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.2868978629409058493.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.2868978629409058493.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.2868978629409058493.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.2868978629409058493.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.2868978629409058493.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.2868978629409058493.tmp/output.sam Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:45.231 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:45.231 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:45.231 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:45.231 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:45.231 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:45.231 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:45.231 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:45.231 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:45 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2868978629409058493.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2868978629409058493.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2868978629409058493.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:45 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2868978629409058493.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2868978629409058493.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2868978629409058493.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:45 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:45 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:45 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 100b aligned to chr1:1-100. WARNING 2024-07-02 11:47:45 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 100b aligned to chr1:1-100. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:45 MarkDuplicatesWithMateCigar Processed 6820 records INFO 2024-07-02 11:47:45 MarkDuplicatesWithMateCigar Processed 6820 records Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:45 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:45 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:45 MarkDuplicatesWithMateCigar Marking 6200 records as duplicates. INFO 2024-07-02 11:47:45 MarkDuplicatesWithMateCigar Marking 6200 records as duplicates. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:45 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:45 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:47:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:46 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testBulkPairsWithDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:47:46 MarkDuplicatesWithMateCigar Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.11094324241965438442.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.11094324241965438442.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.11094324241965438442.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.11094324241965438442.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.11094324241965438442.tmp/input.bam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.11094324241965438442.tmp/output.sam Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:46.063 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:46.063 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:46.063 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:46.063 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:46.064 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:46.064 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:46.064 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:46.064 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:46 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.11094324241965438442.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.11094324241965438442.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.11094324241965438442.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:46 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.11094324241965438442.tmp/input.bam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.11094324241965438442.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.11094324241965438442.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:46 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:46 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:46 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 100b aligned to chr1:1-100. WARNING 2024-07-02 11:47:46 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 100b aligned to chr1:1-100. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:46 MarkDuplicatesWithMateCigar Processed 6820 records INFO 2024-07-02 11:47:46 MarkDuplicatesWithMateCigar Processed 6820 records Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:46 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:46 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:46 MarkDuplicatesWithMateCigar Marking 6200 records as duplicates. INFO 2024-07-02 11:47:46 MarkDuplicatesWithMateCigar Marking 6200 records as duplicates. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:46 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:46 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:47:46 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.02 minutes. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:48 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testBulkPairsWithDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:47:48 MarkDuplicatesWithMateCigar Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.18341658157613067618.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.18341658157613067618.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.18341658157613067618.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester4994375510765021218/input.fasta ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.18341658157613067618.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.18341658157613067618.tmp/input.cram -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.18341658157613067618.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester4994375510765021218/input.fasta Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:48.540 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:48.540 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:48.540 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:48.540 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:48.540 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:48.540 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:48.540 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:48.540 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:48 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.18341658157613067618.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.18341658157613067618.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.18341658157613067618.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 REFERENCE_SEQUENCE=/tmp/SamFileTester4994375510765021218/input.fasta MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:48 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.18341658157613067618.tmp/input.cram] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.18341658157613067618.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.18341658157613067618.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 REFERENCE_SEQUENCE=/tmp/SamFileTester4994375510765021218/input.fasta MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:48 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:48 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:49 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 100b aligned to chr1:1-100. WARNING 2024-07-02 11:47:49 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 100b aligned to chr1:1-100. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:49 MarkDuplicatesWithMateCigar Processed 6820 records INFO 2024-07-02 11:47:49 MarkDuplicatesWithMateCigar Processed 6820 records Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:49 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:49 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:49 MarkDuplicatesWithMateCigar Marking 6200 records as duplicates. INFO 2024-07-02 11:47:49 MarkDuplicatesWithMateCigar Marking 6200 records as duplicates. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:49 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:49 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:47:49 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.02 minutes. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testDifferentChromosomesInOppositeOrder STANDARD_ERROR INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.15070439220232859642.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.15070439220232859642.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.15070439220232859642.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.15070439220232859642.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.15070439220232859642.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.15070439220232859642.tmp/output.sam Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.115 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.115 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.115 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.115 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.115 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.115 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.115 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.115 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.15070439220232859642.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.15070439220232859642.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.15070439220232859642.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.15070439220232859642.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.15070439220232859642.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.15070439220232859642.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:6:101:17616:6888 2/2 101b aligned to chr1:123989-124052. WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:6:101:17616:6888 2/2 101b aligned to chr1:123989-124052. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.2320296082675070580.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.2320296082675070580.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.2320296082675070580.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.2320296082675070580.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.2320296082675070580.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.2320296082675070580.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.196 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.196 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.196 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.196 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.196 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.196 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.196 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.196 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2320296082675070580.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2320296082675070580.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2320296082675070580.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2320296082675070580.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2320296082675070580.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2320296082675070580.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17939:39728 101b aligned to chr2:400-500. WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17939:39728 101b aligned to chr2:400-500. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 11 records INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 11 records Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.10142341208768330000.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.10142341208768330000.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.10142341208768330000.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.10142341208768330000.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.10142341208768330000.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.10142341208768330000.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.298 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.298 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.299 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.299 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.299 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.299 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.299 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.299 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.10142341208768330000.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.10142341208768330000.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.10142341208768330000.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.10142341208768330000.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.10142341208768330000.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.10142341208768330000.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17939:39728 101b aligned to chr2:400-500. WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17939:39728 101b aligned to chr2:400-500. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 11 records INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 11 records Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.13483307838374354170.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.13483307838374354170.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.13483307838374354170.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.13483307838374354170.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.13483307838374354170.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.13483307838374354170.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.372 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.372 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.372 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.372 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.372 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.372 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.372 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.372 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.13483307838374354170.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.13483307838374354170.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.13483307838374354170.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.13483307838374354170.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.13483307838374354170.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.13483307838374354170.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17939:39728 101b aligned to chr2:400-500. WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17939:39728 101b aligned to chr2:400-500. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 11 records INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 11 records Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.15968041325905944942.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.15968041325905944942.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.15968041325905944942.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.15968041325905944942.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.15968041325905944942.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.15968041325905944942.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.429 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.429 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.429 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.429 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.429 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.429 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.429 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.429 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.15968041325905944942.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.15968041325905944942.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.15968041325905944942.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.15968041325905944942.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.15968041325905944942.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.15968041325905944942.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17949:39745 101b aligned to chr2:400-500. WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17949:39745 101b aligned to chr2:400-500. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 11 records INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 11 records Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.13561079705770859452.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.13561079705770859452.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.13561079705770859452.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.13561079705770859452.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.13561079705770859452.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.13561079705770859452.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.470 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.470 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.470 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.470 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.470 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.470 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.470 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.470 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.13561079705770859452.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.13561079705770859452.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.13561079705770859452.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.13561079705770859452.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.13561079705770859452.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.13561079705770859452.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17949:39745 101b aligned to chr2:400-500. WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17949:39745 101b aligned to chr2:400-500. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 11 records INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 11 records Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.9435266003087071178.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.9435266003087071178.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.9435266003087071178.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.9435266003087071178.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.9435266003087071178.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.9435266003087071178.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.517 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.517 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.517 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.517 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.517 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.517 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.517 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.517 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.9435266003087071178.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.9435266003087071178.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.9435266003087071178.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.9435266003087071178.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.9435266003087071178.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.9435266003087071178.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17949:39745 101b aligned to chr2:400-500. WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17949:39745 101b aligned to chr2:400-500. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 11 records INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 11 records Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testMappedFragmentAndMappedPairFirstOfPairNonPrimary STANDARD_ERROR INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.9750965323521987507.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.9750965323521987507.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.9750965323521987507.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.9750965323521987507.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.9750965323521987507.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.9750965323521987507.tmp/output.sam Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.561 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.561 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.561 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.561 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.561 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.561 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.561 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.561 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.9750965323521987507.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.9750965323521987507.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.9750965323521987507.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.9750965323521987507.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.9750965323521987507.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.9750965323521987507.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 76b aligned to chr2:1-76. WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 76b aligned to chr2:1-76. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testMappedFragmentAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.4805878739117319291.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.4805878739117319291.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.4805878739117319291.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.4805878739117319291.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.4805878739117319291.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.4805878739117319291.tmp/output.sam Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.603 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.603 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.603 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.603 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.604 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.604 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.604 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.604 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.4805878739117319291.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.4805878739117319291.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.4805878739117319291.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.4805878739117319291.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.4805878739117319291.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.4805878739117319291.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b unmapped read. WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b unmapped read. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 3 records INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 3 records Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testMappedFragmentAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.330633574146313471.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.330633574146313471.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.330633574146313471.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.330633574146313471.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.330633574146313471.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.330633574146313471.tmp/output.sam Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.648 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.648 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.648 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.648 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.649 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.649 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.649 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.649 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.330633574146313471.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.330633574146313471.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.330633574146313471.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.330633574146313471.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.330633574146313471.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.330633574146313471.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:10049-10122. WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:10049-10122. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 3 records INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 3 records Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testMappedPairAndMappedFragmentAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.3114675136837960777.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.3114675136837960777.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.3114675136837960777.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.3114675136837960777.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.3114675136837960777.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.3114675136837960777.tmp/output.sam Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.711 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.711 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.712 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.712 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.712 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.712 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.712 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.712 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3114675136837960777.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3114675136837960777.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3114675136837960777.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3114675136837960777.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3114675136837960777.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3114675136837960777.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b unmapped read. WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b unmapped read. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testMappedPairAndMappedFragmentAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.9764606025434606319.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.9764606025434606319.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.9764606025434606319.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.9764606025434606319.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.9764606025434606319.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.9764606025434606319.tmp/output.sam Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.747 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.747 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.747 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.747 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.747 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.747 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.748 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.748 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.9764606025434606319.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.9764606025434606319.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.9764606025434606319.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.9764606025434606319.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.9764606025434606319.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.9764606025434606319.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:10040-10115. WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:10040-10115. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.12536902728997955177.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.12536902728997955177.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.12536902728997955177.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.12536902728997955177.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.12536902728997955177.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.12536902728997955177.tmp/output.sam Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.784 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.784 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.784 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.784 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.784 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.784 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.784 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.784 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.12536902728997955177.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.12536902728997955177.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.12536902728997955177.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.12536902728997955177.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.12536902728997955177.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.12536902728997955177.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 101b unmapped read. WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 101b unmapped read. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testMappedPairAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.11368612492509060148.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.11368612492509060148.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.11368612492509060148.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.11368612492509060148.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.11368612492509060148.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.11368612492509060148.tmp/output.sam Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.816 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.816 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.816 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.816 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.816 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.816 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.816 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.816 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.11368612492509060148.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.11368612492509060148.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.11368612492509060148.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.11368612492509060148.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.11368612492509060148.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.11368612492509060148.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b unmapped read. WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b unmapped read. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testMappedPairAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.12394275561515647608.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.12394275561515647608.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.12394275561515647608.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.12394275561515647608.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.12394275561515647608.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.12394275561515647608.tmp/output.sam Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.852 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.852 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.852 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.852 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.852 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.852 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.852 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.852 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.12394275561515647608.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.12394275561515647608.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.12394275561515647608.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.12394275561515647608.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.12394275561515647608.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.12394275561515647608.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:10040-10115. WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:10040-10115. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testMappedPairWithFirstEndSamePositionAndOther STANDARD_ERROR INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.3010770283601408744.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.3010770283601408744.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.3010770283601408744.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.3010770283601408744.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.3010770283601408744.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.3010770283601408744.tmp/output.sam Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.883 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.883 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.883 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.883 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.884 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.884 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.884 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.884 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3010770283601408744.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3010770283601408744.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3010770283601408744.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3010770283601408744.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3010770283601408744.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3010770283601408744.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr1:5604914-5604950. WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr1:5604914-5604950. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testMappedPairWithSamePosition STANDARD_ERROR INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.17295817031051670096.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.17295817031051670096.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.17295817031051670096.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.17295817031051670096.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.17295817031051670096.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.17295817031051670096.tmp/output.sam Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.917 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.917 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.917 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.917 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.917 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.917 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.917 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.917 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.17295817031051670096.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.17295817031051670096.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.17295817031051670096.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.17295817031051670096.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.17295817031051670096.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.17295817031051670096.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:4914-4950. WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:4914-4950. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testMappedPairWithSamePositionSameCigar STANDARD_ERROR INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.2831745041315118362.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.2831745041315118362.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.2831745041315118362.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.2831745041315118362.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.2831745041315118362.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.2831745041315118362.tmp/output.sam Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.948 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.948 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.948 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.948 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.951 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.951 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.951 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.951 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2831745041315118362.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2831745041315118362.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2831745041315118362.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2831745041315118362.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2831745041315118362.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2831745041315118362.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:4914-4950. WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:4914-4950. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.15213362389796019277.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.15213362389796019277.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.15213362389796019277.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.15213362389796019277.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.15213362389796019277.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.15213362389796019277.tmp/output.sam Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.984 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.984 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.984 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.984 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.985 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:50.985 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:50.985 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:50.985 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.15213362389796019277.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.15213362389796019277.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.15213362389796019277.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:50 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.15213362389796019277.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.15213362389796019277.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.15213362389796019277.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:50 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b unmapped read. WARNING 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b unmapped read. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:50 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:50 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.458930371707603812.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.458930371707603812.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.458930371707603812.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.458930371707603812.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.458930371707603812.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.458930371707603812.tmp/output.sam Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.016 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.016 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.016 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.016 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.019 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.019 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.019 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.019 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.458930371707603812.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.458930371707603812.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.458930371707603812.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.458930371707603812.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.458930371707603812.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.458930371707603812.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:10049-10122. WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:10049-10122. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testOpticalDuplicateBehaviorNullRegex STANDARD_ERROR INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.1994013903050605692.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -READ_NAME_REGEX null -INPUT /tmp/MarkDuplicatesWithMateCigarTester.1994013903050605692.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.1994013903050605692.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.1994013903050605692.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -READ_NAME_REGEX null -INPUT /tmp/MarkDuplicatesWithMateCigarTester.1994013903050605692.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.1994013903050605692.tmp/output.sam Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.055 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.055 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.055 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.055 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.055 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.055 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.055 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.055 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.1994013903050605692.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.1994013903050605692.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.1994013903050605692.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH READ_NAME_REGEX=null MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.1994013903050605692.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.1994013903050605692.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.1994013903050605692.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH READ_NAME_REGEX=null MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 2/2 68b aligned to chr3:41212310-41212358. WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 2/2 68b aligned to chr3:41212310-41212358. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testOpticalDuplicateClusterOneEndSamePositionOneCluster STANDARD_ERROR INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.17503013668403528217.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.17503013668403528217.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.17503013668403528217.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.17503013668403528217.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.17503013668403528217.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.17503013668403528217.tmp/output.sam Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.087 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.087 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.087 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.087 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.088 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.088 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.088 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.088 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.17503013668403528217.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.17503013668403528217.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.17503013668403528217.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.17503013668403528217.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.17503013668403528217.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.17503013668403528217.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17939:39728 2/2 101b aligned to chr2:485312-485382. WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:2205:17939:39728 2/2 101b aligned to chr2:485312-485382. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance STANDARD_ERROR INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.13299015703515666797.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.13299015703515666797.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.13299015703515666797.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.13299015703515666797.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.13299015703515666797.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.13299015703515666797.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.141 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.141 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.141 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.141 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.141 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.141 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.141 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.141 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.13299015703515666797.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.13299015703515666797.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.13299015703515666797.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.13299015703515666797.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.13299015703515666797.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.13299015703515666797.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:1203:2884:16835 2/2 101b aligned to chr2:485253-485294. WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:1203:2884:16835 2/2 101b aligned to chr2:485253-485294. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance STANDARD_ERROR INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.9374024595533332007.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.9374024595533332007.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.9374024595533332007.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.9374024595533332007.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.9374024595533332007.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.9374024595533332007.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.164 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.164 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.164 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.164 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.164 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.164 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.164 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.164 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.9374024595533332007.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.9374024595533332007.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.9374024595533332007.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.9374024595533332007.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.9374024595533332007.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.9374024595533332007.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:1203:2884:16835 1/2 45b aligned to chr2:485253-485297. WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:7:1203:2884:16835 1/2 45b aligned to chr2:485253-485297. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate STANDARD_ERROR INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.12352735660440634068.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.12352735660440634068.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.12352735660440634068.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.12352735660440634068.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.12352735660440634068.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.12352735660440634068.tmp/output.sam Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.187 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.187 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.187 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.187 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.187 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.187 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.187 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.187 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.12352735660440634068.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.12352735660440634068.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.12352735660440634068.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.12352735660440634068.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.12352735660440634068.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.12352735660440634068.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 2/2 68b aligned to chr3:41212310-41212358. WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 2/2 68b aligned to chr3:41212310-41212358. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testOpticalDuplicateFinding STANDARD_ERROR INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.13056184085350783482.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.13056184085350783482.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.13056184085350783482.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.13056184085350783482.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.13056184085350783482.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.13056184085350783482.tmp/output.sam Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.210 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.210 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.210 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.210 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.210 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.210 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.210 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.210 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.13056184085350783482.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.13056184085350783482.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.13056184085350783482.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.13056184085350783482.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.13056184085350783482.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.13056184085350783482.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0:1:1:1:1 1/2 50b aligned to chr2:1-50. WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0:1:1:1:1 1/2 50b aligned to chr2:1-50. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 6 records INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 6 records Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testPathologicalOrderingAtTheSamePosition STANDARD_ERROR INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.2597115858621415209.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.2597115858621415209.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.2597115858621415209.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.2597115858621415209.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.2597115858621415209.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.2597115858621415209.tmp/output.sam Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.243 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.243 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.244 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.244 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.244 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.244 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.244 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.244 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2597115858621415209.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2597115858621415209.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2597115858621415209.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2597115858621415209.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2597115858621415209.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2597115858621415209.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:3:1:15013:113051 1/2 68b aligned to chr1:129384554-129384621. WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:3:1:15013:113051 1/2 68b aligned to chr1:129384554-129384621. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testSecondEndIsBeforeFirstInCoordinate STANDARD_ERROR INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.6172602964571590176.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.6172602964571590176.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.6172602964571590176.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.6172602964571590176.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.6172602964571590176.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.6172602964571590176.tmp/output.sam Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.382 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.382 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.382 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.382 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.382 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.382 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.382 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.382 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.6172602964571590176.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.6172602964571590176.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.6172602964571590176.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.6172602964571590176.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.6172602964571590176.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.6172602964571590176.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 68b aligned to chr1:108855323-108855373. WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 68b aligned to chr1:108855323-108855373. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testSingleMappedFragment STANDARD_ERROR INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.3957182162695679239.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.3957182162695679239.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.3957182162695679239.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.3957182162695679239.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.3957182162695679239.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.3957182162695679239.tmp/output.sam Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.432 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.432 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.432 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.432 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.433 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.433 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.433 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.433 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3957182162695679239.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3957182162695679239.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3957182162695679239.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3957182162695679239.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3957182162695679239.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3957182162695679239.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned to chr2:1-50. WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned to chr2:1-50. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 1 records INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 1 records Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testSingleMappedFragmentAndSingleMappedPair STANDARD_ERROR INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.2705320218126745629.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.2705320218126745629.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.2705320218126745629.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.2705320218126745629.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.2705320218126745629.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.2705320218126745629.tmp/output.sam Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.483 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.483 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.483 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.483 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.483 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.483 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.483 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.483 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2705320218126745629.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2705320218126745629.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2705320218126745629.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2705320218126745629.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2705320218126745629.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2705320218126745629.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned to chr2:1-50. WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned to chr2:1-50. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 3 records INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 3 records Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testSingleMappedFragmentAndTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.15353713392378211077.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.15353713392378211077.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.15353713392378211077.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.15353713392378211077.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.15353713392378211077.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.15353713392378211077.tmp/output.sam Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.542 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.542 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.542 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.542 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.542 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.542 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.542 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.542 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.15353713392378211077.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.15353713392378211077.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.15353713392378211077.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.15353713392378211077.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.15353713392378211077.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.15353713392378211077.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned to chr2:1-50. WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned to chr2:1-50. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 3 records as duplicates. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 3 records as duplicates. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testSingleMappedPair STANDARD_ERROR INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.14410025993810461436.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.14410025993810461436.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.14410025993810461436.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.14410025993810461436.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.14410025993810461436.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.14410025993810461436.tmp/output.sam Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.596 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.596 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.596 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.596 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.596 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.596 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.596 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.596 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.14410025993810461436.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.14410025993810461436.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.14410025993810461436.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.14410025993810461436.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.14410025993810461436.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.14410025993810461436.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr2:1-50. WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr2:1-50. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testSingleMappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testSingleUnmappedFragment STANDARD_ERROR INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.110886340498711863.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.110886340498711863.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.110886340498711863.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.110886340498711863.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.110886340498711863.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.110886340498711863.tmp/output.sam Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.648 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.648 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.648 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.648 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.648 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.648 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.648 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.648 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.110886340498711863.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.110886340498711863.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.110886340498711863.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.110886340498711863.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.110886340498711863.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.110886340498711863.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b unmapped read. WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b unmapped read. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 1 records INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 1 records Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testSingleUnmappedPair STANDARD_ERROR INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.11201409274263273116.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.11201409274263273116.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.11201409274263273116.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.11201409274263273116.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.11201409274263273116.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.11201409274263273116.tmp/output.sam Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.719 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.719 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.719 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.719 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.719 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.719 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.719 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.719 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.11201409274263273116.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.11201409274263273116.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.11201409274263273116.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.11201409274263273116.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.11201409274263273116.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.11201409274263273116.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b unmapped read. WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b unmapped read. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testStackOverFlowPairSetSwap STANDARD_ERROR INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.1282732126050762237.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.1282732126050762237.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.1282732126050762237.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.1282732126050762237.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.1282732126050762237.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.1282732126050762237.tmp/output.sam Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.781 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.781 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.781 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.781 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.781 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.781 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.781 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.781 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.1282732126050762237.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.1282732126050762237.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.1282732126050762237.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.1282732126050762237.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.1282732126050762237.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.1282732126050762237.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.1511856580026220846.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.1511856580026220846.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.1511856580026220846.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.1511856580026220846.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.1511856580026220846.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.1511856580026220846.tmp/output.sam Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.838 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.838 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.838 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.838 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.838 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.838 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.838 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.838 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.1511856580026220846.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.1511856580026220846.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.1511856580026220846.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.1511856580026220846.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.1511856580026220846.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.1511856580026220846.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr1:1-50. WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr1:1-50. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 18 records INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 18 records Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 12 records as duplicates. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 12 records as duplicates. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.16672651907797568117.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.16672651907797568117.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.16672651907797568117.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.16672651907797568117.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.16672651907797568117.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.16672651907797568117.tmp/output.sam Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.890 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.890 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.890 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.890 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.890 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.890 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.890 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.890 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.16672651907797568117.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.16672651907797568117.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.16672651907797568117.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.16672651907797568117.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.16672651907797568117.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.16672651907797568117.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr2:1-50. WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr2:1-50. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 6 records INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 6 records Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testThreeMappedPairsWithMatchingSecondMate STANDARD_ERROR INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.9656760943151529416.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.9656760943151529416.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.9656760943151529416.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.9656760943151529416.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.9656760943151529416.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.9656760943151529416.tmp/output.sam Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.940 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.940 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.941 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.941 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.941 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.941 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.941 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.941 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.9656760943151529416.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.9656760943151529416.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.9656760943151529416.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.9656760943151529416.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.9656760943151529416.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.9656760943151529416.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 76b aligned to chr2:10058-10104. WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 76b aligned to chr2:10058-10104. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 6 records INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 6 records Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:51 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.18370760542327981102.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.18370760542327981102.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.18370760542327981102.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.18370760542327981102.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.18370760542327981102.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.18370760542327981102.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.992 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.992 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.992 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.992 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.997 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:51.997 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:51.997 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:51.997 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.18370760542327981102.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.18370760542327981102.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.18370760542327981102.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:51 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.18370760542327981102.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.18370760542327981102.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.18370760542327981102.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:51 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr1:1-50. WARNING 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr1:1-50. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 12 records INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Processed 12 records Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:51 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoGroupsOnDifferentChromosomesOfTwoFragments STANDARD_ERROR INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.2308873056864777400.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.2308873056864777400.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.2308873056864777400.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.2308873056864777400.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.2308873056864777400.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.2308873056864777400.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.044 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.044 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.045 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.045 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.053 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.053 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.053 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.053 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2308873056864777400.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2308873056864777400.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2308873056864777400.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.2308873056864777400.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.2308873056864777400.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.2308873056864777400.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned to chr1:1-50. WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned to chr1:1-50. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.3579832897614185048.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.3579832897614185048.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.3579832897614185048.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.3579832897614185048.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.3579832897614185048.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.3579832897614185048.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.099 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.099 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.099 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.099 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.100 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.100 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.100 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.100 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3579832897614185048.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3579832897614185048.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3579832897614185048.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3579832897614185048.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3579832897614185048.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3579832897614185048.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr1:1-50. WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr1:1-50. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 8 records INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 8 records Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoMappedFragments STANDARD_ERROR INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.17774257649167943255.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.17774257649167943255.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.17774257649167943255.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.17774257649167943255.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.17774257649167943255.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.17774257649167943255.tmp/output.sam Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.156 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.156 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.156 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.156 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.156 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.156 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.156 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.156 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.17774257649167943255.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.17774257649167943255.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.17774257649167943255.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.17774257649167943255.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.17774257649167943255.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.17774257649167943255.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned to chr1:1-50. WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned to chr1:1-50. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoMappedPairWithSamePosition STANDARD_ERROR INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.13014027032443722392.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.13014027032443722392.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.13014027032443722392.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.13014027032443722392.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.13014027032443722392.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.13014027032443722392.tmp/output.sam Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.210 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.210 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.210 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.210 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.211 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.211 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.211 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.211 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.13014027032443722392.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.13014027032443722392.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.13014027032443722392.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.13014027032443722392.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.13014027032443722392.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.13014027032443722392.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr1:5604914-5604950. WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr1:5604914-5604950. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoMappedPairWithSamePositionDifferentStrands STANDARD_ERROR INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.14142469576768159145.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.14142469576768159145.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.14142469576768159145.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.14142469576768159145.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.14142469576768159145.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.14142469576768159145.tmp/output.sam Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.256 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.256 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.256 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.256 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.265 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.265 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.265 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.265 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.14142469576768159145.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.14142469576768159145.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.14142469576768159145.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.14142469576768159145.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.14142469576768159145.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.14142469576768159145.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 50b aligned to chr1:5604914-5604963. WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 50b aligned to chr1:5604914-5604963. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoMappedPairWithSamePositionDifferentStrands2 STANDARD_ERROR INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.17516466049628265675.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.17516466049628265675.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.17516466049628265675.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.17516466049628265675.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.17516466049628265675.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.17516466049628265675.tmp/output.sam Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.320 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.320 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.320 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.320 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.321 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.321 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.321 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.321 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.17516466049628265675.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.17516466049628265675.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.17516466049628265675.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.17516466049628265675.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.17516466049628265675.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.17516466049628265675.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr1:5604914-5604963. WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr1:5604914-5604963. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.14625703592648178874.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.14625703592648178874.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.14625703592648178874.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.14625703592648178874.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.14625703592648178874.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.14625703592648178874.tmp/output.sam Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.379 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.379 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.379 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.379 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.379 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.379 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.379 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.379 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.14625703592648178874.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.14625703592648178874.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.14625703592648178874.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.14625703592648178874.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.14625703592648178874.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.14625703592648178874.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr2:1-50. WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr2:1-50. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoMappedPairsAndMappedSecondaryFragment STANDARD_ERROR INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.5531946390822161236.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.5531946390822161236.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.5531946390822161236.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.5531946390822161236.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.5531946390822161236.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.5531946390822161236.tmp/output.sam Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.441 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.441 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.441 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.441 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.441 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.441 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.441 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.441 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.5531946390822161236.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.5531946390822161236.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.5531946390822161236.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.5531946390822161236.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.5531946390822161236.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.5531946390822161236.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr2:1-50. WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr2:1-50. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoMappedPairsAndTerminalUnmappedFragment STANDARD_ERROR INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.13712719896056598298.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.13712719896056598298.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.13712719896056598298.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.13712719896056598298.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.13712719896056598298.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.13712719896056598298.tmp/output.sam Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.502 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.502 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.502 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.502 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.503 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.503 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.503 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.503 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.13712719896056598298.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.13712719896056598298.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.13712719896056598298.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.13712719896056598298.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.13712719896056598298.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.13712719896056598298.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr2:1-50. WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr2:1-50. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoMappedPairsAndTerminalUnmappedPair STANDARD_ERROR INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.9768334791919180328.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.9768334791919180328.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.9768334791919180328.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.9768334791919180328.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.9768334791919180328.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.9768334791919180328.tmp/output.sam Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.566 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.566 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.566 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.566 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.566 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.566 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.567 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.567 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.9768334791919180328.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.9768334791919180328.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.9768334791919180328.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.9768334791919180328.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.9768334791919180328.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.9768334791919180328.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr2:1-50. WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 50b aligned to chr2:1-50. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 6 records INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 6 records Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoMappedPairsMatesSoftClipped STANDARD_ERROR INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.6620493625491147072.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.6620493625491147072.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.6620493625491147072.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.6620493625491147072.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.6620493625491147072.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.6620493625491147072.tmp/output.sam Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.626 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.626 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.626 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.626 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.626 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.626 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.626 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.626 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.6620493625491147072.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.6620493625491147072.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.6620493625491147072.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.6620493625491147072.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.6620493625491147072.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.6620493625491147072.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:10022-10097. WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:10022-10097. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithOppositeOrientations STANDARD_ERROR INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.5928863406570374948.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.5928863406570374948.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.5928863406570374948.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.5928863406570374948.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.5928863406570374948.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.5928863406570374948.tmp/output.sam Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.694 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.694 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.694 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.694 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.694 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.694 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.694 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.694 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.5928863406570374948.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.5928863406570374948.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.5928863406570374948.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.5928863406570374948.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.5928863406570374948.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.5928863406570374948.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 76b aligned to chr2:10038-10103. WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 76b aligned to chr2:10038-10103. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithOppositeOrientationsNumberTwo STANDARD_ERROR INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.9677701621119348367.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.9677701621119348367.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.9677701621119348367.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.9677701621119348367.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.9677701621119348367.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.9677701621119348367.tmp/output.sam Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.768 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.768 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.768 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.768 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.773 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.773 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.774 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.774 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.9677701621119348367.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.9677701621119348367.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.9677701621119348367.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.9677701621119348367.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.9677701621119348367.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.9677701621119348367.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:10038-10107. WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:10038-10107. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSoftClipping STANDARD_ERROR INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.8200172988750292513.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.8200172988750292513.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.8200172988750292513.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.8200172988750292513.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.8200172988750292513.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.8200172988750292513.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.811 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.811 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.811 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.811 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.812 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.812 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.812 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.812 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.8200172988750292513.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.8200172988750292513.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.8200172988750292513.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.8200172988750292513.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.8200172988750292513.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.8200172988750292513.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:2-43. WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:2-43. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSoftClippingBoth STANDARD_ERROR INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.17149665264768139719.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.17149665264768139719.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.17149665264768139719.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.17149665264768139719.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.17149665264768139719.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.17149665264768139719.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.853 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.853 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.853 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.853 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.854 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.854 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.854 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.854 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.17149665264768139719.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.17149665264768139719.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.17149665264768139719.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.17149665264768139719.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.17149665264768139719.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.17149665264768139719.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:52 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 76b aligned to chr2:10002-10043. WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 2/2 76b aligned to chr2:10002-10043. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar STANDARD_ERROR INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.7316298961226180325.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.7316298961226180325.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.7316298961226180325.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.7316298961226180325.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.7316298961226180325.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.7316298961226180325.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.891 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.891 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.891 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.891 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.892 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.892 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.892 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.892 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.7316298961226180325.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.7316298961226180325.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.7316298961226180325.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.7316298961226180325.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.7316298961226180325.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.7316298961226180325.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:12-53. WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr2:12-53. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 2 records with no mate cigar optional tag. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 2 records with no mate cigar optional tag. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReads[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.11434277348048693191.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.11434277348048693191.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.11434277348048693191.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.11434277348048693191.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.11434277348048693191.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.11434277348048693191.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.927 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.927 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.927 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.927 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.928 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.928 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.928 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.928 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.11434277348048693191.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.11434277348048693191.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.11434277348048693191.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.11434277348048693191.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.11434277348048693191.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.11434277348048693191.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 68b aligned to chr2:400-467. WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 68b aligned to chr2:400-467. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReads[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.3436805768363146720.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.3436805768363146720.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.3436805768363146720.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.3436805768363146720.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.3436805768363146720.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.3436805768363146720.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.960 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.960 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.960 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.960 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.960 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.960 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.960 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.960 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3436805768363146720.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3436805768363146720.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3436805768363146720.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3436805768363146720.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3436805768363146720.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3436805768363146720.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 68b aligned to chr2:400-467. WARNING 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 68b aligned to chr2:400-467. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:52 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReads[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:47:52 MarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.4123432024448108399.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.4123432024448108399.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.4123432024448108399.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.4123432024448108399.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.4123432024448108399.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.4123432024448108399.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.996 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.996 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.997 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.997 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.997 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:52.997 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:52.997 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:52.997 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.4123432024448108399.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.4123432024448108399.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.4123432024448108399.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:52 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.4123432024448108399.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.4123432024448108399.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.4123432024448108399.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 68b aligned to chr2:400-467. WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 68b aligned to chr2:400-467. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReads[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.7908088854500661846.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.7908088854500661846.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.7908088854500661846.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.7908088854500661846.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.7908088854500661846.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.7908088854500661846.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.031 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.031 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.032 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.032 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.032 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.032 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.032 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.032 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.7908088854500661846.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.7908088854500661846.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.7908088854500661846.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.7908088854500661846.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.7908088854500661846.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.7908088854500661846.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:16020:13352 68b aligned to chr2:400-467. WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:16020:13352 68b aligned to chr2:400-467. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReads[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.5108914430376305154.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.5108914430376305154.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.5108914430376305154.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.5108914430376305154.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.5108914430376305154.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.5108914430376305154.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.065 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.065 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.065 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.065 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.065 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.065 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.066 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.066 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.5108914430376305154.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.5108914430376305154.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.5108914430376305154.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.5108914430376305154.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.5108914430376305154.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.5108914430376305154.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:16020:13352 68b aligned to chr2:400-467. WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:16020:13352 68b aligned to chr2:400-467. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReads[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.9493956904345382668.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.9493956904345382668.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.9493956904345382668.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.9493956904345382668.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.9493956904345382668.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.9493956904345382668.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.096 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.096 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.096 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.096 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.096 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.096 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.096 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.096 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.9493956904345382668.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.9493956904345382668.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.9493956904345382668.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.9493956904345382668.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.9493956904345382668.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.9493956904345382668.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:16020:13352 68b aligned to chr2:400-467. WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:16020:13352 68b aligned to chr2:400-467. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.18321785004000741311.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.18321785004000741311.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.18321785004000741311.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.18321785004000741311.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.18321785004000741311.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.18321785004000741311.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.128 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.128 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.129 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.129 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.129 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.129 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.129 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.129 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.18321785004000741311.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.18321785004000741311.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.18321785004000741311.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.18321785004000741311.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.18321785004000741311.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.18321785004000741311.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 2/2 68b aligned to chr3:41212310-41212358. WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 2/2 68b aligned to chr3:41212310-41212358. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.11048194384846177323.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.11048194384846177323.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.11048194384846177323.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.11048194384846177323.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.11048194384846177323.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.11048194384846177323.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.159 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.159 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.159 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.159 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.159 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.159 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.159 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.159 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.11048194384846177323.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.11048194384846177323.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.11048194384846177323.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.11048194384846177323.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.11048194384846177323.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.11048194384846177323.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 2/2 68b aligned to chr3:41212310-41212358. WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 2/2 68b aligned to chr3:41212310-41212358. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.3202764656112963828.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.3202764656112963828.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.3202764656112963828.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.3202764656112963828.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.3202764656112963828.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.3202764656112963828.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.192 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.192 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.192 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.192 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.192 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.192 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.192 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.192 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3202764656112963828.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3202764656112963828.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3202764656112963828.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.3202764656112963828.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.3202764656112963828.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.3202764656112963828.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 2/2 68b aligned to chr3:41212310-41212358. WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 2/2 68b aligned to chr3:41212310-41212358. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.7866458092235611938.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.7866458092235611938.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.7866458092235611938.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.7866458092235611938.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.7866458092235611938.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.7866458092235611938.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.228 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.228 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.228 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.228 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.228 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.228 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.228 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.228 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.7866458092235611938.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.7866458092235611938.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.7866458092235611938.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.7866458092235611938.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.7866458092235611938.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.7866458092235611938.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 2/2 68b aligned to chr3:41212310-41212358. WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 2/2 68b aligned to chr3:41212310-41212358. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.5273083116673551674.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.5273083116673551674.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.5273083116673551674.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.5273083116673551674.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.5273083116673551674.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.5273083116673551674.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.262 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.262 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.262 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.262 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.262 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.262 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.262 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.262 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.5273083116673551674.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.5273083116673551674.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.5273083116673551674.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.5273083116673551674.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.5273083116673551674.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.5273083116673551674.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 2/2 68b aligned to chr3:41212310-41212358. WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 2/2 68b aligned to chr3:41212310-41212358. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.14340096717534103030.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.14340096717534103030.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.14340096717534103030.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.14340096717534103030.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.14340096717534103030.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.14340096717534103030.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.292 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.292 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.292 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.292 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.293 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.293 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.293 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.293 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.14340096717534103030.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.14340096717534103030.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.14340096717534103030.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.14340096717534103030.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.14340096717534103030.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.14340096717534103030.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 2/2 68b aligned to chr3:41212310-41212358. WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: RUNID:1:1:15993:13361 2/2 68b aligned to chr3:41212310-41212358. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoUnmappedFragments STANDARD_ERROR INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.16066855670093578354.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.16066855670093578354.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.16066855670093578354.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.16066855670093578354.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.16066855670093578354.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.16066855670093578354.tmp/output.sam Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.324 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.324 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.324 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.324 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.324 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.324 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.324 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.324 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.16066855670093578354.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.16066855670093578354.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.16066855670093578354.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.16066855670093578354.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.16066855670093578354.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.16066855670093578354.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b unmapped read. WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b unmapped read. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testScoringStrategyForMateReferenceLengthComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testScoringStrategyForMateReferenceLengthComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testScoringStrategyForMateReferenceLengthComparison STANDARD_ERROR INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Test: Test method testScoringStrategyForMateReferenceLengthComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testScoringStrategyForMateReferenceLengthComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScoringStrategyForMateReferenceLengthComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testScoringStrategyForMateReferenceLengthComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScoringStrategyForMateReferenceLengthComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScoringStrategyForMateReferenceLengthComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testScoringStrategyForMateReferenceLengthComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScoringStrategyForMateReferenceLengthComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testScoringStrategyForMateReferenceLengthComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.13805706864121450932.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.13805706864121450932.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.13805706864121450932.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.13805706864121450932.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.13805706864121450932.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.13805706864121450932.tmp/output.sam Test: Test method testScoringStrategyForMateReferenceLengthComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testScoringStrategyForMateReferenceLengthComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testScoringStrategyForMateReferenceLengthComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testScoringStrategyForMateReferenceLengthComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.363 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.363 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScoringStrategyForMateReferenceLengthComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.363 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.363 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScoringStrategyForMateReferenceLengthComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.363 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.363 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScoringStrategyForMateReferenceLengthComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.363 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.363 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScoringStrategyForMateReferenceLengthComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.13805706864121450932.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.13805706864121450932.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.13805706864121450932.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.13805706864121450932.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.13805706864121450932.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.13805706864121450932.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScoringStrategyForMateReferenceLengthComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScoringStrategyForMateReferenceLengthComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:53 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READX. Cause: String 'READX' did not start with a parsable number. WARNING 2024-07-02 11:47:53 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READX. Cause: String 'READX' did not start with a parsable number. Test: Test method testScoringStrategyForMateReferenceLengthComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READX 1/2 50b aligned to chr2:1-50. WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READX 1/2 50b aligned to chr2:1-50. Test: Test method testScoringStrategyForMateReferenceLengthComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testScoringStrategyForMateReferenceLengthComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testScoringStrategyForMateReferenceLengthComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testScoringStrategyForMateReferenceLengthComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testScoringStrategyForMateReferenceLengthComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testScoringStrategyForMateReferenceLengthComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testScoringStrategyForReadNameComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testScoringStrategyForReadNameComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testScoringStrategyForReadNameComparison STANDARD_ERROR INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Test: Test method testScoringStrategyForReadNameComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testScoringStrategyForReadNameComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScoringStrategyForReadNameComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testScoringStrategyForReadNameComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScoringStrategyForReadNameComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScoringStrategyForReadNameComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testScoringStrategyForReadNameComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScoringStrategyForReadNameComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testScoringStrategyForReadNameComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.7922880202953863038.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.7922880202953863038.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.7922880202953863038.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.7922880202953863038.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.7922880202953863038.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.7922880202953863038.tmp/output.sam Test: Test method testScoringStrategyForReadNameComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testScoringStrategyForReadNameComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testScoringStrategyForReadNameComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testScoringStrategyForReadNameComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.396 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.396 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScoringStrategyForReadNameComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.396 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.396 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScoringStrategyForReadNameComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.396 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.396 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScoringStrategyForReadNameComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.396 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.396 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScoringStrategyForReadNameComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.7922880202953863038.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.7922880202953863038.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.7922880202953863038.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.7922880202953863038.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.7922880202953863038.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.7922880202953863038.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScoringStrategyForReadNameComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScoringStrategyForReadNameComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:53 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:53 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testScoringStrategyForReadNameComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned to chr1:1-50. WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 50b aligned to chr1:1-50. Test: Test method testScoringStrategyForReadNameComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testScoringStrategyForReadNameComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testScoringStrategyForReadNameComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. Test: Test method testScoringStrategyForReadNameComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testScoringStrategyForReadNameComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testScoringStrategyForReadNameComparison(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoFragmentsLargeSoftClip(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoFragmentsLargeSoftClip(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoFragmentsLargeSoftClip STANDARD_ERROR INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Test: Test method testTwoFragmentsLargeSoftClip(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoFragmentsLargeSoftClip(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoFragmentsLargeSoftClip(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoFragmentsLargeSoftClip(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoFragmentsLargeSoftClip(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoFragmentsLargeSoftClip(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoFragmentsLargeSoftClip(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoFragmentsLargeSoftClip(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoFragmentsLargeSoftClip(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.7263683030340790496.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.7263683030340790496.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.7263683030340790496.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.7263683030340790496.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.7263683030340790496.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.7263683030340790496.tmp/output.sam Test: Test method testTwoFragmentsLargeSoftClip(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoFragmentsLargeSoftClip(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoFragmentsLargeSoftClip(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoFragmentsLargeSoftClip(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.430 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.430 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoFragmentsLargeSoftClip(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.431 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.431 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoFragmentsLargeSoftClip(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.431 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.431 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoFragmentsLargeSoftClip(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.431 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.431 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoFragmentsLargeSoftClip(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.7263683030340790496.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.7263683030340790496.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.7263683030340790496.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.7263683030340790496.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.7263683030340790496.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.7263683030340790496.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoFragmentsLargeSoftClip(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoFragmentsLargeSoftClip(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:53 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:53 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoFragmentsLargeSoftClip(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: record #1: READ1 0 chr1 2000 255 10S100M * 0 0 CAGTGGCAGCCCTATCGCCAGATCAATCGTCGCTGTGGAACTAGACCCGCCCTACTGTTGTCGCTGACTCCTTACTCCCTCTCAACGTATTCATACAGGCCCTTTTCGAA ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ RG:Z:1 record #1: READ1 0 chr1 2000 255 10S100M * 0 0 CAGTGGCAGCCCTATCGCCAGATCAATCGTCGCTGTGGAACTAGACCCGCCCTACTGTTGTCGCTGACTCCTTACTCCCTCTCAACGTATTCATACAGGCCCTTTTCGAA ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ RG:Z:1 Test: Test method testTwoFragmentsLargeSoftClip(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: record #2: READ2 0 chr1 3000 255 2000S100M * 0 0 TAGCTGGCGTGCACGATTGGCGTGTACATGCTGCCTTTGAGGCACAGTTTCGTAGGGTTTCGTAGCAATGGCTTTGTCTGAAGAGAAGGGGTCTGTCGACAGACACTACGTCCCCAAAGTACCAGCGGGTGATCTCCGCAGACCTCGGAGCCGAGTGCGCTATTCTGGTGACTAGGGGATTAGGTCGGAGCAAGCGGCGTCCGTTAGAAAGCGTCGCTACTAGCCCGCGAGAGGCGACGTCTCACTCCCCGTAACAGCAGGACTGGTCTGGGTACGGCTGGCGCAGGCATGAATGGGATACCCGTGTTCTGCCTTCTGTGTCTACATCCGGTTATGGGAGCTAGCGAAAGTCACGCGAACCAGTAAGGTTAGAGTAGAAACGGAGTACTACTTAGCTATTGAAAAAAGGTGCTGCATCTGAGCCACGCCTAATTGCTGAGCTCTAAGGCTGTGAGTGCGTGAGTAAATGTGATCGGTTAACCTGGCCGAATTGCCCACCTGAGTGCAAGAGTACAAAGCGAAGTATAGTGCAGGCCTCAGCCCCTCCCCGCCAGAATACTACAGGCCGAGGAGGATGAGCTCTTATGGGCGTGTCGTTGGACGATTTATACTGGTGAAGTTGTCTGAAGAACGGTCTTGTTACGACTCACGTCGGGTACCTCTTCCCAGCATCTCGACGCCCCCTTCAGCCTTCGGACCGGTAACCACCGGCCTTGATCTCTGCCCAATAGTAAATGTCGCGGAACTCGTCAGAAATGACGACTCTAGGTGGAGTGTCGCAGTCGAGGTCGGGAGTAGTTCACTACGAACCGTTCGCCTAGGGTGCGAGTGTTCTAGATTCCGCTTGCTCATCGGGCGGAGGGGTCCCTTCGCGGGTGAAAAGCAGTCTCGATTGGGCGATGTTAAGCAATCGGCTGCACCTTGCAGCATCGACTAGAATAAATTGACTGCTCGTATTATTTTGCTCATCGTTGTTCAGTTTTGCGCGCCCAATGTTATTTAAGCTCAAGTGTCTGAAAGACTTCAATATGACGGCTCGATACTGAAGGGACGTCGCGTGCAGCAACACATACTTTTCGTAACGACCAAGTTGCCTCCTCCCTTTAGCACGACCCGGAGTATGCCAGGCCGGCATACTGAGTACACATCCATCATGTGCGTATTCCGGGTTCCTTCGACTCCATAGAGGACTACTGTCAAACGCGAGTCTGAATGGGTCGTTGAATCTACTTACCGTAGGGTGACAGAATGCTGGGCTTTTCTGATTTAGTAAAAGTCAACGCGTGCAAAGTTGCGATCGGGACTCGGCTTGTTCGCAAGGTATTATACTGTAGGATTTCTTTGCACGGTGTGCGACGTTGTCCAATCTGATCTTTCACCGTGTAAGTTCCCTATAGCCTGCACACCGTCAAGACCCGGGTGTCCGCAGACGTTCGCACGTTATCTACGGGTCGATTGTTACACTACCTGTAATACATCTTCATCTGATAGATAGTTTAAGCAATAATCCATGACGCTGCCCGTTGCCAGTAGCCAGCGTTCCGTCCTGCTAGAGCGCCCAAGTCCCACACGGGTAGCGGTTTTCTGGTCCAGGAGGGAAAGTCCTAAATGCAACTGTACACAAGACGGATACCTCTAGCTCCTAAATTCCCGTTGCAGGATGCCAAAAGCTTGACCATCGGGTGAGTGTATCAATGTTGGCGGACATAGGAGGTAGCAGAGACGTCACCGTTTTCGCATGGCCTGTCAAGATCGACTAGAAACAGACTTTATATTATCGGTCAACTATCGCCGATGATGGTCGGAAAGCATTCCTGGGGACCGAGCCGGCGTCCAGGGCGTCAGGGCCAATCCTCCGCATTACCTATAGTTAGGTTACATAGCTCTTGTGGCGTGGGGGTCCTTCCCACCCATCAATCCACTGCCTTGACATGCGCACTGGGGTCTTAGCCCTTTTTATAAACTTTAAACGCATCAGCGCACAAGGTAGAAAGCTGGAACGTAGTTTGTACAAAAAGTCCAGGAGTCCAAGCCGCCATTTCGTTTCCGTTATCGCGACGCTGGACAGAGTGGTGCGAGCTGCACAATCAAGCTGCGGAA ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ RG:Z:1 record #2: READ2 0 chr1 3000 255 2000S100M * 0 0 TAGCTGGCGTGCACGATTGGCGTGTACATGCTGCCTTTGAGGCACAGTTTCGTAGGGTTTCGTAGCAATGGCTTTGTCTGAAGAGAAGGGGTCTGTCGACAGACACTACGTCCCCAAAGTACCAGCGGGTGATCTCCGCAGACCTCGGAGCCGAGTGCGCTATTCTGGTGACTAGGGGATTAGGTCGGAGCAAGCGGCGTCCGTTAGAAAGCGTCGCTACTAGCCCGCGAGAGGCGACGTCTCACTCCCCGTAACAGCAGGACTGGTCTGGGTACGGCTGGCGCAGGCATGAATGGGATACCCGTGTTCTGCCTTCTGTGTCTACATCCGGTTATGGGAGCTAGCGAAAGTCACGCGAACCAGTAAGGTTAGAGTAGAAACGGAGTACTACTTAGCTATTGAAAAAAGGTGCTGCATCTGAGCCACGCCTAATTGCTGAGCTCTAAGGCTGTGAGTGCGTGAGTAAATGTGATCGGTTAACCTGGCCGAATTGCCCACCTGAGTGCAAGAGTACAAAGCGAAGTATAGTGCAGGCCTCAGCCCCTCCCCGCCAGAATACTACAGGCCGAGGAGGATGAGCTCTTATGGGCGTGTCGTTGGACGATTTATACTGGTGAAGTTGTCTGAAGAACGGTCTTGTTACGACTCACGTCGGGTACCTCTTCCCAGCATCTCGACGCCCCCTTCAGCCTTCGGACCGGTAACCACCGGCCTTGATCTCTGCCCAATAGTAAATGTCGCGGAACTCGTCAGAAATGACGACTCTAGGTGGAGTGTCGCAGTCGAGGTCGGGAGTAGTTCACTACGAACCGTTCGCCTAGGGTGCGAGTGTTCTAGATTCCGCTTGCTCATCGGGCGGAGGGGTCCCTTCGCGGGTGAAAAGCAGTCTCGATTGGGCGATGTTAAGCAATCGGCTGCACCTTGCAGCATCGACTAGAATAAATTGACTGCTCGTATTATTTTGCTCATCGTTGTTCAGTTTTGCGCGCCCAATGTTATTTAAGCTCAAGTGTCTGAAAGACTTCAATATGACGGCTCGATACTGAAGGGACGTCGCGTGCAGCAACACATACTTTTCGTAACGACCAAGTTGCCTCCTCCCTTTAGCACGACCCGGAGTATGCCAGGCCGGCATACTGAGTACACATCCATCATGTGCGTATTCCGGGTTCCTTCGACTCCATAGAGGACTACTGTCAAACGCGAGTCTGAATGGGTCGTTGAATCTACTTACCGTAGGGTGACAGAATGCTGGGCTTTTCTGATTTAGTAAAAGTCAACGCGTGCAAAGTTGCGATCGGGACTCGGCTTGTTCGCAAGGTATTATACTGTAGGATTTCTTTGCACGGTGTGCGACGTTGTCCAATCTGATCTTTCACCGTGTAAGTTCCCTATAGCCTGCACACCGTCAAGACCCGGGTGTCCGCAGACGTTCGCACGTTATCTACGGGTCGATTGTTACACTACCTGTAATACATCTTCATCTGATAGATAGTTTAAGCAATAATCCATGACGCTGCCCGTTGCCAGTAGCCAGCGTTCCGTCCTGCTAGAGCGCCCAAGTCCCACACGGGTAGCGGTTTTCTGGTCCAGGAGGGAAAGTCCTAAATGCAACTGTACACAAGACGGATACCTCTAGCTCCTAAATTCCCGTTGCAGGATGCCAAAAGCTTGACCATCGGGTGAGTGTATCAATGTTGGCGGACATAGGAGGTAGCAGAGACGTCACCGTTTTCGCATGGCCTGTCAAGATCGACTAGAAACAGACTTTATATTATCGGTCAACTATCGCCGATGATGGTCGGAAAGCATTCCTGGGGACCGAGCCGGCGTCCAGGGCGTCAGGGCCAATCCTCCGCATTACCTATAGTTAGGTTACATAGCTCTTGTGGCGTGGGGGTCCTTCCCACCCATCAATCCACTGCCTTGACATGCGCACTGGGGTCTTAGCCCTTTTTATAAACTTTAAACGCATCAGCGCACAAGGTAGAAAGCTGGAACGTAGTTTGTACAAAAAGTCCAGGAGTCCAAGCCGCCATTTCGTTTCCGTTATCGCGACGCTGGACAGAGTGGTGCGAGCTGCACAATCAAGCTGCGGAA ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ RG:Z:1 Test: Test method testTwoFragmentsLargeSoftClip(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoFragmentsLargeSoftClip(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Test: Test method testTwoFragmentsLargeSoftClip(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure STANDARD_ERROR INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.16732617365478193499.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -MINIMUM_DISTANCE 989 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.16732617365478193499.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.16732617365478193499.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.16732617365478193499.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -MINIMUM_DISTANCE 989 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.16732617365478193499.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.16732617365478193499.tmp/output.sam Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.468 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.468 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.468 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.468 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.468 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.468 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.468 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.468 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar MINIMUM_DISTANCE=989 BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.16732617365478193499.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.16732617365478193499.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.16732617365478193499.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar MINIMUM_DISTANCE=989 BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.16732617365478193499.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.16732617365478193499.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.16732617365478193499.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:53 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:53 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: record #1: READ1 0 chr1 2000 255 10S100M * 0 0 CAGTGGCAGCCCTATCGCCAGATCAATCGTCGCTGTGGAACTAGACCCGCCCTACTGTTGTCGCTGACTCCTTACTCCCTCTCAACGTATTCATACAGGCCCTTTTCGAA ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ RG:Z:1 record #1: READ1 0 chr1 2000 255 10S100M * 0 0 CAGTGGCAGCCCTATCGCCAGATCAATCGTCGCTGTGGAACTAGACCCGCCCTACTGTTGTCGCTGACTCCTTACTCCCTCTCAACGTATTCATACAGGCCCTTTTCGAA ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ RG:Z:1 Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: record #2: READ2 0 chr1 3000 255 2000S100M * 0 0 TAGCTGGCGTGCACGATTGGCGTGTACATGCTGCCTTTGAGGCACAGTTTCGTAGGGTTTCGTAGCAATGGCTTTGTCTGAAGAGAAGGGGTCTGTCGACAGACACTACGTCCCCAAAGTACCAGCGGGTGATCTCCGCAGACCTCGGAGCCGAGTGCGCTATTCTGGTGACTAGGGGATTAGGTCGGAGCAAGCGGCGTCCGTTAGAAAGCGTCGCTACTAGCCCGCGAGAGGCGACGTCTCACTCCCCGTAACAGCAGGACTGGTCTGGGTACGGCTGGCGCAGGCATGAATGGGATACCCGTGTTCTGCCTTCTGTGTCTACATCCGGTTATGGGAGCTAGCGAAAGTCACGCGAACCAGTAAGGTTAGAGTAGAAACGGAGTACTACTTAGCTATTGAAAAAAGGTGCTGCATCTGAGCCACGCCTAATTGCTGAGCTCTAAGGCTGTGAGTGCGTGAGTAAATGTGATCGGTTAACCTGGCCGAATTGCCCACCTGAGTGCAAGAGTACAAAGCGAAGTATAGTGCAGGCCTCAGCCCCTCCCCGCCAGAATACTACAGGCCGAGGAGGATGAGCTCTTATGGGCGTGTCGTTGGACGATTTATACTGGTGAAGTTGTCTGAAGAACGGTCTTGTTACGACTCACGTCGGGTACCTCTTCCCAGCATCTCGACGCCCCCTTCAGCCTTCGGACCGGTAACCACCGGCCTTGATCTCTGCCCAATAGTAAATGTCGCGGAACTCGTCAGAAATGACGACTCTAGGTGGAGTGTCGCAGTCGAGGTCGGGAGTAGTTCACTACGAACCGTTCGCCTAGGGTGCGAGTGTTCTAGATTCCGCTTGCTCATCGGGCGGAGGGGTCCCTTCGCGGGTGAAAAGCAGTCTCGATTGGGCGATGTTAAGCAATCGGCTGCACCTTGCAGCATCGACTAGAATAAATTGACTGCTCGTATTATTTTGCTCATCGTTGTTCAGTTTTGCGCGCCCAATGTTATTTAAGCTCAAGTGTCTGAAAGACTTCAATATGACGGCTCGATACTGAAGGGACGTCGCGTGCAGCAACACATACTTTTCGTAACGACCAAGTTGCCTCCTCCCTTTAGCACGACCCGGAGTATGCCAGGCCGGCATACTGAGTACACATCCATCATGTGCGTATTCCGGGTTCCTTCGACTCCATAGAGGACTACTGTCAAACGCGAGTCTGAATGGGTCGTTGAATCTACTTACCGTAGGGTGACAGAATGCTGGGCTTTTCTGATTTAGTAAAAGTCAACGCGTGCAAAGTTGCGATCGGGACTCGGCTTGTTCGCAAGGTATTATACTGTAGGATTTCTTTGCACGGTGTGCGACGTTGTCCAATCTGATCTTTCACCGTGTAAGTTCCCTATAGCCTGCACACCGTCAAGACCCGGGTGTCCGCAGACGTTCGCACGTTATCTACGGGTCGATTGTTACACTACCTGTAATACATCTTCATCTGATAGATAGTTTAAGCAATAATCCATGACGCTGCCCGTTGCCAGTAGCCAGCGTTCCGTCCTGCTAGAGCGCCCAAGTCCCACACGGGTAGCGGTTTTCTGGTCCAGGAGGGAAAGTCCTAAATGCAACTGTACACAAGACGGATACCTCTAGCTCCTAAATTCCCGTTGCAGGATGCCAAAAGCTTGACCATCGGGTGAGTGTATCAATGTTGGCGGACATAGGAGGTAGCAGAGACGTCACCGTTTTCGCATGGCCTGTCAAGATCGACTAGAAACAGACTTTATATTATCGGTCAACTATCGCCGATGATGGTCGGAAAGCATTCCTGGGGACCGAGCCGGCGTCCAGGGCGTCAGGGCCAATCCTCCGCATTACCTATAGTTAGGTTACATAGCTCTTGTGGCGTGGGGGTCCTTCCCACCCATCAATCCACTGCCTTGACATGCGCACTGGGGTCTTAGCCCTTTTTATAAACTTTAAACGCATCAGCGCACAAGGTAGAAAGCTGGAACGTAGTTTGTACAAAAAGTCCAGGAGTCCAAGCCGCCATTTCGTTTCCGTTATCGCGACGCTGGACAGAGTGGTGCGAGCTGCACAATCAAGCTGCGGAA ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ RG:Z:1 record #2: READ2 0 chr1 3000 255 2000S100M * 0 0 TAGCTGGCGTGCACGATTGGCGTGTACATGCTGCCTTTGAGGCACAGTTTCGTAGGGTTTCGTAGCAATGGCTTTGTCTGAAGAGAAGGGGTCTGTCGACAGACACTACGTCCCCAAAGTACCAGCGGGTGATCTCCGCAGACCTCGGAGCCGAGTGCGCTATTCTGGTGACTAGGGGATTAGGTCGGAGCAAGCGGCGTCCGTTAGAAAGCGTCGCTACTAGCCCGCGAGAGGCGACGTCTCACTCCCCGTAACAGCAGGACTGGTCTGGGTACGGCTGGCGCAGGCATGAATGGGATACCCGTGTTCTGCCTTCTGTGTCTACATCCGGTTATGGGAGCTAGCGAAAGTCACGCGAACCAGTAAGGTTAGAGTAGAAACGGAGTACTACTTAGCTATTGAAAAAAGGTGCTGCATCTGAGCCACGCCTAATTGCTGAGCTCTAAGGCTGTGAGTGCGTGAGTAAATGTGATCGGTTAACCTGGCCGAATTGCCCACCTGAGTGCAAGAGTACAAAGCGAAGTATAGTGCAGGCCTCAGCCCCTCCCCGCCAGAATACTACAGGCCGAGGAGGATGAGCTCTTATGGGCGTGTCGTTGGACGATTTATACTGGTGAAGTTGTCTGAAGAACGGTCTTGTTACGACTCACGTCGGGTACCTCTTCCCAGCATCTCGACGCCCCCTTCAGCCTTCGGACCGGTAACCACCGGCCTTGATCTCTGCCCAATAGTAAATGTCGCGGAACTCGTCAGAAATGACGACTCTAGGTGGAGTGTCGCAGTCGAGGTCGGGAGTAGTTCACTACGAACCGTTCGCCTAGGGTGCGAGTGTTCTAGATTCCGCTTGCTCATCGGGCGGAGGGGTCCCTTCGCGGGTGAAAAGCAGTCTCGATTGGGCGATGTTAAGCAATCGGCTGCACCTTGCAGCATCGACTAGAATAAATTGACTGCTCGTATTATTTTGCTCATCGTTGTTCAGTTTTGCGCGCCCAATGTTATTTAAGCTCAAGTGTCTGAAAGACTTCAATATGACGGCTCGATACTGAAGGGACGTCGCGTGCAGCAACACATACTTTTCGTAACGACCAAGTTGCCTCCTCCCTTTAGCACGACCCGGAGTATGCCAGGCCGGCATACTGAGTACACATCCATCATGTGCGTATTCCGGGTTCCTTCGACTCCATAGAGGACTACTGTCAAACGCGAGTCTGAATGGGTCGTTGAATCTACTTACCGTAGGGTGACAGAATGCTGGGCTTTTCTGATTTAGTAAAAGTCAACGCGTGCAAAGTTGCGATCGGGACTCGGCTTGTTCGCAAGGTATTATACTGTAGGATTTCTTTGCACGGTGTGCGACGTTGTCCAATCTGATCTTTCACCGTGTAAGTTCCCTATAGCCTGCACACCGTCAAGACCCGGGTGTCCGCAGACGTTCGCACGTTATCTACGGGTCGATTGTTACACTACCTGTAATACATCTTCATCTGATAGATAGTTTAAGCAATAATCCATGACGCTGCCCGTTGCCAGTAGCCAGCGTTCCGTCCTGCTAGAGCGCCCAAGTCCCACACGGGTAGCGGTTTTCTGGTCCAGGAGGGAAAGTCCTAAATGCAACTGTACACAAGACGGATACCTCTAGCTCCTAAATTCCCGTTGCAGGATGCCAAAAGCTTGACCATCGGGTGAGTGTATCAATGTTGGCGGACATAGGAGGTAGCAGAGACGTCACCGTTTTCGCATGGCCTGTCAAGATCGACTAGAAACAGACTTTATATTATCGGTCAACTATCGCCGATGATGGTCGGAAAGCATTCCTGGGGACCGAGCCGGCGTCCAGGGCGTCAGGGCCAATCCTCCGCATTACCTATAGTTAGGTTACATAGCTCTTGTGGCGTGGGGGTCCTTCCCACCCATCAATCCACTGCCTTGACATGCGCACTGGGGTCTTAGCCCTTTTTATAAACTTTAAACGCATCAGCGCACAAGGTAGAAAGCTGGAACGTAGTTTGTACAAAAAGTCCAGGAGTCCAAGCCGCCATTTCGTTTCCGTTATCGCGACGCTGGACAGAGTGGTGCGAGCTGCACAATCAAGCTGCGGAA ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ RG:Z:1 Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceFailure(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceOK(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceOK(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoFragmentsLargeSoftClipWithMinimumDistanceOK STANDARD_ERROR INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceOK(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceOK(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceOK(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceOK(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceOK(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceOK(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceOK(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceOK(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceOK(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.15942561774315775059.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -MINIMUM_DISTANCE 990 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.15942561774315775059.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.15942561774315775059.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.15942561774315775059.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -MINIMUM_DISTANCE 990 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.15942561774315775059.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.15942561774315775059.tmp/output.sam Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceOK(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceOK(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceOK(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceOK(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.547 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.547 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceOK(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.547 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.547 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceOK(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.547 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.547 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceOK(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.547 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.547 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceOK(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar MINIMUM_DISTANCE=990 BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.15942561774315775059.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.15942561774315775059.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.15942561774315775059.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar MINIMUM_DISTANCE=990 BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.15942561774315775059.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.15942561774315775059.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.15942561774315775059.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceOK(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceOK(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:53 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:53 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceOK(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 100b aligned to chr1:1000-1099. WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 100b aligned to chr1:1000-1099. Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceOK(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 3 records INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 3 records Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceOK(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceOK(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceOK(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceOK(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoFragmentsLargeSoftClipWithMinimumDistanceOK(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSoftClippingFirstOfPairOnly STANDARD_ERROR INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.17560403497431705187.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.17560403497431705187.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.17560403497431705187.tmp/output.sam ********** MarkDuplicatesWithMateCigar -METRICS_FILE /tmp/MarkDuplicatesWithMateCigarTester.17560403497431705187.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -BLOCK_SIZE 250 -INPUT /tmp/MarkDuplicatesWithMateCigarTester.17560403497431705187.tmp/input.sam -OUTPUT /tmp/MarkDuplicatesWithMateCigarTester.17560403497431705187.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.618 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.618 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.618 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.618 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.618 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.618 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.619 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.619 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.17560403497431705187.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.17560403497431705187.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.17560403497431705187.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:53 GMT+14:00 2024] MarkDuplicatesWithMateCigar BLOCK_SIZE=250 INPUT=[/tmp/MarkDuplicatesWithMateCigarTester.17560403497431705187.tmp/input.sam] OUTPUT=/tmp/MarkDuplicatesWithMateCigarTester.17560403497431705187.tmp/output.sam METRICS_FILE=/tmp/MarkDuplicatesWithMateCigarTester.17560403497431705187.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MINIMUM_DISTANCE=-1 SKIP_PAIRS_WITH_NO_MATE_CIGAR=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:53 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:47:53 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr1:12-53. WARNING 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Encountered a record with no program record, program group chaining will not occur for this read: READ0 1/2 76b aligned to chr1:12-53. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 records with no mate cigar optional tag. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:53 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:47:53 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnly(picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1334837248 Runtime.totalMemory()=1334837248 Running Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:53 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testBulkFragmentsNoDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:47:53 SimpleMarkDuplicatesWithMateCigar Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.7607292788612327051.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.7607292788612327051.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.7607292788612327051.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.7607292788612327051.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.7607292788612327051.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.7607292788612327051.tmp/output.sam Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.906 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.906 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.907 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.907 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.907 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:53.907 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:53.907 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:53.907 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.7607292788612327051.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7607292788612327051.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7607292788612327051.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:53 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.7607292788612327051.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7607292788612327051.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7607292788612327051.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:55 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:55 MarkDuplicatesWithMateCigar Processed 10000 records INFO 2024-07-02 11:47:55 MarkDuplicatesWithMateCigar Processed 10000 records Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:55 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:47:55 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:55 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:47:55 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.03 minutes. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:56 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testBulkFragmentsNoDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:47:56 SimpleMarkDuplicatesWithMateCigar Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.6716156838122270427.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.6716156838122270427.tmp/input.bam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.6716156838122270427.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.6716156838122270427.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.6716156838122270427.tmp/input.bam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.6716156838122270427.tmp/output.sam Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:56.400 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:56.400 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:56.400 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:56.400 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:56.400 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:56.400 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:56.400 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:56.400 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:56 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.6716156838122270427.tmp/input.bam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6716156838122270427.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6716156838122270427.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:56 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.6716156838122270427.tmp/input.bam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6716156838122270427.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6716156838122270427.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:57 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:57 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:57 MarkDuplicatesWithMateCigar Processed 10000 records INFO 2024-07-02 11:47:57 MarkDuplicatesWithMateCigar Processed 10000 records Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:57 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:47:57 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:57 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:47:57 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.02 minutes. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:58 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testBulkFragmentsNoDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:47:58 SimpleMarkDuplicatesWithMateCigar Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.5036699275247560517.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.5036699275247560517.tmp/input.cram -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.5036699275247560517.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester13609722404645472691/input.fasta ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.5036699275247560517.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.5036699275247560517.tmp/input.cram -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.5036699275247560517.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester13609722404645472691/input.fasta Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:58.195 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:58.195 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:58.195 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:58.195 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:58.195 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:58.195 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:58.195 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:58.195 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:58 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.5036699275247560517.tmp/input.cram] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5036699275247560517.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5036699275247560517.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 REFERENCE_SEQUENCE=/tmp/SamFileTester13609722404645472691/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:58 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.5036699275247560517.tmp/input.cram] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5036699275247560517.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5036699275247560517.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 REFERENCE_SEQUENCE=/tmp/SamFileTester13609722404645472691/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:59 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:47:59 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:59 MarkDuplicatesWithMateCigar Processed 10000 records INFO 2024-07-02 11:47:59 MarkDuplicatesWithMateCigar Processed 10000 records Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:59 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:47:59 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:59 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:47:59 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:47:59 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testBulkFragmentsWithDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:47:59 SimpleMarkDuplicatesWithMateCigar Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.8982630655724075373.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.8982630655724075373.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.8982630655724075373.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.8982630655724075373.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.8982630655724075373.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.8982630655724075373.tmp/output.sam Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:59.400 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:59.400 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:59.400 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:59.400 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:59.400 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:47:59.400 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:47:59.400 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:47:59.400 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:59 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.8982630655724075373.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8982630655724075373.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8982630655724075373.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:47:59 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.8982630655724075373.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8982630655724075373.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8982630655724075373.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:47:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:47:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:00 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:00 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:00 MarkDuplicatesWithMateCigar Processed 21000 records INFO 2024-07-02 11:48:00 MarkDuplicatesWithMateCigar Processed 21000 records Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:00 MarkDuplicatesWithMateCigar Marking 20000 records as duplicates. INFO 2024-07-02 11:48:00 MarkDuplicatesWithMateCigar Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:00 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:48:00 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.02 minutes. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:00 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testBulkFragmentsWithDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:48:00 SimpleMarkDuplicatesWithMateCigar Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.2744078148558440337.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2744078148558440337.tmp/input.bam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2744078148558440337.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.2744078148558440337.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2744078148558440337.tmp/input.bam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2744078148558440337.tmp/output.sam Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:00.971 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:00.971 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:00.971 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:00.971 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:00.971 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:00.971 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:00.971 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:00.971 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:00 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.2744078148558440337.tmp/input.bam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2744078148558440337.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2744078148558440337.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:00 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.2744078148558440337.tmp/input.bam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2744078148558440337.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2744078148558440337.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:01 MarkDuplicatesWithMateCigar Processed 21000 records INFO 2024-07-02 11:48:01 MarkDuplicatesWithMateCigar Processed 21000 records Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:01 MarkDuplicatesWithMateCigar Marking 20000 records as duplicates. INFO 2024-07-02 11:48:01 MarkDuplicatesWithMateCigar Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:01 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:48:01 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:03 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testBulkFragmentsWithDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:48:03 SimpleMarkDuplicatesWithMateCigar Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.15744808690163769629.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.15744808690163769629.tmp/input.cram -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.15744808690163769629.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester2725582913423342951/input.fasta ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.15744808690163769629.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.15744808690163769629.tmp/input.cram -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.15744808690163769629.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester2725582913423342951/input.fasta Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:03.004 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:03.004 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:03.004 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:03.004 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:03.004 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:03.004 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:03.004 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:03.004 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:03 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.15744808690163769629.tmp/input.cram] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.15744808690163769629.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.15744808690163769629.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 REFERENCE_SEQUENCE=/tmp/SamFileTester2725582913423342951/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:03 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.15744808690163769629.tmp/input.cram] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.15744808690163769629.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.15744808690163769629.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 REFERENCE_SEQUENCE=/tmp/SamFileTester2725582913423342951/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:04 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:04 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:04 MarkDuplicatesWithMateCigar Processed 21000 records INFO 2024-07-02 11:48:04 MarkDuplicatesWithMateCigar Processed 21000 records Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:04 MarkDuplicatesWithMateCigar Marking 20000 records as duplicates. INFO 2024-07-02 11:48:04 MarkDuplicatesWithMateCigar Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:04 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:48:04 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.02 minutes. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:04 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testBulkPairsNoDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:48:04 SimpleMarkDuplicatesWithMateCigar Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.11196112045251643014.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11196112045251643014.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11196112045251643014.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.11196112045251643014.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11196112045251643014.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11196112045251643014.tmp/output.sam Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:04.665 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:04.665 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:04.665 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:04.665 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:04.665 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:04.665 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:04.665 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:04.665 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:04 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.11196112045251643014.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11196112045251643014.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11196112045251643014.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:04 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.11196112045251643014.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11196112045251643014.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11196112045251643014.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:05 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:48:05 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:05 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:05 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:05 MarkDuplicatesWithMateCigar Processed 20200 records INFO 2024-07-02 11:48:05 MarkDuplicatesWithMateCigar Processed 20200 records Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:05 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:48:05 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:05 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:48:05 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.02 minutes. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:06 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testBulkPairsNoDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:48:06 SimpleMarkDuplicatesWithMateCigar Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.3563131736584977324.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.3563131736584977324.tmp/input.bam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.3563131736584977324.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.3563131736584977324.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.3563131736584977324.tmp/input.bam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.3563131736584977324.tmp/output.sam Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:06.591 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:06.591 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:06.591 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:06.591 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:06.591 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:06.591 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:06.591 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:06.591 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:06 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.3563131736584977324.tmp/input.bam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3563131736584977324.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3563131736584977324.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:06 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.3563131736584977324.tmp/input.bam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3563131736584977324.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3563131736584977324.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:48:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:07 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:07 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:07 MarkDuplicatesWithMateCigar Processed 20200 records INFO 2024-07-02 11:48:07 MarkDuplicatesWithMateCigar Processed 20200 records Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:07 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:48:07 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:07 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:48:07 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.02 minutes. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:08 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testBulkPairsNoDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:48:08 SimpleMarkDuplicatesWithMateCigar Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.688006382896079453.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.688006382896079453.tmp/input.cram -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.688006382896079453.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester6804512200819202070/input.fasta ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.688006382896079453.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.688006382896079453.tmp/input.cram -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.688006382896079453.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester6804512200819202070/input.fasta Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:08.878 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:08.878 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:08.878 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:08.878 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:08.878 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:08.878 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:08.878 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:08.878 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:08 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.688006382896079453.tmp/input.cram] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.688006382896079453.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.688006382896079453.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 REFERENCE_SEQUENCE=/tmp/SamFileTester6804512200819202070/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:08 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.688006382896079453.tmp/input.cram] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.688006382896079453.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.688006382896079453.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 REFERENCE_SEQUENCE=/tmp/SamFileTester6804512200819202070/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:09 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:48:09 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:10 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:10 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:10 MarkDuplicatesWithMateCigar Processed 20200 records INFO 2024-07-02 11:48:10 MarkDuplicatesWithMateCigar Processed 20200 records Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:10 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:48:10 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:10 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:48:10 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.03 minutes. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:12 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testBulkPairsWithDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:48:12 SimpleMarkDuplicatesWithMateCigar Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.2078861198428854310.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2078861198428854310.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2078861198428854310.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.2078861198428854310.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2078861198428854310.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2078861198428854310.tmp/output.sam Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:12.111 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:12.111 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:12.111 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:12.111 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:12.112 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:12.112 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:12.112 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:12.112 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:12 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.2078861198428854310.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2078861198428854310.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2078861198428854310.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:12 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.2078861198428854310.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2078861198428854310.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2078861198428854310.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:48:13 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:15 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:15 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:15 MarkDuplicatesWithMateCigar Processed 6820 records INFO 2024-07-02 11:48:15 MarkDuplicatesWithMateCigar Processed 6820 records Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:15 MarkDuplicatesWithMateCigar Marking 6200 records as duplicates. INFO 2024-07-02 11:48:15 MarkDuplicatesWithMateCigar Marking 6200 records as duplicates. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:15 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:48:15 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.06 minutes. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:17 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testBulkPairsWithDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:48:17 SimpleMarkDuplicatesWithMateCigar Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.2990890923184514308.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2990890923184514308.tmp/input.bam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2990890923184514308.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.2990890923184514308.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2990890923184514308.tmp/input.bam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2990890923184514308.tmp/output.sam Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:17.461 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:17.461 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:17.461 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:17.461 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:17.461 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:17.461 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:17.461 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:17.461 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:17 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.2990890923184514308.tmp/input.bam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2990890923184514308.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2990890923184514308.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:17 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.2990890923184514308.tmp/input.bam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2990890923184514308.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2990890923184514308.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:18 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:48:18 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:19 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:19 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:19 MarkDuplicatesWithMateCigar Processed 6820 records INFO 2024-07-02 11:48:19 MarkDuplicatesWithMateCigar Processed 6820 records Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:19 MarkDuplicatesWithMateCigar Marking 6200 records as duplicates. INFO 2024-07-02 11:48:19 MarkDuplicatesWithMateCigar Marking 6200 records as duplicates. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:19 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:48:19 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.03 minutes. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:20 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testBulkPairsWithDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:48:20 SimpleMarkDuplicatesWithMateCigar Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.4851624726319606106.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.4851624726319606106.tmp/input.cram -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.4851624726319606106.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester1251171001338692022/input.fasta ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.4851624726319606106.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.4851624726319606106.tmp/input.cram -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.4851624726319606106.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester1251171001338692022/input.fasta Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:20.666 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:20.666 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:20.666 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:20.666 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:20.666 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:20.666 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:20.666 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:20.666 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:20 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.4851624726319606106.tmp/input.cram] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4851624726319606106.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4851624726319606106.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 REFERENCE_SEQUENCE=/tmp/SamFileTester1251171001338692022/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:20 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.4851624726319606106.tmp/input.cram] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4851624726319606106.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4851624726319606106.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 REFERENCE_SEQUENCE=/tmp/SamFileTester1251171001338692022/input.fasta MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:21 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:48:21 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:22 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:22 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:22 MarkDuplicatesWithMateCigar Processed 6820 records INFO 2024-07-02 11:48:22 MarkDuplicatesWithMateCigar Processed 6820 records Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:22 MarkDuplicatesWithMateCigar Marking 6200 records as duplicates. INFO 2024-07-02 11:48:22 MarkDuplicatesWithMateCigar Marking 6200 records as duplicates. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:22 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:48:22 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.03 minutes. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:23 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testDifferentChromosomesInOppositeOrder STANDARD_ERROR INFO 2024-07-02 11:48:23 SimpleMarkDuplicatesWithMateCigar Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.16843409830819722991.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.16843409830819722991.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.16843409830819722991.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.16843409830819722991.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.16843409830819722991.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.16843409830819722991.tmp/output.sam Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:23.102 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:23.102 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:23.102 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:23.102 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:23.103 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:23.103 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:23.103 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:23.103 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:23 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.16843409830819722991.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.16843409830819722991.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.16843409830819722991.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:23 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.16843409830819722991.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.16843409830819722991.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.16843409830819722991.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:23 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:23 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:23 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:48:23 SimpleMarkDuplicatesWithMateCigar Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.16050241230710935991.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.16050241230710935991.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.16050241230710935991.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.16050241230710935991.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.16050241230710935991.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.16050241230710935991.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:23.315 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:23.315 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:23.315 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:23.315 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:23.315 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:23.315 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:23.315 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:23.315 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:23 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.16050241230710935991.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.16050241230710935991.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.16050241230710935991.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:23 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.16050241230710935991.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.16050241230710935991.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.16050241230710935991.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Processed 11 records INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Processed 11 records Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:23 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:23 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:23 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:48:23 SimpleMarkDuplicatesWithMateCigar Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.8938720038991380899.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.8938720038991380899.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.8938720038991380899.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.8938720038991380899.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.8938720038991380899.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.8938720038991380899.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:23.563 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:23.563 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:23.563 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:23.563 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:23.563 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:23.563 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:23.563 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:23.563 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:23 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.8938720038991380899.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8938720038991380899.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8938720038991380899.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:23 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.8938720038991380899.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8938720038991380899.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8938720038991380899.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Processed 11 records INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Processed 11 records Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:23 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:23 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:23 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:48:23 SimpleMarkDuplicatesWithMateCigar Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.4175981390204078908.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.4175981390204078908.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.4175981390204078908.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.4175981390204078908.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.4175981390204078908.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.4175981390204078908.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:23.768 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:23.768 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:23.768 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:23.768 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:23.777 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:23.777 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:23.778 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:23.778 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:23 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.4175981390204078908.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4175981390204078908.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4175981390204078908.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:23 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.4175981390204078908.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4175981390204078908.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4175981390204078908.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Processed 11 records INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Processed 11 records Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:23 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:23 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:23 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:48:23 SimpleMarkDuplicatesWithMateCigar Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.14223645146091390566.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.14223645146091390566.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.14223645146091390566.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.14223645146091390566.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.14223645146091390566.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.14223645146091390566.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:23.905 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:23.905 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:23.922 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:23.922 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:23.923 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:23.923 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:23.923 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:23.923 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:23 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.14223645146091390566.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.14223645146091390566.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.14223645146091390566.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:23 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.14223645146091390566.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.14223645146091390566.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.14223645146091390566.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Processed 11 records INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Processed 11 records Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2024-07-02 11:48:23 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:23 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:23 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:24 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:48:24 SimpleMarkDuplicatesWithMateCigar Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.12062125220623993319.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.12062125220623993319.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.12062125220623993319.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.12062125220623993319.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.12062125220623993319.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.12062125220623993319.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:24.150 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:24.150 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:24.165 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:24.165 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:24.166 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:24.166 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:24.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:24.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:24 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.12062125220623993319.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.12062125220623993319.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.12062125220623993319.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:24 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.12062125220623993319.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.12062125220623993319.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.12062125220623993319.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:24 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2024-07-02 11:48:24 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:24 MarkDuplicatesWithMateCigar Processed 11 records INFO 2024-07-02 11:48:24 MarkDuplicatesWithMateCigar Processed 11 records Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:24 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2024-07-02 11:48:24 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:24 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:24 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:24 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:48:24 SimpleMarkDuplicatesWithMateCigar Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.4431315740379472710.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.4431315740379472710.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.4431315740379472710.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.4431315740379472710.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.4431315740379472710.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.4431315740379472710.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:24.361 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:24.361 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:24.361 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:24.361 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:24.361 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:24.361 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:24.362 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:24.362 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:24 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.4431315740379472710.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4431315740379472710.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4431315740379472710.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:24 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.4431315740379472710.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4431315740379472710.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4431315740379472710.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:24 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2024-07-02 11:48:24 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:24 MarkDuplicatesWithMateCigar Processed 11 records INFO 2024-07-02 11:48:24 MarkDuplicatesWithMateCigar Processed 11 records Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:24 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2024-07-02 11:48:24 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:24 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:24 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:24 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testMappedFragmentAndMappedPairFirstOfPairNonPrimary STANDARD_ERROR INFO 2024-07-02 11:48:24 SimpleMarkDuplicatesWithMateCigar Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.11683849918302795360.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11683849918302795360.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11683849918302795360.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.11683849918302795360.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11683849918302795360.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11683849918302795360.tmp/output.sam Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:24.514 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:24.514 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:24.514 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:24.514 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:24.514 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:24.514 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:24.514 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:24.514 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:24 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.11683849918302795360.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11683849918302795360.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11683849918302795360.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:24 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.11683849918302795360.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11683849918302795360.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11683849918302795360.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:24 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:24 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:24 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:48:24 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:24 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:48:24 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:24 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:24 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:24 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testMappedFragmentAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:48:24 SimpleMarkDuplicatesWithMateCigar Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.10407156104619715048.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.10407156104619715048.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.10407156104619715048.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.10407156104619715048.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.10407156104619715048.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.10407156104619715048.tmp/output.sam Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:24.804 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:24.804 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:24.805 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:24.805 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:24.818 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:24.818 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:24.818 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:24.818 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:24 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.10407156104619715048.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.10407156104619715048.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.10407156104619715048.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:24 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.10407156104619715048.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.10407156104619715048.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.10407156104619715048.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:24 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:24 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:24 MarkDuplicatesWithMateCigar Processed 3 records INFO 2024-07-02 11:48:24 MarkDuplicatesWithMateCigar Processed 3 records Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:24 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2024-07-02 11:48:24 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:24 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:24 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:25 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testMappedFragmentAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:48:25 SimpleMarkDuplicatesWithMateCigar Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.15768952529282854996.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.15768952529282854996.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.15768952529282854996.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.15768952529282854996.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.15768952529282854996.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.15768952529282854996.tmp/output.sam Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:25.135 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:25.135 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:25.136 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:25.136 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:25.136 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:25.136 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:25.136 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:25.136 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:25 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.15768952529282854996.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.15768952529282854996.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.15768952529282854996.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:25 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.15768952529282854996.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.15768952529282854996.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.15768952529282854996.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:25 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:25 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:25 MarkDuplicatesWithMateCigar Processed 3 records INFO 2024-07-02 11:48:25 MarkDuplicatesWithMateCigar Processed 3 records Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:25 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2024-07-02 11:48:25 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:25 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:25 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:25 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testMappedPairAndMappedFragmentAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:48:25 SimpleMarkDuplicatesWithMateCigar Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.9710366052756019131.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.9710366052756019131.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.9710366052756019131.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.9710366052756019131.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.9710366052756019131.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.9710366052756019131.tmp/output.sam Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:25.460 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:25.460 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:25.460 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:25.460 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:25.474 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:25.474 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:25.474 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:25.474 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:25 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.9710366052756019131.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.9710366052756019131.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.9710366052756019131.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:25 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.9710366052756019131.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.9710366052756019131.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.9710366052756019131.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:25 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. WARNING 2024-07-02 11:48:25 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:25 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:25 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:25 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:48:25 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:25 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:25 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:25 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:25 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:25 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testMappedPairAndMappedFragmentAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:48:25 SimpleMarkDuplicatesWithMateCigar Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.1415173353311033727.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1415173353311033727.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1415173353311033727.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.1415173353311033727.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1415173353311033727.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1415173353311033727.tmp/output.sam Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:25.696 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:25.696 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:25.697 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:25.697 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:25.697 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:25.697 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:25.697 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:25.697 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:25 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1415173353311033727.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1415173353311033727.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1415173353311033727.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:25 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1415173353311033727.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1415173353311033727.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1415173353311033727.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:25 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. WARNING 2024-07-02 11:48:25 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:25 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:25 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:25 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:48:25 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:25 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:25 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:25 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:25 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:25 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:48:25 SimpleMarkDuplicatesWithMateCigar Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.2207996102982214915.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2207996102982214915.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2207996102982214915.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.2207996102982214915.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2207996102982214915.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2207996102982214915.tmp/output.sam Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:25.980 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:25.980 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:25.980 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:25.980 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:25.980 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:25.980 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:25.980 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:25.980 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:25 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.2207996102982214915.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2207996102982214915.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2207996102982214915.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:25 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.2207996102982214915.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2207996102982214915.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2207996102982214915.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. WARNING 2024-07-02 11:48:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:26 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:26 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:26 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testMappedPairAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:48:26 SimpleMarkDuplicatesWithMateCigar Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.15942167458685788456.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.15942167458685788456.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.15942167458685788456.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.15942167458685788456.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.15942167458685788456.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.15942167458685788456.tmp/output.sam Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:26.142 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:26.142 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:26.142 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:26.142 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:26.143 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:26.143 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:26.143 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:26.143 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:26 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.15942167458685788456.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.15942167458685788456.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.15942167458685788456.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:26 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.15942167458685788456.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.15942167458685788456.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.15942167458685788456.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. WARNING 2024-07-02 11:48:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:26 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:26 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:26 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testMappedPairAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:48:26 SimpleMarkDuplicatesWithMateCigar Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.1110128323876244995.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1110128323876244995.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1110128323876244995.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.1110128323876244995.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1110128323876244995.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1110128323876244995.tmp/output.sam Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:26.310 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:26.310 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:26.310 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:26.310 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:26.311 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:26.311 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:26.311 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:26.311 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:26 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1110128323876244995.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1110128323876244995.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1110128323876244995.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:26 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1110128323876244995.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1110128323876244995.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1110128323876244995.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. WARNING 2024-07-02 11:48:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:26 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:26 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:26 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testMappedPairWithFirstEndSamePositionAndOther STANDARD_ERROR INFO 2024-07-02 11:48:26 SimpleMarkDuplicatesWithMateCigar Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.8902475347148580461.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.8902475347148580461.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.8902475347148580461.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.8902475347148580461.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.8902475347148580461.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.8902475347148580461.tmp/output.sam Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:26.448 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:26.448 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:26.448 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:26.448 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:26.448 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:26.448 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:26.448 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:26.448 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:26 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.8902475347148580461.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8902475347148580461.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8902475347148580461.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:26 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.8902475347148580461.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8902475347148580461.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8902475347148580461.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. WARNING 2024-07-02 11:48:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:26 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:26 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:26 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testMappedPairWithSamePosition STANDARD_ERROR INFO 2024-07-02 11:48:26 SimpleMarkDuplicatesWithMateCigar Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.16650152154038742820.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.16650152154038742820.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.16650152154038742820.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.16650152154038742820.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.16650152154038742820.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.16650152154038742820.tmp/output.sam Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:26.611 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:26.611 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:26.611 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:26.611 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:26.612 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:26.612 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:26.612 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:26.612 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:26 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.16650152154038742820.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.16650152154038742820.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.16650152154038742820.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:26 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.16650152154038742820.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.16650152154038742820.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.16650152154038742820.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:48:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:26 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:26 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:26 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testMappedPairWithSamePositionSameCigar STANDARD_ERROR INFO 2024-07-02 11:48:26 SimpleMarkDuplicatesWithMateCigar Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.6503578305656440383.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.6503578305656440383.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.6503578305656440383.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.6503578305656440383.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.6503578305656440383.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.6503578305656440383.tmp/output.sam Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:26.776 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:26.776 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:26.776 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:26.776 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:26.789 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:26.789 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:26.790 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:26.790 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:26 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.6503578305656440383.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6503578305656440383.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6503578305656440383.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:26 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.6503578305656440383.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6503578305656440383.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6503578305656440383.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:48:26 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:48:26 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:26 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:26 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:27 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:48:27 SimpleMarkDuplicatesWithMateCigar Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.16327517495761664761.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.16327517495761664761.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.16327517495761664761.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.16327517495761664761.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.16327517495761664761.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.16327517495761664761.tmp/output.sam Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:27.027 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:27.027 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:27.027 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:27.027 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:27.028 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:27.028 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:27.028 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:27.028 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:27 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.16327517495761664761.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.16327517495761664761.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.16327517495761664761.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:27 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.16327517495761664761.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.16327517495761664761.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.16327517495761664761.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:27 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:27 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:27 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:48:27 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:27 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:48:27 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:27 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:27 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:27 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:48:27 SimpleMarkDuplicatesWithMateCigar Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.6922798014703941224.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.6922798014703941224.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.6922798014703941224.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.6922798014703941224.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.6922798014703941224.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.6922798014703941224.tmp/output.sam Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:27.269 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:27.269 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:27.270 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:27.270 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:27.270 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:27.270 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:27.270 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:27.270 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:27 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.6922798014703941224.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6922798014703941224.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6922798014703941224.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:27 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.6922798014703941224.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6922798014703941224.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6922798014703941224.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:27 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:27 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:27 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:48:27 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:27 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:48:27 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:27 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:27 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:27 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testOpticalDuplicateBehaviorNullRegex STANDARD_ERROR INFO 2024-07-02 11:48:27 SimpleMarkDuplicatesWithMateCigar Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.9352726466198496619.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -READ_NAME_REGEX null -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.9352726466198496619.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.9352726466198496619.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.9352726466198496619.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -READ_NAME_REGEX null -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.9352726466198496619.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.9352726466198496619.tmp/output.sam Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:27.497 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:27.497 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:27.498 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:27.498 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:27.498 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:27.498 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:27.498 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:27.498 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:27 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.9352726466198496619.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.9352726466198496619.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.9352726466198496619.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH READ_NAME_REGEX=null MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:27 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.9352726466198496619.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.9352726466198496619.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.9352726466198496619.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH READ_NAME_REGEX=null MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:27 MarkDuplicatesWithMateCigar Skipped optical duplicate cluster discovery; library size estimation may be inaccurate! WARNING 2024-07-02 11:48:27 MarkDuplicatesWithMateCigar Skipped optical duplicate cluster discovery; library size estimation may be inaccurate! Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:27 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:48:27 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:27 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:27 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:27 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:27 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:27 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testOpticalDuplicateClusterOneEndSamePositionOneCluster STANDARD_ERROR INFO 2024-07-02 11:48:27 SimpleMarkDuplicatesWithMateCigar Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.1101073515108496816.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1101073515108496816.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1101073515108496816.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.1101073515108496816.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1101073515108496816.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1101073515108496816.tmp/output.sam Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:27.737 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:27.737 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:27.737 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:27.737 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:27.738 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:27.738 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:27.738 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:27.738 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:27 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1101073515108496816.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1101073515108496816.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1101073515108496816.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:27 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1101073515108496816.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1101073515108496816.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1101073515108496816.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:27 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:48:27 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:27 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:48:27 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:27 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:27 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:27 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:27 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:28 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance STANDARD_ERROR INFO 2024-07-02 11:48:28 SimpleMarkDuplicatesWithMateCigar Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.13581009817857725869.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.13581009817857725869.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.13581009817857725869.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.13581009817857725869.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.13581009817857725869.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.13581009817857725869.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:28.016 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:28.016 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:28.016 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:28.016 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:28.025 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:28.025 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:28.026 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:28.026 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:28 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.13581009817857725869.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.13581009817857725869.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.13581009817857725869.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:28 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.13581009817857725869.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.13581009817857725869.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.13581009817857725869.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:28 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:28 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:28 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance STANDARD_ERROR INFO 2024-07-02 11:48:28 SimpleMarkDuplicatesWithMateCigar Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.1852968437991323862.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1852968437991323862.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1852968437991323862.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.1852968437991323862.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1852968437991323862.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1852968437991323862.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:28.264 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:28.264 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:28.264 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:28.264 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:28.281 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:28.281 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:28.281 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:28.281 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:28 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1852968437991323862.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1852968437991323862.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1852968437991323862.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:28 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1852968437991323862.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1852968437991323862.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1852968437991323862.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:28 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:28 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:28 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate STANDARD_ERROR INFO 2024-07-02 11:48:28 SimpleMarkDuplicatesWithMateCigar Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.11276436434982853305.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11276436434982853305.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11276436434982853305.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.11276436434982853305.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11276436434982853305.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11276436434982853305.tmp/output.sam Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:28.474 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:28.474 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:28.474 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:28.474 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:28.475 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:28.475 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:28.475 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:28.475 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:28 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.11276436434982853305.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11276436434982853305.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11276436434982853305.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:28 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.11276436434982853305.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11276436434982853305.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11276436434982853305.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:28 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:28 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:28 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testOpticalDuplicateFinding STANDARD_ERROR INFO 2024-07-02 11:48:28 SimpleMarkDuplicatesWithMateCigar Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.2682890460546173117.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2682890460546173117.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2682890460546173117.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.2682890460546173117.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2682890460546173117.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2682890460546173117.tmp/output.sam Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:28.684 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:28.684 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:28.684 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:28.684 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:28.685 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:28.685 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:28.697 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:28.697 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:28 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.2682890460546173117.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2682890460546173117.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2682890460546173117.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:28 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.2682890460546173117.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2682890460546173117.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2682890460546173117.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Processed 6 records INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Processed 6 records Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:28 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:28 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:28 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testPathologicalOrderingAtTheSamePosition STANDARD_ERROR INFO 2024-07-02 11:48:28 SimpleMarkDuplicatesWithMateCigar Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.2173112139971663751.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2173112139971663751.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2173112139971663751.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.2173112139971663751.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2173112139971663751.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2173112139971663751.tmp/output.sam Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:28.860 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:28.860 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:28.869 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:28.869 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:28.870 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:28.870 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:28.870 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:28.870 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:28 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.2173112139971663751.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2173112139971663751.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2173112139971663751.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:28 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.2173112139971663751.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2173112139971663751.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2173112139971663751.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:28 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:28 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:28 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testSecondEndIsBeforeFirstInCoordinate STANDARD_ERROR INFO 2024-07-02 11:48:29 SimpleMarkDuplicatesWithMateCigar Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.1201684713536181500.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1201684713536181500.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1201684713536181500.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.1201684713536181500.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1201684713536181500.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1201684713536181500.tmp/output.sam Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.093 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:29.093 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.093 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:29.093 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.094 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:29.094 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.094 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:29.094 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:29 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1201684713536181500.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1201684713536181500.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1201684713536181500.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:29 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1201684713536181500.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1201684713536181500.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1201684713536181500.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:29 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:48:29 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:29 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:29 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testSingleMappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testSingleMappedFragment STANDARD_ERROR INFO 2024-07-02 11:48:29 SimpleMarkDuplicatesWithMateCigar Test: Test method testSingleMappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.6215883098532673715.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.6215883098532673715.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.6215883098532673715.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.6215883098532673715.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.6215883098532673715.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.6215883098532673715.tmp/output.sam Test: Test method testSingleMappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.179 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:29.179 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.179 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:29.179 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.179 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:29.179 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.179 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:29.179 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:29 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.6215883098532673715.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6215883098532673715.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6215883098532673715.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:29 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.6215883098532673715.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6215883098532673715.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6215883098532673715.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Processed 1 records INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Processed 1 records Test: Test method testSingleMappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:29 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:29 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testSingleMappedFragmentAndSingleMappedPair STANDARD_ERROR INFO 2024-07-02 11:48:29 SimpleMarkDuplicatesWithMateCigar Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.11156043936130708846.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11156043936130708846.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11156043936130708846.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.11156043936130708846.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11156043936130708846.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11156043936130708846.tmp/output.sam Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.293 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:29.293 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.293 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:29.293 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.293 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:29.293 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.293 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:29.293 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:29 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.11156043936130708846.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11156043936130708846.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11156043936130708846.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:29 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.11156043936130708846.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11156043936130708846.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11156043936130708846.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:29 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. WARNING 2024-07-02 11:48:29 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Processed 3 records INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Processed 3 records Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:29 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:29 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testSingleMappedFragmentAndTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:48:29 SimpleMarkDuplicatesWithMateCigar Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.13877502607709620265.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.13877502607709620265.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.13877502607709620265.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.13877502607709620265.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.13877502607709620265.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.13877502607709620265.tmp/output.sam Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.458 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:29.458 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.458 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:29.458 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.458 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:29.458 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.458 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:29.458 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:29 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.13877502607709620265.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.13877502607709620265.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.13877502607709620265.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:29 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.13877502607709620265.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.13877502607709620265.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.13877502607709620265.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:29 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. WARNING 2024-07-02 11:48:29 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Marking 3 records as duplicates. INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Marking 3 records as duplicates. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:29 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:29 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testSingleMappedPair STANDARD_ERROR INFO 2024-07-02 11:48:29 SimpleMarkDuplicatesWithMateCigar Test: Test method testSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.2906683522312990930.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2906683522312990930.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2906683522312990930.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.2906683522312990930.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2906683522312990930.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2906683522312990930.tmp/output.sam Test: Test method testSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.556 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:29.556 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.556 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:29.556 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.565 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:29.565 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.565 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:29.565 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:29 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.2906683522312990930.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2906683522312990930.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2906683522312990930.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:29 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.2906683522312990930.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2906683522312990930.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2906683522312990930.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:29 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:48:29 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:29 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:29 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testSingleMappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testSingleUnmappedFragment STANDARD_ERROR INFO 2024-07-02 11:48:29 SimpleMarkDuplicatesWithMateCigar Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.12356932041271428234.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.12356932041271428234.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.12356932041271428234.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.12356932041271428234.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.12356932041271428234.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.12356932041271428234.tmp/output.sam Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.670 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:29.670 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.670 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:29.670 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.670 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:29.670 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.670 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:29.670 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:29 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.12356932041271428234.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.12356932041271428234.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.12356932041271428234.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:29 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.12356932041271428234.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.12356932041271428234.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.12356932041271428234.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Processed 1 records INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Processed 1 records Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:29 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:29 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testSingleUnmappedPair STANDARD_ERROR INFO 2024-07-02 11:48:29 SimpleMarkDuplicatesWithMateCigar Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.3925075468298269935.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.3925075468298269935.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.3925075468298269935.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.3925075468298269935.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.3925075468298269935.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.3925075468298269935.tmp/output.sam Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.771 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:29.771 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.771 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:29.771 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.771 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:29.771 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.771 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:29.771 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:29 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.3925075468298269935.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3925075468298269935.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3925075468298269935.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:29 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.3925075468298269935.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3925075468298269935.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3925075468298269935.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:29 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:29 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testStackOverFlowPairSetSwap STANDARD_ERROR INFO 2024-07-02 11:48:29 SimpleMarkDuplicatesWithMateCigar Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.17199354473612234715.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.17199354473612234715.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.17199354473612234715.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.17199354473612234715.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.17199354473612234715.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.17199354473612234715.tmp/output.sam Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.883 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:29.883 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.884 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:29.884 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.884 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:29.884 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.884 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:29.884 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:29 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.17199354473612234715.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.17199354473612234715.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.17199354473612234715.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:29 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.17199354473612234715.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.17199354473612234715.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.17199354473612234715.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:29 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:29 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:29 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:29 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:48:29 SimpleMarkDuplicatesWithMateCigar Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.10780422069488746704.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.10780422069488746704.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.10780422069488746704.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.10780422069488746704.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.10780422069488746704.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.10780422069488746704.tmp/output.sam Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.994 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:29.994 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.994 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:29.994 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.994 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:29.994 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:29.994 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:29.994 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:29 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.10780422069488746704.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.10780422069488746704.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.10780422069488746704.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:29 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.10780422069488746704.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.10780422069488746704.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.10780422069488746704.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:48:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Processed 18 records INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Processed 18 records Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Marking 12 records as duplicates. INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Marking 12 records as duplicates. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:30 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:30 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:48:30 SimpleMarkDuplicatesWithMateCigar Test: Test method testThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.787738253263171283.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.787738253263171283.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.787738253263171283.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.787738253263171283.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.787738253263171283.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.787738253263171283.tmp/output.sam Test: Test method testThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.106 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:30.106 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.106 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:30.106 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.106 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:30.106 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.107 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:30.107 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:30 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.787738253263171283.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.787738253263171283.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.787738253263171283.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:30 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.787738253263171283.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.787738253263171283.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.787738253263171283.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:48:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Processed 6 records INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Processed 6 records Test: Test method testThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:30 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:30 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testThreeMappedPairsWithMatchingSecondMate STANDARD_ERROR INFO 2024-07-02 11:48:30 SimpleMarkDuplicatesWithMateCigar Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.7718592824630929022.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.7718592824630929022.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.7718592824630929022.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.7718592824630929022.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.7718592824630929022.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.7718592824630929022.tmp/output.sam Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.233 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:30.233 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.233 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:30.233 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.233 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:30.233 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.233 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:30.233 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:30 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.7718592824630929022.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7718592824630929022.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7718592824630929022.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:30 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.7718592824630929022.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7718592824630929022.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.7718592824630929022.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:48:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Processed 6 records INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Processed 6 records Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:30 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:30 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:48:30 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.1615439545034396146.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1615439545034396146.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1615439545034396146.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.1615439545034396146.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1615439545034396146.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1615439545034396146.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.347 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:30.347 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.347 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:30.347 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.347 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:30.347 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.347 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:30.347 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:30 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1615439545034396146.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1615439545034396146.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1615439545034396146.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:30 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1615439545034396146.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1615439545034396146.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1615439545034396146.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:48:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Processed 12 records INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Processed 12 records Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:30 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:30 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoGroupsOnDifferentChromosomesOfTwoFragments STANDARD_ERROR INFO 2024-07-02 11:48:30 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.16428522172323366156.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.16428522172323366156.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.16428522172323366156.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.16428522172323366156.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.16428522172323366156.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.16428522172323366156.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.472 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:30.472 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.481 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:30.481 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.482 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:30.482 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.482 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:30.482 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:30 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.16428522172323366156.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.16428522172323366156.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.16428522172323366156.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:30 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.16428522172323366156.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.16428522172323366156.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.16428522172323366156.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:30 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:30 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:48:30 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.13596779130676903495.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.13596779130676903495.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.13596779130676903495.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.13596779130676903495.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.13596779130676903495.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.13596779130676903495.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.611 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:30.611 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.611 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:30.611 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.612 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:30.612 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.612 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:30.612 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:30 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.13596779130676903495.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.13596779130676903495.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.13596779130676903495.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:30 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.13596779130676903495.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.13596779130676903495.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.13596779130676903495.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:48:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Processed 8 records INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Processed 8 records Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:30 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:30 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoMappedFragments STANDARD_ERROR INFO 2024-07-02 11:48:30 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoMappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.4420680718804533451.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.4420680718804533451.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.4420680718804533451.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.4420680718804533451.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.4420680718804533451.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.4420680718804533451.tmp/output.sam Test: Test method testTwoMappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.768 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:30.768 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.769 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:30.769 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.770 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:30.770 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.770 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:30.770 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:30 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.4420680718804533451.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4420680718804533451.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4420680718804533451.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:30 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.4420680718804533451.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4420680718804533451.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.4420680718804533451.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testTwoMappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:30 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:30 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoMappedPairWithSamePosition STANDARD_ERROR INFO 2024-07-02 11:48:30 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.5330603422824981979.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.5330603422824981979.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.5330603422824981979.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.5330603422824981979.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.5330603422824981979.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.5330603422824981979.tmp/output.sam Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.869 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:30.869 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.869 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:30.869 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.870 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:30.870 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.870 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:30.870 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:30 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.5330603422824981979.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5330603422824981979.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5330603422824981979.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:30 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.5330603422824981979.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5330603422824981979.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.5330603422824981979.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:48:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:30 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:30 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoMappedPairWithSamePositionDifferentStrands STANDARD_ERROR INFO 2024-07-02 11:48:30 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.15361217645332127582.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.15361217645332127582.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.15361217645332127582.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.15361217645332127582.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.15361217645332127582.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.15361217645332127582.tmp/output.sam Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.965 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:30.965 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.965 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:30.965 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.966 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:30.966 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:30.966 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:30.966 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:30 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.15361217645332127582.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.15361217645332127582.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.15361217645332127582.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:30 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.15361217645332127582.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.15361217645332127582.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.15361217645332127582.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:48:30 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:30 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:30 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:30 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:31 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoMappedPairWithSamePositionDifferentStrands2 STANDARD_ERROR INFO 2024-07-02 11:48:31 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.11431569094743907113.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11431569094743907113.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11431569094743907113.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.11431569094743907113.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11431569094743907113.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11431569094743907113.tmp/output.sam Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:31.065 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:31.065 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:31.065 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:31.065 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:31.066 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:31.066 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:31.066 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:31.066 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:31 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.11431569094743907113.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11431569094743907113.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11431569094743907113.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:31 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.11431569094743907113.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11431569094743907113.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11431569094743907113.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:31 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:48:31 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:31 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:31 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:31 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:48:31 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.1973883003564304011.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1973883003564304011.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1973883003564304011.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.1973883003564304011.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1973883003564304011.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1973883003564304011.tmp/output.sam Test: Test method testTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:31.173 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:31.173 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:31.173 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:31.173 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:31.175 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:31.175 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:31.175 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:31.175 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:31 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1973883003564304011.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1973883003564304011.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1973883003564304011.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:31 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1973883003564304011.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1973883003564304011.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1973883003564304011.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:31 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:48:31 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:31 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:31 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:31 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoMappedPairsAndMappedSecondaryFragment STANDARD_ERROR INFO 2024-07-02 11:48:31 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.15244954625645873666.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.15244954625645873666.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.15244954625645873666.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.15244954625645873666.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.15244954625645873666.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.15244954625645873666.tmp/output.sam Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:31.267 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:31.267 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:31.267 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:31.267 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:31.268 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:31.268 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:31.268 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:31.268 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:31 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.15244954625645873666.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.15244954625645873666.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.15244954625645873666.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:31 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.15244954625645873666.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.15244954625645873666.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.15244954625645873666.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:31 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:48:31 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:31 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:31 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:31 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoMappedPairsAndTerminalUnmappedFragment STANDARD_ERROR INFO 2024-07-02 11:48:31 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.15813051108407820721.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.15813051108407820721.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.15813051108407820721.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.15813051108407820721.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.15813051108407820721.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.15813051108407820721.tmp/output.sam Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:31.466 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:31.466 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:31.466 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:31.466 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:31.467 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:31.467 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:31.467 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:31.467 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:31 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.15813051108407820721.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.15813051108407820721.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.15813051108407820721.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:31 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.15813051108407820721.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.15813051108407820721.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.15813051108407820721.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:31 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:48:31 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:31 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:31 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:31 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoMappedPairsAndTerminalUnmappedPair STANDARD_ERROR INFO 2024-07-02 11:48:31 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.9228532772632988915.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.9228532772632988915.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.9228532772632988915.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.9228532772632988915.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.9228532772632988915.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.9228532772632988915.tmp/output.sam Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:31.774 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:31.774 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:31.781 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:31.781 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:31.782 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:31.782 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:31.782 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:31.782 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:31 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.9228532772632988915.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.9228532772632988915.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.9228532772632988915.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:31 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.9228532772632988915.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.9228532772632988915.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.9228532772632988915.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:31 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:48:31 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Processed 6 records INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Processed 6 records Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:31 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:31 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:31 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:32 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoMappedPairsMatesSoftClipped STANDARD_ERROR INFO 2024-07-02 11:48:32 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.1061504622120108778.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1061504622120108778.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1061504622120108778.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.1061504622120108778.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1061504622120108778.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1061504622120108778.tmp/output.sam Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:32.092 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:32.092 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:32.098 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:32.098 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:32.100 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:32.100 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:32.100 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:32.100 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:32 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1061504622120108778.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1061504622120108778.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1061504622120108778.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:32 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1061504622120108778.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1061504622120108778.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1061504622120108778.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:32 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:48:32 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:32 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:32 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:32 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:48:32 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:32 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:48:32 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:32 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:32 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:32 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithOppositeOrientations STANDARD_ERROR INFO 2024-07-02 11:48:32 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.2307435716744337189.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2307435716744337189.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2307435716744337189.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.2307435716744337189.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2307435716744337189.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2307435716744337189.tmp/output.sam Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:32.351 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:32.351 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:32.352 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:32.352 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:32.352 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:32.352 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:32.352 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:32.352 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:32 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.2307435716744337189.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2307435716744337189.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2307435716744337189.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:32 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.2307435716744337189.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2307435716744337189.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2307435716744337189.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:32 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. WARNING 2024-07-02 11:48:32 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:32 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:32 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:32 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:48:32 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:32 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:32 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:32 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:32 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:32 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithOppositeOrientationsNumberTwo STANDARD_ERROR INFO 2024-07-02 11:48:32 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.6975401697634688626.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.6975401697634688626.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.6975401697634688626.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.6975401697634688626.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.6975401697634688626.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.6975401697634688626.tmp/output.sam Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:32.553 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:32.553 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:32.553 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:32.553 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:32.554 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:32.554 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:32.554 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:32.554 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:32 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.6975401697634688626.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6975401697634688626.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6975401697634688626.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:32 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.6975401697634688626.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6975401697634688626.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6975401697634688626.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:32 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:48:32 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:32 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:32 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:32 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:48:32 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:32 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:32 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:32 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:32 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:32 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSoftClipping STANDARD_ERROR INFO 2024-07-02 11:48:32 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.12495189733201744287.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.12495189733201744287.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.12495189733201744287.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.12495189733201744287.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.12495189733201744287.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.12495189733201744287.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:32.787 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:32.787 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:32.787 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:32.787 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:32.788 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:32.788 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:32.788 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:32.788 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:32 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.12495189733201744287.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.12495189733201744287.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.12495189733201744287.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:32 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.12495189733201744287.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.12495189733201744287.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.12495189733201744287.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:32 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:48:32 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:32 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:32 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:32 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:48:32 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:32 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:32 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:32 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:32 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:32 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSoftClippingBoth STANDARD_ERROR INFO 2024-07-02 11:48:32 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.1762851378077338005.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1762851378077338005.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1762851378077338005.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.1762851378077338005.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1762851378077338005.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1762851378077338005.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:33.000 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:33.000 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:33.000 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:33.000 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:33.013 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:33.013 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:33.014 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:33.014 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:33 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1762851378077338005.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1762851378077338005.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1762851378077338005.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:33 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1762851378077338005.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1762851378077338005.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1762851378077338005.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:48:33 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. WARNING 2024-07-02 11:48:33 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:33 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:33 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:33 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReads[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:48:33 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.3703692130065008082.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.3703692130065008082.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.3703692130065008082.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.3703692130065008082.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.3703692130065008082.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.3703692130065008082.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:33.255 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:33.255 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:33.256 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:33.256 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:33.256 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:33.256 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:33.256 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:33.256 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:33 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.3703692130065008082.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3703692130065008082.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3703692130065008082.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:33 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.3703692130065008082.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3703692130065008082.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.3703692130065008082.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:33 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:33 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:33 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReads[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:48:33 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.126149370830587537.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.126149370830587537.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.126149370830587537.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.126149370830587537.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.126149370830587537.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.126149370830587537.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:33.562 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:33.562 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:33.562 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:33.562 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:33.563 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:33.563 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:33.563 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:33.563 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:33 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.126149370830587537.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.126149370830587537.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.126149370830587537.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:33 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.126149370830587537.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.126149370830587537.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.126149370830587537.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:33 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:33 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:33 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReads[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:48:33 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.8192170483306769722.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.8192170483306769722.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.8192170483306769722.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.8192170483306769722.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.8192170483306769722.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.8192170483306769722.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:33.660 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:33.660 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:33.660 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:33.660 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:33.660 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:33.660 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:33.660 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:33.660 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:33 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.8192170483306769722.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8192170483306769722.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8192170483306769722.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:33 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.8192170483306769722.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8192170483306769722.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.8192170483306769722.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:33 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:33 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:33 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReads[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:48:33 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.6283907271398167975.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.6283907271398167975.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.6283907271398167975.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.6283907271398167975.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.6283907271398167975.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.6283907271398167975.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:33.791 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:33.791 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:33.791 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:33.791 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:33.792 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:33.792 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:33.792 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:33.792 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:33 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.6283907271398167975.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6283907271398167975.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6283907271398167975.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:33 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.6283907271398167975.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6283907271398167975.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.6283907271398167975.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:33 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:33 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:33 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReads[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:48:33 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.9547315234219192895.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.9547315234219192895.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.9547315234219192895.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.9547315234219192895.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.9547315234219192895.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.9547315234219192895.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:33.902 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:33.902 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:33.902 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:33.902 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:33.902 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:33.902 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:33.902 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:33.902 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:33 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.9547315234219192895.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.9547315234219192895.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.9547315234219192895.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:33 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.9547315234219192895.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.9547315234219192895.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.9547315234219192895.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:33 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:33 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:33 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReads[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:48:34 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.16292204030746304090.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.16292204030746304090.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.16292204030746304090.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.16292204030746304090.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.16292204030746304090.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.16292204030746304090.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.018 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:34.018 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.018 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:34.018 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.018 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:34.018 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.019 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:34.019 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:34 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.16292204030746304090.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.16292204030746304090.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.16292204030746304090.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:34 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.16292204030746304090.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.16292204030746304090.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.16292204030746304090.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:34 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:34 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:48:34 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.11316948611261382818.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11316948611261382818.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11316948611261382818.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.11316948611261382818.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11316948611261382818.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11316948611261382818.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.131 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:34.131 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.131 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:34.131 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.131 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:34.131 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.131 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:34.131 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:34 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.11316948611261382818.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11316948611261382818.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11316948611261382818.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:34 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.11316948611261382818.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11316948611261382818.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11316948611261382818.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:34 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:34 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:48:34 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.2495897835379344509.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2495897835379344509.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2495897835379344509.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.2495897835379344509.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2495897835379344509.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2495897835379344509.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.231 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:34.231 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.231 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:34.231 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.231 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:34.231 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.231 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:34.231 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:34 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.2495897835379344509.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2495897835379344509.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2495897835379344509.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:34 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.2495897835379344509.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2495897835379344509.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2495897835379344509.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:34 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:34 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:48:34 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.12555092217597740512.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.12555092217597740512.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.12555092217597740512.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.12555092217597740512.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.12555092217597740512.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.12555092217597740512.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.355 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:34.355 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.356 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:34.356 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.356 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:34.356 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.356 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:34.356 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:34 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.12555092217597740512.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.12555092217597740512.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.12555092217597740512.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:34 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.12555092217597740512.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.12555092217597740512.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.12555092217597740512.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:34 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:34 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:48:34 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.11053566469500517782.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11053566469500517782.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11053566469500517782.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.11053566469500517782.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11053566469500517782.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11053566469500517782.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.477 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:34.477 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.477 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:34.477 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.477 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:34.477 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.478 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:34.478 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:34 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.11053566469500517782.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11053566469500517782.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11053566469500517782.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:34 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.11053566469500517782.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11053566469500517782.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11053566469500517782.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:34 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:34 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:48:34 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.2187101220405928665.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2187101220405928665.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2187101220405928665.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.2187101220405928665.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2187101220405928665.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.2187101220405928665.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.683 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:34.683 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.683 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:34.683 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.684 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:34.684 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.684 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:34.684 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:34 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.2187101220405928665.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2187101220405928665.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2187101220405928665.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:34 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.2187101220405928665.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2187101220405928665.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.2187101220405928665.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:34 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:34 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:48:34 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.11121523289606240053.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11121523289606240053.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11121523289606240053.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.11121523289606240053.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11121523289606240053.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.11121523289606240053.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.803 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:34.803 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.804 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:34.804 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.804 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:34.804 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.804 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:34.804 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:34 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.11121523289606240053.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11121523289606240053.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11121523289606240053.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:34 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.11121523289606240053.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11121523289606240053.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.11121523289606240053.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:34 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:34 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoUnmappedFragments STANDARD_ERROR INFO 2024-07-02 11:48:34 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.13913281463337611327.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.13913281463337611327.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.13913281463337611327.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.13913281463337611327.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.13913281463337611327.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.13913281463337611327.tmp/output.sam Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.943 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:34.943 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.943 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:34.943 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.943 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:34.943 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:34.943 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:34.943 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:34 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.13913281463337611327.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.13913281463337611327.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.13913281463337611327.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:34 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.13913281463337611327.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.13913281463337611327.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.13913281463337611327.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:48:34 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:34 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:34 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:35 SimpleMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar STANDARD_ERROR INFO 2024-07-02 11:48:35 SimpleMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.1778655158200843324.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1778655158200843324.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1778655158200843324.tmp/output.sam ********** SimpleMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.1778655158200843324.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -MAX_RECORDS_IN_RAM 1000 -INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1778655158200843324.tmp/input.sam -OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.1778655158200843324.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:35.086 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:35.086 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:35.086 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:35.086 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:35.087 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:35.087 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:35.087 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:35.087 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:35 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1778655158200843324.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1778655158200843324.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1778655158200843324.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:35 GMT+14:00 2024] SimpleMarkDuplicatesWithMateCigar INPUT=[/tmp/SimpleMarkDuplicatesWithMateCigarTester.1778655158200843324.tmp/input.sam] OUTPUT=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1778655158200843324.tmp/output.sam METRICS_FILE=/tmp/SimpleMarkDuplicatesWithMateCigarTester.1778655158200843324.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_RECORDS_IN_RAM=1000 MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=SimpleMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:35 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:48:35 GMT+14:00 2024] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:36 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testBulkFragmentsNoDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:48:36 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7427794228703489980.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7427794228703489980.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7427794228703489980.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7427794228703489980.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7427794228703489980.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7427794228703489980.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7427794228703489980.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7427794228703489980.tmp/output.sam Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:36.206 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:36.206 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:36.206 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:36.206 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:36.207 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:36.207 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:36.207 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:36.207 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:36 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7427794228703489980.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7427794228703489980.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7427794228703489980.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7427794228703489980.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:36 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7427794228703489980.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7427794228703489980.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7427794228703489980.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7427794228703489980.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:40 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:40 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:40 MarkDuplicatesWithMateCigar Processed 10000 records INFO 2024-07-02 11:48:40 MarkDuplicatesWithMateCigar Processed 10000 records Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:40 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:48:40 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:40 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:48:40 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.07 minutes. Test: Test method testBulkFragmentsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:42 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testBulkFragmentsNoDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:48:42 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7419925653653078852.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7419925653653078852.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7419925653653078852.tmp/input.bam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7419925653653078852.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7419925653653078852.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7419925653653078852.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7419925653653078852.tmp/input.bam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7419925653653078852.tmp/output.sam Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:42.254 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:42.254 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:42.255 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:42.255 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:42.255 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:42.255 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:42.255 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:42.255 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:42 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7419925653653078852.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7419925653653078852.tmp/input.bam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7419925653653078852.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7419925653653078852.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:42 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7419925653653078852.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7419925653653078852.tmp/input.bam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7419925653653078852.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7419925653653078852.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:45 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:45 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:45 MarkDuplicatesWithMateCigar Processed 10000 records INFO 2024-07-02 11:48:45 MarkDuplicatesWithMateCigar Processed 10000 records Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:45 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:48:45 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:45 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:48:45 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.05 minutes. Test: Test method testBulkFragmentsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:47 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testBulkFragmentsNoDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:48:47 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7983673604536056868.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7983673604536056868.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7983673604536056868.tmp/input.cram -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7983673604536056868.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester8774646289471651798/input.fasta ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7983673604536056868.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7983673604536056868.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7983673604536056868.tmp/input.cram -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7983673604536056868.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester8774646289471651798/input.fasta Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:47.884 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:47.884 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:47.884 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:47.884 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:47.893 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:47.893 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:47.893 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:47.893 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:47 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7983673604536056868.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7983673604536056868.tmp/input.cram] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7983673604536056868.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7983673604536056868.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester8774646289471651798/input.fasta MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:47 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7983673604536056868.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7983673604536056868.tmp/input.cram] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7983673604536056868.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7983673604536056868.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester8774646289471651798/input.fasta MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:52 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:52 MarkDuplicatesWithMateCigar Processed 10000 records INFO 2024-07-02 11:48:52 MarkDuplicatesWithMateCigar Processed 10000 records Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:52 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:48:52 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:52 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:48:52 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.07 minutes. Test: Test method testBulkFragmentsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:53 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testBulkFragmentsWithDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:48:53 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3955049781016162290.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3955049781016162290.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3955049781016162290.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3955049781016162290.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3955049781016162290.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3955049781016162290.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3955049781016162290.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3955049781016162290.tmp/output.sam Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:53.764 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:53.764 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:53.765 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:53.765 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:53.769 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:48:53.769 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:48:53.769 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:48:53.769 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:53 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3955049781016162290.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3955049781016162290.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3955049781016162290.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3955049781016162290.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:48:53 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3955049781016162290.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3955049781016162290.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3955049781016162290.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3955049781016162290.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:48:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:58 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:48:58 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:58 MarkDuplicatesWithMateCigar Processed 21000 records INFO 2024-07-02 11:48:58 MarkDuplicatesWithMateCigar Processed 21000 records Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:48:58 MarkDuplicatesWithMateCigar Marking 20000 records as duplicates. INFO 2024-07-02 11:48:58 MarkDuplicatesWithMateCigar Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:48:58 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:48:58 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.07 minutes. Test: Test method testBulkFragmentsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Gradle is still running, please be patient... Running Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:01 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testBulkFragmentsWithDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:49:01 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5596619154648481055.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5596619154648481055.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5596619154648481055.tmp/input.bam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5596619154648481055.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5596619154648481055.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5596619154648481055.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5596619154648481055.tmp/input.bam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5596619154648481055.tmp/output.sam Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:01.862 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:01.862 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:01.863 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:01.863 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:01.863 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:01.863 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:01.863 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:01.863 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:01 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5596619154648481055.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5596619154648481055.tmp/input.bam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5596619154648481055.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5596619154648481055.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:01 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5596619154648481055.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5596619154648481055.tmp/input.bam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5596619154648481055.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5596619154648481055.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:04 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:49:04 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:04 MarkDuplicatesWithMateCigar Processed 21000 records INFO 2024-07-02 11:49:04 MarkDuplicatesWithMateCigar Processed 21000 records Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:04 MarkDuplicatesWithMateCigar Marking 20000 records as duplicates. INFO 2024-07-02 11:49:04 MarkDuplicatesWithMateCigar Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:04 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:49:04 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.05 minutes. Test: Test method testBulkFragmentsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:11 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testBulkFragmentsWithDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:49:11 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10694662144055770967.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10694662144055770967.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10694662144055770967.tmp/input.cram -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10694662144055770967.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester17383820975883757105/input.fasta ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10694662144055770967.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10694662144055770967.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10694662144055770967.tmp/input.cram -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10694662144055770967.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester17383820975883757105/input.fasta Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:11.276 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:11.276 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:11.281 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:11.281 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:11.282 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:11.282 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:11.282 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:11.282 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:11 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10694662144055770967.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10694662144055770967.tmp/input.cram] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10694662144055770967.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10694662144055770967.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester17383820975883757105/input.fasta MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:11 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10694662144055770967.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10694662144055770967.tmp/input.cram] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10694662144055770967.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10694662144055770967.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester17383820975883757105/input.fasta MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:17 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:49:17 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:17 MarkDuplicatesWithMateCigar Processed 21000 records INFO 2024-07-02 11:49:17 MarkDuplicatesWithMateCigar Processed 21000 records Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:17 MarkDuplicatesWithMateCigar Marking 20000 records as duplicates. INFO 2024-07-02 11:49:17 MarkDuplicatesWithMateCigar Marking 20000 records as duplicates. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:17 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.10 minutes. [Tue Jul 02 11:49:17 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.10 minutes. Test: Test method testBulkFragmentsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:19 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testBulkPairsNoDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:49:19 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6884531602887932749.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6884531602887932749.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6884531602887932749.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6884531602887932749.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6884531602887932749.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6884531602887932749.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6884531602887932749.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6884531602887932749.tmp/output.sam Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:19.576 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:19.576 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:19.576 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:19.576 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:19.576 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:19.576 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:19.576 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:19.576 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:19 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6884531602887932749.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6884531602887932749.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6884531602887932749.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6884531602887932749.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:19 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6884531602887932749.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6884531602887932749.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6884531602887932749.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6884531602887932749.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:49:20 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:49:20 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:24 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:49:24 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:24 MarkDuplicatesWithMateCigar Processed 20200 records INFO 2024-07-02 11:49:24 MarkDuplicatesWithMateCigar Processed 20200 records Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:24 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:49:24 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:24 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:49:24 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.07 minutes. Test: Test method testBulkPairsNoDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:26 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testBulkPairsNoDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:49:26 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2719697139983689865.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2719697139983689865.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2719697139983689865.tmp/input.bam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2719697139983689865.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2719697139983689865.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2719697139983689865.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2719697139983689865.tmp/input.bam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2719697139983689865.tmp/output.sam Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:26.669 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:26.669 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:26.669 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:26.669 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:26.670 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:26.670 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:26.670 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:26.670 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:26 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2719697139983689865.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2719697139983689865.tmp/input.bam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2719697139983689865.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2719697139983689865.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:26 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2719697139983689865.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2719697139983689865.tmp/input.bam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2719697139983689865.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2719697139983689865.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:49:27 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:49:27 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:30 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:49:30 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:30 MarkDuplicatesWithMateCigar Processed 20200 records INFO 2024-07-02 11:49:30 MarkDuplicatesWithMateCigar Processed 20200 records Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:30 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:49:30 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:30 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:49:30 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.07 minutes. Test: Test method testBulkPairsNoDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:38 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testBulkPairsNoDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:49:38 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12640378086005687733.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12640378086005687733.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12640378086005687733.tmp/input.cram -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12640378086005687733.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester18317473633828385025/input.fasta ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12640378086005687733.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12640378086005687733.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12640378086005687733.tmp/input.cram -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12640378086005687733.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester18317473633828385025/input.fasta Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:38.443 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:38.443 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:38.444 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:38.444 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:38.444 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:38.444 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:38.444 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:38.444 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:38 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12640378086005687733.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12640378086005687733.tmp/input.cram] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12640378086005687733.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12640378086005687733.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester18317473633828385025/input.fasta MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:38 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12640378086005687733.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12640378086005687733.tmp/input.cram] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12640378086005687733.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12640378086005687733.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester18317473633828385025/input.fasta MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:49:42 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:49:42 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:44 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:49:44 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:44 MarkDuplicatesWithMateCigar Processed 20200 records INFO 2024-07-02 11:49:44 MarkDuplicatesWithMateCigar Processed 20200 records Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:44 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:49:44 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:44 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.10 minutes. [Tue Jul 02 11:49:44 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.10 minutes. Test: Test method testBulkPairsNoDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:45 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testBulkPairsWithDuplicates[0](.sam) STANDARD_ERROR INFO 2024-07-02 11:49:45 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18061983029425112002.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18061983029425112002.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18061983029425112002.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18061983029425112002.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18061983029425112002.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18061983029425112002.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18061983029425112002.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18061983029425112002.tmp/output.sam Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:45.734 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:45.734 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:45.734 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:45.734 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:45.735 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:45.735 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:45.735 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:45.735 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:45 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18061983029425112002.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18061983029425112002.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18061983029425112002.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18061983029425112002.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:45 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18061983029425112002.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18061983029425112002.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18061983029425112002.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18061983029425112002.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:49:46 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:49:46 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:47 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:49:47 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:47 MarkDuplicatesWithMateCigar Processed 6820 records INFO 2024-07-02 11:49:47 MarkDuplicatesWithMateCigar Processed 6820 records Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:47 MarkDuplicatesWithMateCigar Marking 6200 records as duplicates. INFO 2024-07-02 11:49:47 MarkDuplicatesWithMateCigar Marking 6200 records as duplicates. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:47 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:49:47 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.02 minutes. Test: Test method testBulkPairsWithDuplicates[0](.sam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:47 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testBulkPairsWithDuplicates[1](.bam) STANDARD_ERROR INFO 2024-07-02 11:49:47 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1177757663431947036.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1177757663431947036.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1177757663431947036.tmp/input.bam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1177757663431947036.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1177757663431947036.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1177757663431947036.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1177757663431947036.tmp/input.bam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1177757663431947036.tmp/output.sam Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:47.560 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:47.560 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:47.560 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:47.560 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:47.560 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:47.560 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:47.560 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:47.560 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:47 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1177757663431947036.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1177757663431947036.tmp/input.bam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1177757663431947036.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1177757663431947036.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:47 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1177757663431947036.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1177757663431947036.tmp/input.bam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1177757663431947036.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1177757663431947036.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:49:48 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:49:48 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:49 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:49:49 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:49 MarkDuplicatesWithMateCigar Processed 6820 records INFO 2024-07-02 11:49:49 MarkDuplicatesWithMateCigar Processed 6820 records Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:49 MarkDuplicatesWithMateCigar Marking 6200 records as duplicates. INFO 2024-07-02 11:49:49 MarkDuplicatesWithMateCigar Marking 6200 records as duplicates. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:49 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:49:49 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.03 minutes. Test: Test method testBulkPairsWithDuplicates[1](.bam)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:53 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testBulkPairsWithDuplicates[2](.cram) STANDARD_ERROR INFO 2024-07-02 11:49:53 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.917085387830046569.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.917085387830046569.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.917085387830046569.tmp/input.cram -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.917085387830046569.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester3054683276086155588/input.fasta ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.917085387830046569.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.917085387830046569.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.917085387830046569.tmp/input.cram -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.917085387830046569.tmp/output.sam -REFERENCE_SEQUENCE /tmp/SamFileTester3054683276086155588/input.fasta Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:53.512 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:53.512 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:53.512 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:53.512 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:53.512 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:53.512 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:53.512 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:53.512 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:53 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.917085387830046569.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.917085387830046569.tmp/input.cram] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.917085387830046569.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.917085387830046569.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester3054683276086155588/input.fasta MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:53 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.917085387830046569.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.917085387830046569.tmp/input.cram] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.917085387830046569.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.917085387830046569.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH REFERENCE_SEQUENCE=/tmp/SamFileTester3054683276086155588/input.fasta MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:49:54 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:49:54 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:56 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:49:56 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:56 MarkDuplicatesWithMateCigar Processed 6820 records INFO 2024-07-02 11:49:56 MarkDuplicatesWithMateCigar Processed 6820 records Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:56 MarkDuplicatesWithMateCigar Marking 6200 records as duplicates. INFO 2024-07-02 11:49:56 MarkDuplicatesWithMateCigar Marking 6200 records as duplicates. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:56 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:49:56 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.05 minutes. Test: Test method testBulkPairsWithDuplicates[2](.cram)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:56 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testDifferentChromosomesInOppositeOrder STANDARD_ERROR INFO 2024-07-02 11:49:56 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6113272111802372721.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6113272111802372721.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6113272111802372721.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6113272111802372721.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6113272111802372721.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6113272111802372721.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6113272111802372721.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6113272111802372721.tmp/output.sam Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:56.975 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:56.975 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:56.975 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:56.975 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:56.975 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:56.975 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:56.976 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:56.976 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:56 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6113272111802372721.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6113272111802372721.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6113272111802372721.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6113272111802372721.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:56 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6113272111802372721.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6113272111802372721.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6113272111802372721.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6113272111802372721.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:56 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:49:56 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:56 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:49:56 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:56 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:49:56 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:57 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:49:57 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testDifferentChromosomesInOppositeOrder(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:57 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:49:57 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9164367507345730954.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9164367507345730954.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9164367507345730954.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9164367507345730954.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9164367507345730954.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9164367507345730954.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9164367507345730954.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9164367507345730954.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:57.124 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:57.124 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:57.124 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:57.124 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:57.125 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:57.125 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:57.125 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:57.125 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:57 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9164367507345730954.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9164367507345730954.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9164367507345730954.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9164367507345730954.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:57 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9164367507345730954.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9164367507345730954.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9164367507345730954.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9164367507345730954.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Processed 11 records INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Processed 11 records Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:57 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:49:57 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:57 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:49:57 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10972661579973340044.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10972661579973340044.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10972661579973340044.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10972661579973340044.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10972661579973340044.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10972661579973340044.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10972661579973340044.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10972661579973340044.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:57.207 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:57.207 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:57.207 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:57.207 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:57.207 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:57.207 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:57.207 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:57.207 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:57 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10972661579973340044.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10972661579973340044.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10972661579973340044.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10972661579973340044.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:57 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10972661579973340044.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10972661579973340044.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10972661579973340044.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10972661579973340044.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Processed 11 records INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Processed 11 records Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:57 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:49:57 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:57 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:49:57 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5332210489444127510.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5332210489444127510.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5332210489444127510.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5332210489444127510.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5332210489444127510.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5332210489444127510.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5332210489444127510.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5332210489444127510.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:57.308 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:57.308 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:57.321 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:57.321 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:57.322 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:57.322 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:57.322 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:57.322 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:57 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5332210489444127510.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5332210489444127510.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5332210489444127510.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5332210489444127510.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:57 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5332210489444127510.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5332210489444127510.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5332210489444127510.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5332210489444127510.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Processed 11 records INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Processed 11 records Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:57 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:49:57 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:57 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:49:57 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1419096117938064491.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1419096117938064491.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1419096117938064491.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1419096117938064491.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1419096117938064491.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1419096117938064491.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1419096117938064491.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1419096117938064491.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:57.439 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:57.439 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:57.439 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:57.439 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:57.440 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:57.440 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:57.440 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:57.440 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:57 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1419096117938064491.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1419096117938064491.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1419096117938064491.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1419096117938064491.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:57 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1419096117938064491.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1419096117938064491.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1419096117938064491.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1419096117938064491.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Processed 11 records INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Processed 11 records Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:57 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:49:57 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:57 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:49:57 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3689432074271518464.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3689432074271518464.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3689432074271518464.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3689432074271518464.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3689432074271518464.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3689432074271518464.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3689432074271518464.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3689432074271518464.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:57.532 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:57.532 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:57.541 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:57.541 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:57.541 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:57.541 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:57.541 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:57.541 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:57 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3689432074271518464.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3689432074271518464.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3689432074271518464.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3689432074271518464.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:57 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3689432074271518464.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3689432074271518464.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3689432074271518464.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3689432074271518464.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Processed 11 records INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Processed 11 records Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:57 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:49:57 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:57 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:49:57 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4954208197777074555.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4954208197777074555.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4954208197777074555.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4954208197777074555.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4954208197777074555.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4954208197777074555.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4954208197777074555.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4954208197777074555.tmp/output.sam Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:57.917 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:57.917 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:57.917 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:57.917 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:57.917 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:57.917 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:57.918 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:57.918 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:57 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4954208197777074555.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4954208197777074555.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4954208197777074555.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4954208197777074555.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:57 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4954208197777074555.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4954208197777074555.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4954208197777074555.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4954208197777074555.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Processed 11 records INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Processed 11 records Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2024-07-02 11:49:57 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:57 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:49:57 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:58 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testMappedFragmentAndMappedPairFirstOfPairNonPrimary STANDARD_ERROR INFO 2024-07-02 11:49:58 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11458382484518696894.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11458382484518696894.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11458382484518696894.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11458382484518696894.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11458382484518696894.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11458382484518696894.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11458382484518696894.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11458382484518696894.tmp/output.sam Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:58.020 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:58.020 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:58.020 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:58.020 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:58.021 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:58.021 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:58.021 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:58.021 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:58 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11458382484518696894.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11458382484518696894.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11458382484518696894.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11458382484518696894.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:58 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11458382484518696894.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11458382484518696894.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11458382484518696894.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11458382484518696894.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:58 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:49:58 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedFragmentAndMappedPairFirstOfPairNonPrimary(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:58 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testMappedFragmentAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:49:58 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6836554976665942336.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6836554976665942336.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6836554976665942336.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6836554976665942336.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6836554976665942336.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6836554976665942336.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6836554976665942336.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6836554976665942336.tmp/output.sam Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:58.247 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:58.247 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:58.247 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:58.247 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:58.248 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:58.248 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:58.248 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:58.248 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:58 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6836554976665942336.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6836554976665942336.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6836554976665942336.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6836554976665942336.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:58 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6836554976665942336.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6836554976665942336.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6836554976665942336.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6836554976665942336.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Processed 3 records INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Processed 3 records Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:58 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:49:58 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:58 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testMappedFragmentAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:49:58 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12112318083046652451.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12112318083046652451.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12112318083046652451.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12112318083046652451.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12112318083046652451.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12112318083046652451.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12112318083046652451.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12112318083046652451.tmp/output.sam Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:58.396 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:58.396 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:58.396 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:58.396 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:58.409 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:58.409 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:58.409 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:58.409 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:58 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12112318083046652451.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12112318083046652451.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12112318083046652451.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12112318083046652451.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:58 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12112318083046652451.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12112318083046652451.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12112318083046652451.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12112318083046652451.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Processed 3 records INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Processed 3 records Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:58 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:49:58 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:58 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testMappedPairAndMappedFragmentAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:49:58 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15789642969924961050.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15789642969924961050.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15789642969924961050.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15789642969924961050.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15789642969924961050.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15789642969924961050.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15789642969924961050.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15789642969924961050.tmp/output.sam Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:58.537 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:58.537 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:58.538 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:58.538 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:58.538 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:58.538 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:58.538 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:58.538 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:58 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15789642969924961050.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15789642969924961050.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15789642969924961050.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15789642969924961050.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:58 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15789642969924961050.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15789642969924961050.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15789642969924961050.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15789642969924961050.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:49:58 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. WARNING 2024-07-02 11:49:58 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:58 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:49:58 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedPairAndMappedFragmentAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:58 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testMappedPairAndMappedFragmentAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:49:58 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13865410566251652235.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13865410566251652235.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13865410566251652235.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13865410566251652235.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13865410566251652235.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13865410566251652235.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13865410566251652235.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13865410566251652235.tmp/output.sam Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:58.691 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:58.691 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:58.691 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:58.691 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:58.692 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:58.692 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:58.692 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:58.692 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:58 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13865410566251652235.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13865410566251652235.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13865410566251652235.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13865410566251652235.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:58 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13865410566251652235.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13865410566251652235.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13865410566251652235.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13865410566251652235.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:49:58 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. WARNING 2024-07-02 11:49:58 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:58 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:49:58 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedPairAndMappedFragmentAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:58 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:49:58 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17867650502614713370.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17867650502614713370.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17867650502614713370.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17867650502614713370.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17867650502614713370.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17867650502614713370.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17867650502614713370.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17867650502614713370.tmp/output.sam Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:58.879 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:58.879 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:58.879 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:58.879 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:58.879 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:58.879 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:58.879 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:58.879 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:58 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17867650502614713370.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17867650502614713370.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17867650502614713370.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17867650502614713370.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:58 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17867650502614713370.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17867650502614713370.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17867650502614713370.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17867650502614713370.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:49:58 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. WARNING 2024-07-02 11:49:58 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:49:58 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:58 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:49:58 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testMappedPairAndMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:49:59 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10770122499414253683.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10770122499414253683.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10770122499414253683.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10770122499414253683.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10770122499414253683.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10770122499414253683.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10770122499414253683.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10770122499414253683.tmp/output.sam Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.085 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:59.085 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.093 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:59.093 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.094 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:59.094 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.094 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:59.094 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10770122499414253683.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10770122499414253683.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10770122499414253683.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10770122499414253683.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:59 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10770122499414253683.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10770122499414253683.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10770122499414253683.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10770122499414253683.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:49:59 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. WARNING 2024-07-02 11:49:59 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:49:59 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedPairAndMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testMappedPairAndMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:49:59 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15993068341027009597.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15993068341027009597.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15993068341027009597.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15993068341027009597.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15993068341027009597.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15993068341027009597.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15993068341027009597.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15993068341027009597.tmp/output.sam Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.180 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:59.180 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.180 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:59.180 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.189 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:59.189 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.189 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:59.189 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15993068341027009597.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15993068341027009597.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15993068341027009597.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15993068341027009597.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:59 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15993068341027009597.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15993068341027009597.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15993068341027009597.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15993068341027009597.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:49:59 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. WARNING 2024-07-02 11:49:59 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:49:59 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedPairAndMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testMappedPairWithFirstEndSamePositionAndOther STANDARD_ERROR INFO 2024-07-02 11:49:59 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16793981555544458611.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16793981555544458611.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16793981555544458611.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16793981555544458611.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16793981555544458611.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16793981555544458611.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16793981555544458611.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16793981555544458611.tmp/output.sam Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.279 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:59.279 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.279 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:59.279 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.280 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:59.280 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.280 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:59.280 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16793981555544458611.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16793981555544458611.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16793981555544458611.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16793981555544458611.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:59 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16793981555544458611.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16793981555544458611.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16793981555544458611.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16793981555544458611.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:49:59 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. WARNING 2024-07-02 11:49:59 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:49:59 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedPairWithFirstEndSamePositionAndOther(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testMappedPairWithSamePosition STANDARD_ERROR INFO 2024-07-02 11:49:59 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1267604495242424168.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1267604495242424168.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1267604495242424168.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1267604495242424168.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1267604495242424168.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1267604495242424168.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1267604495242424168.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1267604495242424168.tmp/output.sam Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.356 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:59.356 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.356 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:59.356 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.365 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:59.365 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.365 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:59.365 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1267604495242424168.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1267604495242424168.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1267604495242424168.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1267604495242424168.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:59 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1267604495242424168.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1267604495242424168.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1267604495242424168.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1267604495242424168.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:49:59 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:49:59 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:49:59 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testMappedPairWithSamePositionSameCigar STANDARD_ERROR INFO 2024-07-02 11:49:59 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16229305852011782300.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16229305852011782300.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16229305852011782300.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16229305852011782300.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16229305852011782300.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16229305852011782300.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16229305852011782300.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16229305852011782300.tmp/output.sam Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.458 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:59.458 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.458 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:59.458 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.458 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:59.458 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.458 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:59.458 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16229305852011782300.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16229305852011782300.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16229305852011782300.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16229305852011782300.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:59 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16229305852011782300.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16229305852011782300.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16229305852011782300.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16229305852011782300.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:49:59 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:49:59 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:49:59 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMappedPairWithSamePositionSameCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testMatePairFirstUnmapped STANDARD_ERROR INFO 2024-07-02 11:49:59 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17578457891088546904.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17578457891088546904.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17578457891088546904.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17578457891088546904.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17578457891088546904.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17578457891088546904.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17578457891088546904.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17578457891088546904.tmp/output.sam Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.544 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:59.544 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.544 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:59.544 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.544 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:59.544 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.544 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:59.544 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17578457891088546904.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17578457891088546904.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17578457891088546904.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17578457891088546904.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:59 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17578457891088546904.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17578457891088546904.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17578457891088546904.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17578457891088546904.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:49:59 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMatePairFirstUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testMatePairSecondUnmapped STANDARD_ERROR INFO 2024-07-02 11:49:59 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002219235031470277.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002219235031470277.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002219235031470277.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002219235031470277.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002219235031470277.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002219235031470277.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002219235031470277.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002219235031470277.tmp/output.sam Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.628 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:59.628 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.641 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:59.641 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.642 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:59.642 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.642 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:59.642 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002219235031470277.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002219235031470277.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002219235031470277.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002219235031470277.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:59 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002219235031470277.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002219235031470277.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002219235031470277.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002219235031470277.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:49:59 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMatePairSecondUnmapped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testOpticalDuplicateBehaviorNullRegex STANDARD_ERROR INFO 2024-07-02 11:49:59 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13125621590821401400.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13125621590821401400.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -READ_NAME_REGEX null -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13125621590821401400.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13125621590821401400.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13125621590821401400.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13125621590821401400.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -READ_NAME_REGEX null -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13125621590821401400.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13125621590821401400.tmp/output.sam Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.720 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:59.720 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.720 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:59.720 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.720 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:59.720 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.720 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:59.720 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13125621590821401400.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13125621590821401400.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13125621590821401400.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13125621590821401400.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH READ_NAME_REGEX=null MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:59 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13125621590821401400.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13125621590821401400.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13125621590821401400.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13125621590821401400.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH READ_NAME_REGEX=null MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Skipped optical duplicate cluster discovery; library size estimation may be inaccurate! WARNING 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Skipped optical duplicate cluster discovery; library size estimation may be inaccurate! Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:49:59 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testOpticalDuplicateBehaviorNullRegex(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testOpticalDuplicateClusterOneEndSamePositionOneCluster STANDARD_ERROR INFO 2024-07-02 11:49:59 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6293506866586047212.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6293506866586047212.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6293506866586047212.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6293506866586047212.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6293506866586047212.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6293506866586047212.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6293506866586047212.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6293506866586047212.tmp/output.sam Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.828 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:59.828 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.828 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:59.828 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.831 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:59.831 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.831 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:59.831 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6293506866586047212.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6293506866586047212.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6293506866586047212.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6293506866586047212.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:59 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6293506866586047212.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6293506866586047212.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6293506866586047212.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6293506866586047212.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:49:59 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testOpticalDuplicateClusterOneEndSamePositionOneCluster(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance STANDARD_ERROR INFO 2024-07-02 11:49:59 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2258229157121191916.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2258229157121191916.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2258229157121191916.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2258229157121191916.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2258229157121191916.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2258229157121191916.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2258229157121191916.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2258229157121191916.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.916 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:59.916 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.916 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:59.916 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.916 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:49:59.916 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:49:59.916 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:49:59.916 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2258229157121191916.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2258229157121191916.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2258229157121191916.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2258229157121191916.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:49:59 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2258229157121191916.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2258229157121191916.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2258229157121191916.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2258229157121191916.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:49:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:49:59 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:49:59 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:49:59 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance STANDARD_ERROR INFO 2024-07-02 11:50:00 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8519028242626946739.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8519028242626946739.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8519028242626946739.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8519028242626946739.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8519028242626946739.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8519028242626946739.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8519028242626946739.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8519028242626946739.tmp/output.sam Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.036 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:00.036 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.036 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:00.036 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.037 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:00.037 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.037 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:00.037 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8519028242626946739.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8519028242626946739.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8519028242626946739.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8519028242626946739.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:00 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8519028242626946739.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8519028242626946739.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8519028242626946739.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8519028242626946739.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:00 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate STANDARD_ERROR INFO 2024-07-02 11:50:00 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16182886627057770418.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16182886627057770418.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16182886627057770418.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16182886627057770418.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16182886627057770418.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16182886627057770418.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16182886627057770418.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16182886627057770418.tmp/output.sam Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.185 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:00.185 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.185 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:00.185 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.186 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:00.186 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.186 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:00.186 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16182886627057770418.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16182886627057770418.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16182886627057770418.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16182886627057770418.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:00 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16182886627057770418.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16182886627057770418.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16182886627057770418.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16182886627057770418.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:00 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testOpticalDuplicateFinding STANDARD_ERROR INFO 2024-07-02 11:50:00 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4890298154321415981.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4890298154321415981.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4890298154321415981.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4890298154321415981.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4890298154321415981.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4890298154321415981.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4890298154321415981.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4890298154321415981.tmp/output.sam Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.416 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:00.416 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.416 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:00.416 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.416 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:00.416 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.416 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:00.416 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4890298154321415981.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4890298154321415981.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4890298154321415981.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4890298154321415981.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:00 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4890298154321415981.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4890298154321415981.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4890298154321415981.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4890298154321415981.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Processed 6 records INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Processed 6 records Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:00 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testOpticalDuplicateFinding(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testPathologicalOrderingAtTheSamePosition STANDARD_ERROR INFO 2024-07-02 11:50:00 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13693295247852518237.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13693295247852518237.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13693295247852518237.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13693295247852518237.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13693295247852518237.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13693295247852518237.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13693295247852518237.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13693295247852518237.tmp/output.sam Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.532 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:00.532 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.536 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:00.536 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.537 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:00.537 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.537 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:00.537 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13693295247852518237.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13693295247852518237.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13693295247852518237.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13693295247852518237.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:00 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13693295247852518237.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13693295247852518237.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13693295247852518237.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13693295247852518237.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:00 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testPathologicalOrderingAtTheSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testSecondEndIsBeforeFirstInCoordinate STANDARD_ERROR INFO 2024-07-02 11:50:00 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5429362965744650950.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5429362965744650950.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5429362965744650950.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5429362965744650950.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5429362965744650950.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5429362965744650950.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5429362965744650950.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5429362965744650950.tmp/output.sam Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.600 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:00.600 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.600 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:00.600 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.600 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:00.600 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.600 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:00.600 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5429362965744650950.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5429362965744650950.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5429362965744650950.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5429362965744650950.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:00 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5429362965744650950.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5429362965744650950.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5429362965744650950.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5429362965744650950.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:00 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:00 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:00 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testSecondEndIsBeforeFirstInCoordinate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testSingleMappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testSingleMappedFragment STANDARD_ERROR INFO 2024-07-02 11:50:00 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testSingleMappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15658407225001323467.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15658407225001323467.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15658407225001323467.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15658407225001323467.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15658407225001323467.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15658407225001323467.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15658407225001323467.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15658407225001323467.tmp/output.sam Test: Test method testSingleMappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.663 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:00.663 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.663 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:00.663 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.664 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:00.664 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.664 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:00.664 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15658407225001323467.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15658407225001323467.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15658407225001323467.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15658407225001323467.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:00 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15658407225001323467.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15658407225001323467.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15658407225001323467.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15658407225001323467.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Processed 1 records INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Processed 1 records Test: Test method testSingleMappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:00 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testSingleMappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testSingleMappedFragmentAndSingleMappedPair STANDARD_ERROR INFO 2024-07-02 11:50:00 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4153159598354444465.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4153159598354444465.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4153159598354444465.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4153159598354444465.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4153159598354444465.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4153159598354444465.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4153159598354444465.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4153159598354444465.tmp/output.sam Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.716 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:00.716 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.716 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:00.716 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.716 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:00.716 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.716 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:00.716 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4153159598354444465.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4153159598354444465.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4153159598354444465.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4153159598354444465.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:00 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4153159598354444465.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4153159598354444465.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4153159598354444465.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4153159598354444465.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:00 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. WARNING 2024-07-02 11:50:00 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Processed 3 records INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Processed 3 records Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:00 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testSingleMappedFragmentAndSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testSingleMappedFragmentAndTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:50:00 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5411054298902167981.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5411054298902167981.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5411054298902167981.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5411054298902167981.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5411054298902167981.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5411054298902167981.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5411054298902167981.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5411054298902167981.tmp/output.sam Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.763 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:00.763 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.764 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:00.764 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.764 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:00.764 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.764 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:00.764 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5411054298902167981.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5411054298902167981.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5411054298902167981.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5411054298902167981.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:00 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5411054298902167981.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5411054298902167981.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5411054298902167981.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5411054298902167981.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:00 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. WARNING 2024-07-02 11:50:00 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Marking 3 records as duplicates. INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Marking 3 records as duplicates. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:00 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testSingleMappedFragmentAndTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testSingleMappedPair STANDARD_ERROR INFO 2024-07-02 11:50:00 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.564537444690593281.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.564537444690593281.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.564537444690593281.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.564537444690593281.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.564537444690593281.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.564537444690593281.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.564537444690593281.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.564537444690593281.tmp/output.sam Test: Test method testSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.815 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:00.815 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.816 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:00.816 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.816 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:00.816 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.816 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:00.816 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.564537444690593281.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.564537444690593281.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.564537444690593281.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.564537444690593281.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:00 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.564537444690593281.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.564537444690593281.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.564537444690593281.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.564537444690593281.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:00 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:00 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:50:00 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:00 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testSingleMappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:00 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testSingleUnmappedFragment STANDARD_ERROR INFO 2024-07-02 11:50:00 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7161708058587906637.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7161708058587906637.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7161708058587906637.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7161708058587906637.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7161708058587906637.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7161708058587906637.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7161708058587906637.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7161708058587906637.tmp/output.sam Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.988 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:00.988 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.988 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:00.988 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.997 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:00.997 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:00.997 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:00.997 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7161708058587906637.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7161708058587906637.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7161708058587906637.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7161708058587906637.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:00 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7161708058587906637.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7161708058587906637.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7161708058587906637.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7161708058587906637.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Processed 1 records INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Processed 1 records Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:01 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:01 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testSingleUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testSingleUnmappedPair STANDARD_ERROR INFO 2024-07-02 11:50:01 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6429368505338548516.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6429368505338548516.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6429368505338548516.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6429368505338548516.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6429368505338548516.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6429368505338548516.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6429368505338548516.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6429368505338548516.tmp/output.sam Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:01.102 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:01.102 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:01.102 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:01.102 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:01.103 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:01.103 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:01.103 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:01.103 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:01 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6429368505338548516.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6429368505338548516.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6429368505338548516.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6429368505338548516.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:01 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6429368505338548516.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6429368505338548516.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6429368505338548516.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6429368505338548516.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:01 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:01 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testSingleUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testStackOverFlowPairSetSwap STANDARD_ERROR INFO 2024-07-02 11:50:01 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11206328552513915300.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11206328552513915300.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11206328552513915300.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11206328552513915300.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11206328552513915300.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11206328552513915300.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11206328552513915300.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11206328552513915300.tmp/output.sam Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:01.222 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:01.222 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:01.230 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:01.230 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:01.231 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:01.231 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:01.231 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:01.231 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:01 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11206328552513915300.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11206328552513915300.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11206328552513915300.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11206328552513915300.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:01 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11206328552513915300.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11206328552513915300.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11206328552513915300.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11206328552513915300.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:01 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:01 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testStackOverFlowPairSetSwap(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:50:01 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7761871189898073036.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7761871189898073036.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7761871189898073036.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7761871189898073036.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7761871189898073036.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7761871189898073036.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7761871189898073036.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7761871189898073036.tmp/output.sam Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:01.332 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:01.332 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:01.332 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:01.332 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:01.332 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:01.332 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:01.332 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:01.332 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:01 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7761871189898073036.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7761871189898073036.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7761871189898073036.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7761871189898073036.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:01 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7761871189898073036.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7761871189898073036.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7761871189898073036.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7761871189898073036.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Processed 18 records INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Processed 18 records Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Marking 12 records as duplicates. INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Marking 12 records as duplicates. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:01 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:01 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:50:01 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1781345851394595721.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1781345851394595721.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1781345851394595721.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1781345851394595721.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1781345851394595721.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1781345851394595721.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1781345851394595721.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1781345851394595721.tmp/output.sam Test: Test method testThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:01.453 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:01.453 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:01.453 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:01.453 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:01.454 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:01.454 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:01.454 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:01.454 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:01 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1781345851394595721.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1781345851394595721.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1781345851394595721.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1781345851394595721.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:01 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1781345851394595721.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1781345851394595721.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1781345851394595721.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1781345851394595721.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Processed 6 records INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Processed 6 records Test: Test method testThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:01 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:01 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testThreeMappedPairsWithMatchingSecondMate STANDARD_ERROR INFO 2024-07-02 11:50:01 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1480823168659838060.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1480823168659838060.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1480823168659838060.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1480823168659838060.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1480823168659838060.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1480823168659838060.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1480823168659838060.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1480823168659838060.tmp/output.sam Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:01.592 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:01.592 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:01.592 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:01.592 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:01.592 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:01.592 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:01.592 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:01.592 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:01 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1480823168659838060.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1480823168659838060.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1480823168659838060.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1480823168659838060.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:01 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1480823168659838060.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1480823168659838060.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1480823168659838060.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1480823168659838060.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Processed 6 records INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Processed 6 records Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:01 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:01 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testThreeMappedPairsWithMatchingSecondMate(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs STANDARD_ERROR INFO 2024-07-02 11:50:01 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9589272177688630657.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9589272177688630657.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9589272177688630657.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9589272177688630657.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9589272177688630657.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9589272177688630657.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9589272177688630657.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9589272177688630657.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:01.761 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:01.761 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:01.762 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:01.762 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:01.762 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:01.762 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:01.762 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:01.762 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:01 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9589272177688630657.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9589272177688630657.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9589272177688630657.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9589272177688630657.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:01 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9589272177688630657.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9589272177688630657.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9589272177688630657.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9589272177688630657.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:01 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Processed 12 records INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Processed 12 records Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:01 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:01 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoGroupsOnDifferentChromosomesOfTwoFragments STANDARD_ERROR INFO 2024-07-02 11:50:01 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7243073309858984035.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7243073309858984035.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7243073309858984035.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7243073309858984035.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7243073309858984035.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7243073309858984035.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7243073309858984035.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7243073309858984035.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:01.943 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:01.943 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:01.944 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:01.944 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:01.944 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:01.944 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:01.944 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:01.944 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:01 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7243073309858984035.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7243073309858984035.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7243073309858984035.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7243073309858984035.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:01 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7243073309858984035.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7243073309858984035.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7243073309858984035.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7243073309858984035.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:01 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:01 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:01 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:02 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:50:02 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8587999099887247539.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8587999099887247539.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8587999099887247539.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8587999099887247539.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8587999099887247539.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8587999099887247539.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8587999099887247539.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8587999099887247539.tmp/output.sam Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:02.112 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:02.112 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:02.112 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:02.112 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:02.121 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:02.121 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:02.122 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:02.122 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:02 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8587999099887247539.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8587999099887247539.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8587999099887247539.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8587999099887247539.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:02 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8587999099887247539.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8587999099887247539.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8587999099887247539.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8587999099887247539.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:02 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:02 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Processed 8 records INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Processed 8 records Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:02 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:02 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:02 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoMappedFragments STANDARD_ERROR INFO 2024-07-02 11:50:02 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoMappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4106324520800024664.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4106324520800024664.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4106324520800024664.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4106324520800024664.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4106324520800024664.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4106324520800024664.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4106324520800024664.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4106324520800024664.tmp/output.sam Test: Test method testTwoMappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:02.318 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:02.318 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:02.318 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:02.318 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:02.318 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:02.318 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:02.318 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:02.318 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:02 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4106324520800024664.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4106324520800024664.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4106324520800024664.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4106324520800024664.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:02 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4106324520800024664.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4106324520800024664.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4106324520800024664.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4106324520800024664.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testTwoMappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:02 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:02 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:02 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoMappedPairWithSamePosition STANDARD_ERROR INFO 2024-07-02 11:50:02 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3830392927616641265.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3830392927616641265.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3830392927616641265.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3830392927616641265.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3830392927616641265.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3830392927616641265.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3830392927616641265.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3830392927616641265.tmp/output.sam Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:02.479 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:02.479 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:02.480 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:02.480 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:02.480 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:02.480 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:02.480 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:02.480 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:02 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3830392927616641265.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3830392927616641265.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3830392927616641265.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3830392927616641265.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:02 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3830392927616641265.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3830392927616641265.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3830392927616641265.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3830392927616641265.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:02 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:02 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:02 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:02 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairWithSamePosition(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:02 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoMappedPairWithSamePositionDifferentStrands STANDARD_ERROR INFO 2024-07-02 11:50:02 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10384693688120452481.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10384693688120452481.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10384693688120452481.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10384693688120452481.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10384693688120452481.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10384693688120452481.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10384693688120452481.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10384693688120452481.tmp/output.sam Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:02.621 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:02.621 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:02.621 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:02.621 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:02.622 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:02.622 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:02.622 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:02.622 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:02 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10384693688120452481.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10384693688120452481.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10384693688120452481.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10384693688120452481.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:02 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10384693688120452481.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10384693688120452481.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10384693688120452481.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10384693688120452481.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:02 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:02 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:02 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:02 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:02 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoMappedPairWithSamePositionDifferentStrands2 STANDARD_ERROR INFO 2024-07-02 11:50:02 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1535712122864420490.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1535712122864420490.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1535712122864420490.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1535712122864420490.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1535712122864420490.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1535712122864420490.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1535712122864420490.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1535712122864420490.tmp/output.sam Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:02.716 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:02.716 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:02.716 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:02.716 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:02.729 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:02.729 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:02.729 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:02.729 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:02 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1535712122864420490.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1535712122864420490.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1535712122864420490.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1535712122864420490.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:02 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1535712122864420490.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1535712122864420490.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1535712122864420490.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1535712122864420490.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:02 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:02 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:02 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:02 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairWithSamePositionDifferentStrands2(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:02 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoMappedPairs STANDARD_ERROR INFO 2024-07-02 11:50:02 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2077307136591762556.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2077307136591762556.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2077307136591762556.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2077307136591762556.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2077307136591762556.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2077307136591762556.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2077307136591762556.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2077307136591762556.tmp/output.sam Test: Test method testTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:02.816 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:02.816 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:02.816 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:02.816 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:02.821 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:02.821 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:02.821 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:02.821 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:02 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2077307136591762556.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2077307136591762556.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2077307136591762556.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2077307136591762556.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:02 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2077307136591762556.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2077307136591762556.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2077307136591762556.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2077307136591762556.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:02 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:02 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:02 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:02 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairs(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:02 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoMappedPairsAndMappedSecondaryFragment STANDARD_ERROR INFO 2024-07-02 11:50:02 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15547143539323374259.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15547143539323374259.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15547143539323374259.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15547143539323374259.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15547143539323374259.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15547143539323374259.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15547143539323374259.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15547143539323374259.tmp/output.sam Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:02.919 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:02.919 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:02.919 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:02.919 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:02.920 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:02.920 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:02.920 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:02.920 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:02 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15547143539323374259.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15547143539323374259.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15547143539323374259.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15547143539323374259.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:02 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15547143539323374259.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15547143539323374259.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15547143539323374259.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15547143539323374259.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:02 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:02 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:02 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:02 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:02 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsAndMappedSecondaryFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoMappedPairsAndTerminalUnmappedFragment STANDARD_ERROR INFO 2024-07-02 11:50:03 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12233908004323632729.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12233908004323632729.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12233908004323632729.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12233908004323632729.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12233908004323632729.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12233908004323632729.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12233908004323632729.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12233908004323632729.tmp/output.sam Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.049 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:03.049 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.050 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:03.050 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.050 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:03.050 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.050 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:03.050 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:03 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12233908004323632729.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12233908004323632729.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12233908004323632729.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12233908004323632729.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:03 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12233908004323632729.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12233908004323632729.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12233908004323632729.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12233908004323632729.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:03 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:03 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsAndTerminalUnmappedFragment(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoMappedPairsAndTerminalUnmappedPair STANDARD_ERROR INFO 2024-07-02 11:50:03 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15721041980168237823.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15721041980168237823.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15721041980168237823.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15721041980168237823.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15721041980168237823.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15721041980168237823.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15721041980168237823.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15721041980168237823.tmp/output.sam Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.164 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:03.164 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.169 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:03.169 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.170 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:03.170 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.170 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:03.170 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:03 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15721041980168237823.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15721041980168237823.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15721041980168237823.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15721041980168237823.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:03 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15721041980168237823.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15721041980168237823.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15721041980168237823.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15721041980168237823.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Processed 6 records INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Processed 6 records Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:03 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:03 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsAndTerminalUnmappedPair(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoMappedPairsMatesSoftClipped STANDARD_ERROR INFO 2024-07-02 11:50:03 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7153835278247550436.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7153835278247550436.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7153835278247550436.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7153835278247550436.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7153835278247550436.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7153835278247550436.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7153835278247550436.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7153835278247550436.tmp/output.sam Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.310 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:03.310 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.310 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:03.310 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.310 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:03.310 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.310 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:03.310 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:03 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7153835278247550436.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7153835278247550436.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7153835278247550436.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7153835278247550436.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:03 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7153835278247550436.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7153835278247550436.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7153835278247550436.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7153835278247550436.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:03 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:03 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsMatesSoftClipped(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithOppositeOrientations STANDARD_ERROR INFO 2024-07-02 11:50:03 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5196694131637405899.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5196694131637405899.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5196694131637405899.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5196694131637405899.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5196694131637405899.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5196694131637405899.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5196694131637405899.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5196694131637405899.tmp/output.sam Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:03.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:03.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:03.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:03.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:03 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5196694131637405899.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5196694131637405899.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5196694131637405899.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5196694131637405899.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:03 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5196694131637405899.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5196694131637405899.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5196694131637405899.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5196694131637405899.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. WARNING 2024-07-02 11:50:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:03 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:03 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithOppositeOrientations(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithOppositeOrientationsNumberTwo STANDARD_ERROR INFO 2024-07-02 11:50:03 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5387624829094572726.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5387624829094572726.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5387624829094572726.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5387624829094572726.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5387624829094572726.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5387624829094572726.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5387624829094572726.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5387624829094572726.tmp/output.sam Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.613 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:03.613 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.613 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:03.613 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.615 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:03.615 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.615 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:03.615 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:03 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5387624829094572726.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5387624829094572726.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5387624829094572726.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5387624829094572726.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:03 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5387624829094572726.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5387624829094572726.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5387624829094572726.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5387624829094572726.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:03 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:03 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithOppositeOrientationsNumberTwo(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSoftClipping STANDARD_ERROR INFO 2024-07-02 11:50:03 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002058693189432493.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002058693189432493.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002058693189432493.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002058693189432493.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002058693189432493.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002058693189432493.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002058693189432493.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002058693189432493.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.712 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:03.712 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.712 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:03.712 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.713 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:03.713 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.713 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:03.713 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:03 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002058693189432493.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002058693189432493.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002058693189432493.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002058693189432493.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:03 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002058693189432493.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002058693189432493.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002058693189432493.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18002058693189432493.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:03 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:03 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSoftClipping(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSoftClippingBoth STANDARD_ERROR INFO 2024-07-02 11:50:03 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5319578347022731510.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5319578347022731510.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5319578347022731510.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5319578347022731510.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5319578347022731510.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5319578347022731510.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5319578347022731510.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5319578347022731510.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.802 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:03.802 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.803 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:03.803 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.803 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:03.803 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.803 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:03.803 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:03 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5319578347022731510.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5319578347022731510.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5319578347022731510.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5319578347022731510.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:03 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5319578347022731510.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5319578347022731510.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5319578347022731510.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5319578347022731510.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. WARNING 2024-07-02 11:50:03 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:03 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:03 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSoftClippingBoth(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReads[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:50:03 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15590630661892059268.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15590630661892059268.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15590630661892059268.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15590630661892059268.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15590630661892059268.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15590630661892059268.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15590630661892059268.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15590630661892059268.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.912 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:03.912 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.925 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:03.925 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.926 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:03.926 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:03.926 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:03.926 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:03 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15590630661892059268.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15590630661892059268.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15590630661892059268.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15590630661892059268.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:03 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15590630661892059268.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15590630661892059268.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15590630661892059268.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15590630661892059268.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:03 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:03 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:03 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:04 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReads[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:50:04 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12023357343335801901.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12023357343335801901.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12023357343335801901.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12023357343335801901.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12023357343335801901.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12023357343335801901.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12023357343335801901.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12023357343335801901.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:04.075 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:04.075 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:04.075 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:04.075 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:04.075 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:04.075 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:04.075 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:04.075 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:04 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12023357343335801901.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12023357343335801901.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12023357343335801901.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12023357343335801901.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:04 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12023357343335801901.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12023357343335801901.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12023357343335801901.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.12023357343335801901.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:04 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:04 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:04 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReads[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:50:04 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9804663675105707057.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9804663675105707057.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9804663675105707057.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9804663675105707057.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9804663675105707057.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9804663675105707057.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9804663675105707057.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9804663675105707057.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:04.215 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:04.215 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:04.215 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:04.215 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:04.215 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:04.215 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:04.215 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:04.215 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:04 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9804663675105707057.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9804663675105707057.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9804663675105707057.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9804663675105707057.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:04 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9804663675105707057.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9804663675105707057.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9804663675105707057.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9804663675105707057.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:04 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:04 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:04 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReads[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:50:04 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7021905945678482261.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7021905945678482261.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7021905945678482261.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7021905945678482261.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7021905945678482261.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7021905945678482261.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7021905945678482261.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7021905945678482261.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:04.329 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:04.329 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:04.329 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:04.329 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:04.330 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:04.330 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:04.330 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:04.330 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:04 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7021905945678482261.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7021905945678482261.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7021905945678482261.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7021905945678482261.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:04 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7021905945678482261.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7021905945678482261.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7021905945678482261.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7021905945678482261.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:04 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:04 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:04 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReads[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:50:04 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8179617982247608608.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8179617982247608608.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8179617982247608608.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8179617982247608608.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8179617982247608608.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8179617982247608608.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8179617982247608608.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8179617982247608608.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:04.417 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:04.417 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:04.429 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:04.429 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:04.429 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:04.429 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:04.429 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:04.429 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:04 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8179617982247608608.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8179617982247608608.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8179617982247608608.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8179617982247608608.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:04 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8179617982247608608.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8179617982247608608.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8179617982247608608.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.8179617982247608608.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:04 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:04 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:04 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReads[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:50:04 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.186081048446023145.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.186081048446023145.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.186081048446023145.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.186081048446023145.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.186081048446023145.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.186081048446023145.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.186081048446023145.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.186081048446023145.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:04.585 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:04.585 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:04.585 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:04.585 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:04.586 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:04.586 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:04.586 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:04.586 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:04 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.186081048446023145.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.186081048446023145.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.186081048446023145.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.186081048446023145.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:04 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.186081048446023145.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.186081048446023145.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.186081048446023145.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.186081048446023145.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:04 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:04 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReads[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:04 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true) STANDARD_ERROR INFO 2024-07-02 11:50:04 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4836612204786652815.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4836612204786652815.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4836612204786652815.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4836612204786652815.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4836612204786652815.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4836612204786652815.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4836612204786652815.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4836612204786652815.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:04.682 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:04.682 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:04.683 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:04.683 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:04.683 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:04.683 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:04.683 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:04.683 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:04 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4836612204786652815.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4836612204786652815.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4836612204786652815.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4836612204786652815.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:04 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4836612204786652815.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4836612204786652815.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4836612204786652815.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4836612204786652815.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:04 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:04 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:04 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true) STANDARD_ERROR INFO 2024-07-02 11:50:04 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16987353554031713473.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16987353554031713473.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16987353554031713473.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16987353554031713473.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16987353554031713473.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16987353554031713473.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16987353554031713473.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16987353554031713473.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:04.793 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:04.793 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:04.793 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:04.793 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:04.794 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:04.794 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:04.794 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:04.794 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:04 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16987353554031713473.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16987353554031713473.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16987353554031713473.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16987353554031713473.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:04 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16987353554031713473.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16987353554031713473.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16987353554031713473.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16987353554031713473.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:04 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:04 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:04 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:05 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true) STANDARD_ERROR INFO 2024-07-02 11:50:05 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10693484783611990648.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10693484783611990648.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10693484783611990648.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10693484783611990648.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10693484783611990648.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10693484783611990648.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10693484783611990648.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10693484783611990648.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:05.041 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:05.041 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:05.041 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:05.041 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:05.042 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:05.042 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:05.042 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:05.042 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:05 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10693484783611990648.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10693484783611990648.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10693484783611990648.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10693484783611990648.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:05 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10693484783611990648.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10693484783611990648.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10693484783611990648.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10693484783611990648.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:05 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:05 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:05 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false) STANDARD_ERROR INFO 2024-07-02 11:50:05 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18111567076826058813.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18111567076826058813.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18111567076826058813.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18111567076826058813.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18111567076826058813.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18111567076826058813.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18111567076826058813.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18111567076826058813.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:05.286 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:05.286 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:05.287 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:05.287 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:05.287 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:05.287 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:05.287 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:05.287 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:05 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18111567076826058813.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18111567076826058813.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18111567076826058813.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18111567076826058813.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:05 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18111567076826058813.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18111567076826058813.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18111567076826058813.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.18111567076826058813.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:05 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:05 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:05 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false) STANDARD_ERROR INFO 2024-07-02 11:50:05 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7855711480708987606.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7855711480708987606.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7855711480708987606.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7855711480708987606.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7855711480708987606.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7855711480708987606.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7855711480708987606.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7855711480708987606.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:05.475 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:05.475 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:05.475 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:05.475 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:05.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:05.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:05.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:05.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:05 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7855711480708987606.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7855711480708987606.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7855711480708987606.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7855711480708987606.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:05 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7855711480708987606.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7855711480708987606.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7855711480708987606.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7855711480708987606.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:05 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:05 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:05 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false) STANDARD_ERROR INFO 2024-07-02 11:50:05 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1142251610044617297.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1142251610044617297.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1142251610044617297.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1142251610044617297.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1142251610044617297.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1142251610044617297.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1142251610044617297.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1142251610044617297.tmp/output.sam Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:05.672 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:05.672 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:05.672 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:05.672 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:05.686 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:05.686 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:05.687 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:05.687 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:05 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1142251610044617297.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1142251610044617297.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1142251610044617297.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1142251610044617297.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:05 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1142251610044617297.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1142251610044617297.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1142251610044617297.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1142251610044617297.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Processed 5 records INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Processed 5 records Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:05 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:05 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:05 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoUnmappedFragments STANDARD_ERROR INFO 2024-07-02 11:50:05 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6439606441734902270.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6439606441734902270.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6439606441734902270.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6439606441734902270.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6439606441734902270.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6439606441734902270.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6439606441734902270.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6439606441734902270.tmp/output.sam Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:05.882 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:05.882 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:05.882 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:05.882 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:05.883 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:05.883 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:05.883 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:05.883 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:05 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6439606441734902270.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6439606441734902270.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6439606441734902270.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6439606441734902270.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:05 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6439606441734902270.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6439606441734902270.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6439606441734902270.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.6439606441734902270.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:50:05 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:05 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:05 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoUnmappedFragments(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:06 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar STANDARD_ERROR INFO 2024-07-02 11:50:06 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9894040487128247658.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9894040487128247658.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9894040487128247658.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9894040487128247658.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9894040487128247658.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9894040487128247658.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9894040487128247658.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9894040487128247658.tmp/output.sam Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:06.019 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:06.019 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:06.020 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:06.020 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:06.020 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:06.020 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:06.020 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:06.020 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:06 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9894040487128247658.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9894040487128247658.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9894040487128247658.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9894040487128247658.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:06 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9894040487128247658.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9894040487128247658.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9894040487128247658.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9894040487128247658.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:06 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:06 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testBadUmis[0]([AAAA, A], [AAAA, A], [false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testBadUmis[0]([AAAA, A], [AAAA, A], [false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:06 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testBadUmis[0]([AAAA, A], [AAAA, A], [false, false], 4) STANDARD_ERROR INFO 2024-07-02 11:50:06 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testBadUmis[0]([AAAA, A], [AAAA, A], [false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBadUmis[0]([AAAA, A], [AAAA, A], [false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadUmis[0]([AAAA, A], [AAAA, A], [false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBadUmis[0]([AAAA, A], [AAAA, A], [false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadUmis[0]([AAAA, A], [AAAA, A], [false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadUmis[0]([AAAA, A], [AAAA, A], [false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBadUmis[0]([AAAA, A], [AAAA, A], [false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadUmis[0]([AAAA, A], [AAAA, A], [false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBadUmis[0]([AAAA, A], [AAAA, A], [false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13969516791784580373.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13969516791784580373.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 4 -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13969516791784580373.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13969516791784580373.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13969516791784580373.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13969516791784580373.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 4 -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13969516791784580373.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13969516791784580373.tmp/output.sam Test: Test method testBadUmis[0]([AAAA, A], [AAAA, A], [false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBadUmis[0]([AAAA, A], [AAAA, A], [false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBadUmis[0]([AAAA, A], [AAAA, A], [false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBadUmis[0]([AAAA, A], [AAAA, A], [false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:06.228 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:06.228 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadUmis[0]([AAAA, A], [AAAA, A], [false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:06.229 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:06.229 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadUmis[0]([AAAA, A], [AAAA, A], [false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:06.229 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:06.229 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadUmis[0]([AAAA, A], [AAAA, A], [false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:06.230 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:06.230 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadUmis[0]([AAAA, A], [AAAA, A], [false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:06 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=4 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13969516791784580373.tmp/umi_metrics.txt INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13969516791784580373.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13969516791784580373.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13969516791784580373.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:06 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=4 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13969516791784580373.tmp/umi_metrics.txt INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13969516791784580373.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13969516791784580373.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13969516791784580373.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBadUmis[0]([AAAA, A], [AAAA, A], [false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBadUmis[0]([AAAA, A], [AAAA, A], [false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:06 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:06 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testBadUmis[0]([AAAA, A], [AAAA, A], [false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testBadUmis[0]([AAAA, A], [AAAA, A], [false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testBadUmis[1]([T, GG], [T, GG], [false, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testBadUmis[1]([T, GG], [T, GG], [false, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:06 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testBadUmis[1]([T, GG], [T, GG], [false, false], 1) STANDARD_ERROR INFO 2024-07-02 11:50:06 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testBadUmis[1]([T, GG], [T, GG], [false, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBadUmis[1]([T, GG], [T, GG], [false, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadUmis[1]([T, GG], [T, GG], [false, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBadUmis[1]([T, GG], [T, GG], [false, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadUmis[1]([T, GG], [T, GG], [false, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadUmis[1]([T, GG], [T, GG], [false, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBadUmis[1]([T, GG], [T, GG], [false, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadUmis[1]([T, GG], [T, GG], [false, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBadUmis[1]([T, GG], [T, GG], [false, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9782109949463079209.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9782109949463079209.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 1 -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9782109949463079209.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9782109949463079209.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9782109949463079209.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9782109949463079209.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 1 -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9782109949463079209.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9782109949463079209.tmp/output.sam Test: Test method testBadUmis[1]([T, GG], [T, GG], [false, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBadUmis[1]([T, GG], [T, GG], [false, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBadUmis[1]([T, GG], [T, GG], [false, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBadUmis[1]([T, GG], [T, GG], [false, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:06.340 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:06.340 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadUmis[1]([T, GG], [T, GG], [false, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:06.340 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:06.340 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadUmis[1]([T, GG], [T, GG], [false, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:06.341 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:06.341 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadUmis[1]([T, GG], [T, GG], [false, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:06.345 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:06.345 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadUmis[1]([T, GG], [T, GG], [false, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:06 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9782109949463079209.tmp/umi_metrics.txt INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9782109949463079209.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9782109949463079209.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9782109949463079209.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:06 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9782109949463079209.tmp/umi_metrics.txt INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9782109949463079209.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9782109949463079209.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.9782109949463079209.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBadUmis[1]([T, GG], [T, GG], [false, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBadUmis[1]([T, GG], [T, GG], [false, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:06 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:06 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testBadUmis[1]([T, GG], [T, GG], [false, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testBadUmis[1]([T, GG], [T, GG], [false, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testBadUmis[2]([TTGA, TTAT, null], [TTGA, TTAT, null], [false, false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testBadUmis[2]([TTGA, TTAT, null], [TTGA, TTAT, null], [false, false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:06 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testBadUmis[2]([TTGA, TTAT, null], [TTGA, TTAT, null], [false, false, false], 4) STANDARD_ERROR INFO 2024-07-02 11:50:06 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testBadUmis[2]([TTGA, TTAT, null], [TTGA, TTAT, null], [false, false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBadUmis[2]([TTGA, TTAT, null], [TTGA, TTAT, null], [false, false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadUmis[2]([TTGA, TTAT, null], [TTGA, TTAT, null], [false, false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBadUmis[2]([TTGA, TTAT, null], [TTGA, TTAT, null], [false, false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadUmis[2]([TTGA, TTAT, null], [TTGA, TTAT, null], [false, false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadUmis[2]([TTGA, TTAT, null], [TTGA, TTAT, null], [false, false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBadUmis[2]([TTGA, TTAT, null], [TTGA, TTAT, null], [false, false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadUmis[2]([TTGA, TTAT, null], [TTGA, TTAT, null], [false, false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBadUmis[2]([TTGA, TTAT, null], [TTGA, TTAT, null], [false, false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7730985880217631880.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7730985880217631880.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 4 -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7730985880217631880.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7730985880217631880.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7730985880217631880.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7730985880217631880.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 4 -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7730985880217631880.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7730985880217631880.tmp/output.sam Test: Test method testBadUmis[2]([TTGA, TTAT, null], [TTGA, TTAT, null], [false, false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testBadUmis[2]([TTGA, TTAT, null], [TTGA, TTAT, null], [false, false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBadUmis[2]([TTGA, TTAT, null], [TTGA, TTAT, null], [false, false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testBadUmis[2]([TTGA, TTAT, null], [TTGA, TTAT, null], [false, false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:06.434 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:06.434 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadUmis[2]([TTGA, TTAT, null], [TTGA, TTAT, null], [false, false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:06.434 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:06.434 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadUmis[2]([TTGA, TTAT, null], [TTGA, TTAT, null], [false, false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:06.435 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:06.435 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadUmis[2]([TTGA, TTAT, null], [TTGA, TTAT, null], [false, false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:06.435 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:06.435 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadUmis[2]([TTGA, TTAT, null], [TTGA, TTAT, null], [false, false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:06 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=4 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7730985880217631880.tmp/umi_metrics.txt INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7730985880217631880.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7730985880217631880.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7730985880217631880.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:06 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=4 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7730985880217631880.tmp/umi_metrics.txt INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7730985880217631880.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7730985880217631880.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7730985880217631880.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBadUmis[2]([TTGA, TTAT, null], [TTGA, TTAT, null], [false, false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBadUmis[2]([TTGA, TTAT, null], [TTGA, TTAT, null], [false, false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:06 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:06 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testBadUmis[2]([TTGA, TTAT, null], [TTGA, TTAT, null], [false, false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testBadUmis[2]([TTGA, TTAT, null], [TTGA, TTAT, null], [false, false, false], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testDuplexUmi[0](true, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testDuplexUmi[0](true, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:06 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testDuplexUmi[0](true, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ) STANDARD_ERROR INFO 2024-07-02 11:50:06 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testDuplexUmi[0](true, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testDuplexUmi[0](true, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDuplexUmi[0](true, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testDuplexUmi[0](true, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDuplexUmi[0](true, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDuplexUmi[0](true, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testDuplexUmi[0](true, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDuplexUmi[0](true, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testDuplexUmi[0](true, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15902464267246068151.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15902464267246068151.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 0 -DUPLEX_UMI true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15902464267246068151.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15902464267246068151.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15902464267246068151.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15902464267246068151.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 0 -DUPLEX_UMI true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15902464267246068151.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15902464267246068151.tmp/output.sam Test: Test method testDuplexUmi[0](true, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testDuplexUmi[0](true, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testDuplexUmi[0](true, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testDuplexUmi[0](true, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:06.556 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:06.556 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDuplexUmi[0](true, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:06.556 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:06.556 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDuplexUmi[0](true, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:06.556 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:06.556 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDuplexUmi[0](true, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:06.556 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:06.556 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDuplexUmi[0](true, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:06 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=0 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15902464267246068151.tmp/umi_metrics.txt DUPLEX_UMI=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15902464267246068151.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15902464267246068151.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15902464267246068151.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:06 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=0 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15902464267246068151.tmp/umi_metrics.txt DUPLEX_UMI=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15902464267246068151.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15902464267246068151.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15902464267246068151.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDuplexUmi[0](true, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDuplexUmi[0](true, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testDuplexUmi[0](true, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:06 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:06 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testDuplexUmi[0](true, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:06 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:50:06 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testDuplexUmi[0](true, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:06 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:06 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testDuplexUmi[0](true, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:06 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:06 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testDuplexUmi[0](true, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testDuplexUmi[1](false, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, false], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0.5 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testDuplexUmi[1](false, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, false], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0.5 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:06 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testDuplexUmi[1](false, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, false], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0.5 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ) STANDARD_ERROR INFO 2024-07-02 11:50:06 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testDuplexUmi[1](false, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, false], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0.5 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testDuplexUmi[1](false, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, false], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0.5 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDuplexUmi[1](false, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, false], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0.5 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testDuplexUmi[1](false, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, false], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0.5 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDuplexUmi[1](false, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, false], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0.5 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDuplexUmi[1](false, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, false], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0.5 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testDuplexUmi[1](false, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, false], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0.5 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDuplexUmi[1](false, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, false], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0.5 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testDuplexUmi[1](false, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, false], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0.5 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2261876172063037061.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2261876172063037061.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 0 -DUPLEX_UMI false -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2261876172063037061.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2261876172063037061.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2261876172063037061.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2261876172063037061.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 0 -DUPLEX_UMI false -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2261876172063037061.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2261876172063037061.tmp/output.sam Test: Test method testDuplexUmi[1](false, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, false], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0.5 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testDuplexUmi[1](false, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, false], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0.5 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testDuplexUmi[1](false, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, false], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0.5 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testDuplexUmi[1](false, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, false], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0.5 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:06.955 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:06.955 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDuplexUmi[1](false, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, false], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0.5 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:06.956 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:06.956 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDuplexUmi[1](false, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, false], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0.5 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:06.956 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:06.956 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDuplexUmi[1](false, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, false], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0.5 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:06.956 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:06.956 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDuplexUmi[1](false, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, false], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0.5 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:06 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=0 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2261876172063037061.tmp/umi_metrics.txt DUPLEX_UMI=false INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2261876172063037061.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2261876172063037061.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2261876172063037061.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:06 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=0 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2261876172063037061.tmp/umi_metrics.txt DUPLEX_UMI=false INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2261876172063037061.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2261876172063037061.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2261876172063037061.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDuplexUmi[1](false, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, false], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0.5 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDuplexUmi[1](false, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, false], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0.5 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:06 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testDuplexUmi[1](false, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, false], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0.5 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:06 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:06 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testDuplexUmi[1](false, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, false], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0.5 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:06 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:50:06 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testDuplexUmi[1](false, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, false], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0.5 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:06 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:50:06 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testDuplexUmi[1](false, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, false], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0.5 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:06 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:06 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testDuplexUmi[1](false, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, false], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0.5 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testDuplexUmi[2](true, 1, [AAA-GGG, GGG-ATA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testDuplexUmi[2](true, 1, [AAA-GGG, GGG-ATA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testDuplexUmi[2](true, 1, [AAA-GGG, GGG-ATA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 ) STANDARD_ERROR INFO 2024-07-02 11:50:07 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testDuplexUmi[2](true, 1, [AAA-GGG, GGG-ATA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testDuplexUmi[2](true, 1, [AAA-GGG, GGG-ATA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDuplexUmi[2](true, 1, [AAA-GGG, GGG-ATA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testDuplexUmi[2](true, 1, [AAA-GGG, GGG-ATA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDuplexUmi[2](true, 1, [AAA-GGG, GGG-ATA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDuplexUmi[2](true, 1, [AAA-GGG, GGG-ATA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testDuplexUmi[2](true, 1, [AAA-GGG, GGG-ATA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDuplexUmi[2](true, 1, [AAA-GGG, GGG-ATA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testDuplexUmi[2](true, 1, [AAA-GGG, GGG-ATA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.245799934587039347.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.245799934587039347.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 1 -DUPLEX_UMI true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.245799934587039347.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.245799934587039347.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.245799934587039347.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.245799934587039347.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 1 -DUPLEX_UMI true -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.245799934587039347.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.245799934587039347.tmp/output.sam Test: Test method testDuplexUmi[2](true, 1, [AAA-GGG, GGG-ATA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testDuplexUmi[2](true, 1, [AAA-GGG, GGG-ATA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testDuplexUmi[2](true, 1, [AAA-GGG, GGG-ATA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testDuplexUmi[2](true, 1, [AAA-GGG, GGG-ATA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.107 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:07.107 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDuplexUmi[2](true, 1, [AAA-GGG, GGG-ATA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.108 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:07.108 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDuplexUmi[2](true, 1, [AAA-GGG, GGG-ATA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.108 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:07.108 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDuplexUmi[2](true, 1, [AAA-GGG, GGG-ATA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.108 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:07.108 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDuplexUmi[2](true, 1, [AAA-GGG, GGG-ATA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:07 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.245799934587039347.tmp/umi_metrics.txt DUPLEX_UMI=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.245799934587039347.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.245799934587039347.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.245799934587039347.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:07 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.245799934587039347.tmp/umi_metrics.txt DUPLEX_UMI=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.245799934587039347.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.245799934587039347.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.245799934587039347.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDuplexUmi[2](true, 1, [AAA-GGG, GGG-ATA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDuplexUmi[2](true, 1, [AAA-GGG, GGG-ATA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testDuplexUmi[2](true, 1, [AAA-GGG, GGG-ATA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testDuplexUmi[2](true, 1, [AAA-GGG, GGG-ATA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testDuplexUmi[2](true, 1, [AAA-GGG, GGG-ATA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testDuplexUmi[2](true, 1, [AAA-GGG, GGG-ATA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:07 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:07 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testDuplexUmi[2](true, 1, [AAA-GGG, GGG-ATA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testEmptyUmis[0]([null, null, null], [null, null, null], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testEmptyUmis[0]([null, null, null], [null, null, null], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testEmptyUmis[0]([null, null, null], [null, null, null], [false, true, true], 4) STANDARD_ERROR INFO 2024-07-02 11:50:07 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testEmptyUmis[0]([null, null, null], [null, null, null], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testEmptyUmis[0]([null, null, null], [null, null, null], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testEmptyUmis[0]([null, null, null], [null, null, null], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testEmptyUmis[0]([null, null, null], [null, null, null], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testEmptyUmis[0]([null, null, null], [null, null, null], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testEmptyUmis[0]([null, null, null], [null, null, null], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testEmptyUmis[0]([null, null, null], [null, null, null], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testEmptyUmis[0]([null, null, null], [null, null, null], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testEmptyUmis[0]([null, null, null], [null, null, null], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1681762143583054674.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1681762143583054674.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -MAX_EDIT_DISTANCE_TO_JOIN 4 -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1681762143583054674.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1681762143583054674.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1681762143583054674.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1681762143583054674.tmp/umi_metrics.txt -ALLOW_MISSING_UMIS true -MAX_EDIT_DISTANCE_TO_JOIN 4 -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1681762143583054674.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1681762143583054674.tmp/output.sam Test: Test method testEmptyUmis[0]([null, null, null], [null, null, null], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testEmptyUmis[0]([null, null, null], [null, null, null], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testEmptyUmis[0]([null, null, null], [null, null, null], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testEmptyUmis[0]([null, null, null], [null, null, null], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.316 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:07.316 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEmptyUmis[0]([null, null, null], [null, null, null], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.329 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:07.329 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEmptyUmis[0]([null, null, null], [null, null, null], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.330 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:07.330 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEmptyUmis[0]([null, null, null], [null, null, null], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.330 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:07.330 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEmptyUmis[0]([null, null, null], [null, null, null], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:07 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=4 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1681762143583054674.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1681762143583054674.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1681762143583054674.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1681762143583054674.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:07 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=4 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1681762143583054674.tmp/umi_metrics.txt ALLOW_MISSING_UMIS=true INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1681762143583054674.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1681762143583054674.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1681762143583054674.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testEmptyUmis[0]([null, null, null], [null, null, null], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testEmptyUmis[0]([null, null, null], [null, null, null], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testEmptyUmis[0]([null, null, null], [null, null, null], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testEmptyUmis[0]([null, null, null], [null, null, null], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Processed 6 records INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Processed 6 records Test: Test method testEmptyUmis[0]([null, null, null], [null, null, null], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. Test: Test method testEmptyUmis[0]([null, null, null], [null, null, null], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:07 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:07 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testEmptyUmis[0]([null, null, null], [null, null, null], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ]) STANDARD_ERROR INFO 2024-07-02 11:50:07 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4696703832214557372.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4696703832214557372.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 1 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4696703832214557372.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4696703832214557372.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4696703832214557372.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4696703832214557372.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 1 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4696703832214557372.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4696703832214557372.tmp/output.sam Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:07.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.478 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:07.478 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.479 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:07.479 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.479 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:07.479 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:07 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4696703832214557372.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4696703832214557372.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4696703832214557372.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4696703832214557372.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:07 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4696703832214557372.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4696703832214557372.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4696703832214557372.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4696703832214557372.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Processed 6 records INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Processed 6 records Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:07 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:07 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 UmiAwareMarkDuplicatesWithMateCigar INFO 2024-07-02 11:50:07 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11131740396111583542.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11131740396111583542.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 1 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11131740396111583542.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11131740396111583542.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11131740396111583542.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11131740396111583542.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 1 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11131740396111583542.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11131740396111583542.tmp/output.sam Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.587 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:07.587 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.588 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:07.588 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.588 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:07.588 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.588 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:07.588 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:07 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11131740396111583542.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11131740396111583542.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11131740396111583542.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11131740396111583542.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:07 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11131740396111583542.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11131740396111583542.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11131740396111583542.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.11131740396111583542.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:07 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:07 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ]) STANDARD_ERROR INFO 2024-07-02 11:50:07 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2045539436382144113.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2045539436382144113.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 1 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2045539436382144113.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2045539436382144113.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2045539436382144113.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2045539436382144113.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 1 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2045539436382144113.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2045539436382144113.tmp/output.sam Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.661 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:07.661 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.661 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:07.661 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.661 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:07.661 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.661 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:07.661 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:07 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2045539436382144113.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2045539436382144113.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2045539436382144113.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2045539436382144113.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:07 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2045539436382144113.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2045539436382144113.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2045539436382144113.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2045539436382144113.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:07 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:07 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 UmiAwareMarkDuplicatesWithMateCigar INFO 2024-07-02 11:50:07 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2179910126509110920.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2179910126509110920.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 1 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2179910126509110920.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2179910126509110920.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2179910126509110920.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2179910126509110920.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 1 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2179910126509110920.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2179910126509110920.tmp/output.sam Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.749 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:07.749 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.749 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:07.749 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.749 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:07.749 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.749 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:07.749 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:07 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2179910126509110920.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2179910126509110920.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2179910126509110920.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2179910126509110920.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:07 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2179910126509110920.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2179910126509110920.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2179910126509110920.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2179910126509110920.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Processed 2 records INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Processed 2 records Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:07 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:07 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 UmiAwareMarkDuplicatesWithMateCigar INFO 2024-07-02 11:50:07 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1409890293453320069.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1409890293453320069.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 1 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1409890293453320069.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1409890293453320069.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1409890293453320069.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1409890293453320069.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 1 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1409890293453320069.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1409890293453320069.tmp/output.sam Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.811 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:07.811 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.812 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:07.812 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.812 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:07.812 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.812 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:07.812 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:07 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1409890293453320069.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1409890293453320069.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1409890293453320069.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1409890293453320069.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:07 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1409890293453320069.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1409890293453320069.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1409890293453320069.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.1409890293453320069.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Processed 6 records INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Processed 6 records Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:07 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:07 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ])(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testUmi[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testUmi[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testUmi[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1) STANDARD_ERROR INFO 2024-07-02 11:50:07 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testUmi[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmi[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testUmi[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testUmi[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testUmi[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testUmi[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16749768150907730535.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16749768150907730535.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 1 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16749768150907730535.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16749768150907730535.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16749768150907730535.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16749768150907730535.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 1 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16749768150907730535.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16749768150907730535.tmp/output.sam Test: Test method testUmi[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmi[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmi[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.894 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:07.894 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUmi[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.895 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:07.895 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUmi[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.895 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:07.895 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUmi[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:07.895 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:07.895 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUmi[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:07 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16749768150907730535.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16749768150907730535.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16749768150907730535.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16749768150907730535.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:07 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16749768150907730535.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16749768150907730535.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16749768150907730535.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16749768150907730535.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testUmi[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testUmi[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:07 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testUmi[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testUmi[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Processed 10 records INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Processed 10 records Test: Test method testUmi[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Marking 6 records as duplicates. INFO 2024-07-02 11:50:07 MarkDuplicatesWithMateCigar Marking 6 records as duplicates. Test: Test method testUmi[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:07 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:07 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testUmi[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testUmi[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testUmi[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:08 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testUmi[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2) STANDARD_ERROR INFO 2024-07-02 11:50:08 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testUmi[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmi[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testUmi[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testUmi[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testUmi[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testUmi[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2654752524478849051.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2654752524478849051.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 2 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2654752524478849051.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2654752524478849051.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2654752524478849051.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2654752524478849051.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 2 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2654752524478849051.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2654752524478849051.tmp/output.sam Test: Test method testUmi[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmi[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmi[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:08.067 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:08.067 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUmi[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:08.067 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:08.067 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUmi[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:08.068 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:08.068 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUmi[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:08.068 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:08.068 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUmi[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:08 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=2 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2654752524478849051.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2654752524478849051.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2654752524478849051.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2654752524478849051.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:08 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=2 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2654752524478849051.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2654752524478849051.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2654752524478849051.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.2654752524478849051.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testUmi[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testUmi[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testUmi[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testUmi[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Processed 10 records INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Processed 10 records Test: Test method testUmi[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. Test: Test method testUmi[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:08 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:08 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testUmi[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testUmi[2]([AAAA, AAAA, AAAT, AAGT, ACGT, TCGT, CCCC], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, CCCC], [false, true, true, true, true, true, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testUmi[2]([AAAA, AAAA, AAAT, AAGT, ACGT, TCGT, CCCC], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, CCCC], [false, true, true, true, true, true, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:08 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testUmi[2]([AAAA, AAAA, AAAT, AAGT, ACGT, TCGT, CCCC], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, CCCC], [false, true, true, true, true, true, false], 1) STANDARD_ERROR INFO 2024-07-02 11:50:08 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testUmi[2]([AAAA, AAAA, AAAT, AAGT, ACGT, TCGT, CCCC], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, CCCC], [false, true, true, true, true, true, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmi[2]([AAAA, AAAA, AAAT, AAGT, ACGT, TCGT, CCCC], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, CCCC], [false, true, true, true, true, true, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testUmi[2]([AAAA, AAAA, AAAT, AAGT, ACGT, TCGT, CCCC], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, CCCC], [false, true, true, true, true, true, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[2]([AAAA, AAAA, AAAT, AAGT, ACGT, TCGT, CCCC], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, CCCC], [false, true, true, true, true, true, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testUmi[2]([AAAA, AAAA, AAAT, AAGT, ACGT, TCGT, CCCC], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, CCCC], [false, true, true, true, true, true, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testUmi[2]([AAAA, AAAA, AAAT, AAGT, ACGT, TCGT, CCCC], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, CCCC], [false, true, true, true, true, true, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[2]([AAAA, AAAA, AAAT, AAGT, ACGT, TCGT, CCCC], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, CCCC], [false, true, true, true, true, true, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testUmi[2]([AAAA, AAAA, AAAT, AAGT, ACGT, TCGT, CCCC], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, CCCC], [false, true, true, true, true, true, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[2]([AAAA, AAAA, AAAT, AAGT, ACGT, TCGT, CCCC], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, CCCC], [false, true, true, true, true, true, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16507144028269039100.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16507144028269039100.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 1 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16507144028269039100.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16507144028269039100.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16507144028269039100.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16507144028269039100.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 1 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16507144028269039100.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16507144028269039100.tmp/output.sam Test: Test method testUmi[2]([AAAA, AAAA, AAAT, AAGT, ACGT, TCGT, CCCC], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, CCCC], [false, true, true, true, true, true, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[2]([AAAA, AAAA, AAAT, AAGT, ACGT, TCGT, CCCC], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, CCCC], [false, true, true, true, true, true, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmi[2]([AAAA, AAAA, AAAT, AAGT, ACGT, TCGT, CCCC], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, CCCC], [false, true, true, true, true, true, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmi[2]([AAAA, AAAA, AAAT, AAGT, ACGT, TCGT, CCCC], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, CCCC], [false, true, true, true, true, true, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:08.277 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:08.277 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUmi[2]([AAAA, AAAA, AAAT, AAGT, ACGT, TCGT, CCCC], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, CCCC], [false, true, true, true, true, true, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:08.277 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:08.277 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUmi[2]([AAAA, AAAA, AAAT, AAGT, ACGT, TCGT, CCCC], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, CCCC], [false, true, true, true, true, true, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:08.278 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:08.278 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUmi[2]([AAAA, AAAA, AAAT, AAGT, ACGT, TCGT, CCCC], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, CCCC], [false, true, true, true, true, true, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:08.278 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:08.278 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUmi[2]([AAAA, AAAA, AAAT, AAGT, ACGT, TCGT, CCCC], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, CCCC], [false, true, true, true, true, true, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:08 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16507144028269039100.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16507144028269039100.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16507144028269039100.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16507144028269039100.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:08 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16507144028269039100.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16507144028269039100.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16507144028269039100.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.16507144028269039100.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testUmi[2]([AAAA, AAAA, AAAT, AAGT, ACGT, TCGT, CCCC], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, CCCC], [false, true, true, true, true, true, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testUmi[2]([AAAA, AAAA, AAAT, AAGT, ACGT, TCGT, CCCC], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, CCCC], [false, true, true, true, true, true, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testUmi[2]([AAAA, AAAA, AAAT, AAGT, ACGT, TCGT, CCCC], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, CCCC], [false, true, true, true, true, true, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testUmi[2]([AAAA, AAAA, AAAT, AAGT, ACGT, TCGT, CCCC], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, CCCC], [false, true, true, true, true, true, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Processed 14 records INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Processed 14 records Test: Test method testUmi[2]([AAAA, AAAA, AAAT, AAGT, ACGT, TCGT, CCCC], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, CCCC], [false, true, true, true, true, true, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Marking 10 records as duplicates. INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Marking 10 records as duplicates. Test: Test method testUmi[2]([AAAA, AAAA, AAAT, AAGT, ACGT, TCGT, CCCC], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, CCCC], [false, true, true, true, true, true, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:08 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:08 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testUmi[2]([AAAA, AAAA, AAAT, AAGT, ACGT, TCGT, CCCC], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, CCCC], [false, true, true, true, true, true, false], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testUmi[3]([A, A, T, G, G, C, C, A], [A, A, A, A, A, A, A, A], [false, true, true, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testUmi[3]([A, A, T, G, G, C, C, A], [A, A, A, A, A, A, A, A], [false, true, true, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:08 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testUmi[3]([A, A, T, G, G, C, C, A], [A, A, A, A, A, A, A, A], [false, true, true, true, true, true, true, true], 1) STANDARD_ERROR INFO 2024-07-02 11:50:08 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testUmi[3]([A, A, T, G, G, C, C, A], [A, A, A, A, A, A, A, A], [false, true, true, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmi[3]([A, A, T, G, G, C, C, A], [A, A, A, A, A, A, A, A], [false, true, true, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testUmi[3]([A, A, T, G, G, C, C, A], [A, A, A, A, A, A, A, A], [false, true, true, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[3]([A, A, T, G, G, C, C, A], [A, A, A, A, A, A, A, A], [false, true, true, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testUmi[3]([A, A, T, G, G, C, C, A], [A, A, A, A, A, A, A, A], [false, true, true, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testUmi[3]([A, A, T, G, G, C, C, A], [A, A, A, A, A, A, A, A], [false, true, true, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[3]([A, A, T, G, G, C, C, A], [A, A, A, A, A, A, A, A], [false, true, true, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testUmi[3]([A, A, T, G, G, C, C, A], [A, A, A, A, A, A, A, A], [false, true, true, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[3]([A, A, T, G, G, C, C, A], [A, A, A, A, A, A, A, A], [false, true, true, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10913631157865368750.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10913631157865368750.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 1 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10913631157865368750.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10913631157865368750.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10913631157865368750.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10913631157865368750.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 1 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10913631157865368750.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10913631157865368750.tmp/output.sam Test: Test method testUmi[3]([A, A, T, G, G, C, C, A], [A, A, A, A, A, A, A, A], [false, true, true, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[3]([A, A, T, G, G, C, C, A], [A, A, A, A, A, A, A, A], [false, true, true, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmi[3]([A, A, T, G, G, C, C, A], [A, A, A, A, A, A, A, A], [false, true, true, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmi[3]([A, A, T, G, G, C, C, A], [A, A, A, A, A, A, A, A], [false, true, true, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:08.590 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:08.590 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUmi[3]([A, A, T, G, G, C, C, A], [A, A, A, A, A, A, A, A], [false, true, true, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:08.590 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:08.590 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUmi[3]([A, A, T, G, G, C, C, A], [A, A, A, A, A, A, A, A], [false, true, true, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:08.591 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:08.591 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUmi[3]([A, A, T, G, G, C, C, A], [A, A, A, A, A, A, A, A], [false, true, true, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:08.591 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:08.591 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUmi[3]([A, A, T, G, G, C, C, A], [A, A, A, A, A, A, A, A], [false, true, true, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:08 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10913631157865368750.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10913631157865368750.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10913631157865368750.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10913631157865368750.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:08 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10913631157865368750.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10913631157865368750.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10913631157865368750.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10913631157865368750.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testUmi[3]([A, A, T, G, G, C, C, A], [A, A, A, A, A, A, A, A], [false, true, true, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testUmi[3]([A, A, T, G, G, C, C, A], [A, A, A, A, A, A, A, A], [false, true, true, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testUmi[3]([A, A, T, G, G, C, C, A], [A, A, A, A, A, A, A, A], [false, true, true, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testUmi[3]([A, A, T, G, G, C, C, A], [A, A, A, A, A, A, A, A], [false, true, true, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Processed 16 records INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Processed 16 records Test: Test method testUmi[3]([A, A, T, G, G, C, C, A], [A, A, A, A, A, A, A, A], [false, true, true, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Marking 14 records as duplicates. INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Marking 14 records as duplicates. Test: Test method testUmi[3]([A, A, T, G, G, C, C, A], [A, A, A, A, A, A, A, A], [false, true, true, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:08 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:08 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testUmi[3]([A, A, T, G, G, C, C, A], [A, A, A, A, A, A, A, A], [false, true, true, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testUmi[4]([A, A, T, G, G, C, C, A], [A, A, T, G, G, C, C, A], [false, true, false, false, true, false, true, true], 0)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testUmi[4]([A, A, T, G, G, C, C, A], [A, A, T, G, G, C, C, A], [false, true, false, false, true, false, true, true], 0)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:08 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testUmi[4]([A, A, T, G, G, C, C, A], [A, A, T, G, G, C, C, A], [false, true, false, false, true, false, true, true], 0) STANDARD_ERROR INFO 2024-07-02 11:50:08 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testUmi[4]([A, A, T, G, G, C, C, A], [A, A, T, G, G, C, C, A], [false, true, false, false, true, false, true, true], 0)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmi[4]([A, A, T, G, G, C, C, A], [A, A, T, G, G, C, C, A], [false, true, false, false, true, false, true, true], 0)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testUmi[4]([A, A, T, G, G, C, C, A], [A, A, T, G, G, C, C, A], [false, true, false, false, true, false, true, true], 0)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[4]([A, A, T, G, G, C, C, A], [A, A, T, G, G, C, C, A], [false, true, false, false, true, false, true, true], 0)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testUmi[4]([A, A, T, G, G, C, C, A], [A, A, T, G, G, C, C, A], [false, true, false, false, true, false, true, true], 0)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testUmi[4]([A, A, T, G, G, C, C, A], [A, A, T, G, G, C, C, A], [false, true, false, false, true, false, true, true], 0)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[4]([A, A, T, G, G, C, C, A], [A, A, T, G, G, C, C, A], [false, true, false, false, true, false, true, true], 0)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testUmi[4]([A, A, T, G, G, C, C, A], [A, A, T, G, G, C, C, A], [false, true, false, false, true, false, true, true], 0)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[4]([A, A, T, G, G, C, C, A], [A, A, T, G, G, C, C, A], [false, true, false, false, true, false, true, true], 0)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4649556107269137859.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4649556107269137859.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 0 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4649556107269137859.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4649556107269137859.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4649556107269137859.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4649556107269137859.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 0 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4649556107269137859.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4649556107269137859.tmp/output.sam Test: Test method testUmi[4]([A, A, T, G, G, C, C, A], [A, A, T, G, G, C, C, A], [false, true, false, false, true, false, true, true], 0)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[4]([A, A, T, G, G, C, C, A], [A, A, T, G, G, C, C, A], [false, true, false, false, true, false, true, true], 0)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmi[4]([A, A, T, G, G, C, C, A], [A, A, T, G, G, C, C, A], [false, true, false, false, true, false, true, true], 0)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmi[4]([A, A, T, G, G, C, C, A], [A, A, T, G, G, C, C, A], [false, true, false, false, true, false, true, true], 0)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:08.703 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:08.703 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUmi[4]([A, A, T, G, G, C, C, A], [A, A, T, G, G, C, C, A], [false, true, false, false, true, false, true, true], 0)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:08.703 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:08.703 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUmi[4]([A, A, T, G, G, C, C, A], [A, A, T, G, G, C, C, A], [false, true, false, false, true, false, true, true], 0)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:08.704 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:08.704 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUmi[4]([A, A, T, G, G, C, C, A], [A, A, T, G, G, C, C, A], [false, true, false, false, true, false, true, true], 0)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:08.704 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:08.704 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUmi[4]([A, A, T, G, G, C, C, A], [A, A, T, G, G, C, C, A], [false, true, false, false, true, false, true, true], 0)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:08 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=0 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4649556107269137859.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4649556107269137859.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4649556107269137859.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4649556107269137859.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:08 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=0 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4649556107269137859.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4649556107269137859.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4649556107269137859.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4649556107269137859.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testUmi[4]([A, A, T, G, G, C, C, A], [A, A, T, G, G, C, C, A], [false, true, false, false, true, false, true, true], 0)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testUmi[4]([A, A, T, G, G, C, C, A], [A, A, T, G, G, C, C, A], [false, true, false, false, true, false, true, true], 0)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testUmi[4]([A, A, T, G, G, C, C, A], [A, A, T, G, G, C, C, A], [false, true, false, false, true, false, true, true], 0)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testUmi[4]([A, A, T, G, G, C, C, A], [A, A, T, G, G, C, C, A], [false, true, false, false, true, false, true, true], 0)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Processed 16 records INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Processed 16 records Test: Test method testUmi[4]([A, A, T, G, G, C, C, A], [A, A, T, G, G, C, C, A], [false, true, false, false, true, false, true, true], 0)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. Test: Test method testUmi[4]([A, A, T, G, G, C, C, A], [A, A, T, G, G, C, C, A], [false, true, false, false, true, false, true, true], 0)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:08 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:08 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testUmi[4]([A, A, T, G, G, C, C, A], [A, A, T, G, G, C, C, A], [false, true, false, false, true, false, true, true], 0)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testUmi[5]([TTGACATCCA, ATGCCATCGA, AAGTCACCGT], [TTGACATCCA, TTGACATCCA, TTGACATCCA], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testUmi[5]([TTGACATCCA, ATGCCATCGA, AAGTCACCGT], [TTGACATCCA, TTGACATCCA, TTGACATCCA], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:08 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testUmi[5]([TTGACATCCA, ATGCCATCGA, AAGTCACCGT], [TTGACATCCA, TTGACATCCA, TTGACATCCA], [false, true, true], 4) STANDARD_ERROR INFO 2024-07-02 11:50:08 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testUmi[5]([TTGACATCCA, ATGCCATCGA, AAGTCACCGT], [TTGACATCCA, TTGACATCCA, TTGACATCCA], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmi[5]([TTGACATCCA, ATGCCATCGA, AAGTCACCGT], [TTGACATCCA, TTGACATCCA, TTGACATCCA], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testUmi[5]([TTGACATCCA, ATGCCATCGA, AAGTCACCGT], [TTGACATCCA, TTGACATCCA, TTGACATCCA], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[5]([TTGACATCCA, ATGCCATCGA, AAGTCACCGT], [TTGACATCCA, TTGACATCCA, TTGACATCCA], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testUmi[5]([TTGACATCCA, ATGCCATCGA, AAGTCACCGT], [TTGACATCCA, TTGACATCCA, TTGACATCCA], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testUmi[5]([TTGACATCCA, ATGCCATCGA, AAGTCACCGT], [TTGACATCCA, TTGACATCCA, TTGACATCCA], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[5]([TTGACATCCA, ATGCCATCGA, AAGTCACCGT], [TTGACATCCA, TTGACATCCA, TTGACATCCA], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testUmi[5]([TTGACATCCA, ATGCCATCGA, AAGTCACCGT], [TTGACATCCA, TTGACATCCA, TTGACATCCA], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[5]([TTGACATCCA, ATGCCATCGA, AAGTCACCGT], [TTGACATCCA, TTGACATCCA, TTGACATCCA], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4623690535223903777.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4623690535223903777.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 4 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4623690535223903777.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4623690535223903777.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4623690535223903777.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4623690535223903777.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 4 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4623690535223903777.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4623690535223903777.tmp/output.sam Test: Test method testUmi[5]([TTGACATCCA, ATGCCATCGA, AAGTCACCGT], [TTGACATCCA, TTGACATCCA, TTGACATCCA], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[5]([TTGACATCCA, ATGCCATCGA, AAGTCACCGT], [TTGACATCCA, TTGACATCCA, TTGACATCCA], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmi[5]([TTGACATCCA, ATGCCATCGA, AAGTCACCGT], [TTGACATCCA, TTGACATCCA, TTGACATCCA], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmi[5]([TTGACATCCA, ATGCCATCGA, AAGTCACCGT], [TTGACATCCA, TTGACATCCA, TTGACATCCA], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:08.829 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:08.829 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUmi[5]([TTGACATCCA, ATGCCATCGA, AAGTCACCGT], [TTGACATCCA, TTGACATCCA, TTGACATCCA], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:08.830 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:08.830 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUmi[5]([TTGACATCCA, ATGCCATCGA, AAGTCACCGT], [TTGACATCCA, TTGACATCCA, TTGACATCCA], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:08.830 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:08.830 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUmi[5]([TTGACATCCA, ATGCCATCGA, AAGTCACCGT], [TTGACATCCA, TTGACATCCA, TTGACATCCA], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:08.830 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:08.830 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUmi[5]([TTGACATCCA, ATGCCATCGA, AAGTCACCGT], [TTGACATCCA, TTGACATCCA, TTGACATCCA], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:08 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=4 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4623690535223903777.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4623690535223903777.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4623690535223903777.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4623690535223903777.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:08 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=4 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4623690535223903777.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4623690535223903777.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4623690535223903777.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.4623690535223903777.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testUmi[5]([TTGACATCCA, ATGCCATCGA, AAGTCACCGT], [TTGACATCCA, TTGACATCCA, TTGACATCCA], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testUmi[5]([TTGACATCCA, ATGCCATCGA, AAGTCACCGT], [TTGACATCCA, TTGACATCCA, TTGACATCCA], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:08 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testUmi[5]([TTGACATCCA, ATGCCATCGA, AAGTCACCGT], [TTGACATCCA, TTGACATCCA, TTGACATCCA], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testUmi[5]([TTGACATCCA, ATGCCATCGA, AAGTCACCGT], [TTGACATCCA, TTGACATCCA, TTGACATCCA], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Processed 6 records INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Processed 6 records Test: Test method testUmi[5]([TTGACATCCA, ATGCCATCGA, AAGTCACCGT], [TTGACATCCA, TTGACATCCA, TTGACATCCA], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. INFO 2024-07-02 11:50:08 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. Test: Test method testUmi[5]([TTGACATCCA, ATGCCATCGA, AAGTCACCGT], [TTGACATCCA, TTGACATCCA, TTGACATCCA], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:08 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:08 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testUmi[5]([TTGACATCCA, ATGCCATCGA, AAGTCACCGT], [TTGACATCCA, TTGACATCCA, TTGACATCCA], [false, true, true], 4)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testUmi[6]([AAAN, AANN], [AAAN, AAAN], [false, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testUmi[6]([AAAN, AANN], [AAAN, AAAN], [false, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:08 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testUmi[6]([AAAN, AANN], [AAAN, AAAN], [false, true], 1) STANDARD_ERROR INFO 2024-07-02 11:50:08 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testUmi[6]([AAAN, AANN], [AAAN, AAAN], [false, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmi[6]([AAAN, AANN], [AAAN, AAAN], [false, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testUmi[6]([AAAN, AANN], [AAAN, AAAN], [false, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[6]([AAAN, AANN], [AAAN, AAAN], [false, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testUmi[6]([AAAN, AANN], [AAAN, AAAN], [false, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testUmi[6]([AAAN, AANN], [AAAN, AAAN], [false, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[6]([AAAN, AANN], [AAAN, AAAN], [false, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testUmi[6]([AAAN, AANN], [AAAN, AAAN], [false, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[6]([AAAN, AANN], [AAAN, AAAN], [false, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13320360652698965226.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13320360652698965226.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 1 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13320360652698965226.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13320360652698965226.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13320360652698965226.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13320360652698965226.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 1 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13320360652698965226.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13320360652698965226.tmp/output.sam Test: Test method testUmi[6]([AAAN, AANN], [AAAN, AAAN], [false, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[6]([AAAN, AANN], [AAAN, AAAN], [false, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmi[6]([AAAN, AANN], [AAAN, AAAN], [false, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmi[6]([AAAN, AANN], [AAAN, AAAN], [false, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:08.991 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:08.991 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUmi[6]([AAAN, AANN], [AAAN, AAAN], [false, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:08.991 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:08.991 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUmi[6]([AAAN, AANN], [AAAN, AAAN], [false, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:08.991 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:08.991 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUmi[6]([AAAN, AANN], [AAAN, AAAN], [false, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:08.991 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:08.991 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUmi[6]([AAAN, AANN], [AAAN, AAAN], [false, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:08 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13320360652698965226.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13320360652698965226.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13320360652698965226.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13320360652698965226.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:08 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13320360652698965226.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13320360652698965226.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13320360652698965226.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.13320360652698965226.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testUmi[6]([AAAN, AANN], [AAAN, AAAN], [false, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testUmi[6]([AAAN, AANN], [AAAN, AAAN], [false, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:09 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:09 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testUmi[6]([AAAN, AANN], [AAAN, AAAN], [false, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testUmi[6]([AAAN, AANN], [AAAN, AAAN], [false, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Processed 4 records INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Processed 4 records Test: Test method testUmi[6]([AAAN, AANN], [AAAN, AAAN], [false, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. Test: Test method testUmi[6]([AAAN, AANN], [AAAN, AAAN], [false, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:09 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testUmi[6]([AAAN, AANN], [AAAN, AAAN], [false, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testUmi[7]([AAAN, AAAN, AAAA, AAAA, AAAN], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testUmi[7]([AAAN, AAAN, AAAA, AAAA, AAAN], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:09 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testUmi[7]([AAAN, AAAN, AAAA, AAAA, AAAN], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 1) STANDARD_ERROR INFO 2024-07-02 11:50:09 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testUmi[7]([AAAN, AAAN, AAAA, AAAA, AAAN], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmi[7]([AAAN, AAAN, AAAA, AAAA, AAAN], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testUmi[7]([AAAN, AAAN, AAAA, AAAA, AAAN], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[7]([AAAN, AAAN, AAAA, AAAA, AAAN], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testUmi[7]([AAAN, AAAN, AAAA, AAAA, AAAN], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testUmi[7]([AAAN, AAAN, AAAA, AAAA, AAAN], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[7]([AAAN, AAAN, AAAA, AAAA, AAAN], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testUmi[7]([AAAN, AAAN, AAAA, AAAA, AAAN], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[7]([AAAN, AAAN, AAAA, AAAA, AAAN], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3665009473048294813.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3665009473048294813.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 1 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3665009473048294813.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3665009473048294813.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3665009473048294813.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3665009473048294813.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 1 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3665009473048294813.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3665009473048294813.tmp/output.sam Test: Test method testUmi[7]([AAAN, AAAN, AAAA, AAAA, AAAN], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[7]([AAAN, AAAN, AAAA, AAAA, AAAN], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmi[7]([AAAN, AAAN, AAAA, AAAA, AAAN], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmi[7]([AAAN, AAAN, AAAA, AAAA, AAAN], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:09.099 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:09.099 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUmi[7]([AAAN, AAAN, AAAA, AAAA, AAAN], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:09.099 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:09.099 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUmi[7]([AAAN, AAAN, AAAA, AAAA, AAAN], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:09.099 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:09.099 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUmi[7]([AAAN, AAAN, AAAA, AAAA, AAAN], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:09.099 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:09.099 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUmi[7]([AAAN, AAAN, AAAA, AAAA, AAAN], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3665009473048294813.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3665009473048294813.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3665009473048294813.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3665009473048294813.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:09 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3665009473048294813.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3665009473048294813.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3665009473048294813.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.3665009473048294813.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testUmi[7]([AAAN, AAAN, AAAA, AAAA, AAAN], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testUmi[7]([AAAN, AAAN, AAAA, AAAA, AAAN], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:09 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:09 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testUmi[7]([AAAN, AAAN, AAAA, AAAA, AAAN], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testUmi[7]([AAAN, AAAN, AAAA, AAAA, AAAN], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Processed 10 records INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Processed 10 records Test: Test method testUmi[7]([AAAN, AAAN, AAAA, AAAA, AAAN], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. Test: Test method testUmi[7]([AAAN, AAAN, AAAA, AAAA, AAAN], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:09 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testUmi[7]([AAAN, AAAN, AAAA, AAAA, AAAN], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testUmi[8]([AAAN, AAAN, AANN, AANN, AANN], [AAAN, AAAN, AAAN, AAAN, AAAN], [false, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testUmi[8]([AAAN, AAAN, AANN, AANN, AANN], [AAAN, AAAN, AAAN, AAAN, AAAN], [false, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:09 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testUmi[8]([AAAN, AAAN, AANN, AANN, AANN], [AAAN, AAAN, AAAN, AAAN, AAAN], [false, true, true, true, true, true], 1) STANDARD_ERROR INFO 2024-07-02 11:50:09 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testUmi[8]([AAAN, AAAN, AANN, AANN, AANN], [AAAN, AAAN, AAAN, AAAN, AAAN], [false, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmi[8]([AAAN, AAAN, AANN, AANN, AANN], [AAAN, AAAN, AAAN, AAAN, AAAN], [false, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testUmi[8]([AAAN, AAAN, AANN, AANN, AANN], [AAAN, AAAN, AAAN, AAAN, AAAN], [false, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[8]([AAAN, AAAN, AANN, AANN, AANN], [AAAN, AAAN, AAAN, AAAN, AAAN], [false, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testUmi[8]([AAAN, AAAN, AANN, AANN, AANN], [AAAN, AAAN, AAAN, AAAN, AAAN], [false, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testUmi[8]([AAAN, AAAN, AANN, AANN, AANN], [AAAN, AAAN, AAAN, AAAN, AAAN], [false, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[8]([AAAN, AAAN, AANN, AANN, AANN], [AAAN, AAAN, AAAN, AAAN, AAAN], [false, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testUmi[8]([AAAN, AAAN, AANN, AANN, AANN], [AAAN, AAAN, AAAN, AAAN, AAAN], [false, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[8]([AAAN, AAAN, AANN, AANN, AANN], [AAAN, AAAN, AAAN, AAAN, AAAN], [false, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17708160277085061886.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17708160277085061886.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 1 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17708160277085061886.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17708160277085061886.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17708160277085061886.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17708160277085061886.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 1 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17708160277085061886.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17708160277085061886.tmp/output.sam Test: Test method testUmi[8]([AAAN, AAAN, AANN, AANN, AANN], [AAAN, AAAN, AAAN, AAAN, AAAN], [false, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmi[8]([AAAN, AAAN, AANN, AANN, AANN], [AAAN, AAAN, AAAN, AAAN, AAAN], [false, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmi[8]([AAAN, AAAN, AANN, AANN, AANN], [AAAN, AAAN, AAAN, AAAN, AAAN], [false, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmi[8]([AAAN, AAAN, AANN, AANN, AANN], [AAAN, AAAN, AAAN, AAAN, AAAN], [false, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:09.169 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:09.169 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUmi[8]([AAAN, AAAN, AANN, AANN, AANN], [AAAN, AAAN, AAAN, AAAN, AAAN], [false, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:09.170 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:09.170 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUmi[8]([AAAN, AAAN, AANN, AANN, AANN], [AAAN, AAAN, AAAN, AAAN, AAAN], [false, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:09.170 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:09.170 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUmi[8]([AAAN, AAAN, AANN, AANN, AANN], [AAAN, AAAN, AAAN, AAAN, AAAN], [false, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:09.170 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:09.170 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUmi[8]([AAAN, AAAN, AANN, AANN, AANN], [AAAN, AAAN, AAAN, AAAN, AAAN], [false, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17708160277085061886.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17708160277085061886.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17708160277085061886.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17708160277085061886.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:09 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17708160277085061886.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17708160277085061886.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17708160277085061886.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.17708160277085061886.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testUmi[8]([AAAN, AAAN, AANN, AANN, AANN], [AAAN, AAAN, AAAN, AAAN, AAAN], [false, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testUmi[8]([AAAN, AAAN, AANN, AANN, AANN], [AAAN, AAAN, AAAN, AAAN, AAAN], [false, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:09 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:09 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testUmi[8]([AAAN, AAAN, AANN, AANN, AANN], [AAAN, AAAN, AAAN, AAAN, AAAN], [false, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testUmi[8]([AAAN, AAAN, AANN, AANN, AANN], [AAAN, AAAN, AAAN, AAAN, AAAN], [false, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Processed 10 records INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Processed 10 records Test: Test method testUmi[8]([AAAN, AAAN, AANN, AANN, AANN], [AAAN, AAAN, AAAN, AAAN, AAAN], [false, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. Test: Test method testUmi[8]([AAAN, AAAN, AANN, AANN, AANN], [AAAN, AAAN, AAAN, AAAN, AAAN], [false, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:09 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testUmi[8]([AAAN, AAAN, AANN, AANN, AANN], [AAAN, AAAN, AAAN, AAAN, AAAN], [false, true, true, true, true, true], 1)(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testUmiMetrics[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0.360964 UMI_BASE_QUALITIES 13 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testUmiMetrics[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0.360964 UMI_BASE_QUALITIES 13 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:09 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testUmiMetrics[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0.360964 UMI_BASE_QUALITIES 13 PCT_UMI_WITH_N 0 ) STANDARD_ERROR INFO 2024-07-02 11:50:09 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testUmiMetrics[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0.360964 UMI_BASE_QUALITIES 13 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmiMetrics[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0.360964 UMI_BASE_QUALITIES 13 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testUmiMetrics[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0.360964 UMI_BASE_QUALITIES 13 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmiMetrics[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0.360964 UMI_BASE_QUALITIES 13 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testUmiMetrics[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0.360964 UMI_BASE_QUALITIES 13 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testUmiMetrics[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0.360964 UMI_BASE_QUALITIES 13 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmiMetrics[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0.360964 UMI_BASE_QUALITIES 13 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testUmiMetrics[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0.360964 UMI_BASE_QUALITIES 13 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmiMetrics[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0.360964 UMI_BASE_QUALITIES 13 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10130482553772277192.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10130482553772277192.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 1 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10130482553772277192.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10130482553772277192.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10130482553772277192.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10130482553772277192.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 1 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10130482553772277192.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10130482553772277192.tmp/output.sam Test: Test method testUmiMetrics[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0.360964 UMI_BASE_QUALITIES 13 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmiMetrics[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0.360964 UMI_BASE_QUALITIES 13 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmiMetrics[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0.360964 UMI_BASE_QUALITIES 13 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmiMetrics[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0.360964 UMI_BASE_QUALITIES 13 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:09.238 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:09.238 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUmiMetrics[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0.360964 UMI_BASE_QUALITIES 13 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:09.239 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:09.239 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUmiMetrics[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0.360964 UMI_BASE_QUALITIES 13 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:09.239 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:09.239 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUmiMetrics[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0.360964 UMI_BASE_QUALITIES 13 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:09.239 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:09.239 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUmiMetrics[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0.360964 UMI_BASE_QUALITIES 13 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10130482553772277192.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10130482553772277192.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10130482553772277192.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10130482553772277192.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:09 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=1 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10130482553772277192.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10130482553772277192.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10130482553772277192.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.10130482553772277192.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testUmiMetrics[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0.360964 UMI_BASE_QUALITIES 13 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testUmiMetrics[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0.360964 UMI_BASE_QUALITIES 13 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:09 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:09 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testUmiMetrics[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0.360964 UMI_BASE_QUALITIES 13 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testUmiMetrics[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0.360964 UMI_BASE_QUALITIES 13 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Processed 10 records INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Processed 10 records Test: Test method testUmiMetrics[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0.360964 UMI_BASE_QUALITIES 13 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Marking 6 records as duplicates. INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Marking 6 records as duplicates. Test: Test method testUmiMetrics[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0.360964 UMI_BASE_QUALITIES 13 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:09 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testUmiMetrics[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0.360964 UMI_BASE_QUALITIES 13 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testUmiMetrics[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 6 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 8 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testUmiMetrics[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 6 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 8 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:09 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testUmiMetrics[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 6 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 8 PCT_UMI_WITH_N 0 ) STANDARD_ERROR INFO 2024-07-02 11:50:09 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testUmiMetrics[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 6 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 8 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmiMetrics[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 6 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 8 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testUmiMetrics[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 6 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 8 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmiMetrics[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 6 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 8 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testUmiMetrics[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 6 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 8 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testUmiMetrics[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 6 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 8 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmiMetrics[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 6 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 8 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testUmiMetrics[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 6 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 8 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmiMetrics[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 6 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 8 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15728790645245607968.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15728790645245607968.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 2 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15728790645245607968.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15728790645245607968.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15728790645245607968.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15728790645245607968.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 2 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15728790645245607968.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15728790645245607968.tmp/output.sam Test: Test method testUmiMetrics[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 6 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 8 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmiMetrics[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 6 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 8 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmiMetrics[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 6 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 8 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmiMetrics[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 6 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 8 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:09.293 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:09.293 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUmiMetrics[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 6 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 8 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:09.293 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:09.293 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUmiMetrics[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 6 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 8 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:09.294 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:09.294 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUmiMetrics[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 6 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 8 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:09.294 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:09.294 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUmiMetrics[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 6 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 8 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=2 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15728790645245607968.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15728790645245607968.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15728790645245607968.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15728790645245607968.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:09 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=2 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15728790645245607968.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15728790645245607968.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15728790645245607968.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.15728790645245607968.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testUmiMetrics[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 6 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 8 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testUmiMetrics[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 6 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 8 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:09 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:09 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testUmiMetrics[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 6 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 8 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testUmiMetrics[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 6 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 8 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Processed 10 records INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Processed 10 records Test: Test method testUmiMetrics[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 6 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 8 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. Test: Test method testUmiMetrics[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 6 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 8 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:09 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testUmiMetrics[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 6 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 8 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testUmiMetrics[2]([AAAA, AAAA, AANA, ANNA, ATTA, AAAA, ANAT], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 4 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.405639 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 9 PCT_UMI_WITH_N 0.428571 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testUmiMetrics[2]([AAAA, AAAA, AANA, ANNA, ATTA, AAAA, ANAT], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 4 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.405639 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 9 PCT_UMI_WITH_N 0.428571 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:09 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testUmiMetrics[2]([AAAA, AAAA, AANA, ANNA, ATTA, AAAA, ANAT], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 4 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.405639 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 9 PCT_UMI_WITH_N 0.428571 ) STANDARD_ERROR INFO 2024-07-02 11:50:09 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testUmiMetrics[2]([AAAA, AAAA, AANA, ANNA, ATTA, AAAA, ANAT], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 4 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.405639 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 9 PCT_UMI_WITH_N 0.428571 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmiMetrics[2]([AAAA, AAAA, AANA, ANNA, ATTA, AAAA, ANAT], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 4 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.405639 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 9 PCT_UMI_WITH_N 0.428571 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testUmiMetrics[2]([AAAA, AAAA, AANA, ANNA, ATTA, AAAA, ANAT], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 4 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.405639 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 9 PCT_UMI_WITH_N 0.428571 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmiMetrics[2]([AAAA, AAAA, AANA, ANNA, ATTA, AAAA, ANAT], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 4 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.405639 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 9 PCT_UMI_WITH_N 0.428571 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testUmiMetrics[2]([AAAA, AAAA, AANA, ANNA, ATTA, AAAA, ANAT], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 4 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.405639 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 9 PCT_UMI_WITH_N 0.428571 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testUmiMetrics[2]([AAAA, AAAA, AANA, ANNA, ATTA, AAAA, ANAT], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 4 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.405639 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 9 PCT_UMI_WITH_N 0.428571 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmiMetrics[2]([AAAA, AAAA, AANA, ANNA, ATTA, AAAA, ANAT], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 4 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.405639 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 9 PCT_UMI_WITH_N 0.428571 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testUmiMetrics[2]([AAAA, AAAA, AANA, ANNA, ATTA, AAAA, ANAT], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 4 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.405639 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 9 PCT_UMI_WITH_N 0.428571 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmiMetrics[2]([AAAA, AAAA, AANA, ANNA, ATTA, AAAA, ANAT], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 4 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.405639 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 9 PCT_UMI_WITH_N 0.428571 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5298101138896081805.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5298101138896081805.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 2 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5298101138896081805.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5298101138896081805.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5298101138896081805.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5298101138896081805.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 2 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5298101138896081805.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5298101138896081805.tmp/output.sam Test: Test method testUmiMetrics[2]([AAAA, AAAA, AANA, ANNA, ATTA, AAAA, ANAT], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 4 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.405639 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 9 PCT_UMI_WITH_N 0.428571 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmiMetrics[2]([AAAA, AAAA, AANA, ANNA, ATTA, AAAA, ANAT], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 4 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.405639 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 9 PCT_UMI_WITH_N 0.428571 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmiMetrics[2]([AAAA, AAAA, AANA, ANNA, ATTA, AAAA, ANAT], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 4 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.405639 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 9 PCT_UMI_WITH_N 0.428571 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmiMetrics[2]([AAAA, AAAA, AANA, ANNA, ATTA, AAAA, ANAT], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 4 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.405639 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 9 PCT_UMI_WITH_N 0.428571 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:09.356 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:09.356 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUmiMetrics[2]([AAAA, AAAA, AANA, ANNA, ATTA, AAAA, ANAT], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 4 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.405639 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 9 PCT_UMI_WITH_N 0.428571 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:09.356 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:09.356 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUmiMetrics[2]([AAAA, AAAA, AANA, ANNA, ATTA, AAAA, ANAT], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 4 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.405639 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 9 PCT_UMI_WITH_N 0.428571 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:09.356 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:09.356 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUmiMetrics[2]([AAAA, AAAA, AANA, ANNA, ATTA, AAAA, ANAT], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 4 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.405639 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 9 PCT_UMI_WITH_N 0.428571 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:09.356 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:09.356 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUmiMetrics[2]([AAAA, AAAA, AANA, ANNA, ATTA, AAAA, ANAT], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 4 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.405639 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 9 PCT_UMI_WITH_N 0.428571 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=2 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5298101138896081805.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5298101138896081805.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5298101138896081805.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5298101138896081805.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:09 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=2 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5298101138896081805.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5298101138896081805.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5298101138896081805.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.5298101138896081805.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testUmiMetrics[2]([AAAA, AAAA, AANA, ANNA, ATTA, AAAA, ANAT], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 4 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.405639 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 9 PCT_UMI_WITH_N 0.428571 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testUmiMetrics[2]([AAAA, AAAA, AANA, ANNA, ATTA, AAAA, ANAT], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 4 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.405639 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 9 PCT_UMI_WITH_N 0.428571 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:09 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. WARNING 2024-07-02 11:50:09 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. Test: Test method testUmiMetrics[2]([AAAA, AAAA, AANA, ANNA, ATTA, AAAA, ANAT], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 4 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.405639 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 9 PCT_UMI_WITH_N 0.428571 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testUmiMetrics[2]([AAAA, AAAA, AANA, ANNA, ATTA, AAAA, ANAT], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 4 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.405639 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 9 PCT_UMI_WITH_N 0.428571 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Processed 14 records INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Processed 14 records Test: Test method testUmiMetrics[2]([AAAA, AAAA, AANA, ANNA, ATTA, AAAA, ANAT], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 4 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.405639 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 9 PCT_UMI_WITH_N 0.428571 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Marking 12 records as duplicates. INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Marking 12 records as duplicates. Test: Test method testUmiMetrics[2]([AAAA, AAAA, AANA, ANNA, ATTA, AAAA, ANAT], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 4 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.405639 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 9 PCT_UMI_WITH_N 0.428571 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:09 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testUmiMetrics[2]([AAAA, AAAA, AANA, ANNA, ATTA, AAAA, ANAT], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 4 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.405639 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 9 PCT_UMI_WITH_N 0.428571 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testUmiMetrics[3]([AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], 0, LIBRARY A MEAN_UMI_LENGTH 2 OBSERVED_UNIQUE_UMIS 16 INFERRED_UNIQUE_UMIS 16 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 32 OBSERVED_UMI_ENTROPY 2 INFERRED_UMI_ENTROPY 2 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) Test: Test method testUmiMetrics[3]([AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], 0, LIBRARY A MEAN_UMI_LENGTH 2 OBSERVED_UNIQUE_UMIS 16 INFERRED_UNIQUE_UMIS 16 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 32 OBSERVED_UMI_ENTROPY 2 INFERRED_UMI_ENTROPY 2 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:09 UmiAwareMarkDuplicatesWithMateCigar Gradle suite > Gradle test > picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testUmiMetrics[3]([AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], 0, LIBRARY A MEAN_UMI_LENGTH 2 OBSERVED_UNIQUE_UMIS 16 INFERRED_UNIQUE_UMIS 16 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 32 OBSERVED_UMI_ENTROPY 2 INFERRED_UMI_ENTROPY 2 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ) STANDARD_ERROR INFO 2024-07-02 11:50:09 UmiAwareMarkDuplicatesWithMateCigar Test: Test method testUmiMetrics[3]([AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], 0, LIBRARY A MEAN_UMI_LENGTH 2 OBSERVED_UNIQUE_UMIS 16 INFERRED_UNIQUE_UMIS 16 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 32 OBSERVED_UMI_ENTROPY 2 INFERRED_UMI_ENTROPY 2 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmiMetrics[3]([AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], 0, LIBRARY A MEAN_UMI_LENGTH 2 OBSERVED_UNIQUE_UMIS 16 INFERRED_UNIQUE_UMIS 16 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 32 OBSERVED_UMI_ENTROPY 2 INFERRED_UMI_ENTROPY 2 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testUmiMetrics[3]([AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], 0, LIBRARY A MEAN_UMI_LENGTH 2 OBSERVED_UNIQUE_UMIS 16 INFERRED_UNIQUE_UMIS 16 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 32 OBSERVED_UMI_ENTROPY 2 INFERRED_UMI_ENTROPY 2 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmiMetrics[3]([AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], 0, LIBRARY A MEAN_UMI_LENGTH 2 OBSERVED_UNIQUE_UMIS 16 INFERRED_UNIQUE_UMIS 16 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 32 OBSERVED_UMI_ENTROPY 2 INFERRED_UMI_ENTROPY 2 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testUmiMetrics[3]([AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], 0, LIBRARY A MEAN_UMI_LENGTH 2 OBSERVED_UNIQUE_UMIS 16 INFERRED_UNIQUE_UMIS 16 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 32 OBSERVED_UMI_ENTROPY 2 INFERRED_UMI_ENTROPY 2 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testUmiMetrics[3]([AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], 0, LIBRARY A MEAN_UMI_LENGTH 2 OBSERVED_UNIQUE_UMIS 16 INFERRED_UNIQUE_UMIS 16 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 32 OBSERVED_UMI_ENTROPY 2 INFERRED_UMI_ENTROPY 2 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmiMetrics[3]([AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], 0, LIBRARY A MEAN_UMI_LENGTH 2 OBSERVED_UNIQUE_UMIS 16 INFERRED_UNIQUE_UMIS 16 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 32 OBSERVED_UMI_ENTROPY 2 INFERRED_UMI_ENTROPY 2 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testUmiMetrics[3]([AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], 0, LIBRARY A MEAN_UMI_LENGTH 2 OBSERVED_UNIQUE_UMIS 16 INFERRED_UNIQUE_UMIS 16 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 32 OBSERVED_UMI_ENTROPY 2 INFERRED_UMI_ENTROPY 2 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmiMetrics[3]([AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], 0, LIBRARY A MEAN_UMI_LENGTH 2 OBSERVED_UNIQUE_UMIS 16 INFERRED_UNIQUE_UMIS 16 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 32 OBSERVED_UMI_ENTROPY 2 INFERRED_UMI_ENTROPY 2 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7998962458856938916.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7998962458856938916.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 0 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7998962458856938916.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7998962458856938916.tmp/output.sam ********** UmiAwareMarkDuplicatesWithMateCigar -METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7998962458856938916.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH -UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7998962458856938916.tmp/umi_metrics.txt -MAX_EDIT_DISTANCE_TO_JOIN 0 -MOLECULAR_IDENTIFIER_TAG MI -INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7998962458856938916.tmp/input.sam -OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7998962458856938916.tmp/output.sam Test: Test method testUmiMetrics[3]([AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], 0, LIBRARY A MEAN_UMI_LENGTH 2 OBSERVED_UNIQUE_UMIS 16 INFERRED_UNIQUE_UMIS 16 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 32 OBSERVED_UMI_ENTROPY 2 INFERRED_UMI_ENTROPY 2 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: ********** ********** Test: Test method testUmiMetrics[3]([AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], 0, LIBRARY A MEAN_UMI_LENGTH 2 OBSERVED_UNIQUE_UMIS 16 INFERRED_UNIQUE_UMIS 16 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 32 OBSERVED_UMI_ENTROPY 2 INFERRED_UMI_ENTROPY 2 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmiMetrics[3]([AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], 0, LIBRARY A MEAN_UMI_LENGTH 2 OBSERVED_UNIQUE_UMIS 16 INFERRED_UNIQUE_UMIS 16 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 32 OBSERVED_UMI_ENTROPY 2 INFERRED_UMI_ENTROPY 2 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Test: Test method testUmiMetrics[3]([AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], 0, LIBRARY A MEAN_UMI_LENGTH 2 OBSERVED_UNIQUE_UMIS 16 INFERRED_UNIQUE_UMIS 16 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 32 OBSERVED_UMI_ENTROPY 2 INFERRED_UMI_ENTROPY 2 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:09.486 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:09.486 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUmiMetrics[3]([AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], 0, LIBRARY A MEAN_UMI_LENGTH 2 OBSERVED_UNIQUE_UMIS 16 INFERRED_UNIQUE_UMIS 16 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 32 OBSERVED_UMI_ENTROPY 2 INFERRED_UMI_ENTROPY 2 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:09.486 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:09.486 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUmiMetrics[3]([AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], 0, LIBRARY A MEAN_UMI_LENGTH 2 OBSERVED_UNIQUE_UMIS 16 INFERRED_UNIQUE_UMIS 16 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 32 OBSERVED_UMI_ENTROPY 2 INFERRED_UMI_ENTROPY 2 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:09.486 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:09.486 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUmiMetrics[3]([AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], 0, LIBRARY A MEAN_UMI_LENGTH 2 OBSERVED_UNIQUE_UMIS 16 INFERRED_UNIQUE_UMIS 16 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 32 OBSERVED_UMI_ENTROPY 2 INFERRED_UMI_ENTROPY 2 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: 11:50:09.486 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:09.486 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUmiMetrics[3]([AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], 0, LIBRARY A MEAN_UMI_LENGTH 2 OBSERVED_UNIQUE_UMIS 16 INFERRED_UNIQUE_UMIS 16 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 32 OBSERVED_UMI_ENTROPY 2 INFERRED_UMI_ENTROPY 2 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=0 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7998962458856938916.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7998962458856938916.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7998962458856938916.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7998962458856938916.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:09 GMT+14:00 2024] UmiAwareMarkDuplicatesWithMateCigar MAX_EDIT_DISTANCE_TO_JOIN=0 UMI_METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7998962458856938916.tmp/umi_metrics.txt MOLECULAR_IDENTIFIER_TAG=MI INPUT=[/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7998962458856938916.tmp/input.sam] OUTPUT=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7998962458856938916.tmp/output.sam METRICS_FILE=/tmp/UmiAwareMarkDuplicatesWithMateCigarTester.7998962458856938916.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=TOTAL_MAPPED_REFERENCE_LENGTH UMI_TAG_NAME=RX ALLOW_MISSING_UMIS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=UmiAwareMarkDuplicatesWithMateCigar READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testUmiMetrics[3]([AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], 0, LIBRARY A MEAN_UMI_LENGTH 2 OBSERVED_UNIQUE_UMIS 16 INFERRED_UNIQUE_UMIS 16 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 32 OBSERVED_UMI_ENTROPY 2 INFERRED_UMI_ENTROPY 2 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testUmiMetrics[3]([AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], 0, LIBRARY A MEAN_UMI_LENGTH 2 OBSERVED_UNIQUE_UMIS 16 INFERRED_UNIQUE_UMIS 16 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 32 OBSERVED_UMI_ENTROPY 2 INFERRED_UMI_ENTROPY 2 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: WARNING 2024-07-02 11:50:09 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ5. Cause: String 'READ5' did not start with a parsable number. WARNING 2024-07-02 11:50:09 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ5. Cause: String 'READ5' did not start with a parsable number. Test: Test method testUmiMetrics[3]([AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], 0, LIBRARY A MEAN_UMI_LENGTH 2 OBSERVED_UNIQUE_UMIS 16 INFERRED_UNIQUE_UMIS 16 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 32 OBSERVED_UMI_ENTROPY 2 INFERRED_UMI_ENTROPY 2 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. Test: Test method testUmiMetrics[3]([AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], 0, LIBRARY A MEAN_UMI_LENGTH 2 OBSERVED_UNIQUE_UMIS 16 INFERRED_UNIQUE_UMIS 16 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 32 OBSERVED_UMI_ENTROPY 2 INFERRED_UMI_ENTROPY 2 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Processed 32 records INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Processed 32 records Test: Test method testUmiMetrics[3]([AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], 0, LIBRARY A MEAN_UMI_LENGTH 2 OBSERVED_UNIQUE_UMIS 16 INFERRED_UNIQUE_UMIS 16 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 32 OBSERVED_UMI_ENTROPY 2 INFERRED_UMI_ENTROPY 2 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. INFO 2024-07-02 11:50:09 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. Test: Test method testUmiMetrics[3]([AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], 0, LIBRARY A MEAN_UMI_LENGTH 2 OBSERVED_UNIQUE_UMIS 16 INFERRED_UNIQUE_UMIS 16 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 32 OBSERVED_UMI_ENTROPY 2 INFERRED_UMI_ENTROPY 2 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:09 GMT+14:00 2024] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Test: Test method testUmiMetrics[3]([AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], 0, LIBRARY A MEAN_UMI_LENGTH 2 OBSERVED_UNIQUE_UMIS 16 INFERRED_UNIQUE_UMIS 16 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 32 OBSERVED_UMI_ENTROPY 2 INFERRED_UMI_ENTROPY 2 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 )(picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testFailsOnDissimilarContigLists(picard.vcf.MergeVcfsTest) Test: Test method testFailsOnDissimilarContigLists(picard.vcf.MergeVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:09 MergeVcfs Gradle suite > Gradle test > picard.vcf.MergeVcfsTest.testFailsOnDissimilarContigLists STANDARD_ERROR INFO 2024-07-02 11:50:09 MergeVcfs Test: Test method testFailsOnDissimilarContigLists(picard.vcf.MergeVcfsTest) produced standard out/err: Test: Test method testFailsOnDissimilarContigLists(picard.vcf.MergeVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFailsOnDissimilarContigLists(picard.vcf.MergeVcfsTest) produced standard out/err: ********** ********** Test: Test method testFailsOnDissimilarContigLists(picard.vcf.MergeVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFailsOnDissimilarContigLists(picard.vcf.MergeVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFailsOnDissimilarContigLists(picard.vcf.MergeVcfsTest) produced standard out/err: ********** ********** Test: Test method testFailsOnDissimilarContigLists(picard.vcf.MergeVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFailsOnDissimilarContigLists(picard.vcf.MergeVcfsTest) produced standard out/err: ********** ********** Test: Test method testFailsOnDissimilarContigLists(picard.vcf.MergeVcfsTest) produced standard out/err: ********** MergeVcfs -INPUT testdata/picard/vcf/CEUTrio-indels-dissimilar-contigs.vcf -INPUT testdata/picard/vcf/CEUTrio-snps.vcf -OUTPUT /dev/null/blah -CREATE_INDEX false ********** MergeVcfs -INPUT testdata/picard/vcf/CEUTrio-indels-dissimilar-contigs.vcf -INPUT testdata/picard/vcf/CEUTrio-snps.vcf -OUTPUT /dev/null/blah -CREATE_INDEX false Test: Test method testFailsOnDissimilarContigLists(picard.vcf.MergeVcfsTest) produced standard out/err: ********** ********** Test: Test method testFailsOnDissimilarContigLists(picard.vcf.MergeVcfsTest) produced standard out/err: Test: Test method testFailsOnDissimilarContigLists(picard.vcf.MergeVcfsTest) produced standard out/err: Test: Test method testFailsOnDissimilarContigLists(picard.vcf.MergeVcfsTest) produced standard out/err: 11:50:09.527 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:09.527 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFailsOnDissimilarContigLists(picard.vcf.MergeVcfsTest) produced standard out/err: 11:50:09.528 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:09.528 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFailsOnDissimilarContigLists(picard.vcf.MergeVcfsTest) produced standard out/err: 11:50:09.528 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:09.528 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFailsOnDissimilarContigLists(picard.vcf.MergeVcfsTest) produced standard out/err: 11:50:09.528 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:09.528 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFailsOnDissimilarContigLists(picard.vcf.MergeVcfsTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] MergeVcfs INPUT=[testdata/picard/vcf/CEUTrio-indels-dissimilar-contigs.vcf, testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/dev/null/blah CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:09 GMT+14:00 2024] MergeVcfs INPUT=[testdata/picard/vcf/CEUTrio-indels-dissimilar-contigs.vcf, testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/dev/null/blah CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFailsOnDissimilarContigLists(picard.vcf.MergeVcfsTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFailsOnDissimilarContigLists(picard.vcf.MergeVcfsTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] picard.vcf.MergeVcfs done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:09 GMT+14:00 2024] picard.vcf.MergeVcfs done. Elapsed time: 0.00 minutes. Test: Test method testFailsOnDissimilarContigLists(picard.vcf.MergeVcfsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testFailsOnDissimilarContigLists(picard.vcf.MergeVcfsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.MergeVcfsTest) Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.MergeVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:09 MergeVcfs Gradle suite > Gradle test > picard.vcf.MergeVcfsTest.testFailsOnDissimilarSampleLists STANDARD_ERROR INFO 2024-07-02 11:50:09 MergeVcfs Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.MergeVcfsTest) produced standard out/err: Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.MergeVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.MergeVcfsTest) produced standard out/err: ********** ********** Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.MergeVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.MergeVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.MergeVcfsTest) produced standard out/err: ********** ********** Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.MergeVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.MergeVcfsTest) produced standard out/err: ********** ********** Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.MergeVcfsTest) produced standard out/err: ********** MergeVcfs -INPUT testdata/picard/vcf/CEUTrio-indels-bad-samples.vcf -INPUT testdata/picard/vcf/CEUTrio-snps.vcf -OUTPUT /dev/null ********** MergeVcfs -INPUT testdata/picard/vcf/CEUTrio-indels-bad-samples.vcf -INPUT testdata/picard/vcf/CEUTrio-snps.vcf -OUTPUT /dev/null Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.MergeVcfsTest) produced standard out/err: ********** ********** Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.MergeVcfsTest) produced standard out/err: Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.MergeVcfsTest) produced standard out/err: Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.MergeVcfsTest) produced standard out/err: 11:50:09.595 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:09.595 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.MergeVcfsTest) produced standard out/err: 11:50:09.595 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:09.595 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.MergeVcfsTest) produced standard out/err: 11:50:09.595 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:09.595 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.MergeVcfsTest) produced standard out/err: 11:50:09.595 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:09.595 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.MergeVcfsTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] MergeVcfs INPUT=[testdata/picard/vcf/CEUTrio-indels-bad-samples.vcf, testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/dev/null VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:09 GMT+14:00 2024] MergeVcfs INPUT=[testdata/picard/vcf/CEUTrio-indels-bad-samples.vcf, testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/dev/null VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.MergeVcfsTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.MergeVcfsTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] picard.vcf.MergeVcfs done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:09 GMT+14:00 2024] picard.vcf.MergeVcfs done. Elapsed time: 0.00 minutes. Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.MergeVcfsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.MergeVcfsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testFailsOnNoContigList(picard.vcf.MergeVcfsTest) Test: Test method testFailsOnNoContigList(picard.vcf.MergeVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:09 MergeVcfs Gradle suite > Gradle test > picard.vcf.MergeVcfsTest.testFailsOnNoContigList STANDARD_ERROR INFO 2024-07-02 11:50:09 MergeVcfs Test: Test method testFailsOnNoContigList(picard.vcf.MergeVcfsTest) produced standard out/err: Test: Test method testFailsOnNoContigList(picard.vcf.MergeVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFailsOnNoContigList(picard.vcf.MergeVcfsTest) produced standard out/err: ********** ********** Test: Test method testFailsOnNoContigList(picard.vcf.MergeVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFailsOnNoContigList(picard.vcf.MergeVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFailsOnNoContigList(picard.vcf.MergeVcfsTest) produced standard out/err: ********** ********** Test: Test method testFailsOnNoContigList(picard.vcf.MergeVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFailsOnNoContigList(picard.vcf.MergeVcfsTest) produced standard out/err: ********** ********** Test: Test method testFailsOnNoContigList(picard.vcf.MergeVcfsTest) produced standard out/err: ********** MergeVcfs -INPUT testdata/picard/vcf/CEUTrio-indels-no-contigs.vcf -INPUT testdata/picard/vcf/CEUTrio-snps.vcf -OUTPUT /dev/null ********** MergeVcfs -INPUT testdata/picard/vcf/CEUTrio-indels-no-contigs.vcf -INPUT testdata/picard/vcf/CEUTrio-snps.vcf -OUTPUT /dev/null Test: Test method testFailsOnNoContigList(picard.vcf.MergeVcfsTest) produced standard out/err: ********** ********** Test: Test method testFailsOnNoContigList(picard.vcf.MergeVcfsTest) produced standard out/err: Test: Test method testFailsOnNoContigList(picard.vcf.MergeVcfsTest) produced standard out/err: Test: Test method testFailsOnNoContigList(picard.vcf.MergeVcfsTest) produced standard out/err: 11:50:09.648 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:09.648 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFailsOnNoContigList(picard.vcf.MergeVcfsTest) produced standard out/err: 11:50:09.657 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:09.657 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFailsOnNoContigList(picard.vcf.MergeVcfsTest) produced standard out/err: 11:50:09.657 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:09.657 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFailsOnNoContigList(picard.vcf.MergeVcfsTest) produced standard out/err: 11:50:09.657 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:09.657 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFailsOnNoContigList(picard.vcf.MergeVcfsTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] MergeVcfs INPUT=[testdata/picard/vcf/CEUTrio-indels-no-contigs.vcf, testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/dev/null VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:09 GMT+14:00 2024] MergeVcfs INPUT=[testdata/picard/vcf/CEUTrio-indels-no-contigs.vcf, testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/dev/null VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFailsOnNoContigList(picard.vcf.MergeVcfsTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFailsOnNoContigList(picard.vcf.MergeVcfsTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] picard.vcf.MergeVcfs done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:09 GMT+14:00 2024] picard.vcf.MergeVcfs done. Elapsed time: 0.00 minutes. Test: Test method testFailsOnNoContigList(picard.vcf.MergeVcfsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testFailsOnNoContigList(picard.vcf.MergeVcfsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMergeIndelsSnps(picard.vcf.MergeVcfsTest) Test: Test method testMergeIndelsSnps(picard.vcf.MergeVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:09 MergeVcfs Gradle suite > Gradle test > picard.vcf.MergeVcfsTest.testMergeIndelsSnps STANDARD_ERROR INFO 2024-07-02 11:50:09 MergeVcfs Test: Test method testMergeIndelsSnps(picard.vcf.MergeVcfsTest) produced standard out/err: Test: Test method testMergeIndelsSnps(picard.vcf.MergeVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMergeIndelsSnps(picard.vcf.MergeVcfsTest) produced standard out/err: ********** ********** Test: Test method testMergeIndelsSnps(picard.vcf.MergeVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMergeIndelsSnps(picard.vcf.MergeVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMergeIndelsSnps(picard.vcf.MergeVcfsTest) produced standard out/err: ********** ********** Test: Test method testMergeIndelsSnps(picard.vcf.MergeVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMergeIndelsSnps(picard.vcf.MergeVcfsTest) produced standard out/err: ********** ********** Test: Test method testMergeIndelsSnps(picard.vcf.MergeVcfsTest) produced standard out/err: ********** MergeVcfs -INPUT testdata/picard/vcf/CEUTrio-indels.vcf -INPUT testdata/picard/vcf/CEUTrio-snps.vcf -OUTPUT /tmp/merge-indels-snps-test-output.18079081536197127636.vcf -CREATE_INDEX false ********** MergeVcfs -INPUT testdata/picard/vcf/CEUTrio-indels.vcf -INPUT testdata/picard/vcf/CEUTrio-snps.vcf -OUTPUT /tmp/merge-indels-snps-test-output.18079081536197127636.vcf -CREATE_INDEX false Test: Test method testMergeIndelsSnps(picard.vcf.MergeVcfsTest) produced standard out/err: ********** ********** Test: Test method testMergeIndelsSnps(picard.vcf.MergeVcfsTest) produced standard out/err: Test: Test method testMergeIndelsSnps(picard.vcf.MergeVcfsTest) produced standard out/err: Test: Test method testMergeIndelsSnps(picard.vcf.MergeVcfsTest) produced standard out/err: 11:50:09.840 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:09.840 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMergeIndelsSnps(picard.vcf.MergeVcfsTest) produced standard out/err: 11:50:09.840 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:09.840 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMergeIndelsSnps(picard.vcf.MergeVcfsTest) produced standard out/err: 11:50:09.840 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:09.840 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMergeIndelsSnps(picard.vcf.MergeVcfsTest) produced standard out/err: 11:50:09.840 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:09.840 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMergeIndelsSnps(picard.vcf.MergeVcfsTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] MergeVcfs INPUT=[testdata/picard/vcf/CEUTrio-indels.vcf, testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/tmp/merge-indels-snps-test-output.18079081536197127636.vcf CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:09 GMT+14:00 2024] MergeVcfs INPUT=[testdata/picard/vcf/CEUTrio-indels.vcf, testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/tmp/merge-indels-snps-test-output.18079081536197127636.vcf CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMergeIndelsSnps(picard.vcf.MergeVcfsTest) produced standard out/err: [Tue Jul 02 11:50:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMergeIndelsSnps(picard.vcf.MergeVcfsTest) produced standard out/err: [Tue Jul 02 11:50:10 GMT+14:00 2024] picard.vcf.MergeVcfs done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:50:10 GMT+14:00 2024] picard.vcf.MergeVcfs done. Elapsed time: 0.01 minutes. Test: Test method testMergeIndelsSnps(picard.vcf.MergeVcfsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMergeRandomScatter(picard.vcf.MergeVcfsTest) Test: Test method testMergeRandomScatter(picard.vcf.MergeVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:10 MergeVcfs Gradle suite > Gradle test > picard.vcf.MergeVcfsTest.testMergeRandomScatter STANDARD_ERROR INFO 2024-07-02 11:50:10 MergeVcfs Test: Test method testMergeRandomScatter(picard.vcf.MergeVcfsTest) produced standard out/err: Test: Test method testMergeRandomScatter(picard.vcf.MergeVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMergeRandomScatter(picard.vcf.MergeVcfsTest) produced standard out/err: ********** ********** Test: Test method testMergeRandomScatter(picard.vcf.MergeVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMergeRandomScatter(picard.vcf.MergeVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMergeRandomScatter(picard.vcf.MergeVcfsTest) produced standard out/err: ********** ********** Test: Test method testMergeRandomScatter(picard.vcf.MergeVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMergeRandomScatter(picard.vcf.MergeVcfsTest) produced standard out/err: ********** ********** Test: Test method testMergeRandomScatter(picard.vcf.MergeVcfsTest) produced standard out/err: ********** MergeVcfs -INPUT testdata/picard/vcf/CEUTrio-random-scatter-0.vcf -INPUT testdata/picard/vcf/CEUTrio-random-scatter-1.vcf -INPUT testdata/picard/vcf/CEUTrio-random-scatter-2.vcf -INPUT testdata/picard/vcf/CEUTrio-random-scatter-3.vcf -INPUT testdata/picard/vcf/CEUTrio-random-scatter-4.vcf -INPUT testdata/picard/vcf/CEUTrio-random-scatter-5.vcf -OUTPUT /tmp/random-scatter-test-output.4791684391941490066.vcf -CREATE_INDEX false ********** MergeVcfs -INPUT testdata/picard/vcf/CEUTrio-random-scatter-0.vcf -INPUT testdata/picard/vcf/CEUTrio-random-scatter-1.vcf -INPUT testdata/picard/vcf/CEUTrio-random-scatter-2.vcf -INPUT testdata/picard/vcf/CEUTrio-random-scatter-3.vcf -INPUT testdata/picard/vcf/CEUTrio-random-scatter-4.vcf -INPUT testdata/picard/vcf/CEUTrio-random-scatter-5.vcf -OUTPUT /tmp/random-scatter-test-output.4791684391941490066.vcf -CREATE_INDEX false Test: Test method testMergeRandomScatter(picard.vcf.MergeVcfsTest) produced standard out/err: ********** ********** Test: Test method testMergeRandomScatter(picard.vcf.MergeVcfsTest) produced standard out/err: Test: Test method testMergeRandomScatter(picard.vcf.MergeVcfsTest) produced standard out/err: Test: Test method testMergeRandomScatter(picard.vcf.MergeVcfsTest) produced standard out/err: 11:50:10.355 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:10.355 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMergeRandomScatter(picard.vcf.MergeVcfsTest) produced standard out/err: 11:50:10.355 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:10.355 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMergeRandomScatter(picard.vcf.MergeVcfsTest) produced standard out/err: 11:50:10.355 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:10.355 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMergeRandomScatter(picard.vcf.MergeVcfsTest) produced standard out/err: 11:50:10.355 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:10.355 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMergeRandomScatter(picard.vcf.MergeVcfsTest) produced standard out/err: [Tue Jul 02 11:50:10 GMT+14:00 2024] MergeVcfs INPUT=[testdata/picard/vcf/CEUTrio-random-scatter-0.vcf, testdata/picard/vcf/CEUTrio-random-scatter-1.vcf, testdata/picard/vcf/CEUTrio-random-scatter-2.vcf, testdata/picard/vcf/CEUTrio-random-scatter-3.vcf, testdata/picard/vcf/CEUTrio-random-scatter-4.vcf, testdata/picard/vcf/CEUTrio-random-scatter-5.vcf] OUTPUT=/tmp/random-scatter-test-output.4791684391941490066.vcf CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:10 GMT+14:00 2024] MergeVcfs INPUT=[testdata/picard/vcf/CEUTrio-random-scatter-0.vcf, testdata/picard/vcf/CEUTrio-random-scatter-1.vcf, testdata/picard/vcf/CEUTrio-random-scatter-2.vcf, testdata/picard/vcf/CEUTrio-random-scatter-3.vcf, testdata/picard/vcf/CEUTrio-random-scatter-4.vcf, testdata/picard/vcf/CEUTrio-random-scatter-5.vcf] OUTPUT=/tmp/random-scatter-test-output.4791684391941490066.vcf CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMergeRandomScatter(picard.vcf.MergeVcfsTest) produced standard out/err: [Tue Jul 02 11:50:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMergeRandomScatter(picard.vcf.MergeVcfsTest) produced standard out/err: [Tue Jul 02 11:50:10 GMT+14:00 2024] picard.vcf.MergeVcfs done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:50:10 GMT+14:00 2024] picard.vcf.MergeVcfs done. Elapsed time: 0.01 minutes. Test: Test method testMergeRandomScatter(picard.vcf.MergeVcfsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.MergeVcfsTest) Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.MergeVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:10 MergeVcfs Gradle suite > Gradle test > picard.vcf.MergeVcfsTest.testSucceedsWithProvidedSequenceDictionary STANDARD_ERROR INFO 2024-07-02 11:50:10 MergeVcfs Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.MergeVcfsTest) produced standard out/err: Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.MergeVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.MergeVcfsTest) produced standard out/err: ********** ********** Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.MergeVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.MergeVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.MergeVcfsTest) produced standard out/err: ********** ********** Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.MergeVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.MergeVcfsTest) produced standard out/err: ********** ********** Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.MergeVcfsTest) produced standard out/err: ********** MergeVcfs -INPUT testdata/picard/vcf/noSeqDict.vcf -OUTPUT /dev/null -CREATE_INDEX false -SEQUENCE_DICTIONARY testdata/picard/reference/test.dict ********** MergeVcfs -INPUT testdata/picard/vcf/noSeqDict.vcf -OUTPUT /dev/null -CREATE_INDEX false -SEQUENCE_DICTIONARY testdata/picard/reference/test.dict Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.MergeVcfsTest) produced standard out/err: ********** ********** Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.MergeVcfsTest) produced standard out/err: Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.MergeVcfsTest) produced standard out/err: Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.MergeVcfsTest) produced standard out/err: 11:50:10.796 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:10.796 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.MergeVcfsTest) produced standard out/err: 11:50:10.796 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:10.796 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.MergeVcfsTest) produced standard out/err: 11:50:10.796 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:10.796 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.MergeVcfsTest) produced standard out/err: 11:50:10.796 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:10.796 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.MergeVcfsTest) produced standard out/err: [Tue Jul 02 11:50:10 GMT+14:00 2024] MergeVcfs INPUT=[testdata/picard/vcf/noSeqDict.vcf] OUTPUT=/dev/null SEQUENCE_DICTIONARY=testdata/picard/reference/test.dict CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:10 GMT+14:00 2024] MergeVcfs INPUT=[testdata/picard/vcf/noSeqDict.vcf] OUTPUT=/dev/null SEQUENCE_DICTIONARY=testdata/picard/reference/test.dict CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.MergeVcfsTest) produced standard out/err: [Tue Jul 02 11:50:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.MergeVcfsTest) produced standard out/err: [Tue Jul 02 11:50:10 GMT+14:00 2024] picard.vcf.MergeVcfs done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:10 GMT+14:00 2024] picard.vcf.MergeVcfs done. Elapsed time: 0.00 minutes. Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.MergeVcfsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method TestComments(picard.vcf.MergeVcfsTest) Test: Test method TestComments(picard.vcf.MergeVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:10 MergeVcfs Gradle suite > Gradle test > picard.vcf.MergeVcfsTest.TestComments STANDARD_ERROR INFO 2024-07-02 11:50:10 MergeVcfs Test: Test method TestComments(picard.vcf.MergeVcfsTest) produced standard out/err: Test: Test method TestComments(picard.vcf.MergeVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestComments(picard.vcf.MergeVcfsTest) produced standard out/err: ********** ********** Test: Test method TestComments(picard.vcf.MergeVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestComments(picard.vcf.MergeVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestComments(picard.vcf.MergeVcfsTest) produced standard out/err: ********** ********** Test: Test method TestComments(picard.vcf.MergeVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestComments(picard.vcf.MergeVcfsTest) produced standard out/err: ********** ********** Test: Test method TestComments(picard.vcf.MergeVcfsTest) produced standard out/err: ********** MergeVcfs -INPUT testdata/picard/vcf/mini.vcf -OUTPUT /tmp/result4679486221935357555.vcf -COMMENT This is a comment ********** MergeVcfs -INPUT testdata/picard/vcf/mini.vcf -OUTPUT /tmp/result4679486221935357555.vcf -COMMENT This is a comment Test: Test method TestComments(picard.vcf.MergeVcfsTest) produced standard out/err: ********** ********** Test: Test method TestComments(picard.vcf.MergeVcfsTest) produced standard out/err: Test: Test method TestComments(picard.vcf.MergeVcfsTest) produced standard out/err: Test: Test method TestComments(picard.vcf.MergeVcfsTest) produced standard out/err: 11:50:10.827 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:10.827 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestComments(picard.vcf.MergeVcfsTest) produced standard out/err: 11:50:10.827 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:10.827 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestComments(picard.vcf.MergeVcfsTest) produced standard out/err: 11:50:10.827 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:10.827 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestComments(picard.vcf.MergeVcfsTest) produced standard out/err: 11:50:10.827 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:10.827 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestComments(picard.vcf.MergeVcfsTest) produced standard out/err: [Tue Jul 02 11:50:10 GMT+14:00 2024] MergeVcfs INPUT=[testdata/picard/vcf/mini.vcf] OUTPUT=/tmp/result4679486221935357555.vcf COMMENT=[This is a comment] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:10 GMT+14:00 2024] MergeVcfs INPUT=[testdata/picard/vcf/mini.vcf] OUTPUT=/tmp/result4679486221935357555.vcf COMMENT=[This is a comment] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestComments(picard.vcf.MergeVcfsTest) produced standard out/err: [Tue Jul 02 11:50:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestComments(picard.vcf.MergeVcfsTest) produced standard out/err: [Tue Jul 02 11:50:11 GMT+14:00 2024] picard.vcf.MergeVcfs done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:11 GMT+14:00 2024] picard.vcf.MergeVcfs done. Elapsed time: 0.00 minutes. Test: Test method TestComments(picard.vcf.MergeVcfsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testFailsOnDissimilarContigLists(picard.vcf.SortVcfsTest) Test: Test method testFailsOnDissimilarContigLists(picard.vcf.SortVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:11 SortVcf Gradle suite > Gradle test > picard.vcf.SortVcfsTest.testFailsOnDissimilarContigLists STANDARD_ERROR INFO 2024-07-02 11:50:11 SortVcf Test: Test method testFailsOnDissimilarContigLists(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testFailsOnDissimilarContigLists(picard.vcf.SortVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFailsOnDissimilarContigLists(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testFailsOnDissimilarContigLists(picard.vcf.SortVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFailsOnDissimilarContigLists(picard.vcf.SortVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFailsOnDissimilarContigLists(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testFailsOnDissimilarContigLists(picard.vcf.SortVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFailsOnDissimilarContigLists(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testFailsOnDissimilarContigLists(picard.vcf.SortVcfsTest) produced standard out/err: ********** SortVcf -INPUT testdata/picard/vcf/CEUTrio-indels-dissimilar-contigs.vcf -INPUT testdata/picard/vcf/CEUTrio-snps.vcf -OUTPUT /dev/null/blah -CREATE_INDEX false ********** SortVcf -INPUT testdata/picard/vcf/CEUTrio-indels-dissimilar-contigs.vcf -INPUT testdata/picard/vcf/CEUTrio-snps.vcf -OUTPUT /dev/null/blah -CREATE_INDEX false Test: Test method testFailsOnDissimilarContigLists(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testFailsOnDissimilarContigLists(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testFailsOnDissimilarContigLists(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testFailsOnDissimilarContigLists(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:11.138 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:11.138 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFailsOnDissimilarContigLists(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:11.139 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:11.139 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFailsOnDissimilarContigLists(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:11.139 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:11.139 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFailsOnDissimilarContigLists(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:11.139 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:11.139 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFailsOnDissimilarContigLists(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:11 GMT+14:00 2024] SortVcf INPUT=[testdata/picard/vcf/CEUTrio-indels-dissimilar-contigs.vcf, testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/dev/null/blah CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:11 GMT+14:00 2024] SortVcf INPUT=[testdata/picard/vcf/CEUTrio-indels-dissimilar-contigs.vcf, testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/dev/null/blah CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFailsOnDissimilarContigLists(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFailsOnDissimilarContigLists(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:11 GMT+14:00 2024] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:11 GMT+14:00 2024] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes. Test: Test method testFailsOnDissimilarContigLists(picard.vcf.SortVcfsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testFailsOnDissimilarContigLists(picard.vcf.SortVcfsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.SortVcfsTest) Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.SortVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:11 SortVcf Gradle suite > Gradle test > picard.vcf.SortVcfsTest.testFailsOnDissimilarSampleLists STANDARD_ERROR INFO 2024-07-02 11:50:11 SortVcf Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.SortVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.SortVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.SortVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.SortVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.SortVcfsTest) produced standard out/err: ********** SortVcf -INPUT testdata/picard/vcf/CEUTrio-indels-bad-samples.vcf -INPUT testdata/picard/vcf/CEUTrio-snps.vcf -OUTPUT /dev/null ********** SortVcf -INPUT testdata/picard/vcf/CEUTrio-indels-bad-samples.vcf -INPUT testdata/picard/vcf/CEUTrio-snps.vcf -OUTPUT /dev/null Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:11.153 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:11.153 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:11.154 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:11.154 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:11.154 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:11.154 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:11.154 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:11.154 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:11 GMT+14:00 2024] SortVcf INPUT=[testdata/picard/vcf/CEUTrio-indels-bad-samples.vcf, testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/dev/null VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:11 GMT+14:00 2024] SortVcf INPUT=[testdata/picard/vcf/CEUTrio-indels-bad-samples.vcf, testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/dev/null VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:11 GMT+14:00 2024] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:11 GMT+14:00 2024] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes. Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.SortVcfsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testFailsOnDissimilarSampleLists(picard.vcf.SortVcfsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testFailsOnNoContigList(picard.vcf.SortVcfsTest) Test: Test method testFailsOnNoContigList(picard.vcf.SortVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:11 SortVcf Gradle suite > Gradle test > picard.vcf.SortVcfsTest.testFailsOnNoContigList STANDARD_ERROR INFO 2024-07-02 11:50:11 SortVcf Test: Test method testFailsOnNoContigList(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testFailsOnNoContigList(picard.vcf.SortVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFailsOnNoContigList(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testFailsOnNoContigList(picard.vcf.SortVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFailsOnNoContigList(picard.vcf.SortVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFailsOnNoContigList(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testFailsOnNoContigList(picard.vcf.SortVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFailsOnNoContigList(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testFailsOnNoContigList(picard.vcf.SortVcfsTest) produced standard out/err: ********** SortVcf -INPUT testdata/picard/vcf/CEUTrio-indels-no-contigs.vcf -INPUT testdata/picard/vcf/CEUTrio-snps.vcf -OUTPUT /dev/null ********** SortVcf -INPUT testdata/picard/vcf/CEUTrio-indels-no-contigs.vcf -INPUT testdata/picard/vcf/CEUTrio-snps.vcf -OUTPUT /dev/null Test: Test method testFailsOnNoContigList(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testFailsOnNoContigList(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testFailsOnNoContigList(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testFailsOnNoContigList(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:11.165 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:11.165 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFailsOnNoContigList(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:11.165 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:11.165 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFailsOnNoContigList(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:11.166 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:11.166 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFailsOnNoContigList(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:11.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:11.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFailsOnNoContigList(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:11 GMT+14:00 2024] SortVcf INPUT=[testdata/picard/vcf/CEUTrio-indels-no-contigs.vcf, testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/dev/null VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:11 GMT+14:00 2024] SortVcf INPUT=[testdata/picard/vcf/CEUTrio-indels-no-contigs.vcf, testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/dev/null VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFailsOnNoContigList(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFailsOnNoContigList(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:11 GMT+14:00 2024] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:11 GMT+14:00 2024] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes. Test: Test method testFailsOnNoContigList(picard.vcf.SortVcfsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testFailsOnNoContigList(picard.vcf.SortVcfsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMergeIndelsSnps(picard.vcf.SortVcfsTest) Test: Test method testMergeIndelsSnps(picard.vcf.SortVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:11 SortVcf Gradle suite > Gradle test > picard.vcf.SortVcfsTest.testMergeIndelsSnps STANDARD_ERROR INFO 2024-07-02 11:50:11 SortVcf Test: Test method testMergeIndelsSnps(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testMergeIndelsSnps(picard.vcf.SortVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMergeIndelsSnps(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testMergeIndelsSnps(picard.vcf.SortVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMergeIndelsSnps(picard.vcf.SortVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMergeIndelsSnps(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testMergeIndelsSnps(picard.vcf.SortVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMergeIndelsSnps(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testMergeIndelsSnps(picard.vcf.SortVcfsTest) produced standard out/err: ********** SortVcf -INPUT testdata/picard/vcf/CEUTrio-indels.vcf -INPUT testdata/picard/vcf/CEUTrio-snps.vcf -OUTPUT /tmp/merge-indels-snps-test-output.14395466536298416042.vcf -CREATE_INDEX false ********** SortVcf -INPUT testdata/picard/vcf/CEUTrio-indels.vcf -INPUT testdata/picard/vcf/CEUTrio-snps.vcf -OUTPUT /tmp/merge-indels-snps-test-output.14395466536298416042.vcf -CREATE_INDEX false Test: Test method testMergeIndelsSnps(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testMergeIndelsSnps(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testMergeIndelsSnps(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testMergeIndelsSnps(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:11.192 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:11.192 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMergeIndelsSnps(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:11.192 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:11.192 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMergeIndelsSnps(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:11.193 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:11.193 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMergeIndelsSnps(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:11.193 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:11.193 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMergeIndelsSnps(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:11 GMT+14:00 2024] SortVcf INPUT=[testdata/picard/vcf/CEUTrio-indels.vcf, testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/tmp/merge-indels-snps-test-output.14395466536298416042.vcf CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:11 GMT+14:00 2024] SortVcf INPUT=[testdata/picard/vcf/CEUTrio-indels.vcf, testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/tmp/merge-indels-snps-test-output.14395466536298416042.vcf CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMergeIndelsSnps(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMergeIndelsSnps(picard.vcf.SortVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:11 SortVcf Reading entries from input file 1 INFO 2024-07-02 11:50:11 SortVcf Reading entries from input file 1 Test: Test method testMergeIndelsSnps(picard.vcf.SortVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:11 SortVcf Reading entries from input file 2 INFO 2024-07-02 11:50:11 SortVcf Reading entries from input file 2 Test: Test method testMergeIndelsSnps(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:11 GMT+14:00 2024] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:11 GMT+14:00 2024] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes. Test: Test method testMergeIndelsSnps(picard.vcf.SortVcfsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMergeRandomScatter(picard.vcf.SortVcfsTest) Test: Test method testMergeRandomScatter(picard.vcf.SortVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:11 SortVcf Gradle suite > Gradle test > picard.vcf.SortVcfsTest.testMergeRandomScatter STANDARD_ERROR INFO 2024-07-02 11:50:11 SortVcf Test: Test method testMergeRandomScatter(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testMergeRandomScatter(picard.vcf.SortVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMergeRandomScatter(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testMergeRandomScatter(picard.vcf.SortVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMergeRandomScatter(picard.vcf.SortVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMergeRandomScatter(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testMergeRandomScatter(picard.vcf.SortVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMergeRandomScatter(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testMergeRandomScatter(picard.vcf.SortVcfsTest) produced standard out/err: ********** SortVcf -INPUT testdata/picard/vcf/CEUTrio-random-scatter-0.vcf -INPUT testdata/picard/vcf/CEUTrio-random-scatter-1.vcf -INPUT testdata/picard/vcf/CEUTrio-random-scatter-2.vcf -INPUT testdata/picard/vcf/CEUTrio-random-scatter-3.vcf -INPUT testdata/picard/vcf/CEUTrio-random-scatter-4.vcf -INPUT testdata/picard/vcf/CEUTrio-random-scatter-5.vcf -OUTPUT /tmp/random-scatter-test-output.13784081632131530570.vcf -CREATE_INDEX false ********** SortVcf -INPUT testdata/picard/vcf/CEUTrio-random-scatter-0.vcf -INPUT testdata/picard/vcf/CEUTrio-random-scatter-1.vcf -INPUT testdata/picard/vcf/CEUTrio-random-scatter-2.vcf -INPUT testdata/picard/vcf/CEUTrio-random-scatter-3.vcf -INPUT testdata/picard/vcf/CEUTrio-random-scatter-4.vcf -INPUT testdata/picard/vcf/CEUTrio-random-scatter-5.vcf -OUTPUT /tmp/random-scatter-test-output.13784081632131530570.vcf -CREATE_INDEX false Test: Test method testMergeRandomScatter(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testMergeRandomScatter(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testMergeRandomScatter(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testMergeRandomScatter(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:11.652 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:11.652 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMergeRandomScatter(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:11.652 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:11.652 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMergeRandomScatter(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:11.665 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:11.665 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMergeRandomScatter(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:11.665 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:11.665 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMergeRandomScatter(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:11 GMT+14:00 2024] SortVcf INPUT=[testdata/picard/vcf/CEUTrio-random-scatter-0.vcf, testdata/picard/vcf/CEUTrio-random-scatter-1.vcf, testdata/picard/vcf/CEUTrio-random-scatter-2.vcf, testdata/picard/vcf/CEUTrio-random-scatter-3.vcf, testdata/picard/vcf/CEUTrio-random-scatter-4.vcf, testdata/picard/vcf/CEUTrio-random-scatter-5.vcf] OUTPUT=/tmp/random-scatter-test-output.13784081632131530570.vcf CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:11 GMT+14:00 2024] SortVcf INPUT=[testdata/picard/vcf/CEUTrio-random-scatter-0.vcf, testdata/picard/vcf/CEUTrio-random-scatter-1.vcf, testdata/picard/vcf/CEUTrio-random-scatter-2.vcf, testdata/picard/vcf/CEUTrio-random-scatter-3.vcf, testdata/picard/vcf/CEUTrio-random-scatter-4.vcf, testdata/picard/vcf/CEUTrio-random-scatter-5.vcf] OUTPUT=/tmp/random-scatter-test-output.13784081632131530570.vcf CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMergeRandomScatter(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMergeRandomScatter(picard.vcf.SortVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:12 SortVcf Reading entries from input file 1 INFO 2024-07-02 11:50:12 SortVcf Reading entries from input file 1 Test: Test method testMergeRandomScatter(picard.vcf.SortVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:12 SortVcf Reading entries from input file 2 INFO 2024-07-02 11:50:12 SortVcf Reading entries from input file 2 Test: Test method testMergeRandomScatter(picard.vcf.SortVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:12 SortVcf Reading entries from input file 3 INFO 2024-07-02 11:50:12 SortVcf Reading entries from input file 3 Test: Test method testMergeRandomScatter(picard.vcf.SortVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:12 SortVcf Reading entries from input file 4 INFO 2024-07-02 11:50:12 SortVcf Reading entries from input file 4 Test: Test method testMergeRandomScatter(picard.vcf.SortVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:12 SortVcf Reading entries from input file 5 INFO 2024-07-02 11:50:12 SortVcf Reading entries from input file 5 Test: Test method testMergeRandomScatter(picard.vcf.SortVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:12 SortVcf Reading entries from input file 6 INFO 2024-07-02 11:50:12 SortVcf Reading entries from input file 6 Test: Test method testMergeRandomScatter(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:12 GMT+14:00 2024] picard.vcf.SortVcf done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:50:12 GMT+14:00 2024] picard.vcf.SortVcf done. Elapsed time: 0.01 minutes. Test: Test method testMergeRandomScatter(picard.vcf.SortVcfsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.SortVcfsTest) Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.SortVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:12 SortVcf Gradle suite > Gradle test > picard.vcf.SortVcfsTest.testSucceedsWithProvidedSequenceDictionary STANDARD_ERROR INFO 2024-07-02 11:50:12 SortVcf Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.SortVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.SortVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.SortVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.SortVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.SortVcfsTest) produced standard out/err: ********** SortVcf -INPUT testdata/picard/vcf/noSeqDict.vcf -OUTPUT /dev/null -CREATE_INDEX false -SEQUENCE_DICTIONARY testdata/picard/reference/test.dict ********** SortVcf -INPUT testdata/picard/vcf/noSeqDict.vcf -OUTPUT /dev/null -CREATE_INDEX false -SEQUENCE_DICTIONARY testdata/picard/reference/test.dict Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:12.554 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:12.554 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:12.554 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:12.554 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:12.555 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:12.555 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:12.555 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:12.555 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:12 GMT+14:00 2024] SortVcf INPUT=[testdata/picard/vcf/noSeqDict.vcf] OUTPUT=/dev/null SEQUENCE_DICTIONARY=testdata/picard/reference/test.dict CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:12 GMT+14:00 2024] SortVcf INPUT=[testdata/picard/vcf/noSeqDict.vcf] OUTPUT=/dev/null SEQUENCE_DICTIONARY=testdata/picard/reference/test.dict CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.SortVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:12 SortVcf Reading entries from input file 1 INFO 2024-07-02 11:50:12 SortVcf Reading entries from input file 1 Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:12 GMT+14:00 2024] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:12 GMT+14:00 2024] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes. Test: Test method testSucceedsWithProvidedSequenceDictionary(picard.vcf.SortVcfsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testPresortedFile(picard.vcf.SortVcfsTest) Test: Test method testPresortedFile(picard.vcf.SortVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:12 SortVcf Gradle suite > Gradle test > picard.vcf.SortVcfsTest.testPresortedFile STANDARD_ERROR INFO 2024-07-02 11:50:12 SortVcf Test: Test method testPresortedFile(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testPresortedFile(picard.vcf.SortVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPresortedFile(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testPresortedFile(picard.vcf.SortVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPresortedFile(picard.vcf.SortVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPresortedFile(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testPresortedFile(picard.vcf.SortVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPresortedFile(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testPresortedFile(picard.vcf.SortVcfsTest) produced standard out/err: ********** SortVcf -INPUT testdata/picard/vcf/CEUTrio-snps.vcf -OUTPUT /tmp/sort-presorted-test-output.15590902408831534230.vcf -CREATE_INDEX false ********** SortVcf -INPUT testdata/picard/vcf/CEUTrio-snps.vcf -OUTPUT /tmp/sort-presorted-test-output.15590902408831534230.vcf -CREATE_INDEX false Test: Test method testPresortedFile(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testPresortedFile(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testPresortedFile(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testPresortedFile(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:12.664 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:12.664 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPresortedFile(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:12.673 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:12.673 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPresortedFile(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:12.674 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:12.674 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPresortedFile(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:12.674 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:12.674 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPresortedFile(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:12 GMT+14:00 2024] SortVcf INPUT=[testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/tmp/sort-presorted-test-output.15590902408831534230.vcf CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:12 GMT+14:00 2024] SortVcf INPUT=[testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/tmp/sort-presorted-test-output.15590902408831534230.vcf CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPresortedFile(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPresortedFile(picard.vcf.SortVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:12 SortVcf Reading entries from input file 1 INFO 2024-07-02 11:50:12 SortVcf Reading entries from input file 1 Test: Test method testPresortedFile(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:12 GMT+14:00 2024] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:12 GMT+14:00 2024] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes. Test: Test method testPresortedFile(picard.vcf.SortVcfsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testScrambledSnpsAndOrderedIndels(picard.vcf.SortVcfsTest) Test: Test method testScrambledSnpsAndOrderedIndels(picard.vcf.SortVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:13 SortVcf Gradle suite > Gradle test > picard.vcf.SortVcfsTest.testScrambledSnpsAndOrderedIndels STANDARD_ERROR INFO 2024-07-02 11:50:13 SortVcf Test: Test method testScrambledSnpsAndOrderedIndels(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testScrambledSnpsAndOrderedIndels(picard.vcf.SortVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScrambledSnpsAndOrderedIndels(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testScrambledSnpsAndOrderedIndels(picard.vcf.SortVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScrambledSnpsAndOrderedIndels(picard.vcf.SortVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScrambledSnpsAndOrderedIndels(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testScrambledSnpsAndOrderedIndels(picard.vcf.SortVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScrambledSnpsAndOrderedIndels(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testScrambledSnpsAndOrderedIndels(picard.vcf.SortVcfsTest) produced standard out/err: ********** SortVcf -INPUT testdata/picard/vcf/CEUTrio-indels.vcf -INPUT testdata/picard/vcf/CEUTrio-snps-scrambled.1.vcf -OUTPUT /tmp/sort-scrambled-indels-snps-test-output.7303256627366834219.vcf -CREATE_INDEX false ********** SortVcf -INPUT testdata/picard/vcf/CEUTrio-indels.vcf -INPUT testdata/picard/vcf/CEUTrio-snps-scrambled.1.vcf -OUTPUT /tmp/sort-scrambled-indels-snps-test-output.7303256627366834219.vcf -CREATE_INDEX false Test: Test method testScrambledSnpsAndOrderedIndels(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testScrambledSnpsAndOrderedIndels(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testScrambledSnpsAndOrderedIndels(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testScrambledSnpsAndOrderedIndels(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:13.213 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:13.213 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScrambledSnpsAndOrderedIndels(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:13.214 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:13.214 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScrambledSnpsAndOrderedIndels(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:13.215 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:13.215 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScrambledSnpsAndOrderedIndels(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:13.215 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:13.215 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScrambledSnpsAndOrderedIndels(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:13 GMT+14:00 2024] SortVcf INPUT=[testdata/picard/vcf/CEUTrio-indels.vcf, testdata/picard/vcf/CEUTrio-snps-scrambled.1.vcf] OUTPUT=/tmp/sort-scrambled-indels-snps-test-output.7303256627366834219.vcf CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:13 GMT+14:00 2024] SortVcf INPUT=[testdata/picard/vcf/CEUTrio-indels.vcf, testdata/picard/vcf/CEUTrio-snps-scrambled.1.vcf] OUTPUT=/tmp/sort-scrambled-indels-snps-test-output.7303256627366834219.vcf CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScrambledSnpsAndOrderedIndels(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScrambledSnpsAndOrderedIndels(picard.vcf.SortVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:13 SortVcf Reading entries from input file 1 INFO 2024-07-02 11:50:13 SortVcf Reading entries from input file 1 Test: Test method testScrambledSnpsAndOrderedIndels(picard.vcf.SortVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:13 SortVcf Reading entries from input file 2 INFO 2024-07-02 11:50:13 SortVcf Reading entries from input file 2 Test: Test method testScrambledSnpsAndOrderedIndels(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:13 GMT+14:00 2024] picard.vcf.SortVcf done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:50:13 GMT+14:00 2024] picard.vcf.SortVcf done. Elapsed time: 0.01 minutes. Test: Test method testScrambledSnpsAndOrderedIndels(picard.vcf.SortVcfsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testScrambledSnpsAndScrambledIndels(picard.vcf.SortVcfsTest) Test: Test method testScrambledSnpsAndScrambledIndels(picard.vcf.SortVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:13 SortVcf Gradle suite > Gradle test > picard.vcf.SortVcfsTest.testScrambledSnpsAndScrambledIndels STANDARD_ERROR INFO 2024-07-02 11:50:13 SortVcf Test: Test method testScrambledSnpsAndScrambledIndels(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testScrambledSnpsAndScrambledIndels(picard.vcf.SortVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScrambledSnpsAndScrambledIndels(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testScrambledSnpsAndScrambledIndels(picard.vcf.SortVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScrambledSnpsAndScrambledIndels(picard.vcf.SortVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScrambledSnpsAndScrambledIndels(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testScrambledSnpsAndScrambledIndels(picard.vcf.SortVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScrambledSnpsAndScrambledIndels(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testScrambledSnpsAndScrambledIndels(picard.vcf.SortVcfsTest) produced standard out/err: ********** SortVcf -INPUT testdata/picard/vcf/CEUTrio-indels-scrambled.1.vcf -INPUT testdata/picard/vcf/CEUTrio-snps-scrambled.1.vcf -OUTPUT /tmp/merge-indels-snps-test-output.5675826814998677066.vcf -CREATE_INDEX false ********** SortVcf -INPUT testdata/picard/vcf/CEUTrio-indels-scrambled.1.vcf -INPUT testdata/picard/vcf/CEUTrio-snps-scrambled.1.vcf -OUTPUT /tmp/merge-indels-snps-test-output.5675826814998677066.vcf -CREATE_INDEX false Test: Test method testScrambledSnpsAndScrambledIndels(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testScrambledSnpsAndScrambledIndels(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testScrambledSnpsAndScrambledIndels(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testScrambledSnpsAndScrambledIndels(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:13.621 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:13.621 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScrambledSnpsAndScrambledIndels(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:13.621 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:13.621 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScrambledSnpsAndScrambledIndels(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:13.622 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:13.622 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScrambledSnpsAndScrambledIndels(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:13.622 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:13.622 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScrambledSnpsAndScrambledIndels(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:13 GMT+14:00 2024] SortVcf INPUT=[testdata/picard/vcf/CEUTrio-indels-scrambled.1.vcf, testdata/picard/vcf/CEUTrio-snps-scrambled.1.vcf] OUTPUT=/tmp/merge-indels-snps-test-output.5675826814998677066.vcf CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:13 GMT+14:00 2024] SortVcf INPUT=[testdata/picard/vcf/CEUTrio-indels-scrambled.1.vcf, testdata/picard/vcf/CEUTrio-snps-scrambled.1.vcf] OUTPUT=/tmp/merge-indels-snps-test-output.5675826814998677066.vcf CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScrambledSnpsAndScrambledIndels(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScrambledSnpsAndScrambledIndels(picard.vcf.SortVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:13 SortVcf Reading entries from input file 1 INFO 2024-07-02 11:50:13 SortVcf Reading entries from input file 1 Test: Test method testScrambledSnpsAndScrambledIndels(picard.vcf.SortVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:13 SortVcf Reading entries from input file 2 INFO 2024-07-02 11:50:13 SortVcf Reading entries from input file 2 Test: Test method testScrambledSnpsAndScrambledIndels(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:13 GMT+14:00 2024] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:13 GMT+14:00 2024] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes. Test: Test method testScrambledSnpsAndScrambledIndels(picard.vcf.SortVcfsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSingleScrambledFile(picard.vcf.SortVcfsTest) Test: Test method testSingleScrambledFile(picard.vcf.SortVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:13 SortVcf Gradle suite > Gradle test > picard.vcf.SortVcfsTest.testSingleScrambledFile STANDARD_ERROR INFO 2024-07-02 11:50:13 SortVcf Test: Test method testSingleScrambledFile(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testSingleScrambledFile(picard.vcf.SortVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleScrambledFile(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testSingleScrambledFile(picard.vcf.SortVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleScrambledFile(picard.vcf.SortVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleScrambledFile(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testSingleScrambledFile(picard.vcf.SortVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleScrambledFile(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testSingleScrambledFile(picard.vcf.SortVcfsTest) produced standard out/err: ********** SortVcf -INPUT testdata/picard/vcf/CEUTrio-snps-scrambled.1.vcf -OUTPUT /tmp/sort-single-scrambled-test-output.5749018245668307251.vcf -CREATE_INDEX false ********** SortVcf -INPUT testdata/picard/vcf/CEUTrio-snps-scrambled.1.vcf -OUTPUT /tmp/sort-single-scrambled-test-output.5749018245668307251.vcf -CREATE_INDEX false Test: Test method testSingleScrambledFile(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testSingleScrambledFile(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testSingleScrambledFile(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testSingleScrambledFile(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:13.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:13.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleScrambledFile(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:13.743 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:13.743 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleScrambledFile(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:13.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:13.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleScrambledFile(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:13.743 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:13.743 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleScrambledFile(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:13 GMT+14:00 2024] SortVcf INPUT=[testdata/picard/vcf/CEUTrio-snps-scrambled.1.vcf] OUTPUT=/tmp/sort-single-scrambled-test-output.5749018245668307251.vcf CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:13 GMT+14:00 2024] SortVcf INPUT=[testdata/picard/vcf/CEUTrio-snps-scrambled.1.vcf] OUTPUT=/tmp/sort-single-scrambled-test-output.5749018245668307251.vcf CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleScrambledFile(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleScrambledFile(picard.vcf.SortVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:13 SortVcf Reading entries from input file 1 INFO 2024-07-02 11:50:13 SortVcf Reading entries from input file 1 Test: Test method testSingleScrambledFile(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:13 GMT+14:00 2024] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:13 GMT+14:00 2024] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes. Test: Test method testSingleScrambledFile(picard.vcf.SortVcfsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTwoScrambledSnpFiles(picard.vcf.SortVcfsTest) Test: Test method testTwoScrambledSnpFiles(picard.vcf.SortVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:13 SortVcf Gradle suite > Gradle test > picard.vcf.SortVcfsTest.testTwoScrambledSnpFiles STANDARD_ERROR INFO 2024-07-02 11:50:13 SortVcf Test: Test method testTwoScrambledSnpFiles(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testTwoScrambledSnpFiles(picard.vcf.SortVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTwoScrambledSnpFiles(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testTwoScrambledSnpFiles(picard.vcf.SortVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTwoScrambledSnpFiles(picard.vcf.SortVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTwoScrambledSnpFiles(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testTwoScrambledSnpFiles(picard.vcf.SortVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTwoScrambledSnpFiles(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testTwoScrambledSnpFiles(picard.vcf.SortVcfsTest) produced standard out/err: ********** SortVcf -INPUT testdata/picard/vcf/CEUTrio-snps-scrambled.1.vcf -INPUT testdata/picard/vcf/vcfFormatTest.scrambled.vcf -OUTPUT /tmp/sort-multiple-scrambled-test-output.14915907719876270992.vcf -CREATE_INDEX false ********** SortVcf -INPUT testdata/picard/vcf/CEUTrio-snps-scrambled.1.vcf -INPUT testdata/picard/vcf/vcfFormatTest.scrambled.vcf -OUTPUT /tmp/sort-multiple-scrambled-test-output.14915907719876270992.vcf -CREATE_INDEX false Test: Test method testTwoScrambledSnpFiles(picard.vcf.SortVcfsTest) produced standard out/err: ********** ********** Test: Test method testTwoScrambledSnpFiles(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testTwoScrambledSnpFiles(picard.vcf.SortVcfsTest) produced standard out/err: Test: Test method testTwoScrambledSnpFiles(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:13.989 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:13.989 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoScrambledSnpFiles(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:13.989 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:13.989 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoScrambledSnpFiles(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:13.989 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:13.989 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTwoScrambledSnpFiles(picard.vcf.SortVcfsTest) produced standard out/err: 11:50:13.990 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:13.990 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTwoScrambledSnpFiles(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:13 GMT+14:00 2024] SortVcf INPUT=[testdata/picard/vcf/CEUTrio-snps-scrambled.1.vcf, testdata/picard/vcf/vcfFormatTest.scrambled.vcf] OUTPUT=/tmp/sort-multiple-scrambled-test-output.14915907719876270992.vcf CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:13 GMT+14:00 2024] SortVcf INPUT=[testdata/picard/vcf/CEUTrio-snps-scrambled.1.vcf, testdata/picard/vcf/vcfFormatTest.scrambled.vcf] OUTPUT=/tmp/sort-multiple-scrambled-test-output.14915907719876270992.vcf CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTwoScrambledSnpFiles(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTwoScrambledSnpFiles(picard.vcf.SortVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:14 SortVcf Reading entries from input file 1 INFO 2024-07-02 11:50:14 SortVcf Reading entries from input file 1 Test: Test method testTwoScrambledSnpFiles(picard.vcf.SortVcfsTest) produced standard out/err: INFO 2024-07-02 11:50:14 SortVcf Reading entries from input file 2 INFO 2024-07-02 11:50:14 SortVcf Reading entries from input file 2 Test: Test method testTwoScrambledSnpFiles(picard.vcf.SortVcfsTest) produced standard out/err: [Tue Jul 02 11:50:14 GMT+14:00 2024] picard.vcf.SortVcf done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:50:14 GMT+14:00 2024] picard.vcf.SortVcf done. Elapsed time: 0.01 minutes. Test: Test method testTwoScrambledSnpFiles(picard.vcf.SortVcfsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testForCollectorWithoutData(picard.analysis.AbstractWgsMetricsCollectorTest) Running Test: Test method testForExceptionWithNegativeCoverage(picard.analysis.AbstractWgsMetricsCollectorTest) Running Test: Test method testForRefBaseN(picard.analysis.AbstractWgsMetricsCollectorTest) Running Test: Test method testForSetCounter(picard.analysis.AbstractWgsMetricsCollectorTest) Running Test: Test method testForStop(picard.analysis.AbstractWgsMetricsCollectorTest) Running Test: Test method testMerge[0]([testdata/picard/vcf/mergeTest.shard1, testdata/picard/vcf/mergeTest.shard2])(picard.vcf.AccumulateVariantCallingMetricsTest) Running Test: Test method testMerge[1]([testdata/picard/vcf/mergeTest.shard1, testdata/picard/vcf/mergeTest.shard2, testdata/picard/vcf/mergeTest.emptyShard])(picard.vcf.AccumulateVariantCallingMetricsTest) Running Test: Test method test(picard.vcf.processor.AccumulatorExecutorTest) Running Test: Test method testAdapterReads[0](AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAAGAGGTTGTGGGTATGGGGGGGGGGGGGGGGGGGGTGGGGAAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[1](GATCGGAAGAGCACACGTCTGAACTCCAGTAACGCACATCTATCTCGTATTCCGTCTTCTTCTTGAACAGGGGTGGGTGGGGGGGGGGGGTGGGGGGGGGGGGGG, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[2](CTGAACTCCAGTCACGCACATCTATCGCGTATGCCGTCTTCTGCTTGAAAAGGGGGGGGGGGTGGGGGGGGGGG, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[3](GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAAGAGGTTGTGGGGGTGAAGGGGGGGGGGGGGGG, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[4](AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTGGGGGGGGGGGGTGGGTCCA, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[5](AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTGGGGGGGGGGGGTGGGTCCA, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[6](CTCGTATGCCGTCTTCTGCTTGGGGGGGGGGGGTGGGTCCA, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[7](GAGCTCGTATGCCGTCTTCTGCTTGGGGGGGGGGGGTGGGTCCA, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[8](AGATCGGAAGAGCGTCGTGTAGGGaaaGAGTGTAAGAGGTTGTGGGTATGGGGGGGGGGGGGGGGGGGGTGGGGAAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[9](GATCggaAGAGCACACGTCTGAACTCCAGTAACGCACATCTATCTCGTATTCCGTCTTCTTCTTGAACAGGGGTGGGTGGGGGGGGGGGGTGGGGGGGGGGGGGG, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[10](agatcggaagagctcgtatgccgtcttctgcttggggggggggggtgggtcca, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[11](AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[12](AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[13](AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[14](AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[15](AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[16](AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[17](GAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAACTTACTATCC, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[18](GCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTA, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[19](CTCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCT, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[20](TACCCTTCATTATTGCAGCCCTAGCAGCACTCCACCTCCTATTCTTGCAC, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[21](GAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAAT, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[22](CACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCT, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[23](TCCTTCTCTCCTTAATGACATTAACACTATTCTCACCAGACCTCCTAGGC, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[24](GACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCCTCCCCACAT, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[25](CAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCC, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[26](CTAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTA, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[27](GCAATAATCCCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCG, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[28](CCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTC, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[29](TAACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGA, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[30](CAAGTAGCATCCGTACTATACTTCACAACAATCCTAATCCTAATACCAAC, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[31](TATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGTA, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[32](TAAACTAATACACCAGTCTTGTAAACCGGAGACGAAAACCTTTTTCCAAG, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[33](GACAAATCAGAGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAA, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[34](GATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGG, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[35](TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[36](ATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCA, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[37](CCTGTAGTACATAAAAACCCAACCCACATCAAACCCCCCCCCCCCATGCT, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[38](TACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAAC, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[39](TCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTT, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReads[40](AACAGTACATAGTACATAAAGTCATTTACCGTACATAGCACATTACAGTC, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[0](AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAAGAGGTTGTGGGTATGGGGGGGGGGGGGGGGGGGGTGGGGAAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[1](GATCGGAAGAGCACACGTCTGAACTCCAGTAACGCACATCTATCTCGTATTCCGTCTTCTTCTTGAACAGGGGTGGGTGGGGGGGGGGGGTGGGGGGGGGGGGGG, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[2](CTGAACTCCAGTCACGCACATCTATCGCGTATGCCGTCTTCTGCTTGAAAAGGGGGGGGGGGTGGGGGGGGGGG, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[3](GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAAGAGGTTGTGGGGGTGAAGGGGGGGGGGGGGGG, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[4](AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTGGGGGGGGGGGGTGGGTCCA, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[5](AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTGGGGGGGGGGGGTGGGTCCA, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[6](CTCGTATGCCGTCTTCTGCTTGGGGGGGGGGGGTGGGTCCA, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[7](GAGCTCGTATGCCGTCTTCTGCTTGGGGGGGGGGGGTGGGTCCA, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[8](AGATCGGAAGAGCGTCGTGTAGGGaaaGAGTGTAAGAGGTTGTGGGTATGGGGGGGGGGGGGGGGGGGGTGGGGAAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[9](GATCggaAGAGCACACGTCTGAACTCCAGTAACGCACATCTATCTCGTATTCCGTCTTCTTCTTGAACAGGGGTGGGTGGGGGGGGGGGGTGGGGGGGGGGGGGG, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[10](agatcggaagagctcgtatgccgtcttctgcttggggggggggggtgggtcca, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[11](AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[12](AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[13](AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[14](AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[15](AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[16](AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, true)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[17](GAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAACTTACTATCC, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[18](GCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTA, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[19](CTCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCT, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[20](TACCCTTCATTATTGCAGCCCTAGCAGCACTCCACCTCCTATTCTTGCAC, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[21](GAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAAT, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[22](CACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCT, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[23](TCCTTCTCTCCTTAATGACATTAACACTATTCTCACCAGACCTCCTAGGC, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[24](GACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCCTCCCCACAT, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[25](CAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCC, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[26](CTAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTA, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[27](GCAATAATCCCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCG, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[28](CCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTC, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[29](TAACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGA, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[30](CAAGTAGCATCCGTACTATACTTCACAACAATCCTAATCCTAATACCAAC, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[31](TATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGTA, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[32](TAAACTAATACACCAGTCTTGTAAACCGGAGACGAAAACCTTTTTCCAAG, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[33](GACAAATCAGAGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAA, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[34](GATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGG, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[35](TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[36](ATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCA, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[37](CCTGTAGTACATAAAAACCCAACCCACATCAAACCCCCCCCCCCCATGCT, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[38](TACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAAC, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[39](TCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTT, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAdapterReadsRevComp[40](AACAGTACATAGTACATAAAGTCATTTACCGTACATAGCACATTACAGTC, false)(picard.analysis.AdapterUtilityTest) Running Test: Test method testAddCommentsToBam(picard.sam.AddCommentsToBamTest) Test: Test method testAddCommentsToBam(picard.sam.AddCommentsToBamTest) produced standard out/err: INFO 2024-07-02 11:50:25 AddCommentsToBam Gradle suite > Gradle test > picard.sam.AddCommentsToBamTest.testAddCommentsToBam STANDARD_ERROR INFO 2024-07-02 11:50:25 AddCommentsToBam Test: Test method testAddCommentsToBam(picard.sam.AddCommentsToBamTest) produced standard out/err: Test: Test method testAddCommentsToBam(picard.sam.AddCommentsToBamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testAddCommentsToBam(picard.sam.AddCommentsToBamTest) produced standard out/err: ********** ********** Test: Test method testAddCommentsToBam(picard.sam.AddCommentsToBamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testAddCommentsToBam(picard.sam.AddCommentsToBamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testAddCommentsToBam(picard.sam.AddCommentsToBamTest) produced standard out/err: ********** ********** Test: Test method testAddCommentsToBam(picard.sam.AddCommentsToBamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testAddCommentsToBam(picard.sam.AddCommentsToBamTest) produced standard out/err: ********** ********** Test: Test method testAddCommentsToBam(picard.sam.AddCommentsToBamTest) produced standard out/err: ********** AddCommentsToBam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/aligned_queryname_sorted.bam -OUTPUT /tmp/addCommentsToBamTest.5596505145346782481.bam -COMMENT test1 -COMMENT test2 -COMMENT test3 ********** AddCommentsToBam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/aligned_queryname_sorted.bam -OUTPUT /tmp/addCommentsToBamTest.5596505145346782481.bam -COMMENT test1 -COMMENT test2 -COMMENT test3 Test: Test method testAddCommentsToBam(picard.sam.AddCommentsToBamTest) produced standard out/err: ********** ********** Test: Test method testAddCommentsToBam(picard.sam.AddCommentsToBamTest) produced standard out/err: Test: Test method testAddCommentsToBam(picard.sam.AddCommentsToBamTest) produced standard out/err: Test: Test method testAddCommentsToBam(picard.sam.AddCommentsToBamTest) produced standard out/err: 11:50:25.127 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:25.127 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAddCommentsToBam(picard.sam.AddCommentsToBamTest) produced standard out/err: 11:50:25.127 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:25.127 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAddCommentsToBam(picard.sam.AddCommentsToBamTest) produced standard out/err: 11:50:25.128 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:25.128 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAddCommentsToBam(picard.sam.AddCommentsToBamTest) produced standard out/err: 11:50:25.128 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:25.128 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAddCommentsToBam(picard.sam.AddCommentsToBamTest) produced standard out/err: [Tue Jul 02 11:50:25 GMT+14:00 2024] AddCommentsToBam INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/aligned_queryname_sorted.bam OUTPUT=/tmp/addCommentsToBamTest.5596505145346782481.bam COMMENT=[test1, test2, test3] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:25 GMT+14:00 2024] AddCommentsToBam INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/aligned_queryname_sorted.bam OUTPUT=/tmp/addCommentsToBamTest.5596505145346782481.bam COMMENT=[test1, test2, test3] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testAddCommentsToBam(picard.sam.AddCommentsToBamTest) produced standard out/err: [Tue Jul 02 11:50:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testAddCommentsToBam(picard.sam.AddCommentsToBamTest) produced standard out/err: [Tue Jul 02 11:50:25 GMT+14:00 2024] picard.sam.AddCommentsToBam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:25 GMT+14:00 2024] picard.sam.AddCommentsToBam done. Elapsed time: 0.00 minutes. Test: Test method testAddCommentsToBam(picard.sam.AddCommentsToBamTest) produced standard out/err: Runtime.totalMemory()=1116733440 Runtime.totalMemory()=1116733440 Running Test: Test method testUsingNewlines(picard.sam.AddCommentsToBamTest) Test: Test method testUsingNewlines(picard.sam.AddCommentsToBamTest) produced standard out/err: INFO 2024-07-02 11:50:25 AddCommentsToBam Gradle suite > Gradle test > picard.sam.AddCommentsToBamTest.testUsingNewlines STANDARD_ERROR INFO 2024-07-02 11:50:25 AddCommentsToBam Test: Test method testUsingNewlines(picard.sam.AddCommentsToBamTest) produced standard out/err: Test: Test method testUsingNewlines(picard.sam.AddCommentsToBamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testUsingNewlines(picard.sam.AddCommentsToBamTest) produced standard out/err: ********** ********** Test: Test method testUsingNewlines(picard.sam.AddCommentsToBamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testUsingNewlines(picard.sam.AddCommentsToBamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testUsingNewlines(picard.sam.AddCommentsToBamTest) produced standard out/err: ********** ********** Test: Test method testUsingNewlines(picard.sam.AddCommentsToBamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testUsingNewlines(picard.sam.AddCommentsToBamTest) produced standard out/err: ********** ********** Test: Test method testUsingNewlines(picard.sam.AddCommentsToBamTest) produced standard out/err: ********** AddCommentsToBam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test2.sam -OUTPUT /tmp/addCommentsToBamTest.mewLine3750488943752539308.bam -COMMENT this is ********** AddCommentsToBam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test2.sam -OUTPUT /tmp/addCommentsToBamTest.mewLine3750488943752539308.bam -COMMENT this is Test: Test method testUsingNewlines(picard.sam.AddCommentsToBamTest) produced standard out/err: a crazy a crazy Test: Test method testUsingNewlines(picard.sam.AddCommentsToBamTest) produced standard out/err: test test Test: Test method testUsingNewlines(picard.sam.AddCommentsToBamTest) produced standard out/err: ********** ********** Test: Test method testUsingNewlines(picard.sam.AddCommentsToBamTest) produced standard out/err: Test: Test method testUsingNewlines(picard.sam.AddCommentsToBamTest) produced standard out/err: Running Test: Test method testUsingSam(picard.sam.AddCommentsToBamTest) Test: Test method testUsingSam(picard.sam.AddCommentsToBamTest) produced standard out/err: INFO 2024-07-02 11:50:25 AddCommentsToBam Gradle suite > Gradle test > picard.sam.AddCommentsToBamTest.testUsingSam STANDARD_ERROR INFO 2024-07-02 11:50:25 AddCommentsToBam Test: Test method testUsingSam(picard.sam.AddCommentsToBamTest) produced standard out/err: Test: Test method testUsingSam(picard.sam.AddCommentsToBamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testUsingSam(picard.sam.AddCommentsToBamTest) produced standard out/err: ********** ********** Test: Test method testUsingSam(picard.sam.AddCommentsToBamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testUsingSam(picard.sam.AddCommentsToBamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testUsingSam(picard.sam.AddCommentsToBamTest) produced standard out/err: ********** ********** Test: Test method testUsingSam(picard.sam.AddCommentsToBamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testUsingSam(picard.sam.AddCommentsToBamTest) produced standard out/err: ********** ********** Test: Test method testUsingSam(picard.sam.AddCommentsToBamTest) produced standard out/err: ********** AddCommentsToBam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test2.sam -OUTPUT /tmp/addCommentsToBamTest.samFile3563238998690788053.bam -COMMENT test1 -COMMENT test2 -COMMENT test3 ********** AddCommentsToBam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test2.sam -OUTPUT /tmp/addCommentsToBamTest.samFile3563238998690788053.bam -COMMENT test1 -COMMENT test2 -COMMENT test3 Test: Test method testUsingSam(picard.sam.AddCommentsToBamTest) produced standard out/err: ********** ********** Test: Test method testUsingSam(picard.sam.AddCommentsToBamTest) produced standard out/err: Test: Test method testUsingSam(picard.sam.AddCommentsToBamTest) produced standard out/err: Test: Test method testUsingSam(picard.sam.AddCommentsToBamTest) produced standard out/err: 11:50:25.425 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:25.425 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUsingSam(picard.sam.AddCommentsToBamTest) produced standard out/err: 11:50:25.425 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:25.425 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUsingSam(picard.sam.AddCommentsToBamTest) produced standard out/err: 11:50:25.425 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:25.425 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUsingSam(picard.sam.AddCommentsToBamTest) produced standard out/err: 11:50:25.425 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:25.425 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUsingSam(picard.sam.AddCommentsToBamTest) produced standard out/err: [Tue Jul 02 11:50:25 GMT+14:00 2024] AddCommentsToBam INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test2.sam OUTPUT=/tmp/addCommentsToBamTest.samFile3563238998690788053.bam COMMENT=[test1, test2, test3] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:25 GMT+14:00 2024] AddCommentsToBam INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test2.sam OUTPUT=/tmp/addCommentsToBamTest.samFile3563238998690788053.bam COMMENT=[test1, test2, test3] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testUsingSam(picard.sam.AddCommentsToBamTest) produced standard out/err: [Tue Jul 02 11:50:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testUsingSam(picard.sam.AddCommentsToBamTest) produced standard out/err: [Tue Jul 02 11:50:25 GMT+14:00 2024] picard.sam.AddCommentsToBam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:25 GMT+14:00 2024] picard.sam.AddCommentsToBam done. Elapsed time: 0.00 minutes. Test: Test method testUsingSam(picard.sam.AddCommentsToBamTest) produced standard out/err: Runtime.totalMemory()=1116733440 Runtime.totalMemory()=1116733440 Test: Test method testUsingSam(picard.sam.AddCommentsToBamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testIntervalList[0](testdata/picard/sam/aligned.sam, null, testdata/picard/sam/AddOATag/aligned_no_intervals.sam)(picard.sam.AddOATagTest) Test: Test method testIntervalList[0](testdata/picard/sam/aligned.sam, null, testdata/picard/sam/AddOATag/aligned_no_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: INFO 2024-07-02 11:50:25 AddOATag Gradle suite > Gradle test > picard.sam.AddOATagTest.testIntervalList[0](testdata/picard/sam/aligned.sam, null, testdata/picard/sam/AddOATag/aligned_no_intervals.sam) STANDARD_ERROR INFO 2024-07-02 11:50:25 AddOATag Test: Test method testIntervalList[0](testdata/picard/sam/aligned.sam, null, testdata/picard/sam/AddOATag/aligned_no_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: Test: Test method testIntervalList[0](testdata/picard/sam/aligned.sam, null, testdata/picard/sam/AddOATag/aligned_no_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIntervalList[0](testdata/picard/sam/aligned.sam, null, testdata/picard/sam/AddOATag/aligned_no_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** ********** Test: Test method testIntervalList[0](testdata/picard/sam/aligned.sam, null, testdata/picard/sam/AddOATag/aligned_no_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIntervalList[0](testdata/picard/sam/aligned.sam, null, testdata/picard/sam/AddOATag/aligned_no_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIntervalList[0](testdata/picard/sam/aligned.sam, null, testdata/picard/sam/AddOATag/aligned_no_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** ********** Test: Test method testIntervalList[0](testdata/picard/sam/aligned.sam, null, testdata/picard/sam/AddOATag/aligned_no_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIntervalList[0](testdata/picard/sam/aligned.sam, null, testdata/picard/sam/AddOATag/aligned_no_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** ********** Test: Test method testIntervalList[0](testdata/picard/sam/aligned.sam, null, testdata/picard/sam/AddOATag/aligned_no_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** AddOATag -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/AddOATag2526038457663953132.bam ********** AddOATag -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/AddOATag2526038457663953132.bam Test: Test method testIntervalList[0](testdata/picard/sam/aligned.sam, null, testdata/picard/sam/AddOATag/aligned_no_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** ********** Test: Test method testIntervalList[0](testdata/picard/sam/aligned.sam, null, testdata/picard/sam/AddOATag/aligned_no_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: Test: Test method testIntervalList[0](testdata/picard/sam/aligned.sam, null, testdata/picard/sam/AddOATag/aligned_no_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: Test: Test method testIntervalList[0](testdata/picard/sam/aligned.sam, null, testdata/picard/sam/AddOATag/aligned_no_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: 11:50:25.442 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:25.442 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIntervalList[0](testdata/picard/sam/aligned.sam, null, testdata/picard/sam/AddOATag/aligned_no_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: 11:50:25.442 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:25.442 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIntervalList[0](testdata/picard/sam/aligned.sam, null, testdata/picard/sam/AddOATag/aligned_no_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: 11:50:25.442 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:25.442 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIntervalList[0](testdata/picard/sam/aligned.sam, null, testdata/picard/sam/AddOATag/aligned_no_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: 11:50:25.442 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:25.442 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIntervalList[0](testdata/picard/sam/aligned.sam, null, testdata/picard/sam/AddOATag/aligned_no_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: [Tue Jul 02 11:50:25 GMT+14:00 2024] AddOATag INPUT=testdata/picard/sam/aligned.sam OUTPUT=/tmp/AddOATag2526038457663953132.bam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:25 GMT+14:00 2024] AddOATag INPUT=testdata/picard/sam/aligned.sam OUTPUT=/tmp/AddOATag2526038457663953132.bam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIntervalList[0](testdata/picard/sam/aligned.sam, null, testdata/picard/sam/AddOATag/aligned_no_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: [Tue Jul 02 11:50:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIntervalList[0](testdata/picard/sam/aligned.sam, null, testdata/picard/sam/AddOATag/aligned_no_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: [Tue Jul 02 11:50:25 GMT+14:00 2024] picard.sam.AddOATag done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:25 GMT+14:00 2024] picard.sam.AddOATag done. Elapsed time: 0.00 minutes. Test: Test method testIntervalList[0](testdata/picard/sam/aligned.sam, null, testdata/picard/sam/AddOATag/aligned_no_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: Runtime.totalMemory()=1116733440 Runtime.totalMemory()=1116733440 Running Test: Test method testIntervalList[1](testdata/picard/sam/aligned.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, testdata/picard/sam/aligned.sam)(picard.sam.AddOATagTest) Test: Test method testIntervalList[1](testdata/picard/sam/aligned.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, testdata/picard/sam/aligned.sam)(picard.sam.AddOATagTest) produced standard out/err: INFO 2024-07-02 11:50:25 AddOATag Gradle suite > Gradle test > picard.sam.AddOATagTest.testIntervalList[1](testdata/picard/sam/aligned.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, testdata/picard/sam/aligned.sam) STANDARD_ERROR INFO 2024-07-02 11:50:25 AddOATag Test: Test method testIntervalList[1](testdata/picard/sam/aligned.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, testdata/picard/sam/aligned.sam)(picard.sam.AddOATagTest) produced standard out/err: Test: Test method testIntervalList[1](testdata/picard/sam/aligned.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, testdata/picard/sam/aligned.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIntervalList[1](testdata/picard/sam/aligned.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, testdata/picard/sam/aligned.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** ********** Test: Test method testIntervalList[1](testdata/picard/sam/aligned.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, testdata/picard/sam/aligned.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIntervalList[1](testdata/picard/sam/aligned.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, testdata/picard/sam/aligned.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIntervalList[1](testdata/picard/sam/aligned.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, testdata/picard/sam/aligned.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** ********** Test: Test method testIntervalList[1](testdata/picard/sam/aligned.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, testdata/picard/sam/aligned.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIntervalList[1](testdata/picard/sam/aligned.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, testdata/picard/sam/aligned.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** ********** Test: Test method testIntervalList[1](testdata/picard/sam/aligned.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, testdata/picard/sam/aligned.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** AddOATag -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/AddOATag526370880548777514.bam -INTERVAL_LIST testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list ********** AddOATag -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/AddOATag526370880548777514.bam -INTERVAL_LIST testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list Test: Test method testIntervalList[1](testdata/picard/sam/aligned.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, testdata/picard/sam/aligned.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** ********** Test: Test method testIntervalList[1](testdata/picard/sam/aligned.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, testdata/picard/sam/aligned.sam)(picard.sam.AddOATagTest) produced standard out/err: Test: Test method testIntervalList[1](testdata/picard/sam/aligned.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, testdata/picard/sam/aligned.sam)(picard.sam.AddOATagTest) produced standard out/err: Test: Test method testIntervalList[1](testdata/picard/sam/aligned.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, testdata/picard/sam/aligned.sam)(picard.sam.AddOATagTest) produced standard out/err: 11:50:25.504 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:25.504 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIntervalList[1](testdata/picard/sam/aligned.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, testdata/picard/sam/aligned.sam)(picard.sam.AddOATagTest) produced standard out/err: 11:50:25.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:25.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIntervalList[1](testdata/picard/sam/aligned.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, testdata/picard/sam/aligned.sam)(picard.sam.AddOATagTest) produced standard out/err: 11:50:25.504 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:25.504 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIntervalList[1](testdata/picard/sam/aligned.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, testdata/picard/sam/aligned.sam)(picard.sam.AddOATagTest) produced standard out/err: 11:50:25.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:25.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIntervalList[1](testdata/picard/sam/aligned.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, testdata/picard/sam/aligned.sam)(picard.sam.AddOATagTest) produced standard out/err: [Tue Jul 02 11:50:25 GMT+14:00 2024] AddOATag INPUT=testdata/picard/sam/aligned.sam OUTPUT=/tmp/AddOATag526370880548777514.bam INTERVAL_LIST=testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:25 GMT+14:00 2024] AddOATag INPUT=testdata/picard/sam/aligned.sam OUTPUT=/tmp/AddOATag526370880548777514.bam INTERVAL_LIST=testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIntervalList[1](testdata/picard/sam/aligned.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, testdata/picard/sam/aligned.sam)(picard.sam.AddOATagTest) produced standard out/err: [Tue Jul 02 11:50:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIntervalList[1](testdata/picard/sam/aligned.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, testdata/picard/sam/aligned.sam)(picard.sam.AddOATagTest) produced standard out/err: [Tue Jul 02 11:50:25 GMT+14:00 2024] picard.sam.AddOATag done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:25 GMT+14:00 2024] picard.sam.AddOATag done. Elapsed time: 0.00 minutes. Test: Test method testIntervalList[1](testdata/picard/sam/aligned.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, testdata/picard/sam/aligned.sam)(picard.sam.AddOATagTest) produced standard out/err: Runtime.totalMemory()=1116733440 Runtime.totalMemory()=1116733440 Running Test: Test method testIntervalList[2](testdata/picard/sam/aligned.sam, testdata/picard/sam/contiguous.interval_list, testdata/picard/sam/AddOATag/aligned_with_intervals.sam)(picard.sam.AddOATagTest) Test: Test method testIntervalList[2](testdata/picard/sam/aligned.sam, testdata/picard/sam/contiguous.interval_list, testdata/picard/sam/AddOATag/aligned_with_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: INFO 2024-07-02 11:50:25 AddOATag Gradle suite > Gradle test > picard.sam.AddOATagTest.testIntervalList[2](testdata/picard/sam/aligned.sam, testdata/picard/sam/contiguous.interval_list, testdata/picard/sam/AddOATag/aligned_with_intervals.sam) STANDARD_ERROR INFO 2024-07-02 11:50:25 AddOATag Test: Test method testIntervalList[2](testdata/picard/sam/aligned.sam, testdata/picard/sam/contiguous.interval_list, testdata/picard/sam/AddOATag/aligned_with_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: Test: Test method testIntervalList[2](testdata/picard/sam/aligned.sam, testdata/picard/sam/contiguous.interval_list, testdata/picard/sam/AddOATag/aligned_with_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIntervalList[2](testdata/picard/sam/aligned.sam, testdata/picard/sam/contiguous.interval_list, testdata/picard/sam/AddOATag/aligned_with_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** ********** Test: Test method testIntervalList[2](testdata/picard/sam/aligned.sam, testdata/picard/sam/contiguous.interval_list, testdata/picard/sam/AddOATag/aligned_with_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIntervalList[2](testdata/picard/sam/aligned.sam, testdata/picard/sam/contiguous.interval_list, testdata/picard/sam/AddOATag/aligned_with_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIntervalList[2](testdata/picard/sam/aligned.sam, testdata/picard/sam/contiguous.interval_list, testdata/picard/sam/AddOATag/aligned_with_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** ********** Test: Test method testIntervalList[2](testdata/picard/sam/aligned.sam, testdata/picard/sam/contiguous.interval_list, testdata/picard/sam/AddOATag/aligned_with_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIntervalList[2](testdata/picard/sam/aligned.sam, testdata/picard/sam/contiguous.interval_list, testdata/picard/sam/AddOATag/aligned_with_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** ********** Test: Test method testIntervalList[2](testdata/picard/sam/aligned.sam, testdata/picard/sam/contiguous.interval_list, testdata/picard/sam/AddOATag/aligned_with_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** AddOATag -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/AddOATag13179509203164116617.bam -INTERVAL_LIST testdata/picard/sam/contiguous.interval_list ********** AddOATag -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/AddOATag13179509203164116617.bam -INTERVAL_LIST testdata/picard/sam/contiguous.interval_list Test: Test method testIntervalList[2](testdata/picard/sam/aligned.sam, testdata/picard/sam/contiguous.interval_list, testdata/picard/sam/AddOATag/aligned_with_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** ********** Test: Test method testIntervalList[2](testdata/picard/sam/aligned.sam, testdata/picard/sam/contiguous.interval_list, testdata/picard/sam/AddOATag/aligned_with_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: Test: Test method testIntervalList[2](testdata/picard/sam/aligned.sam, testdata/picard/sam/contiguous.interval_list, testdata/picard/sam/AddOATag/aligned_with_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: Test: Test method testIntervalList[2](testdata/picard/sam/aligned.sam, testdata/picard/sam/contiguous.interval_list, testdata/picard/sam/AddOATag/aligned_with_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: 11:50:25.552 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:25.552 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIntervalList[2](testdata/picard/sam/aligned.sam, testdata/picard/sam/contiguous.interval_list, testdata/picard/sam/AddOATag/aligned_with_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: 11:50:25.553 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:25.553 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIntervalList[2](testdata/picard/sam/aligned.sam, testdata/picard/sam/contiguous.interval_list, testdata/picard/sam/AddOATag/aligned_with_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: 11:50:25.565 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:25.565 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIntervalList[2](testdata/picard/sam/aligned.sam, testdata/picard/sam/contiguous.interval_list, testdata/picard/sam/AddOATag/aligned_with_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: 11:50:25.565 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:25.565 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIntervalList[2](testdata/picard/sam/aligned.sam, testdata/picard/sam/contiguous.interval_list, testdata/picard/sam/AddOATag/aligned_with_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: [Tue Jul 02 11:50:25 GMT+14:00 2024] AddOATag INPUT=testdata/picard/sam/aligned.sam OUTPUT=/tmp/AddOATag13179509203164116617.bam INTERVAL_LIST=testdata/picard/sam/contiguous.interval_list VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:25 GMT+14:00 2024] AddOATag INPUT=testdata/picard/sam/aligned.sam OUTPUT=/tmp/AddOATag13179509203164116617.bam INTERVAL_LIST=testdata/picard/sam/contiguous.interval_list VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIntervalList[2](testdata/picard/sam/aligned.sam, testdata/picard/sam/contiguous.interval_list, testdata/picard/sam/AddOATag/aligned_with_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: [Tue Jul 02 11:50:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIntervalList[2](testdata/picard/sam/aligned.sam, testdata/picard/sam/contiguous.interval_list, testdata/picard/sam/AddOATag/aligned_with_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: [Tue Jul 02 11:50:25 GMT+14:00 2024] picard.sam.AddOATag done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:25 GMT+14:00 2024] picard.sam.AddOATag done. Elapsed time: 0.00 minutes. Test: Test method testIntervalList[2](testdata/picard/sam/aligned.sam, testdata/picard/sam/contiguous.interval_list, testdata/picard/sam/AddOATag/aligned_with_intervals.sam)(picard.sam.AddOATagTest) produced standard out/err: Runtime.totalMemory()=1116733440 Runtime.totalMemory()=1116733440 Running Test: Test method testWritingOATag[0](testdata/picard/sam/AddOATag/aligned_withoutOA.sam, testdata/picard/sam/AddOATag/aligned_withOA.sam)(picard.sam.AddOATagTest) Test: Test method testWritingOATag[0](testdata/picard/sam/AddOATag/aligned_withoutOA.sam, testdata/picard/sam/AddOATag/aligned_withOA.sam)(picard.sam.AddOATagTest) produced standard out/err: INFO 2024-07-02 11:50:25 AddOATag Gradle suite > Gradle test > picard.sam.AddOATagTest.testWritingOATag[0](testdata/picard/sam/AddOATag/aligned_withoutOA.sam, testdata/picard/sam/AddOATag/aligned_withOA.sam) STANDARD_ERROR INFO 2024-07-02 11:50:25 AddOATag Test: Test method testWritingOATag[0](testdata/picard/sam/AddOATag/aligned_withoutOA.sam, testdata/picard/sam/AddOATag/aligned_withOA.sam)(picard.sam.AddOATagTest) produced standard out/err: Test: Test method testWritingOATag[0](testdata/picard/sam/AddOATag/aligned_withoutOA.sam, testdata/picard/sam/AddOATag/aligned_withOA.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWritingOATag[0](testdata/picard/sam/AddOATag/aligned_withoutOA.sam, testdata/picard/sam/AddOATag/aligned_withOA.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** ********** Test: Test method testWritingOATag[0](testdata/picard/sam/AddOATag/aligned_withoutOA.sam, testdata/picard/sam/AddOATag/aligned_withOA.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWritingOATag[0](testdata/picard/sam/AddOATag/aligned_withoutOA.sam, testdata/picard/sam/AddOATag/aligned_withOA.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWritingOATag[0](testdata/picard/sam/AddOATag/aligned_withoutOA.sam, testdata/picard/sam/AddOATag/aligned_withOA.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** ********** Test: Test method testWritingOATag[0](testdata/picard/sam/AddOATag/aligned_withoutOA.sam, testdata/picard/sam/AddOATag/aligned_withOA.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWritingOATag[0](testdata/picard/sam/AddOATag/aligned_withoutOA.sam, testdata/picard/sam/AddOATag/aligned_withOA.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** ********** Test: Test method testWritingOATag[0](testdata/picard/sam/AddOATag/aligned_withoutOA.sam, testdata/picard/sam/AddOATag/aligned_withOA.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** AddOATag -INPUT testdata/picard/sam/AddOATag/aligned_withoutOA.sam -OUTPUT /tmp/AddOATag16014382398826197651.bam ********** AddOATag -INPUT testdata/picard/sam/AddOATag/aligned_withoutOA.sam -OUTPUT /tmp/AddOATag16014382398826197651.bam Test: Test method testWritingOATag[0](testdata/picard/sam/AddOATag/aligned_withoutOA.sam, testdata/picard/sam/AddOATag/aligned_withOA.sam)(picard.sam.AddOATagTest) produced standard out/err: ********** ********** Test: Test method testWritingOATag[0](testdata/picard/sam/AddOATag/aligned_withoutOA.sam, testdata/picard/sam/AddOATag/aligned_withOA.sam)(picard.sam.AddOATagTest) produced standard out/err: Test: Test method testWritingOATag[0](testdata/picard/sam/AddOATag/aligned_withoutOA.sam, testdata/picard/sam/AddOATag/aligned_withOA.sam)(picard.sam.AddOATagTest) produced standard out/err: Test: Test method testWritingOATag[0](testdata/picard/sam/AddOATag/aligned_withoutOA.sam, testdata/picard/sam/AddOATag/aligned_withOA.sam)(picard.sam.AddOATagTest) produced standard out/err: 11:50:25.626 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:25.626 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWritingOATag[0](testdata/picard/sam/AddOATag/aligned_withoutOA.sam, testdata/picard/sam/AddOATag/aligned_withOA.sam)(picard.sam.AddOATagTest) produced standard out/err: 11:50:25.626 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:25.626 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWritingOATag[0](testdata/picard/sam/AddOATag/aligned_withoutOA.sam, testdata/picard/sam/AddOATag/aligned_withOA.sam)(picard.sam.AddOATagTest) produced standard out/err: 11:50:25.627 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:25.627 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWritingOATag[0](testdata/picard/sam/AddOATag/aligned_withoutOA.sam, testdata/picard/sam/AddOATag/aligned_withOA.sam)(picard.sam.AddOATagTest) produced standard out/err: 11:50:25.627 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:25.627 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWritingOATag[0](testdata/picard/sam/AddOATag/aligned_withoutOA.sam, testdata/picard/sam/AddOATag/aligned_withOA.sam)(picard.sam.AddOATagTest) produced standard out/err: [Tue Jul 02 11:50:25 GMT+14:00 2024] AddOATag INPUT=testdata/picard/sam/AddOATag/aligned_withoutOA.sam OUTPUT=/tmp/AddOATag16014382398826197651.bam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:25 GMT+14:00 2024] AddOATag INPUT=testdata/picard/sam/AddOATag/aligned_withoutOA.sam OUTPUT=/tmp/AddOATag16014382398826197651.bam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWritingOATag[0](testdata/picard/sam/AddOATag/aligned_withoutOA.sam, testdata/picard/sam/AddOATag/aligned_withOA.sam)(picard.sam.AddOATagTest) produced standard out/err: [Tue Jul 02 11:50:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWritingOATag[0](testdata/picard/sam/AddOATag/aligned_withoutOA.sam, testdata/picard/sam/AddOATag/aligned_withOA.sam)(picard.sam.AddOATagTest) produced standard out/err: [Tue Jul 02 11:50:25 GMT+14:00 2024] picard.sam.AddOATag done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:25 GMT+14:00 2024] picard.sam.AddOATag done. Elapsed time: 0.00 minutes. Test: Test method testWritingOATag[0](testdata/picard/sam/AddOATag/aligned_withoutOA.sam, testdata/picard/sam/AddOATag/aligned_withOA.sam)(picard.sam.AddOATagTest) produced standard out/err: Runtime.totalMemory()=1116733440 Runtime.totalMemory()=1116733440 Running Test: Test method testGet3PrimeSoftClip[0](20M, true, 0)(picard.analysis.AlignmentSummaryMetricsCollectorTest) Running Test: Test method testGet3PrimeSoftClip[1](20M, false, 0)(picard.analysis.AlignmentSummaryMetricsCollectorTest) Running Test: Test method testGet3PrimeSoftClip[2](5H2S, true, 0)(picard.analysis.AlignmentSummaryMetricsCollectorTest) Running Test: Test method testGet3PrimeSoftClip[3](5H2S, false, 0)(picard.analysis.AlignmentSummaryMetricsCollectorTest) Running Test: Test method testGet3PrimeSoftClip[4](5H2S6H, false, 0)(picard.analysis.AlignmentSummaryMetricsCollectorTest) Running Test: Test method testGet3PrimeSoftClip[5](5H2S6H, true, 0)(picard.analysis.AlignmentSummaryMetricsCollectorTest) Running Test: Test method testGet3PrimeSoftClip[6](2H20M, true, 0)(picard.analysis.AlignmentSummaryMetricsCollectorTest) Running Test: Test method testGet3PrimeSoftClip[7](2H20M, false, 0)(picard.analysis.AlignmentSummaryMetricsCollectorTest) Running Test: Test method testGet3PrimeSoftClip[8](2S20M, false, 0)(picard.analysis.AlignmentSummaryMetricsCollectorTest) Running Test: Test method testGet3PrimeSoftClip[9](2S20M, true, 2)(picard.analysis.AlignmentSummaryMetricsCollectorTest) Running Test: Test method testGet3PrimeSoftClip[10](20M2S, true, 0)(picard.analysis.AlignmentSummaryMetricsCollectorTest) Running Test: Test method testGet3PrimeSoftClip[11](20M2S, false, 2)(picard.analysis.AlignmentSummaryMetricsCollectorTest) Running Test: Test method testGet3PrimeSoftClip[12](20M2S4S, false, 6)(picard.analysis.AlignmentSummaryMetricsCollectorTest) Running Test: Test method testGet3PrimeSoftClip[13](20M2S4S, true, 0)(picard.analysis.AlignmentSummaryMetricsCollectorTest) Running Test: Test method testGet3PrimeSoftClip[14](2S20M5S, false, 5)(picard.analysis.AlignmentSummaryMetricsCollectorTest) Running Test: Test method testGet3PrimeSoftClip[15](2S20M4S, true, 2)(picard.analysis.AlignmentSummaryMetricsCollectorTest) Running Test: Test method testGet3PrimeSoftClip[16](4S20M2S, true, 4)(picard.analysis.AlignmentSummaryMetricsCollectorTest) Running Test: Test method testGet3PrimeSoftClip[17](4S20M2S, false, 2)(picard.analysis.AlignmentSummaryMetricsCollectorTest) Running Test: Test method testGet3PrimeSoftClip[18](2H3S10M4S5H, false, 4)(picard.analysis.AlignmentSummaryMetricsCollectorTest) Running Test: Test method testGet3PrimeSoftClip[19](2H3S10M4S5H, true, 3)(picard.analysis.AlignmentSummaryMetricsCollectorTest) Running Test: Test method testSwapAlleles[0]([VC test @ 20:10 Q. of type=SNP alleles=[A*, C] attr={} GT=[] filters=, C, G, [VC test @ 20:10 Q. of type=SNP alleles=[A*, G] attr={} GT=[] filters=, true)(picard.util.AlleleSubsettingUtilsTest) Running Test: Test method testSwapAlleles[1]([VC test @ 20:10 Q. of type=SNP alleles=[A*, C] attr={} GT=[[NA12878 A*/C GQ 100 DP 10]] filters=, C, G, [VC test @ 20:10 Q. of type=SNP alleles=[A*, G] attr={} GT=[[NA12878 A*/G GQ 100 DP 10]] filters=, true)(picard.util.AlleleSubsettingUtilsTest) Running Test: Test method testSwapAlleles[2]([VC test @ 20:10 Q. of type=SNP alleles=[A*, C] attr={} GT=[[NA12878 A*/A* GQ 100 DP 10]] filters=, C, G, [VC test @ 20:10 Q. of type=SNP alleles=[A*, G] attr={} GT=[[NA12878 A*/A* GQ 100 DP 10]] filters=, true)(picard.util.AlleleSubsettingUtilsTest) Running Test: Test method testSwapAlleles[3]([VC test @ 20:10 Q. of type=SNP alleles=[A*, C] attr={} GT=[[NA12878 C/C GQ 100 DP 10]] filters=, C, G, [VC test @ 20:10 Q. of type=SNP alleles=[A*, G] attr={} GT=[[NA12878 G/G GQ 100 DP 10]] filters=, true)(picard.util.AlleleSubsettingUtilsTest) Running Test: Test method testSwapAlleles[4]([VC test @ 20:10 Q. of type=SNP alleles=[A*, C] attr={} GT=[] filters=, , G, null, false)(picard.util.AlleleSubsettingUtilsTest) Running Test: Test method testUpdatePLsAndADData[0]([VC test @ 20:10 Q. of type=SNP alleles=[A*, C] attr={} GT=[[NA12878 A*/A* GQ 8 DP 10 AD 10,2 PL 1000,900,0]] filters=, [VC test @ 20:10 Q. of type=SNP alleles=[A*, C] attr={} GT=[] filters=, [[NA12878 A*/A* GQ 8 DP 10 AD 10,2 PL 1000,900,0]])(picard.util.AlleleSubsettingUtilsTest) Running Test: Test method testUpdatePLsAndADData[1]([VC test @ 20:10 Q. of type=SNP alleles=[A*, C] attr={} GT=[[NA12878 A*/C GQ 8 DP 10 AD 10,2 PL 900,1000,0]] filters=, [VC test @ 20:10 Q. of type=SNP alleles=[A*, C] attr={} GT=[] filters=, [[NA12878 A*/C GQ 8 DP 10 AD 10,2 PL 900,1000,0]])(picard.util.AlleleSubsettingUtilsTest) Running Test: Test method testUpdatePLsAndADData[2]([VC test @ 20:10 Q. of type=SNP alleles=[A*, C] attr={} GT=[[NA12878 C/C GQ 8 DP 10 AD 10,2 PL 0,900,1000]] filters=, [VC test @ 20:10 Q. of type=SNP alleles=[A*, C] attr={} GT=[] filters=, [[NA12878 C/C GQ 8 DP 10 AD 10,2 PL 0,900,1000]])(picard.util.AlleleSubsettingUtilsTest) Running Test: Test method testUpdatePLsAndADData[3]([VC test @ 20:10 Q. of type=SNP alleles=[A*, C] attr={} GT=[[NA12878 C/C GQ 0 DP 10 PL 0,0,0]] filters=, [VC test @ 20:10 Q. of type=SNP alleles=[A*, C] attr={} GT=[] filters=, [[NA12878 C/C GQ 0 DP 10 PL 0,0,0]])(picard.util.AlleleSubsettingUtilsTest) Running Test: Test method testUpdatePLsAndADData[4]([VC test @ 20:10 Q. of type=SNP alleles=[A*, C] attr={} GT=[[NA12878 ./. DP 10]] filters=, [VC test @ 20:10 Q. of type=SNP alleles=[A*, C] attr={} GT=[] filters=, [[NA12878 ./. DP 10]])(picard.util.AlleleSubsettingUtilsTest) Running Test: Test method testUpdatePLsAndADData[5]([VC test-0 @ 20:10 Q. of type=SNP alleles=[A*, C, G] attr={} GT=[[NA12878 A*/A* GQ 100 DP 10 AD 20,0,1 PL 0,100,200,300,400,500]] filters=, [VC test-1 @ 20:10 Q. of type=SNP alleles=[A*, C] attr={} GT=[] filters=, [[NA12878 A*/A* GQ 100 DP 10 AD 20,0 PL 0,100,200]])(picard.util.AlleleSubsettingUtilsTest) Running Test: Test method testUpdatePLsAndADData[6]([VC test-1 @ 20:10 Q. of type=SNP alleles=[A*, C, G] attr={} GT=[[NA12878 A*/A* GQ 100 DP 10 AD 10,10,1 PL 100,0,200,300,400,500]] filters=, [VC test-2 @ 20:10 Q. of type=SNP alleles=[A*, C] attr={} GT=[] filters=, [[NA12878 A*/C GQ 100 DP 10 AD 10,10 PL 100,0,200]])(picard.util.AlleleSubsettingUtilsTest) Running Test: Test method testUpdatePLsAndADData[7]([VC test-2 @ 20:10 Q. of type=SNP alleles=[A*, C, G] attr={} GT=[[NA12878 A*/A* GQ 100 DP 10 AD 0,20,1 PL 200,100,0,300,400,500]] filters=, [VC test-3 @ 20:10 Q. of type=SNP alleles=[A*, C] attr={} GT=[] filters=, [[NA12878 C/C GQ 100 DP 10 AD 0,20 PL 200,100,0]])(picard.util.AlleleSubsettingUtilsTest) Running Test: Test method testUpdatePLsAndADData[8]([VC test-3 @ 20:10 Q. of type=SNP alleles=[A*, C, G] attr={} GT=[[NA12878 A*/A* GQ 100 DP 10 AD 10,0,11 PL 200,100,300,0,400,500]] filters=, [VC test-4 @ 20:10 Q. of type=SNP alleles=[A*, G] attr={} GT=[] filters=, [[NA12878 A*/G GQ 200 DP 10 AD 10,11 PL 200,0,500]])(picard.util.AlleleSubsettingUtilsTest) Running Test: Test method testUpdatePLsAndADData[9]([VC test-4 @ 20:10 Q. of type=SNP alleles=[A*, C, G] attr={} GT=[[NA12878 A*/A* GQ 100 DP 10 AD 0,12,11 PL 200,100,300,400,0,500]] filters=, [VC test-5 @ 20:10 Q. of type=SNP alleles=[A*, G] attr={} GT=[] filters=, [[NA12878 A*/A* GQ 200 DP 10 AD 0,11 PL 0,200,300]])(picard.util.AlleleSubsettingUtilsTest) Running Test: Test method testUpdatePLsAndADData[10]([VC test-5 @ 20:10 Q. of type=SNP alleles=[A*, C, G] attr={} GT=[[NA12878 A*/A* GQ 100 DP 10 AD 0,1,21 PL 200,100,300,400,500,0]] filters=, [VC test-6 @ 20:10 Q. of type=SNP alleles=[A*, G] attr={} GT=[] filters=, [[NA12878 G/G GQ 200 DP 10 AD 0,21 PL 200,400,0]])(picard.util.AlleleSubsettingUtilsTest) Running Test: Test method testUpdatePLsAndADData[11]([VC test-6 @ 20:10 Q. of type=SNP alleles=[A*, C, G] attr={} GT=[[NA12878 A*/A* GQ 100 DP 10 AD 0,1,21]] filters=, [VC test-7 @ 20:10 Q. of type=SNP alleles=[A*, G] attr={} GT=[] filters=, [[NA12878 ./. DP 10 AD 0,21]])(picard.util.AlleleSubsettingUtilsTest) Running Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: INFO 2024-07-02 11:50:25 CollectDuplicateMetrics Gradle suite > Gradle test > picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest.testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam) STANDARD_ERROR INFO 2024-07-02 11:50:25 CollectDuplicateMetrics Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** CollectDuplicateMetrics -METRICS_FILE /tmp/CollectDuplicateMetricsTester.16593901160161862863.tmp/metrics.txt -INPUT /tmp/CollectDuplicateMetrics782315403235689099.sam ********** CollectDuplicateMetrics -METRICS_FILE /tmp/CollectDuplicateMetricsTester.16593901160161862863.tmp/metrics.txt -INPUT /tmp/CollectDuplicateMetrics782315403235689099.sam Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:25.952 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:25.952 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:25.952 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:25.952 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:25.952 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:25.952 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:25.953 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:25.953 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: [Tue Jul 02 11:50:25 GMT+14:00 2024] CollectDuplicateMetrics METRICS_FILE=/tmp/CollectDuplicateMetricsTester.16593901160161862863.tmp/metrics.txt INPUT=/tmp/CollectDuplicateMetrics782315403235689099.sam ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:25 GMT+14:00 2024] CollectDuplicateMetrics METRICS_FILE=/tmp/CollectDuplicateMetricsTester.16593901160161862863.tmp/metrics.txt INPUT=/tmp/CollectDuplicateMetrics782315403235689099.sam ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: [Tue Jul 02 11:50:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: WARNING 2024-07-02 11:50:25 SinglePassSamProgram File reports sort order 'unknown', assuming it's coordinate sorted anyway. WARNING 2024-07-02 11:50:25 SinglePassSamProgram File reports sort order 'unknown', assuming it's coordinate sorted anyway. Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: [Tue Jul 02 11:50:25 GMT+14:00 2024] picard.sam.markduplicates.CollectDuplicateMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:25 GMT+14:00 2024] picard.sam.markduplicates.CollectDuplicateMetrics done. Elapsed time: 0.00 minutes. Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Runtime.totalMemory()=1116733440 Runtime.totalMemory()=1116733440 Running Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: INFO 2024-07-02 11:50:26 CollectDuplicateMetrics Gradle suite > Gradle test > picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest.testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam) STANDARD_ERROR INFO 2024-07-02 11:50:26 CollectDuplicateMetrics Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** CollectDuplicateMetrics -METRICS_FILE /tmp/CollectDuplicateMetricsTester.12579908985130270761.tmp/metrics.txt -INPUT /tmp/CollectDuplicateMetrics8786145636210157229.sam ********** CollectDuplicateMetrics -METRICS_FILE /tmp/CollectDuplicateMetricsTester.12579908985130270761.tmp/metrics.txt -INPUT /tmp/CollectDuplicateMetrics8786145636210157229.sam Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:26.090 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:26.090 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:26.090 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:26.090 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:26.091 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:26.091 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:26.091 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:26.091 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: [Tue Jul 02 11:50:26 GMT+14:00 2024] CollectDuplicateMetrics METRICS_FILE=/tmp/CollectDuplicateMetricsTester.12579908985130270761.tmp/metrics.txt INPUT=/tmp/CollectDuplicateMetrics8786145636210157229.sam ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:26 GMT+14:00 2024] CollectDuplicateMetrics METRICS_FILE=/tmp/CollectDuplicateMetricsTester.12579908985130270761.tmp/metrics.txt INPUT=/tmp/CollectDuplicateMetrics8786145636210157229.sam ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: [Tue Jul 02 11:50:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: WARNING 2024-07-02 11:50:26 SinglePassSamProgram File reports sort order 'unknown', assuming it's coordinate sorted anyway. WARNING 2024-07-02 11:50:26 SinglePassSamProgram File reports sort order 'unknown', assuming it's coordinate sorted anyway. Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: [Tue Jul 02 11:50:26 GMT+14:00 2024] picard.sam.markduplicates.CollectDuplicateMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:26 GMT+14:00 2024] picard.sam.markduplicates.CollectDuplicateMetrics done. Elapsed time: 0.00 minutes. Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Runtime.totalMemory()=1116733440 Runtime.totalMemory()=1116733440 Running Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: INFO 2024-07-02 11:50:26 CollectDuplicateMetrics Gradle suite > Gradle test > picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest.testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam) STANDARD_ERROR INFO 2024-07-02 11:50:26 CollectDuplicateMetrics Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** CollectDuplicateMetrics -METRICS_FILE /tmp/CollectDuplicateMetricsTester.9420278599825680093.tmp/metrics.txt -INPUT /tmp/CollectDuplicateMetrics2063707336169386611.sam ********** CollectDuplicateMetrics -METRICS_FILE /tmp/CollectDuplicateMetricsTester.9420278599825680093.tmp/metrics.txt -INPUT /tmp/CollectDuplicateMetrics2063707336169386611.sam Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:26.164 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:26.164 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:26.164 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:26.164 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:26.164 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:26.164 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:26.164 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:26.164 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: [Tue Jul 02 11:50:26 GMT+14:00 2024] CollectDuplicateMetrics METRICS_FILE=/tmp/CollectDuplicateMetricsTester.9420278599825680093.tmp/metrics.txt INPUT=/tmp/CollectDuplicateMetrics2063707336169386611.sam ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:26 GMT+14:00 2024] CollectDuplicateMetrics METRICS_FILE=/tmp/CollectDuplicateMetricsTester.9420278599825680093.tmp/metrics.txt INPUT=/tmp/CollectDuplicateMetrics2063707336169386611.sam ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: [Tue Jul 02 11:50:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: WARNING 2024-07-02 11:50:26 SinglePassSamProgram File reports sort order 'queryname', assuming it's coordinate sorted anyway. WARNING 2024-07-02 11:50:26 SinglePassSamProgram File reports sort order 'queryname', assuming it's coordinate sorted anyway. Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: [Tue Jul 02 11:50:26 GMT+14:00 2024] picard.sam.markduplicates.CollectDuplicateMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:26 GMT+14:00 2024] picard.sam.markduplicates.CollectDuplicateMetrics done. Elapsed time: 0.00 minutes. Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Runtime.totalMemory()=1116733440 Runtime.totalMemory()=1116733440 Running Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: INFO 2024-07-02 11:50:26 CollectDuplicateMetrics Gradle suite > Gradle test > picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest.testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam) STANDARD_ERROR INFO 2024-07-02 11:50:26 CollectDuplicateMetrics Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** CollectDuplicateMetrics -METRICS_FILE /tmp/CollectDuplicateMetricsTester.10256221582742286216.tmp/metrics.txt -INPUT /tmp/CollectDuplicateMetrics13126649998975002712.sam ********** CollectDuplicateMetrics -METRICS_FILE /tmp/CollectDuplicateMetricsTester.10256221582742286216.tmp/metrics.txt -INPUT /tmp/CollectDuplicateMetrics13126649998975002712.sam Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:26.220 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:26.220 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:26.221 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:26.221 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:26.221 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:26.221 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:26.221 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:26.221 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: [Tue Jul 02 11:50:26 GMT+14:00 2024] CollectDuplicateMetrics METRICS_FILE=/tmp/CollectDuplicateMetricsTester.10256221582742286216.tmp/metrics.txt INPUT=/tmp/CollectDuplicateMetrics13126649998975002712.sam ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:26 GMT+14:00 2024] CollectDuplicateMetrics METRICS_FILE=/tmp/CollectDuplicateMetricsTester.10256221582742286216.tmp/metrics.txt INPUT=/tmp/CollectDuplicateMetrics13126649998975002712.sam ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: [Tue Jul 02 11:50:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: WARNING 2024-07-02 11:50:26 SinglePassSamProgram File reports sort order 'queryname', assuming it's coordinate sorted anyway. WARNING 2024-07-02 11:50:26 SinglePassSamProgram File reports sort order 'queryname', assuming it's coordinate sorted anyway. Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: [Tue Jul 02 11:50:26 GMT+14:00 2024] picard.sam.markduplicates.CollectDuplicateMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:26 GMT+14:00 2024] picard.sam.markduplicates.CollectDuplicateMetrics done. Elapsed time: 0.00 minutes. Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Runtime.totalMemory()=1116733440 Runtime.totalMemory()=1116733440 Running Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: INFO 2024-07-02 11:50:26 CollectDuplicateMetrics Gradle suite > Gradle test > picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest.testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam) STANDARD_ERROR INFO 2024-07-02 11:50:26 CollectDuplicateMetrics Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** CollectDuplicateMetrics -METRICS_FILE /tmp/CollectDuplicateMetricsTester.4716656919222742041.tmp/metrics.txt -INPUT /tmp/CollectDuplicateMetrics16245563892769044306.sam ********** CollectDuplicateMetrics -METRICS_FILE /tmp/CollectDuplicateMetricsTester.4716656919222742041.tmp/metrics.txt -INPUT /tmp/CollectDuplicateMetrics16245563892769044306.sam Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:26.267 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:26.267 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:26.268 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:26.268 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:26.268 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:26.268 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:26.268 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:26.268 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: [Tue Jul 02 11:50:26 GMT+14:00 2024] CollectDuplicateMetrics METRICS_FILE=/tmp/CollectDuplicateMetricsTester.4716656919222742041.tmp/metrics.txt INPUT=/tmp/CollectDuplicateMetrics16245563892769044306.sam ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:26 GMT+14:00 2024] CollectDuplicateMetrics METRICS_FILE=/tmp/CollectDuplicateMetricsTester.4716656919222742041.tmp/metrics.txt INPUT=/tmp/CollectDuplicateMetrics16245563892769044306.sam ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: [Tue Jul 02 11:50:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: [Tue Jul 02 11:50:26 GMT+14:00 2024] picard.sam.markduplicates.CollectDuplicateMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:26 GMT+14:00 2024] picard.sam.markduplicates.CollectDuplicateMetrics done. Elapsed time: 0.00 minutes. Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Runtime.totalMemory()=1116733440 Runtime.totalMemory()=1116733440 Running Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: INFO 2024-07-02 11:50:26 CollectDuplicateMetrics Gradle suite > Gradle test > picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest.testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam) STANDARD_ERROR INFO 2024-07-02 11:50:26 CollectDuplicateMetrics Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** CollectDuplicateMetrics -METRICS_FILE /tmp/CollectDuplicateMetricsTester.5248276295938028360.tmp/metrics.txt -INPUT /tmp/CollectDuplicateMetrics7398090402005440640.sam ********** CollectDuplicateMetrics -METRICS_FILE /tmp/CollectDuplicateMetricsTester.5248276295938028360.tmp/metrics.txt -INPUT /tmp/CollectDuplicateMetrics7398090402005440640.sam Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:26.378 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:26.378 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:26.379 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:26.379 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:26.379 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:26.379 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:26.379 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:26.379 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: [Tue Jul 02 11:50:26 GMT+14:00 2024] CollectDuplicateMetrics METRICS_FILE=/tmp/CollectDuplicateMetricsTester.5248276295938028360.tmp/metrics.txt INPUT=/tmp/CollectDuplicateMetrics7398090402005440640.sam ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:26 GMT+14:00 2024] CollectDuplicateMetrics METRICS_FILE=/tmp/CollectDuplicateMetricsTester.5248276295938028360.tmp/metrics.txt INPUT=/tmp/CollectDuplicateMetrics7398090402005440640.sam ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: [Tue Jul 02 11:50:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: [Tue Jul 02 11:50:26 GMT+14:00 2024] picard.sam.markduplicates.CollectDuplicateMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:26 GMT+14:00 2024] picard.sam.markduplicates.CollectDuplicateMetrics done. Elapsed time: 0.00 minutes. Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Runtime.totalMemory()=1116733440 Runtime.totalMemory()=1116733440 Running Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: INFO 2024-07-02 11:50:26 CollectDuplicateMetrics Gradle suite > Gradle test > picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest.testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam) STANDARD_ERROR INFO 2024-07-02 11:50:26 CollectDuplicateMetrics Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** CollectDuplicateMetrics -METRICS_FILE /tmp/CollectDuplicateMetricsTester.12350277040702712891.tmp/metrics.txt -INPUT /tmp/CollectDuplicateMetrics17368193429178240242.sam ********** CollectDuplicateMetrics -METRICS_FILE /tmp/CollectDuplicateMetricsTester.12350277040702712891.tmp/metrics.txt -INPUT /tmp/CollectDuplicateMetrics17368193429178240242.sam Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:26.540 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:26.540 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:26.540 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:26.540 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:26.549 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:26.549 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:26.549 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:26.549 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: [Tue Jul 02 11:50:26 GMT+14:00 2024] CollectDuplicateMetrics METRICS_FILE=/tmp/CollectDuplicateMetricsTester.12350277040702712891.tmp/metrics.txt INPUT=/tmp/CollectDuplicateMetrics17368193429178240242.sam ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:26 GMT+14:00 2024] CollectDuplicateMetrics METRICS_FILE=/tmp/CollectDuplicateMetricsTester.12350277040702712891.tmp/metrics.txt INPUT=/tmp/CollectDuplicateMetrics17368193429178240242.sam ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: [Tue Jul 02 11:50:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: [Tue Jul 02 11:50:26 GMT+14:00 2024] picard.sam.markduplicates.CollectDuplicateMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:26 GMT+14:00 2024] picard.sam.markduplicates.CollectDuplicateMetrics done. Elapsed time: 0.00 minutes. Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Runtime.totalMemory()=1116733440 Runtime.totalMemory()=1116733440 Running Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: INFO 2024-07-02 11:50:26 CollectDuplicateMetrics Gradle suite > Gradle test > picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest.testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam) STANDARD_ERROR INFO 2024-07-02 11:50:26 CollectDuplicateMetrics Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** CollectDuplicateMetrics -METRICS_FILE /tmp/CollectDuplicateMetricsTester.7066287554447282658.tmp/metrics.txt -INPUT /tmp/CollectDuplicateMetrics4749046298000184636.sam ********** CollectDuplicateMetrics -METRICS_FILE /tmp/CollectDuplicateMetricsTester.7066287554447282658.tmp/metrics.txt -INPUT /tmp/CollectDuplicateMetrics4749046298000184636.sam Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:26.654 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:26.654 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:26.654 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:26.654 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:26.655 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:26.655 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: 11:50:26.655 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:26.655 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: [Tue Jul 02 11:50:26 GMT+14:00 2024] CollectDuplicateMetrics METRICS_FILE=/tmp/CollectDuplicateMetricsTester.7066287554447282658.tmp/metrics.txt INPUT=/tmp/CollectDuplicateMetrics4749046298000184636.sam ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:26 GMT+14:00 2024] CollectDuplicateMetrics METRICS_FILE=/tmp/CollectDuplicateMetricsTester.7066287554447282658.tmp/metrics.txt INPUT=/tmp/CollectDuplicateMetrics4749046298000184636.sam ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: [Tue Jul 02 11:50:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: [Tue Jul 02 11:50:26 GMT+14:00 2024] picard.sam.markduplicates.CollectDuplicateMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:26 GMT+14:00 2024] picard.sam.markduplicates.CollectDuplicateMetrics done. Elapsed time: 0.00 minutes. Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest) produced standard out/err: Runtime.totalMemory()=1116733440 Runtime.totalMemory()=1116733440 Running Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:26 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.AsIsMarkDuplicatesTest.testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam) STANDARD_ERROR INFO 2024-07-02 11:50:26 MarkDuplicates Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/BySumOfBaseQAndInOriginalOrderMDTester.5326243587998413179.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.5326243587998413179.tmp/input.sam -OUTPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.5326243587998413179.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/BySumOfBaseQAndInOriginalOrderMDTester.5326243587998413179.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.5326243587998413179.tmp/input.sam -OUTPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.5326243587998413179.tmp/output.sam Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:26.762 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:26.762 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:26.762 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:26.762 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:26.763 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:26.763 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:26.763 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:26.763 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:50:26 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/BySumOfBaseQAndInOriginalOrderMDTester.5326243587998413179.tmp/input.sam] OUTPUT=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.5326243587998413179.tmp/output.sam METRICS_FILE=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.5326243587998413179.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:26 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/BySumOfBaseQAndInOriginalOrderMDTester.5326243587998413179.tmp/input.sam] OUTPUT=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.5326243587998413179.tmp/output.sam METRICS_FILE=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.5326243587998413179.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:50:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:27 MarkDuplicates Start of doWork freeMemory: 1024649336; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:27 MarkDuplicates Start of doWork freeMemory: 1024649336; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:27 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:50:27 MarkDuplicates Reading input file and constructing read end information. Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:27 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:50:27 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:27 MarkDuplicates Read 12 records. 0 pairs never matched. INFO 2024-07-02 11:50:27 MarkDuplicates Read 12 records. 0 pairs never matched. Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 963167056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:27 MarkDuplicates After buildSortedReadEndLists freeMemory: 963167056; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:50:28 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:28 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:50:28 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:28 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:50:28 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:28 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:50:28 MarkDuplicates Sorting list of duplicate records. Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 487117280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 487117280; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:29 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:50:29 MarkDuplicates Marking 1 records as duplicates. Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:29 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:29 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:29 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:50:29 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:29 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:50:29 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:29 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:50:29 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:29 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:50:29 MarkDuplicates Duplicate Index cleanup. Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:29 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:50:29 MarkDuplicates Getting Memory Stats. Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:29 MarkDuplicates Before output close freeMemory: 756446384; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:29 MarkDuplicates Before output close freeMemory: 756446384; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:29 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:50:29 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:29 MarkDuplicates After output close freeMemory: 756601056; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:29 MarkDuplicates After output close freeMemory: 756601056; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:50:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:50:29 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testQueryGroupedInput[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:29 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.AsIsMarkDuplicatesTest.testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam) STANDARD_ERROR INFO 2024-07-02 11:50:29 MarkDuplicates Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/BySumOfBaseQAndInOriginalOrderMDTester.4678396395368785108.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.4678396395368785108.tmp/input.sam -OUTPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.4678396395368785108.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/BySumOfBaseQAndInOriginalOrderMDTester.4678396395368785108.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES -TAGGING_POLICY OpticalOnly -ASSUME_SORT_ORDER queryname -INPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.4678396395368785108.tmp/input.sam -OUTPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.4678396395368785108.tmp/output.sam Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:29.985 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:29.985 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:29.985 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:29.985 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:29.986 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:29.986 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:29.986 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:29.986 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:50:29 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/BySumOfBaseQAndInOriginalOrderMDTester.4678396395368785108.tmp/input.sam] OUTPUT=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.4678396395368785108.tmp/output.sam METRICS_FILE=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.4678396395368785108.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:29 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/BySumOfBaseQAndInOriginalOrderMDTester.4678396395368785108.tmp/input.sam] OUTPUT=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.4678396395368785108.tmp/output.sam METRICS_FILE=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.4678396395368785108.tmp/metrics.txt ASSUME_SORT_ORDER=queryname DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:50:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:30 MarkDuplicates Start of doWork freeMemory: 1026105672; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:30 MarkDuplicates Start of doWork freeMemory: 1026105672; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:30 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:50:30 MarkDuplicates Reading input file and constructing read end information. Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:30 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:50:30 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:30 MarkDuplicates Read 12 records. 0 pairs never matched. INFO 2024-07-02 11:50:30 MarkDuplicates Read 12 records. 0 pairs never matched. Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 963169480; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:30 MarkDuplicates After buildSortedReadEndLists freeMemory: 963169480; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:50:31 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:31 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:50:31 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:31 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:50:31 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:31 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:50:31 MarkDuplicates Sorting list of duplicate records. Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 487116648; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:32 MarkDuplicates After generateDuplicateIndexes freeMemory: 487116648; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:32 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:50:32 MarkDuplicates Marking 1 records as duplicates. Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:32 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:32 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:32 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:50:32 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:32 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query INFO 2024-07-02 11:50:32 MarkDuplicates Output will not be re-sorted. Output header will state SO:unknown GO:query Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:32 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:50:32 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:32 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:50:32 MarkDuplicates Duplicate Index cleanup. Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:32 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:50:32 MarkDuplicates Getting Memory Stats. Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:32 MarkDuplicates Before output close freeMemory: 756441280; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:32 MarkDuplicates Before output close freeMemory: 756441280; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:32 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:50:32 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:32 MarkDuplicates After output close freeMemory: 756597352; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:32 MarkDuplicates After output close freeMemory: 756597352; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:50:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:50:32 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testQueryGroupedInput[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndQueryNameGroupedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:32 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.AsIsMarkDuplicatesTest.testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam) STANDARD_ERROR INFO 2024-07-02 11:50:32 MarkDuplicates Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/BySumOfBaseQAndInOriginalOrderMDTester.8694979103803309817.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES -TAGGING_POLICY OpticalOnly -INPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.8694979103803309817.tmp/input.sam -OUTPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.8694979103803309817.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/BySumOfBaseQAndInOriginalOrderMDTester.8694979103803309817.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES -TAGGING_POLICY OpticalOnly -INPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.8694979103803309817.tmp/input.sam -OUTPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.8694979103803309817.tmp/output.sam Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:32.823 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:32.823 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:32.823 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:32.823 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:32.824 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:32.824 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:32.824 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:32.824 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:50:32 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/BySumOfBaseQAndInOriginalOrderMDTester.8694979103803309817.tmp/input.sam] OUTPUT=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.8694979103803309817.tmp/output.sam METRICS_FILE=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.8694979103803309817.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:32 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/BySumOfBaseQAndInOriginalOrderMDTester.8694979103803309817.tmp/input.sam] OUTPUT=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.8694979103803309817.tmp/output.sam METRICS_FILE=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.8694979103803309817.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:50:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:33 MarkDuplicates Start of doWork freeMemory: 1026511656; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:33 MarkDuplicates Start of doWork freeMemory: 1026511656; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:33 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:50:33 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:33 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:50:33 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:33 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:50:33 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 963575608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:33 MarkDuplicates After buildSortedReadEndLists freeMemory: 963575608; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:50:33 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:34 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:50:34 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:34 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:50:34 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:34 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:50:34 MarkDuplicates Sorting list of duplicate records. Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 487525424; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:34 MarkDuplicates After generateDuplicateIndexes freeMemory: 487525424; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:34 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:50:34 MarkDuplicates Marking 1 records as duplicates. Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:34 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:34 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:34 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:50:34 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:34 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:50:34 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:34 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:50:34 MarkDuplicates Duplicate Index cleanup. Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:34 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:50:34 MarkDuplicates Getting Memory Stats. Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:35 MarkDuplicates Before output close freeMemory: 756851944; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:35 MarkDuplicates Before output close freeMemory: 756851944; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:35 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:50:35 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:35 MarkDuplicates After output close freeMemory: 757007168; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:35 MarkDuplicates After output close freeMemory: 757007168; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:50:35 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:50:35 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:35 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.AsIsMarkDuplicatesTest.testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam) STANDARD_ERROR INFO 2024-07-02 11:50:35 MarkDuplicates Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/BySumOfBaseQAndInOriginalOrderMDTester.5372781065450398544.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES -TAGGING_POLICY OpticalOnly -INPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.5372781065450398544.tmp/input.sam -OUTPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.5372781065450398544.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/BySumOfBaseQAndInOriginalOrderMDTester.5372781065450398544.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES -TAGGING_POLICY OpticalOnly -INPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.5372781065450398544.tmp/input.sam -OUTPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.5372781065450398544.tmp/output.sam Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:35.583 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:35.583 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:35.583 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:35.583 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:35.583 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:35.583 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:35.583 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:35.583 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:50:35 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/BySumOfBaseQAndInOriginalOrderMDTester.5372781065450398544.tmp/input.sam] OUTPUT=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.5372781065450398544.tmp/output.sam METRICS_FILE=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.5372781065450398544.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:35 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/BySumOfBaseQAndInOriginalOrderMDTester.5372781065450398544.tmp/input.sam] OUTPUT=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.5372781065450398544.tmp/output.sam METRICS_FILE=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.5372781065450398544.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:50:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:35 MarkDuplicates Start of doWork freeMemory: 1026508488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:35 MarkDuplicates Start of doWork freeMemory: 1026508488; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:35 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:50:35 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:35 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:50:35 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:35 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:50:35 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 963577880; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:36 MarkDuplicates After buildSortedReadEndLists freeMemory: 963577880; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:50:36 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:36 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:50:36 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:36 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:50:36 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:36 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:50:36 MarkDuplicates Sorting list of duplicate records. Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 487524832; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:37 MarkDuplicates After generateDuplicateIndexes freeMemory: 487524832; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:37 MarkDuplicates Marking 1 records as duplicates. INFO 2024-07-02 11:50:37 MarkDuplicates Marking 1 records as duplicates. Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:37 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:37 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:37 MarkDuplicates Reads are assumed to be ordered by: queryname INFO 2024-07-02 11:50:37 MarkDuplicates Reads are assumed to be ordered by: queryname Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:37 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:50:37 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:37 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:50:37 MarkDuplicates Duplicate Index cleanup. Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:37 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:50:37 MarkDuplicates Getting Memory Stats. Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:37 MarkDuplicates Before output close freeMemory: 756852816; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:37 MarkDuplicates Before output close freeMemory: 756852816; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:37 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:50:37 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:37 MarkDuplicates After output close freeMemory: 757008608; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:37 MarkDuplicates After output close freeMemory: 757008608; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:50:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:50:37 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:37 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.AsIsMarkDuplicatesTest.testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam) STANDARD_ERROR INFO 2024-07-02 11:50:37 MarkDuplicates Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/BySumOfBaseQAndInOriginalOrderMDTester.1301566323035329324.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES -TAGGING_POLICY OpticalOnly -INPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.1301566323035329324.tmp/input.sam -OUTPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.1301566323035329324.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/BySumOfBaseQAndInOriginalOrderMDTester.1301566323035329324.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES -TAGGING_POLICY OpticalOnly -INPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.1301566323035329324.tmp/input.sam -OUTPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.1301566323035329324.tmp/output.sam Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:37.842 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:37.842 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:37.842 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:37.842 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:37.843 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:37.843 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:37.843 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:37.843 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:50:37 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/BySumOfBaseQAndInOriginalOrderMDTester.1301566323035329324.tmp/input.sam] OUTPUT=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.1301566323035329324.tmp/output.sam METRICS_FILE=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.1301566323035329324.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:37 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/BySumOfBaseQAndInOriginalOrderMDTester.1301566323035329324.tmp/input.sam] OUTPUT=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.1301566323035329324.tmp/output.sam METRICS_FILE=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.1301566323035329324.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:50:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:38 MarkDuplicates Start of doWork freeMemory: 1026513464; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:38 MarkDuplicates Start of doWork freeMemory: 1026513464; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:38 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:50:38 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:38 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:50:38 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:38 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:50:38 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 963577416; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:38 MarkDuplicates After buildSortedReadEndLists freeMemory: 963577416; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:50:38 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:39 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:50:39 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:39 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:50:39 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:39 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:50:39 MarkDuplicates Sorting list of duplicate records. Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 487524368; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:39 MarkDuplicates After generateDuplicateIndexes freeMemory: 487524368; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:39 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:50:39 MarkDuplicates Marking 2 records as duplicates. Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:39 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:39 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:39 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:50:39 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:39 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:50:39 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:39 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:50:39 MarkDuplicates Duplicate Index cleanup. Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:39 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:50:39 MarkDuplicates Getting Memory Stats. Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:39 MarkDuplicates Before output close freeMemory: 756852568; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:39 MarkDuplicates Before output close freeMemory: 756852568; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:39 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:50:39 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:40 MarkDuplicates After output close freeMemory: 757008272; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:40 MarkDuplicates After output close freeMemory: 757008272; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:50:40 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. [Tue Jul 02 11:50:40 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.05 minutes. Test: Test method testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:40 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.AsIsMarkDuplicatesTest.testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam) STANDARD_ERROR INFO 2024-07-02 11:50:40 MarkDuplicates Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/BySumOfBaseQAndInOriginalOrderMDTester.4295862512300661908.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES -TAGGING_POLICY OpticalOnly -INPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.4295862512300661908.tmp/input.sam -OUTPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.4295862512300661908.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/BySumOfBaseQAndInOriginalOrderMDTester.4295862512300661908.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES -TAGGING_POLICY OpticalOnly -INPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.4295862512300661908.tmp/input.sam -OUTPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.4295862512300661908.tmp/output.sam Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:40.807 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:40.807 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:40.817 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:40.817 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:40.817 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:40.817 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:40.817 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:40.817 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:50:40 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/BySumOfBaseQAndInOriginalOrderMDTester.4295862512300661908.tmp/input.sam] OUTPUT=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.4295862512300661908.tmp/output.sam METRICS_FILE=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.4295862512300661908.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:40 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/BySumOfBaseQAndInOriginalOrderMDTester.4295862512300661908.tmp/input.sam] OUTPUT=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.4295862512300661908.tmp/output.sam METRICS_FILE=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.4295862512300661908.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:50:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:41 MarkDuplicates Start of doWork freeMemory: 1026512680; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:41 MarkDuplicates Start of doWork freeMemory: 1026512680; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:41 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:50:41 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:41 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:50:41 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:41 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:50:41 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 963576632; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:41 MarkDuplicates After buildSortedReadEndLists freeMemory: 963576632; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:50:41 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:42 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:50:42 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:42 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:50:42 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:42 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:50:42 MarkDuplicates Sorting list of duplicate records. Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 487523584; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:42 MarkDuplicates After generateDuplicateIndexes freeMemory: 487523584; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:42 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:50:42 MarkDuplicates Marking 2 records as duplicates. Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:42 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:42 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:42 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:50:42 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:42 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:50:42 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:42 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:50:42 MarkDuplicates Duplicate Index cleanup. Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:42 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:50:42 MarkDuplicates Getting Memory Stats. Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:42 MarkDuplicates Before output close freeMemory: 756851152; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:42 MarkDuplicates Before output close freeMemory: 756851152; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:42 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:50:42 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:43 MarkDuplicates After output close freeMemory: 757007488; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:43 MarkDuplicates After output close freeMemory: 757007488; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:50:43 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:50:43 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:43 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.AsIsMarkDuplicatesTest.testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam) STANDARD_ERROR INFO 2024-07-02 11:50:43 MarkDuplicates Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/BySumOfBaseQAndInOriginalOrderMDTester.3455952612593257561.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES -TAGGING_POLICY OpticalOnly -INPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.3455952612593257561.tmp/input.sam -OUTPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.3455952612593257561.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/BySumOfBaseQAndInOriginalOrderMDTester.3455952612593257561.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES -TAGGING_POLICY OpticalOnly -INPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.3455952612593257561.tmp/input.sam -OUTPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.3455952612593257561.tmp/output.sam Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:43.101 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:43.101 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:43.101 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:43.101 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:43.102 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:43.102 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:43.102 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:43.102 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:50:43 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/BySumOfBaseQAndInOriginalOrderMDTester.3455952612593257561.tmp/input.sam] OUTPUT=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.3455952612593257561.tmp/output.sam METRICS_FILE=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.3455952612593257561.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:43 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/BySumOfBaseQAndInOriginalOrderMDTester.3455952612593257561.tmp/input.sam] OUTPUT=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.3455952612593257561.tmp/output.sam METRICS_FILE=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.3455952612593257561.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:50:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:43 MarkDuplicates Start of doWork freeMemory: 1026511960; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:43 MarkDuplicates Start of doWork freeMemory: 1026511960; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:43 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:50:43 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:43 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:50:43 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:43 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:50:43 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 963575696; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:43 MarkDuplicates After buildSortedReadEndLists freeMemory: 963575696; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:50:44 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:44 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:50:44 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:44 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:50:44 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:44 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:50:44 MarkDuplicates Sorting list of duplicate records. Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 615449136; totalMemory: 1201668096; maxMemory: 2147483648 INFO 2024-07-02 11:50:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 615449136; totalMemory: 1201668096; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:44 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:50:44 MarkDuplicates Marking 2 records as duplicates. Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:44 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:44 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:44 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:50:44 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:44 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:50:44 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:44 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:50:44 MarkDuplicates Duplicate Index cleanup. Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:44 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:50:44 MarkDuplicates Getting Memory Stats. Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:45 MarkDuplicates Before output close freeMemory: 756849472; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:45 MarkDuplicates Before output close freeMemory: 756849472; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:45 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:50:45 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:45 MarkDuplicates After output close freeMemory: 757006768; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:45 MarkDuplicates After output close freeMemory: 757006768; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:50:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:50:45 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:45 MarkDuplicates Gradle suite > Gradle test > picard.sam.markduplicates.AsIsMarkDuplicatesTest.testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam) STANDARD_ERROR INFO 2024-07-02 11:50:45 MarkDuplicates Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** MarkDuplicates -METRICS_FILE /tmp/BySumOfBaseQAndInOriginalOrderMDTester.18010859115982533598.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES -TAGGING_POLICY OpticalOnly -INPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.18010859115982533598.tmp/input.sam -OUTPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.18010859115982533598.tmp/output.sam ********** MarkDuplicates -METRICS_FILE /tmp/BySumOfBaseQAndInOriginalOrderMDTester.18010859115982533598.tmp/metrics.txt -DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES -TAGGING_POLICY OpticalOnly -INPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.18010859115982533598.tmp/input.sam -OUTPUT /tmp/BySumOfBaseQAndInOriginalOrderMDTester.18010859115982533598.tmp/output.sam Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: ********** ********** Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:45.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:45.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:45.743 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:45.743 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:45.744 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:45.744 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: 11:50:45.744 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:45.744 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:50:45 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/BySumOfBaseQAndInOriginalOrderMDTester.18010859115982533598.tmp/input.sam] OUTPUT=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.18010859115982533598.tmp/output.sam METRICS_FILE=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.18010859115982533598.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:45 GMT+14:00 2024] MarkDuplicates TAGGING_POLICY=OpticalOnly INPUT=[/tmp/BySumOfBaseQAndInOriginalOrderMDTester.18010859115982533598.tmp/input.sam] OUTPUT=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.18010859115982533598.tmp/output.sam METRICS_FILE=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.18010859115982533598.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:50:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:46 MarkDuplicates Start of doWork freeMemory: 1026505792; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:46 MarkDuplicates Start of doWork freeMemory: 1026505792; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:46 MarkDuplicates Reading input file and constructing read end information. INFO 2024-07-02 11:50:46 MarkDuplicates Reading input file and constructing read end information. Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:46 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. INFO 2024-07-02 11:50:46 MarkDuplicates Will retain up to 7780737 data points before spilling to disk. Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:46 MarkDuplicates Read 4 records. 0 pairs never matched. INFO 2024-07-02 11:50:46 MarkDuplicates Read 4 records. 0 pairs never matched. Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 963574896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 963574896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. INFO 2024-07-02 11:50:46 MarkDuplicates Will retain up to 33554432 duplicate indices before spilling to disk. Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:47 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2024-07-02 11:50:47 MarkDuplicates Traversing read pair information and detecting duplicates. Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:47 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2024-07-02 11:50:47 MarkDuplicates Traversing fragment information and detecting duplicates. Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:47 MarkDuplicates Sorting list of duplicate records. INFO 2024-07-02 11:50:47 MarkDuplicates Sorting list of duplicate records. Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 487522064; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:47 MarkDuplicates After generateDuplicateIndexes freeMemory: 487522064; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:47 MarkDuplicates Marking 2 records as duplicates. INFO 2024-07-02 11:50:47 MarkDuplicates Marking 2 records as duplicates. Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:47 MarkDuplicates Found 0 optical duplicate clusters. INFO 2024-07-02 11:50:47 MarkDuplicates Found 0 optical duplicate clusters. Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:47 MarkDuplicates Reads are assumed to be ordered by: coordinate INFO 2024-07-02 11:50:47 MarkDuplicates Reads are assumed to be ordered by: coordinate Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:47 MarkDuplicates Writing complete. Closing input iterator. INFO 2024-07-02 11:50:47 MarkDuplicates Writing complete. Closing input iterator. Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:47 MarkDuplicates Duplicate Index cleanup. INFO 2024-07-02 11:50:47 MarkDuplicates Duplicate Index cleanup. Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:47 MarkDuplicates Getting Memory Stats. INFO 2024-07-02 11:50:47 MarkDuplicates Getting Memory Stats. Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:47 MarkDuplicates Before output close freeMemory: 756850240; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:47 MarkDuplicates Before output close freeMemory: 756850240; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:47 MarkDuplicates Closed outputs. Getting more Memory Stats. INFO 2024-07-02 11:50:47 MarkDuplicates Closed outputs. Getting more Memory Stats. Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: INFO 2024-07-02 11:50:48 MarkDuplicates After output close freeMemory: 757005896; totalMemory: 1073741824; maxMemory: 2147483648 INFO 2024-07-02 11:50:48 MarkDuplicates After output close freeMemory: 757005896; totalMemory: 1073741824; maxMemory: 2147483648 Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: [Tue Jul 02 11:50:48 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:50:48 GMT+14:00 2024] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.04 minutes. Test: Test method testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam)(picard.sam.markduplicates.AsIsMarkDuplicatesTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBamToBfq[0](testdata/picard/sam/aligned_queryname_sorted.bam, false, bam_to_bfq_test)(picard.fastq.BamToBfqTest) Test: Test method testBamToBfq[0](testdata/picard/sam/aligned_queryname_sorted.bam, false, bam_to_bfq_test)(picard.fastq.BamToBfqTest) produced standard out/err: INFO 2024-07-02 11:50:48 BamToBfq Gradle suite > Gradle test > picard.fastq.BamToBfqTest.testBamToBfq[0](testdata/picard/sam/aligned_queryname_sorted.bam, false, bam_to_bfq_test) STANDARD_ERROR INFO 2024-07-02 11:50:48 BamToBfq Test: Test method testBamToBfq[0](testdata/picard/sam/aligned_queryname_sorted.bam, false, bam_to_bfq_test)(picard.fastq.BamToBfqTest) produced standard out/err: Test: Test method testBamToBfq[0](testdata/picard/sam/aligned_queryname_sorted.bam, false, bam_to_bfq_test)(picard.fastq.BamToBfqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBamToBfq[0](testdata/picard/sam/aligned_queryname_sorted.bam, false, bam_to_bfq_test)(picard.fastq.BamToBfqTest) produced standard out/err: ********** ********** Test: Test method testBamToBfq[0](testdata/picard/sam/aligned_queryname_sorted.bam, false, bam_to_bfq_test)(picard.fastq.BamToBfqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBamToBfq[0](testdata/picard/sam/aligned_queryname_sorted.bam, false, bam_to_bfq_test)(picard.fastq.BamToBfqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBamToBfq[0](testdata/picard/sam/aligned_queryname_sorted.bam, false, bam_to_bfq_test)(picard.fastq.BamToBfqTest) produced standard out/err: ********** ********** Test: Test method testBamToBfq[0](testdata/picard/sam/aligned_queryname_sorted.bam, false, bam_to_bfq_test)(picard.fastq.BamToBfqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBamToBfq[0](testdata/picard/sam/aligned_queryname_sorted.bam, false, bam_to_bfq_test)(picard.fastq.BamToBfqTest) produced standard out/err: ********** ********** Test: Test method testBamToBfq[0](testdata/picard/sam/aligned_queryname_sorted.bam, false, bam_to_bfq_test)(picard.fastq.BamToBfqTest) produced standard out/err: ********** BamToBfq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/aligned_queryname_sorted.bam -ANALYSIS_DIR /tmp/BamToBfqTest18056296248998845414.dir -OUTPUT_FILE_PREFIX bam_to_bfq_test -PAIRED_RUN false -READS_TO_ALIGN 8 ********** BamToBfq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/aligned_queryname_sorted.bam -ANALYSIS_DIR /tmp/BamToBfqTest18056296248998845414.dir -OUTPUT_FILE_PREFIX bam_to_bfq_test -PAIRED_RUN false -READS_TO_ALIGN 8 Test: Test method testBamToBfq[0](testdata/picard/sam/aligned_queryname_sorted.bam, false, bam_to_bfq_test)(picard.fastq.BamToBfqTest) produced standard out/err: ********** ********** Test: Test method testBamToBfq[0](testdata/picard/sam/aligned_queryname_sorted.bam, false, bam_to_bfq_test)(picard.fastq.BamToBfqTest) produced standard out/err: Test: Test method testBamToBfq[0](testdata/picard/sam/aligned_queryname_sorted.bam, false, bam_to_bfq_test)(picard.fastq.BamToBfqTest) produced standard out/err: Test: Test method testBamToBfq[0](testdata/picard/sam/aligned_queryname_sorted.bam, false, bam_to_bfq_test)(picard.fastq.BamToBfqTest) produced standard out/err: 11:50:48.168 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:48.168 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBamToBfq[0](testdata/picard/sam/aligned_queryname_sorted.bam, false, bam_to_bfq_test)(picard.fastq.BamToBfqTest) produced standard out/err: 11:50:48.168 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:48.168 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBamToBfq[0](testdata/picard/sam/aligned_queryname_sorted.bam, false, bam_to_bfq_test)(picard.fastq.BamToBfqTest) produced standard out/err: 11:50:48.168 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:48.168 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBamToBfq[0](testdata/picard/sam/aligned_queryname_sorted.bam, false, bam_to_bfq_test)(picard.fastq.BamToBfqTest) produced standard out/err: 11:50:48.168 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:48.168 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBamToBfq[0](testdata/picard/sam/aligned_queryname_sorted.bam, false, bam_to_bfq_test)(picard.fastq.BamToBfqTest) produced standard out/err: [Tue Jul 02 11:50:48 GMT+14:00 2024] BamToBfq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/aligned_queryname_sorted.bam ANALYSIS_DIR=/tmp/BamToBfqTest18056296248998845414.dir OUTPUT_FILE_PREFIX=bam_to_bfq_test READS_TO_ALIGN=8 PAIRED_RUN=false READ_CHUNK_SIZE=2000000 INCLUDE_NON_PF_READS=false CLIP_ADAPTERS=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:48 GMT+14:00 2024] BamToBfq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/aligned_queryname_sorted.bam ANALYSIS_DIR=/tmp/BamToBfqTest18056296248998845414.dir OUTPUT_FILE_PREFIX=bam_to_bfq_test READS_TO_ALIGN=8 PAIRED_RUN=false READ_CHUNK_SIZE=2000000 INCLUDE_NON_PF_READS=false CLIP_ADAPTERS=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBamToBfq[0](testdata/picard/sam/aligned_queryname_sorted.bam, false, bam_to_bfq_test)(picard.fastq.BamToBfqTest) produced standard out/err: [Tue Jul 02 11:50:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBamToBfq[0](testdata/picard/sam/aligned_queryname_sorted.bam, false, bam_to_bfq_test)(picard.fastq.BamToBfqTest) produced standard out/err: INFO 2024-07-02 11:50:48 BamToBfqWriter Now writing to file /tmp/BamToBfqTest18056296248998845414.dir/bam_to_bfq_test.0.1.bfq INFO 2024-07-02 11:50:48 BamToBfqWriter Now writing to file /tmp/BamToBfqTest18056296248998845414.dir/bam_to_bfq_test.0.1.bfq Test: Test method testBamToBfq[0](testdata/picard/sam/aligned_queryname_sorted.bam, false, bam_to_bfq_test)(picard.fastq.BamToBfqTest) produced standard out/err: INFO 2024-07-02 11:50:48 BamToBfqWriter Wrote 8 bfq records. INFO 2024-07-02 11:50:48 BamToBfqWriter Wrote 8 bfq records. Test: Test method testBamToBfq[0](testdata/picard/sam/aligned_queryname_sorted.bam, false, bam_to_bfq_test)(picard.fastq.BamToBfqTest) produced standard out/err: [Tue Jul 02 11:50:48 GMT+14:00 2024] picard.fastq.BamToBfq done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:48 GMT+14:00 2024] picard.fastq.BamToBfq done. Elapsed time: 0.00 minutes. Test: Test method testBamToBfq[0](testdata/picard/sam/aligned_queryname_sorted.bam, false, bam_to_bfq_test)(picard.fastq.BamToBfqTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBamToBfq[1](testdata/picard/sam/aligned_queryname_sorted.bam, true, bam_to_bfq_paired_test)(picard.fastq.BamToBfqTest) Test: Test method testBamToBfq[1](testdata/picard/sam/aligned_queryname_sorted.bam, true, bam_to_bfq_paired_test)(picard.fastq.BamToBfqTest) produced standard out/err: INFO 2024-07-02 11:50:48 BamToBfq Gradle suite > Gradle test > picard.fastq.BamToBfqTest.testBamToBfq[1](testdata/picard/sam/aligned_queryname_sorted.bam, true, bam_to_bfq_paired_test) STANDARD_ERROR INFO 2024-07-02 11:50:48 BamToBfq Test: Test method testBamToBfq[1](testdata/picard/sam/aligned_queryname_sorted.bam, true, bam_to_bfq_paired_test)(picard.fastq.BamToBfqTest) produced standard out/err: Test: Test method testBamToBfq[1](testdata/picard/sam/aligned_queryname_sorted.bam, true, bam_to_bfq_paired_test)(picard.fastq.BamToBfqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBamToBfq[1](testdata/picard/sam/aligned_queryname_sorted.bam, true, bam_to_bfq_paired_test)(picard.fastq.BamToBfqTest) produced standard out/err: ********** ********** Test: Test method testBamToBfq[1](testdata/picard/sam/aligned_queryname_sorted.bam, true, bam_to_bfq_paired_test)(picard.fastq.BamToBfqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBamToBfq[1](testdata/picard/sam/aligned_queryname_sorted.bam, true, bam_to_bfq_paired_test)(picard.fastq.BamToBfqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBamToBfq[1](testdata/picard/sam/aligned_queryname_sorted.bam, true, bam_to_bfq_paired_test)(picard.fastq.BamToBfqTest) produced standard out/err: ********** ********** Test: Test method testBamToBfq[1](testdata/picard/sam/aligned_queryname_sorted.bam, true, bam_to_bfq_paired_test)(picard.fastq.BamToBfqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBamToBfq[1](testdata/picard/sam/aligned_queryname_sorted.bam, true, bam_to_bfq_paired_test)(picard.fastq.BamToBfqTest) produced standard out/err: ********** ********** Test: Test method testBamToBfq[1](testdata/picard/sam/aligned_queryname_sorted.bam, true, bam_to_bfq_paired_test)(picard.fastq.BamToBfqTest) produced standard out/err: ********** BamToBfq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/aligned_queryname_sorted.bam -ANALYSIS_DIR /tmp/BamToBfqTest11582152548911123979.dir -OUTPUT_FILE_PREFIX bam_to_bfq_paired_test -PAIRED_RUN true -READS_TO_ALIGN 8 ********** BamToBfq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/aligned_queryname_sorted.bam -ANALYSIS_DIR /tmp/BamToBfqTest11582152548911123979.dir -OUTPUT_FILE_PREFIX bam_to_bfq_paired_test -PAIRED_RUN true -READS_TO_ALIGN 8 Test: Test method testBamToBfq[1](testdata/picard/sam/aligned_queryname_sorted.bam, true, bam_to_bfq_paired_test)(picard.fastq.BamToBfqTest) produced standard out/err: ********** ********** Test: Test method testBamToBfq[1](testdata/picard/sam/aligned_queryname_sorted.bam, true, bam_to_bfq_paired_test)(picard.fastq.BamToBfqTest) produced standard out/err: Test: Test method testBamToBfq[1](testdata/picard/sam/aligned_queryname_sorted.bam, true, bam_to_bfq_paired_test)(picard.fastq.BamToBfqTest) produced standard out/err: Test: Test method testBamToBfq[1](testdata/picard/sam/aligned_queryname_sorted.bam, true, bam_to_bfq_paired_test)(picard.fastq.BamToBfqTest) produced standard out/err: 11:50:48.228 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:48.228 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBamToBfq[1](testdata/picard/sam/aligned_queryname_sorted.bam, true, bam_to_bfq_paired_test)(picard.fastq.BamToBfqTest) produced standard out/err: 11:50:48.228 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:48.228 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBamToBfq[1](testdata/picard/sam/aligned_queryname_sorted.bam, true, bam_to_bfq_paired_test)(picard.fastq.BamToBfqTest) produced standard out/err: 11:50:48.241 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:48.241 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBamToBfq[1](testdata/picard/sam/aligned_queryname_sorted.bam, true, bam_to_bfq_paired_test)(picard.fastq.BamToBfqTest) produced standard out/err: 11:50:48.241 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:48.241 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBamToBfq[1](testdata/picard/sam/aligned_queryname_sorted.bam, true, bam_to_bfq_paired_test)(picard.fastq.BamToBfqTest) produced standard out/err: [Tue Jul 02 11:50:48 GMT+14:00 2024] BamToBfq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/aligned_queryname_sorted.bam ANALYSIS_DIR=/tmp/BamToBfqTest11582152548911123979.dir OUTPUT_FILE_PREFIX=bam_to_bfq_paired_test READS_TO_ALIGN=8 PAIRED_RUN=true READ_CHUNK_SIZE=2000000 INCLUDE_NON_PF_READS=false CLIP_ADAPTERS=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:48 GMT+14:00 2024] BamToBfq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/aligned_queryname_sorted.bam ANALYSIS_DIR=/tmp/BamToBfqTest11582152548911123979.dir OUTPUT_FILE_PREFIX=bam_to_bfq_paired_test READS_TO_ALIGN=8 PAIRED_RUN=true READ_CHUNK_SIZE=2000000 INCLUDE_NON_PF_READS=false CLIP_ADAPTERS=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBamToBfq[1](testdata/picard/sam/aligned_queryname_sorted.bam, true, bam_to_bfq_paired_test)(picard.fastq.BamToBfqTest) produced standard out/err: [Tue Jul 02 11:50:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBamToBfq[1](testdata/picard/sam/aligned_queryname_sorted.bam, true, bam_to_bfq_paired_test)(picard.fastq.BamToBfqTest) produced standard out/err: INFO 2024-07-02 11:50:48 BamToBfqWriter Now writing to file /tmp/BamToBfqTest11582152548911123979.dir/bam_to_bfq_paired_test.0.1.bfq INFO 2024-07-02 11:50:48 BamToBfqWriter Now writing to file /tmp/BamToBfqTest11582152548911123979.dir/bam_to_bfq_paired_test.0.1.bfq Test: Test method testBamToBfq[1](testdata/picard/sam/aligned_queryname_sorted.bam, true, bam_to_bfq_paired_test)(picard.fastq.BamToBfqTest) produced standard out/err: INFO 2024-07-02 11:50:48 BamToBfqWriter Now writing to file /tmp/BamToBfqTest11582152548911123979.dir/bam_to_bfq_paired_test.0.2.bfq INFO 2024-07-02 11:50:48 BamToBfqWriter Now writing to file /tmp/BamToBfqTest11582152548911123979.dir/bam_to_bfq_paired_test.0.2.bfq Test: Test method testBamToBfq[1](testdata/picard/sam/aligned_queryname_sorted.bam, true, bam_to_bfq_paired_test)(picard.fastq.BamToBfqTest) produced standard out/err: INFO 2024-07-02 11:50:48 BamToBfqWriter Wrote 4 bfq records. INFO 2024-07-02 11:50:48 BamToBfqWriter Wrote 4 bfq records. Test: Test method testBamToBfq[1](testdata/picard/sam/aligned_queryname_sorted.bam, true, bam_to_bfq_paired_test)(picard.fastq.BamToBfqTest) produced standard out/err: [Tue Jul 02 11:50:48 GMT+14:00 2024] picard.fastq.BamToBfq done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:48 GMT+14:00 2024] picard.fastq.BamToBfq done. Elapsed time: 0.00 minutes. Test: Test method testBamToBfq[1](testdata/picard/sam/aligned_queryname_sorted.bam, true, bam_to_bfq_paired_test)(picard.fastq.BamToBfqTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBaseErrorAggregation(picard.sam.SamErrorMetric.BaseErrorAggregationTest) Running Test: Test method testBaseErrorAggregation2(picard.sam.SamErrorMetric.BaseErrorAggregationTest) Running Test: Test method testBaseErrorAggregation3(picard.sam.SamErrorMetric.BaseErrorAggregationTest) Running Test: Test method testOverlappingErrorCalculator(picard.sam.SamErrorMetric.BaseErrorCalculationTest) Running Test: Test method testOverlappingErrorCalculatorWithManyReads[0](/tmp/Overlapping1281265390033890182.bam)(picard.sam.SamErrorMetric.BaseErrorCalculationTest) Running Test: Test method testSimpleErrorCalculator(picard.sam.SamErrorMetric.BaseErrorCalculationTest) Running Test: Test method testFileLengthMatchesHeaderLength(picard.illumina.parser.fakers.BclFileFakerTest) Running Test: Test method testGZFileIsActuallyGZipped(picard.illumina.parser.fakers.BclFileFakerTest) Running Test: Test method eamssParsingTestNoGSeries[0](BasesAndQuals( G G G G G G G G G , 13,7,35,32,31,33,31,26,29,, 13,7,35,32,31,33,31,26,29,))(picard.illumina.parser.BclParserTest) Running Test: Test method eamssParsingTestNoGSeries[1](BasesAndQuals( G G G G G G G G G , 13,7,35,26,18,19,35,8,33,, 13,7,35,26,18,19,35,8,33,))(picard.illumina.parser.BclParserTest) Running Test: Test method eamssParsingTestNoGSeries[2](BasesAndQuals( A C C C C C C C C C C C T G G C T A A , 7,8,33,7,2,33,16,17,19,7,6,5,35,2,33,22,18,16,25,, 7,8,33,7,2,33,16,17,19,7,6,5,35,2,33,22,18,16,25,))(picard.illumina.parser.BclParserTest) Running Test: Test method eamssParsingTestNoGSeries[3](BasesAndQuals( T G G G G G G G . . G G G G G G G T A A G G G , 7,8,33,7,2,33,16,17,2,2,6,5,35,2,33,22,18,16,25,33,32,16,18,, 7,8,33,7,2,33,16,17,2,2,6,5,35,2,33,22,18,16,25,33,32,16,18,))(picard.illumina.parser.BclParserTest) Running Test: Test method eamssParsingTestNoGSeries[4](BasesAndQuals( T A C , 25,16,16,, 25,16,16,))(picard.illumina.parser.BclParserTest) Running Test: Test method eamssParsingTestNoGSeries[5](BasesAndQuals( T A C G G . . T C C C C T T T G G G A T G C A T A C G G . . T C C C C T T T G G G A T G C A , 25,16,16,33,22,2,2,33,35,3,31,38,22,19,25,16,16,31,30,2,2,33,26,3,31,38,22,19,2,2,30,27,28,16,2,2,30,16,19,21,22,17,19,16,16,16,, 25,16,16,33,22,2,2,33,35,3,31,38,22,19,25,16,16,31,30,2,2,33,26,3,31,38,22,19,2,2,30,27,28,16,2,2,30,16,19,21,22,17,19,16,16,16,))(picard.illumina.parser.BclParserTest) Running Test: Test method eamssParsingTestNoGSeries[6](BasesAndQuals( G G G G G G G G G , 13,7,35,32,2,16,33,14,19,, 13,7,35,32,2,16,33,2,2,))(picard.illumina.parser.BclParserTest) Running Test: Test method eamssParsingTestNoGSeries[7](BasesAndQuals( G G G G G G G G G , 13,7,35,33,18,2,6,8,33,, 13,7,35,33,2,2,2,2,2,))(picard.illumina.parser.BclParserTest) Running Test: Test method eamssParsingTestNoGSeries[8](BasesAndQuals( A C C C C C C C C C C C T G G C T A A , 7,8,33,7,2,33,16,17,19,32,33,5,8,2,2,2,33,16,25,, 7,8,33,7,2,33,16,17,19,32,33,2,2,2,2,2,2,2,2,))(picard.illumina.parser.BclParserTest) Running Test: Test method eamssParsingTestNoGSeries[9](BasesAndQuals( T G G G G G G G . . G G G G G G G T A A G G G , 7,8,33,7,2,33,16,17,2,2,6,5,35,2,33,30,13,16,7,2,2,16,18,, 7,8,33,7,2,33,16,17,2,2,6,5,35,2,33,30,2,2,2,2,2,2,2,))(picard.illumina.parser.BclParserTest) Running Test: Test method eamssParsingTestNoGSeries[10](BasesAndQuals( T A C , 2,11,13,, 2,2,2,))(picard.illumina.parser.BclParserTest) Running Test: Test method eamssParsingTestNoGSeries[11](BasesAndQuals( T A C G G . . T C C C C T T T G G G A T G C A T A C G G . . T C C C C T T T G G G A T G C A , 25,16,16,33,22,2,2,33,35,3,31,38,22,19,25,16,16,31,30,2,2,33,26,3,31,38,22,19,2,2,30,27,28,16,2,2,30,16,19,21,22,2,19,16,2,2,, 25,16,16,33,22,2,2,33,35,3,31,38,22,19,25,16,16,31,30,2,2,33,26,3,31,38,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,))(picard.illumina.parser.BclParserTest) Running Test: Test method eamssParsingTestWithGSeries[0](BasesAndQuals( A C G G T G G G G G G G G G A C T , 7,8,33,7,12,33,16,17,2,2,32,35,35,35,2,15,9,, 7,8,33,7,12,2,2,2,2,2,2,2,2,2,2,2,2,))(picard.illumina.parser.BclParserTest) Running Test: Test method eamssParsingTestWithGSeries[1](BasesAndQuals( A C G G T G G G G G G G G G A C T , 7,8,2,7,2,2,16,17,2,2,32,35,35,35,2,15,9,, 2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,))(picard.illumina.parser.BclParserTest) Running Test: Test method eamssParsingTestWithGSeries[2](BasesAndQuals( A C G G T G G G G G G G G G A C T , 7,8,2,7,2,2,16,17,2,2,32,35,35,35,33,15,9,, 7,8,2,7,2,2,16,17,2,2,32,35,35,35,33,2,2,))(picard.illumina.parser.BclParserTest) Running Test: Test method eamssParsingTestWithGSeries[3](BasesAndQuals( A C C G C C G G G G G G G G G G T T A , 33,31,29,32,28,27,30,18,18,18,18,19,19,19,33,18,9,9,19,, 33,31,29,32,28,27,2,2,2,2,2,2,2,2,2,2,2,2,2,))(picard.illumina.parser.BclParserTest) Running Test: Test method eamssParsingTestWithGSeries[4](BasesAndQuals( A C C G C C G G G G G G G G G G T T A , 33,31,29,32,28,27,30,18,18,18,18,19,19,19,33,18,33,32,34,, 33,31,29,32,28,27,30,18,18,18,18,19,19,19,33,18,33,32,34,))(picard.illumina.parser.BclParserTest) Running Test: Test method eamssParsingTestWithGSeries[5](BasesAndQuals( A C C G C C G G G G A G G G G G T T A , 33,31,29,32,28,27,30,18,18,18,18,19,19,19,33,18,9,9,19,, 33,31,29,32,28,27,2,2,2,2,2,2,2,2,2,2,2,2,2,))(picard.illumina.parser.BclParserTest) Running Test: Test method eamssParsingTestWithGSeries[6](BasesAndQuals( A C G G G C G G G G G G G G G G T T A , 33,31,29,32,28,16,33,18,18,18,18,19,19,19,33,18,3,9,19,, 33,31,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,))(picard.illumina.parser.BclParserTest) Running Test: Test method eamssParsingTestWithGSeries[7](BasesAndQuals( A C G G C C G G G G G G G G G G G G G , 33,31,29,32,28,16,33,18,18,18,18,19,19,19,33,34,33,33,3,, 33,31,29,32,28,16,2,2,2,2,2,2,2,2,2,2,2,2,2,))(picard.illumina.parser.BclParserTest) Running Test: Test method eamssParsingTestWithGSeries[8](BasesAndQuals( A C G G C C G G G G G G G G G G G G G T A C T T G G G G G G G G G G G G G , 33,31,29,32,28,16,33,18,18,18,18,19,19,19,33,34,33,33,3,33,34,2,4,8,33,7,35,15,16,31,30,38,16,15,22,29,25,, 33,31,29,32,28,16,33,18,18,18,18,19,19,19,33,34,33,33,3,33,34,2,4,8,33,7,35,15,16,31,30,38,16,15,22,29,25,))(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTest[0]([I@6b06ad17, 180, -1, -1, -1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTest[1]([I@506dfc8e, 180, -1, -1, -1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTest[2]([I@6af3c8c5, 120, -1, -1, -1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTest[3]([I@54897d16, 120, -1, -1, -1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTest[4]([I@396dc6fa, 60, -1, -1, -1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTest[5]([I@3617013f, 206, 25, 0, 0)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTest[6]([I@484cfdd9, 206, 25, 0, 0)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTest[7]([I@2297d93f, 80, 19, 0, 1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTest[8]([I@1f5f419c, 156, 35, 0, 0)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTest[9]([I@16d41331, 66, 5, 0, 0)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWBadDeletedSkips[0]([I@5515a428, 180, -1, -1, -1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWBadDeletedSkips[1]([I@70a3fd4e, 180, -1, -1, -1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWBadDeletedSkips[2]([I@6e6f02bf, 120, -1, -1, -1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWBadDeletedSkips[3]([I@f839efa, 120, -1, -1, -1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWBadDeletedSkips[4]([I@68ed609a, 60, -1, -1, -1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWBadDeletedSkips[5]([I@31d479f6, 206, 25, 0, 0)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWBadDeletedSkips[6]([I@4336c0e5, 206, 25, 0, 0)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWBadDeletedSkips[7]([I@698c69af, 80, 19, 0, 1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWBadDeletedSkips[8]([I@38bec7d9, 156, 35, 0, 0)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWBadDeletedSkips[9]([I@64810bed, 66, 5, 0, 0)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWDeletedSkips[0]([I@37139924, 180, -1, -1, -1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWDeletedSkips[1]([I@6367dbae, 180, -1, -1, -1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWDeletedSkips[2]([I@5994e89b, 120, -1, -1, -1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWDeletedSkips[3]([I@203cb1fa, 120, -1, -1, -1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWDeletedSkips[4]([I@3c08c, 60, -1, -1, -1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWDeletedSkips[5]([I@6574285c, 206, 25, 0, 0)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWDeletedSkips[6]([I@6c2860d5, 206, 25, 0, 0)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWDeletedSkips[7]([I@1f99aa38, 80, 19, 0, 1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWDeletedSkips[8]([I@4c989eab, 156, 35, 0, 0)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWDeletedSkips[9]([I@1f96fe5d, 66, 5, 0, 0)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWPartiallyDeletedSkips[0]([I@3f64a3ab, 180, -1, -1, -1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWPartiallyDeletedSkips[1]([I@38a6d08a, 180, -1, -1, -1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWPartiallyDeletedSkips[2]([I@1d0a9b3b, 120, -1, -1, -1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWPartiallyDeletedSkips[3]([I@568f9d18, 120, -1, -1, -1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWPartiallyDeletedSkips[4]([I@507f08a2, 60, -1, -1, -1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWPartiallyDeletedSkips[5]([I@3b703dcd, 206, 25, 0, 0)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWPartiallyDeletedSkips[6]([I@266d088b, 206, 25, 0, 0)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWPartiallyDeletedSkips[7]([I@652031ec, 80, 19, 0, 1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWPartiallyDeletedSkips[8]([I@5c90ade8, 156, 35, 0, 0)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWPartiallyDeletedSkips[9]([I@402b850e, 66, 5, 0, 0)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWSkips[0]([I@3565f855, 180, -1, -1, -1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWSkips[1]([I@ec49471, 180, -1, -1, -1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWSkips[2]([I@6777b77a, 120, -1, -1, -1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWSkips[3]([I@42ee08c, 120, -1, -1, -1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWSkips[4]([I@71a3855b, 60, -1, -1, -1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWSkips[5]([I@305a4d58, 206, 25, 0, 0)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWSkips[6]([I@5fd04e18, 206, 25, 0, 0)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWSkips[7]([I@61a44da2, 80, 19, 0, 1)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWSkips[8]([I@2a99fb78, 156, 35, 0, 0)(picard.illumina.parser.BclParserTest) Running Test: Test method fullBclParserTestWSkips[9]([I@5dd1b72e, 66, 5, 0, 0)(picard.illumina.parser.BclParserTest) Running Test: Test method failingFileTest[0](testdata/picard/illumina/readerTests/bcl_failing.bcl)(picard.illumina.parser.readers.BclReaderTest) Running Test: Test method failingFileTest[1](testdata/picard/illumina/readerTests/bcl_failing2.bcl)(picard.illumina.parser.readers.BclReaderTest) Running Test: Test method failingFileTest[2](testdata/picard/illumina/readerTests/SomeNoneExistentFile.bcl)(picard.illumina.parser.readers.BclReaderTest) Running Test: Test method failingFileTest[3](testdata/picard/illumina/readerTests/bcl_tooLong.bcl)(picard.illumina.parser.readers.BclReaderTest) Running Test: Test method failingFileTest[4](testdata/picard/illumina/readerTests/bcl_tooShort.bcl)(picard.illumina.parser.readers.BclReaderTest) Running Test: Test method lowQualityAndFailingTest(picard.illumina.parser.readers.BclReaderTest) Running Test: Test method lowQualityButPassingTest(picard.illumina.parser.readers.BclReaderTest) Running Test: Test method readValidFile(picard.illumina.parser.readers.BclReaderTest) Running Test: Test method testBedToIntervalList[0](simple.bed)(picard.util.BedToIntervalListTest) Test: Test method testBedToIntervalList[0](simple.bed)(picard.util.BedToIntervalListTest) produced standard out/err: INFO 2024-07-02 11:50:56 BedToIntervalList Wrote 2 intervals spanning a total of 2900 bases Gradle suite > Gradle test > picard.util.BedToIntervalListTest.testBedToIntervalList[0](simple.bed) STANDARD_ERROR INFO 2024-07-02 11:50:56 BedToIntervalList Wrote 2 intervals spanning a total of 2900 bases Running Test: Test method testBedToIntervalList[1](overlapping.bed)(picard.util.BedToIntervalListTest) Test: Test method testBedToIntervalList[1](overlapping.bed)(picard.util.BedToIntervalListTest) produced standard out/err: INFO 2024-07-02 11:50:56 BedToIntervalList Wrote 1 intervals spanning a total of 3900 bases Gradle suite > Gradle test > picard.util.BedToIntervalListTest.testBedToIntervalList[1](overlapping.bed) STANDARD_ERROR INFO 2024-07-02 11:50:56 BedToIntervalList Wrote 1 intervals spanning a total of 3900 bases Running Test: Test method testBedToIntervalList[2](extended.bed)(picard.util.BedToIntervalListTest) Test: Test method testBedToIntervalList[2](extended.bed)(picard.util.BedToIntervalListTest) produced standard out/err: INFO 2024-07-02 11:50:56 BedToIntervalList Wrote 2 intervals spanning a total of 2900 bases Gradle suite > Gradle test > picard.util.BedToIntervalListTest.testBedToIntervalList[2](extended.bed) STANDARD_ERROR INFO 2024-07-02 11:50:56 BedToIntervalList Wrote 2 intervals spanning a total of 2900 bases Running Test: Test method testBedToIntervalList[3](one_base_interval.bed)(picard.util.BedToIntervalListTest) Test: Test method testBedToIntervalList[3](one_base_interval.bed)(picard.util.BedToIntervalListTest) produced standard out/err: INFO 2024-07-02 11:50:56 BedToIntervalList Wrote 1 intervals spanning a total of 1 bases Gradle suite > Gradle test > picard.util.BedToIntervalListTest.testBedToIntervalList[3](one_base_interval.bed) STANDARD_ERROR INFO 2024-07-02 11:50:56 BedToIntervalList Wrote 1 intervals spanning a total of 1 bases Running Test: Test method testBedToIntervalList[4](zero_base_interval.bed)(picard.util.BedToIntervalListTest) Test: Test method testBedToIntervalList[4](zero_base_interval.bed)(picard.util.BedToIntervalListTest) produced standard out/err: INFO 2024-07-02 11:50:56 BedToIntervalList Wrote 1 intervals spanning a total of 0 bases Gradle suite > Gradle test > picard.util.BedToIntervalListTest.testBedToIntervalList[4](zero_base_interval.bed) STANDARD_ERROR INFO 2024-07-02 11:50:56 BedToIntervalList Wrote 1 intervals spanning a total of 0 bases Running Test: Test method testBedToIntervalList[5](first_base_in_contig.bed)(picard.util.BedToIntervalListTest) Test: Test method testBedToIntervalList[5](first_base_in_contig.bed)(picard.util.BedToIntervalListTest) produced standard out/err: INFO 2024-07-02 11:50:56 BedToIntervalList Wrote 1 intervals spanning a total of 100 bases Gradle suite > Gradle test > picard.util.BedToIntervalListTest.testBedToIntervalList[5](first_base_in_contig.bed) STANDARD_ERROR INFO 2024-07-02 11:50:56 BedToIntervalList Wrote 1 intervals spanning a total of 100 bases Running Test: Test method testBedToIntervalList[6](zero_length_interval_at_first_position_in_contig.bed)(picard.util.BedToIntervalListTest) Test: Test method testBedToIntervalList[6](zero_length_interval_at_first_position_in_contig.bed)(picard.util.BedToIntervalListTest) produced standard out/err: INFO 2024-07-02 11:50:56 BedToIntervalList Wrote 1 intervals spanning a total of 0 bases Gradle suite > Gradle test > picard.util.BedToIntervalListTest.testBedToIntervalList[6](zero_length_interval_at_first_position_in_contig.bed) STANDARD_ERROR INFO 2024-07-02 11:50:56 BedToIntervalList Wrote 1 intervals spanning a total of 0 bases Running Test: Test method testBedToIntervalList[7](last_base_in_contig.bed)(picard.util.BedToIntervalListTest) Test: Test method testBedToIntervalList[7](last_base_in_contig.bed)(picard.util.BedToIntervalListTest) produced standard out/err: INFO 2024-07-02 11:50:56 BedToIntervalList Wrote 1 intervals spanning a total of 1000000 bases Gradle suite > Gradle test > picard.util.BedToIntervalListTest.testBedToIntervalList[7](last_base_in_contig.bed) STANDARD_ERROR INFO 2024-07-02 11:50:56 BedToIntervalList Wrote 1 intervals spanning a total of 1000000 bases Running Test: Test method testBedToIntervalList[8](multi_contig.bed)(picard.util.BedToIntervalListTest) Test: Test method testBedToIntervalList[8](multi_contig.bed)(picard.util.BedToIntervalListTest) produced standard out/err: INFO 2024-07-02 11:50:56 BedToIntervalList Wrote 4 intervals spanning a total of 5800 bases Gradle suite > Gradle test > picard.util.BedToIntervalListTest.testBedToIntervalList[8](multi_contig.bed) STANDARD_ERROR INFO 2024-07-02 11:50:56 BedToIntervalList Wrote 4 intervals spanning a total of 5800 bases Running Test: Test method testBedToIntervalListBadSequenceDictionary[0](seq_dict_test.dictionary.bad)(picard.util.BedToIntervalListTest) Running Test: Test method testBedToIntervalListBadSequenceDictionary[1](seq_dict_test.dictionary.bad.vcf)(picard.util.BedToIntervalListTest) Running Test: Test method testBedToIntervalListOutOfBounds[0](end_after_chr.bed)(picard.util.BedToIntervalListTest) Running Test: Test method testBedToIntervalListOutOfBounds[1](end_before_chr.bed)(picard.util.BedToIntervalListTest) Running Test: Test method testBedToIntervalListOutOfBounds[2](missing_chr.bed)(picard.util.BedToIntervalListTest) Running Test: Test method testBedToIntervalListOutOfBounds[3](start_after_chr.bed)(picard.util.BedToIntervalListTest) Running Test: Test method testBedToIntervalListOutOfBounds[4](start_before_chr.bed)(picard.util.BedToIntervalListTest) Running Test: Test method testBedToIntervalListOutOfBounds[5](off_by_one_interval.bed)(picard.util.BedToIntervalListTest) Running Test: Test method testBedToIntervalListSequenceDictionary[0](seq_dict_test.dictionary.interval_list)(picard.util.BedToIntervalListTest) Test: Test method testBedToIntervalListSequenceDictionary[0](seq_dict_test.dictionary.interval_list)(picard.util.BedToIntervalListTest) produced standard out/err: INFO 2024-07-02 11:50:57 BedToIntervalList Wrote 3 intervals spanning a total of 3000 bases Gradle suite > Gradle test > picard.util.BedToIntervalListTest.testBedToIntervalListSequenceDictionary[0](seq_dict_test.dictionary.interval_list) STANDARD_ERROR INFO 2024-07-02 11:50:57 BedToIntervalList Wrote 3 intervals spanning a total of 3000 bases Running Test: Test method testBedToIntervalListSequenceDictionary[1](seq_dict_test.dictionary.fasta)(picard.util.BedToIntervalListTest) Test: Test method testBedToIntervalListSequenceDictionary[1](seq_dict_test.dictionary.fasta)(picard.util.BedToIntervalListTest) produced standard out/err: INFO 2024-07-02 11:50:57 BedToIntervalList Wrote 3 intervals spanning a total of 3000 bases Gradle suite > Gradle test > picard.util.BedToIntervalListTest.testBedToIntervalListSequenceDictionary[1](seq_dict_test.dictionary.fasta) STANDARD_ERROR INFO 2024-07-02 11:50:57 BedToIntervalList Wrote 3 intervals spanning a total of 3000 bases Running Test: Test method testBedToIntervalListSequenceDictionary[2](seq_dict_test.dictionary.dict)(picard.util.BedToIntervalListTest) Test: Test method testBedToIntervalListSequenceDictionary[2](seq_dict_test.dictionary.dict)(picard.util.BedToIntervalListTest) produced standard out/err: INFO 2024-07-02 11:50:57 BedToIntervalList Wrote 3 intervals spanning a total of 3000 bases Gradle suite > Gradle test > picard.util.BedToIntervalListTest.testBedToIntervalListSequenceDictionary[2](seq_dict_test.dictionary.dict) STANDARD_ERROR INFO 2024-07-02 11:50:57 BedToIntervalList Wrote 3 intervals spanning a total of 3000 bases Running Test: Test method testBedToIntervalListSequenceDictionary[3](seq_dict_test.dictionary.sam)(picard.util.BedToIntervalListTest) Test: Test method testBedToIntervalListSequenceDictionary[3](seq_dict_test.dictionary.sam)(picard.util.BedToIntervalListTest) produced standard out/err: INFO 2024-07-02 11:50:57 BedToIntervalList Wrote 3 intervals spanning a total of 3000 bases Gradle suite > Gradle test > picard.util.BedToIntervalListTest.testBedToIntervalListSequenceDictionary[3](seq_dict_test.dictionary.sam) STANDARD_ERROR INFO 2024-07-02 11:50:57 BedToIntervalList Wrote 3 intervals spanning a total of 3000 bases Running Test: Test method testBedToIntervalListSequenceDictionary[4](seq_dict_test.dictionary.vcf)(picard.util.BedToIntervalListTest) Test: Test method testBedToIntervalListSequenceDictionary[4](seq_dict_test.dictionary.vcf)(picard.util.BedToIntervalListTest) produced standard out/err: INFO 2024-07-02 11:50:57 BedToIntervalList Wrote 3 intervals spanning a total of 3000 bases Gradle suite > Gradle test > picard.util.BedToIntervalListTest.testBedToIntervalListSequenceDictionary[4](seq_dict_test.dictionary.vcf) STANDARD_ERROR INFO 2024-07-02 11:50:57 BedToIntervalList Wrote 3 intervals spanning a total of 3000 bases Running Test: Test method testBuild37ExtendedIlluminaManifest[0](HumanExome-12v1-1_A.1.3.extended.csv, HumanExome-12v1-1_A.bpm, 4/23/2012, Infinium HD Ultra, 8, 1.3, 6)(picard.arrays.illumina.Build37ExtendedIlluminaManifestTest) Running Test: Test method testBuild37ExtendedIlluminaManifest[1](MEG_AllofUs_20002558X351448_A2.1.4.extended.csv, MEG_AllofUs_20002558X351448_A2.bpm, 2/13/2019, Infinium LCG, 5, 1.4, 1)(picard.arrays.illumina.Build37ExtendedIlluminaManifestTest) Running Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: INFO 2024-07-02 11:50:57 SamFormatConverter Gradle suite > Gradle test > picard.sam.BuildBamIndexTest.testBuildBamIndexFail STANDARD_ERROR INFO 2024-07-02 11:50:57 SamFormatConverter Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: ********** ********** Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: ********** ********** Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: ********** ********** Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: ********** SamFormatConverter -INPUT testdata/picard/indices/index_test.sam -OUTPUT testdata/picard/indices/index_test_unsorted.bam ********** SamFormatConverter -INPUT testdata/picard/indices/index_test.sam -OUTPUT testdata/picard/indices/index_test_unsorted.bam Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: ********** ********** Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: 11:50:57.128 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:57.128 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: 11:50:57.128 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:57.128 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: 11:50:57.131 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:57.131 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: 11:50:57.131 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:57.131 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: [Tue Jul 02 11:50:57 GMT+14:00 2024] SamFormatConverter INPUT=testdata/picard/indices/index_test.sam OUTPUT=testdata/picard/indices/index_test_unsorted.bam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:57 GMT+14:00 2024] SamFormatConverter INPUT=testdata/picard/indices/index_test.sam OUTPUT=testdata/picard/indices/index_test_unsorted.bam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: [Tue Jul 02 11:50:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: [Tue Jul 02 11:50:57 GMT+14:00 2024] picard.sam.SamFormatConverter done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:57 GMT+14:00 2024] picard.sam.SamFormatConverter done. Elapsed time: 0.00 minutes. Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: INFO 2024-07-02 11:50:57 BuildBamIndex INFO 2024-07-02 11:50:57 BuildBamIndex Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: ********** ********** Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: ********** ********** Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: ********** ********** Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: ********** BuildBamIndex -INPUT testdata/picard/indices/index_test_unsorted.bam -OUTPUT testdata/picard/indices/index_test.bam.bai ********** BuildBamIndex -INPUT testdata/picard/indices/index_test_unsorted.bam -OUTPUT testdata/picard/indices/index_test.bam.bai Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: ********** ********** Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: 11:50:57.159 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:57.159 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: 11:50:57.159 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:57.159 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: 11:50:57.160 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:57.160 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: 11:50:57.160 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:57.160 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: [Tue Jul 02 11:50:57 GMT+14:00 2024] BuildBamIndex INPUT=testdata/picard/indices/index_test_unsorted.bam OUTPUT=testdata/picard/indices/index_test.bam.bai VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:57 GMT+14:00 2024] BuildBamIndex INPUT=testdata/picard/indices/index_test_unsorted.bam OUTPUT=testdata/picard/indices/index_test.bam.bai VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: [Tue Jul 02 11:50:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: [Tue Jul 02 11:50:57 GMT+14:00 2024] picard.sam.BuildBamIndex done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:57 GMT+14:00 2024] picard.sam.BuildBamIndex done. Elapsed time: 0.00 minutes. Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testBuildBamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: INFO 2024-07-02 11:50:57 SortSam Gradle suite > Gradle test > picard.sam.BuildBamIndexTest.testBuildBamIndexOK STANDARD_ERROR INFO 2024-07-02 11:50:57 SortSam Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: ********** ********** Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: ********** ********** Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: ********** ********** Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: ********** SortSam -I testdata/picard/indices/index_test.sam -O testdata/picard/indices/index_test_sorted.bam -SORT_ORDER coordinate ********** SortSam -I testdata/picard/indices/index_test.sam -O testdata/picard/indices/index_test_sorted.bam -SORT_ORDER coordinate Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: ********** ********** Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: 11:50:57.164 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:57.164 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: 11:50:57.164 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:57.164 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: 11:50:57.164 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:57.164 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: 11:50:57.164 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:57.164 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: [Tue Jul 02 11:50:57 GMT+14:00 2024] SortSam INPUT=testdata/picard/indices/index_test.sam OUTPUT=testdata/picard/indices/index_test_sorted.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:57 GMT+14:00 2024] SortSam INPUT=testdata/picard/indices/index_test.sam OUTPUT=testdata/picard/indices/index_test_sorted.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: [Tue Jul 02 11:50:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: INFO 2024-07-02 11:50:57 SortSam Finished reading inputs, merging and writing to output now. INFO 2024-07-02 11:50:57 SortSam Finished reading inputs, merging and writing to output now. Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: [Tue Jul 02 11:50:57 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:57 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.00 minutes. Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: INFO 2024-07-02 11:50:57 BuildBamIndex INFO 2024-07-02 11:50:57 BuildBamIndex Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: ********** ********** Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: ********** ********** Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: ********** ********** Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: ********** BuildBamIndex -INPUT testdata/picard/indices/index_test_sorted.bam -OUTPUT testdata/picard/indices/index_test.bam.bai ********** BuildBamIndex -INPUT testdata/picard/indices/index_test_sorted.bam -OUTPUT testdata/picard/indices/index_test.bam.bai Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: ********** ********** Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: 11:50:57.194 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:57.194 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: 11:50:57.195 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:57.195 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: 11:50:57.195 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:57.195 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: 11:50:57.195 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:57.195 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: [Tue Jul 02 11:50:57 GMT+14:00 2024] BuildBamIndex INPUT=testdata/picard/indices/index_test_sorted.bam OUTPUT=testdata/picard/indices/index_test.bam.bai VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:57 GMT+14:00 2024] BuildBamIndex INPUT=testdata/picard/indices/index_test_sorted.bam OUTPUT=testdata/picard/indices/index_test.bam.bai VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: [Tue Jul 02 11:50:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: INFO 2024-07-02 11:50:57 BuildBamIndex Successfully wrote bam index file testdata/picard/indices/index_test.bam.bai INFO 2024-07-02 11:50:57 BuildBamIndex Successfully wrote bam index file testdata/picard/indices/index_test.bam.bai Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: [Tue Jul 02 11:50:57 GMT+14:00 2024] picard.sam.BuildBamIndex done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:57 GMT+14:00 2024] picard.sam.BuildBamIndex done. Elapsed time: 0.00 minutes. Test: Test method testBuildBamIndexOK(picard.sam.BuildBamIndexTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBuildSamIndexFail(picard.sam.BuildBamIndexTest) Test: Test method testBuildSamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: INFO 2024-07-02 11:50:57 BuildBamIndex Gradle suite > Gradle test > picard.sam.BuildBamIndexTest.testBuildSamIndexFail STANDARD_ERROR INFO 2024-07-02 11:50:57 BuildBamIndex Test: Test method testBuildSamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: Test: Test method testBuildSamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBuildSamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: ********** ********** Test: Test method testBuildSamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBuildSamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBuildSamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: ********** ********** Test: Test method testBuildSamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBuildSamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: ********** ********** Test: Test method testBuildSamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: ********** BuildBamIndex -INPUT testdata/picard/indices/index_test.sam -OUTPUT testdata/picard/indices/index_test.bam.bai ********** BuildBamIndex -INPUT testdata/picard/indices/index_test.sam -OUTPUT testdata/picard/indices/index_test.bam.bai Test: Test method testBuildSamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: ********** ********** Test: Test method testBuildSamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: Test: Test method testBuildSamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: Test: Test method testBuildSamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: 11:50:57.239 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:57.239 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBuildSamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: 11:50:57.239 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:57.239 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBuildSamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: 11:50:57.239 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:57.239 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBuildSamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: 11:50:57.239 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:57.239 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBuildSamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: [Tue Jul 02 11:50:57 GMT+14:00 2024] BuildBamIndex INPUT=testdata/picard/indices/index_test.sam OUTPUT=testdata/picard/indices/index_test.bam.bai VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:57 GMT+14:00 2024] BuildBamIndex INPUT=testdata/picard/indices/index_test.sam OUTPUT=testdata/picard/indices/index_test.bam.bai VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBuildSamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: [Tue Jul 02 11:50:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBuildSamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: [Tue Jul 02 11:50:57 GMT+14:00 2024] picard.sam.BuildBamIndex done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:57 GMT+14:00 2024] picard.sam.BuildBamIndex done. Elapsed time: 0.00 minutes. Test: Test method testBuildSamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testBuildSamIndexFail(picard.sam.BuildBamIndexTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testEmptyIntervalList(picard.vcf.ByIntervalListVariantContextIteratorTest) Running Test: Test method testNoOverlapDifferentContig(picard.vcf.ByIntervalListVariantContextIteratorTest) Running Test: Test method testNoVariants(picard.vcf.ByIntervalListVariantContextIteratorTest) Running Test: Test method testSimpleEnclosing(picard.vcf.ByIntervalListVariantContextIteratorTest) Running Test: Test method testSimpleOverlap(picard.vcf.ByIntervalListVariantContextIteratorTest) Running Test: Test method testVariantOverlappingMultipleIntervalsIsReturnedOnlyOnce(picard.vcf.ByIntervalListVariantContextIteratorTest) Running Test: Test method test(picard.vcf.processor.ByWholeContigTest) Running Test: Test method testFingerprintMetric[0](testdata/picard/fingerprint/NA12892.g.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) Test: Test method testFingerprintMetric[0](testdata/picard/fingerprint/NA12892.g.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: INFO 2024-07-02 11:50:57 CalculateFingerprintMetrics Gradle suite > Gradle test > picard.fingerprint.CalculateFingerprintMetricsTest.testFingerprintMetric[0](testdata/picard/fingerprint/NA12892.g.vcf) STANDARD_ERROR INFO 2024-07-02 11:50:57 CalculateFingerprintMetrics Test: Test method testFingerprintMetric[0](testdata/picard/fingerprint/NA12892.g.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: Test: Test method testFingerprintMetric[0](testdata/picard/fingerprint/NA12892.g.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFingerprintMetric[0](testdata/picard/fingerprint/NA12892.g.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** ********** Test: Test method testFingerprintMetric[0](testdata/picard/fingerprint/NA12892.g.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFingerprintMetric[0](testdata/picard/fingerprint/NA12892.g.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFingerprintMetric[0](testdata/picard/fingerprint/NA12892.g.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** ********** Test: Test method testFingerprintMetric[0](testdata/picard/fingerprint/NA12892.g.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFingerprintMetric[0](testdata/picard/fingerprint/NA12892.g.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** ********** Test: Test method testFingerprintMetric[0](testdata/picard/fingerprint/NA12892.g.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** CalculateFingerprintMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf -OUTPUT /tmp/testFingerprintMetric7051699800128040393fingerprint_metric -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt ********** CalculateFingerprintMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf -OUTPUT /tmp/testFingerprintMetric7051699800128040393fingerprint_metric -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt Test: Test method testFingerprintMetric[0](testdata/picard/fingerprint/NA12892.g.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** ********** Test: Test method testFingerprintMetric[0](testdata/picard/fingerprint/NA12892.g.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: Test: Test method testFingerprintMetric[0](testdata/picard/fingerprint/NA12892.g.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: Test: Test method testFingerprintMetric[0](testdata/picard/fingerprint/NA12892.g.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: 11:50:57.335 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:57.335 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFingerprintMetric[0](testdata/picard/fingerprint/NA12892.g.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: 11:50:57.335 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:57.335 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFingerprintMetric[0](testdata/picard/fingerprint/NA12892.g.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: 11:50:57.335 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:57.335 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFingerprintMetric[0](testdata/picard/fingerprint/NA12892.g.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: 11:50:57.335 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:57.335 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFingerprintMetric[0](testdata/picard/fingerprint/NA12892.g.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: [Tue Jul 02 11:50:57 GMT+14:00 2024] CalculateFingerprintMetrics INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf] OUTPUT=/tmp/testFingerprintMetric7051699800128040393fingerprint_metric HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt CALCULATE_BY=READGROUP GENOTYPE_LOD_THRESHOLD=3.0 NUMBER_OF_SAMPLING=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:57 GMT+14:00 2024] CalculateFingerprintMetrics INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf] OUTPUT=/tmp/testFingerprintMetric7051699800128040393fingerprint_metric HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt CALCULATE_BY=READGROUP GENOTYPE_LOD_THRESHOLD=3.0 NUMBER_OF_SAMPLING=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFingerprintMetric[0](testdata/picard/fingerprint/NA12892.g.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: [Tue Jul 02 11:50:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFingerprintMetric[0](testdata/picard/fingerprint/NA12892.g.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: WARNING 2024-07-02 11:50:57 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf going to read through it all. WARNING 2024-07-02 11:50:57 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf going to read through it all. Test: Test method testFingerprintMetric[0](testdata/picard/fingerprint/NA12892.g.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: INFO 2024-07-02 11:50:57 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:50:57 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testFingerprintMetric[0](testdata/picard/fingerprint/NA12892.g.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: [Tue Jul 02 11:50:57 GMT+14:00 2024] picard.fingerprint.CalculateFingerprintMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:57 GMT+14:00 2024] picard.fingerprint.CalculateFingerprintMetrics done. Elapsed time: 0.00 minutes. Test: Test method testFingerprintMetric[0](testdata/picard/fingerprint/NA12892.g.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testFingerprintMetric[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) Test: Test method testFingerprintMetric[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: INFO 2024-07-02 11:50:57 CalculateFingerprintMetrics Gradle suite > Gradle test > picard.fingerprint.CalculateFingerprintMetricsTest.testFingerprintMetric[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam) STANDARD_ERROR INFO 2024-07-02 11:50:57 CalculateFingerprintMetrics Test: Test method testFingerprintMetric[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: Test: Test method testFingerprintMetric[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFingerprintMetric[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** ********** Test: Test method testFingerprintMetric[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFingerprintMetric[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFingerprintMetric[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** ********** Test: Test method testFingerprintMetric[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFingerprintMetric[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** ********** Test: Test method testFingerprintMetric[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** CalculateFingerprintMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam -OUTPUT /tmp/testFingerprintMetric10071580892655198583fingerprint_metric -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt ********** CalculateFingerprintMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam -OUTPUT /tmp/testFingerprintMetric10071580892655198583fingerprint_metric -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt Test: Test method testFingerprintMetric[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** ********** Test: Test method testFingerprintMetric[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: Test: Test method testFingerprintMetric[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: Test: Test method testFingerprintMetric[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: 11:50:57.615 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:57.615 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFingerprintMetric[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: 11:50:57.615 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:57.615 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFingerprintMetric[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: 11:50:57.615 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:57.615 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFingerprintMetric[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: 11:50:57.615 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:57.615 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFingerprintMetric[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: [Tue Jul 02 11:50:57 GMT+14:00 2024] CalculateFingerprintMetrics INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam] OUTPUT=/tmp/testFingerprintMetric10071580892655198583fingerprint_metric HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt CALCULATE_BY=READGROUP GENOTYPE_LOD_THRESHOLD=3.0 NUMBER_OF_SAMPLING=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:57 GMT+14:00 2024] CalculateFingerprintMetrics INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam] OUTPUT=/tmp/testFingerprintMetric10071580892655198583fingerprint_metric HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt CALCULATE_BY=READGROUP GENOTYPE_LOD_THRESHOLD=3.0 NUMBER_OF_SAMPLING=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFingerprintMetric[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: [Tue Jul 02 11:50:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFingerprintMetric[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: WARNING 2024-07-02 11:50:57 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam) WARNING 2024-07-02 11:50:57 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam) Test: Test method testFingerprintMetric[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: INFO 2024-07-02 11:50:58 FingerprintChecker Processed files. 27 fingerprints found in map. INFO 2024-07-02 11:50:58 FingerprintChecker Processed files. 27 fingerprints found in map. Test: Test method testFingerprintMetric[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: [Tue Jul 02 11:50:58 GMT+14:00 2024] picard.fingerprint.CalculateFingerprintMetrics done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:50:58 GMT+14:00 2024] picard.fingerprint.CalculateFingerprintMetrics done. Elapsed time: 0.01 minutes. Test: Test method testFingerprintMetric[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testFingerprintMetric[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) Test: Test method testFingerprintMetric[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: INFO 2024-07-02 11:50:58 CalculateFingerprintMetrics Gradle suite > Gradle test > picard.fingerprint.CalculateFingerprintMetricsTest.testFingerprintMetric[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) STANDARD_ERROR INFO 2024-07-02 11:50:58 CalculateFingerprintMetrics Test: Test method testFingerprintMetric[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: Test: Test method testFingerprintMetric[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFingerprintMetric[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** ********** Test: Test method testFingerprintMetric[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFingerprintMetric[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFingerprintMetric[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** ********** Test: Test method testFingerprintMetric[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFingerprintMetric[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** ********** Test: Test method testFingerprintMetric[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** CalculateFingerprintMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -OUTPUT /tmp/testFingerprintMetric5519157432861290854fingerprint_metric -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt ********** CalculateFingerprintMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -OUTPUT /tmp/testFingerprintMetric5519157432861290854fingerprint_metric -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt Test: Test method testFingerprintMetric[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** ********** Test: Test method testFingerprintMetric[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: Test: Test method testFingerprintMetric[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: Test: Test method testFingerprintMetric[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: 11:50:58.542 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:58.542 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFingerprintMetric[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: 11:50:58.542 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:58.542 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFingerprintMetric[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: 11:50:58.542 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:58.542 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFingerprintMetric[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: 11:50:58.542 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:58.542 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFingerprintMetric[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: [Tue Jul 02 11:50:58 GMT+14:00 2024] CalculateFingerprintMetrics INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam] OUTPUT=/tmp/testFingerprintMetric5519157432861290854fingerprint_metric HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt CALCULATE_BY=READGROUP GENOTYPE_LOD_THRESHOLD=3.0 NUMBER_OF_SAMPLING=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:58 GMT+14:00 2024] CalculateFingerprintMetrics INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam] OUTPUT=/tmp/testFingerprintMetric5519157432861290854fingerprint_metric HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt CALCULATE_BY=READGROUP GENOTYPE_LOD_THRESHOLD=3.0 NUMBER_OF_SAMPLING=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFingerprintMetric[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: [Tue Jul 02 11:50:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFingerprintMetric[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: WARNING 2024-07-02 11:50:58 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) WARNING 2024-07-02 11:50:58 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) Test: Test method testFingerprintMetric[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: INFO 2024-07-02 11:50:58 FingerprintChecker Processed files. 25 fingerprints found in map. INFO 2024-07-02 11:50:58 FingerprintChecker Processed files. 25 fingerprints found in map. Test: Test method testFingerprintMetric[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] picard.fingerprint.CalculateFingerprintMetrics done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:50:59 GMT+14:00 2024] picard.fingerprint.CalculateFingerprintMetrics done. Elapsed time: 0.01 minutes. Test: Test method testFingerprintMetric[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testFingerprintMetric[3](testdata/picard/fingerprint/NA12891.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) Test: Test method testFingerprintMetric[3](testdata/picard/fingerprint/NA12891.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: INFO 2024-07-02 11:50:59 CalculateFingerprintMetrics Gradle suite > Gradle test > picard.fingerprint.CalculateFingerprintMetricsTest.testFingerprintMetric[3](testdata/picard/fingerprint/NA12891.fp.vcf) STANDARD_ERROR INFO 2024-07-02 11:50:59 CalculateFingerprintMetrics Test: Test method testFingerprintMetric[3](testdata/picard/fingerprint/NA12891.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: Test: Test method testFingerprintMetric[3](testdata/picard/fingerprint/NA12891.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFingerprintMetric[3](testdata/picard/fingerprint/NA12891.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** ********** Test: Test method testFingerprintMetric[3](testdata/picard/fingerprint/NA12891.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFingerprintMetric[3](testdata/picard/fingerprint/NA12891.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFingerprintMetric[3](testdata/picard/fingerprint/NA12891.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** ********** Test: Test method testFingerprintMetric[3](testdata/picard/fingerprint/NA12891.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFingerprintMetric[3](testdata/picard/fingerprint/NA12891.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** ********** Test: Test method testFingerprintMetric[3](testdata/picard/fingerprint/NA12891.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** CalculateFingerprintMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf -OUTPUT /tmp/testFingerprintMetric9841600033150220613fingerprint_metric -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt ********** CalculateFingerprintMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf -OUTPUT /tmp/testFingerprintMetric9841600033150220613fingerprint_metric -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt Test: Test method testFingerprintMetric[3](testdata/picard/fingerprint/NA12891.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** ********** Test: Test method testFingerprintMetric[3](testdata/picard/fingerprint/NA12891.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: Test: Test method testFingerprintMetric[3](testdata/picard/fingerprint/NA12891.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: Test: Test method testFingerprintMetric[3](testdata/picard/fingerprint/NA12891.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: 11:50:59.303 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:59.303 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFingerprintMetric[3](testdata/picard/fingerprint/NA12891.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: 11:50:59.303 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:59.303 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFingerprintMetric[3](testdata/picard/fingerprint/NA12891.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: 11:50:59.303 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:59.303 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFingerprintMetric[3](testdata/picard/fingerprint/NA12891.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: 11:50:59.303 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:59.303 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFingerprintMetric[3](testdata/picard/fingerprint/NA12891.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] CalculateFingerprintMetrics INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf] OUTPUT=/tmp/testFingerprintMetric9841600033150220613fingerprint_metric HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt CALCULATE_BY=READGROUP GENOTYPE_LOD_THRESHOLD=3.0 NUMBER_OF_SAMPLING=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:59 GMT+14:00 2024] CalculateFingerprintMetrics INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf] OUTPUT=/tmp/testFingerprintMetric9841600033150220613fingerprint_metric HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt CALCULATE_BY=READGROUP GENOTYPE_LOD_THRESHOLD=3.0 NUMBER_OF_SAMPLING=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFingerprintMetric[3](testdata/picard/fingerprint/NA12891.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFingerprintMetric[3](testdata/picard/fingerprint/NA12891.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: WARNING 2024-07-02 11:50:59 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf going to read through it all. WARNING 2024-07-02 11:50:59 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf going to read through it all. Test: Test method testFingerprintMetric[3](testdata/picard/fingerprint/NA12891.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: INFO 2024-07-02 11:50:59 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:50:59 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testFingerprintMetric[3](testdata/picard/fingerprint/NA12891.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] picard.fingerprint.CalculateFingerprintMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:59 GMT+14:00 2024] picard.fingerprint.CalculateFingerprintMetrics done. Elapsed time: 0.00 minutes. Test: Test method testFingerprintMetric[3](testdata/picard/fingerprint/NA12891.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testFingerprintMetric[4](testdata/picard/fingerprint/NA12892.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) Test: Test method testFingerprintMetric[4](testdata/picard/fingerprint/NA12892.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: INFO 2024-07-02 11:50:59 CalculateFingerprintMetrics Gradle suite > Gradle test > picard.fingerprint.CalculateFingerprintMetricsTest.testFingerprintMetric[4](testdata/picard/fingerprint/NA12892.fp.vcf) STANDARD_ERROR INFO 2024-07-02 11:50:59 CalculateFingerprintMetrics Test: Test method testFingerprintMetric[4](testdata/picard/fingerprint/NA12892.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: Test: Test method testFingerprintMetric[4](testdata/picard/fingerprint/NA12892.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFingerprintMetric[4](testdata/picard/fingerprint/NA12892.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** ********** Test: Test method testFingerprintMetric[4](testdata/picard/fingerprint/NA12892.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFingerprintMetric[4](testdata/picard/fingerprint/NA12892.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFingerprintMetric[4](testdata/picard/fingerprint/NA12892.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** ********** Test: Test method testFingerprintMetric[4](testdata/picard/fingerprint/NA12892.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFingerprintMetric[4](testdata/picard/fingerprint/NA12892.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** ********** Test: Test method testFingerprintMetric[4](testdata/picard/fingerprint/NA12892.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** CalculateFingerprintMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.fp.vcf -OUTPUT /tmp/testFingerprintMetric11919841445732743500fingerprint_metric -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt ********** CalculateFingerprintMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.fp.vcf -OUTPUT /tmp/testFingerprintMetric11919841445732743500fingerprint_metric -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt Test: Test method testFingerprintMetric[4](testdata/picard/fingerprint/NA12892.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: ********** ********** Test: Test method testFingerprintMetric[4](testdata/picard/fingerprint/NA12892.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: Test: Test method testFingerprintMetric[4](testdata/picard/fingerprint/NA12892.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: Test: Test method testFingerprintMetric[4](testdata/picard/fingerprint/NA12892.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: 11:50:59.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:59.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFingerprintMetric[4](testdata/picard/fingerprint/NA12892.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: 11:50:59.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:59.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFingerprintMetric[4](testdata/picard/fingerprint/NA12892.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: 11:50:59.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:59.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFingerprintMetric[4](testdata/picard/fingerprint/NA12892.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: 11:50:59.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:59.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFingerprintMetric[4](testdata/picard/fingerprint/NA12892.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] CalculateFingerprintMetrics INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.fp.vcf] OUTPUT=/tmp/testFingerprintMetric11919841445732743500fingerprint_metric HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt CALCULATE_BY=READGROUP GENOTYPE_LOD_THRESHOLD=3.0 NUMBER_OF_SAMPLING=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:59 GMT+14:00 2024] CalculateFingerprintMetrics INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.fp.vcf] OUTPUT=/tmp/testFingerprintMetric11919841445732743500fingerprint_metric HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt CALCULATE_BY=READGROUP GENOTYPE_LOD_THRESHOLD=3.0 NUMBER_OF_SAMPLING=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFingerprintMetric[4](testdata/picard/fingerprint/NA12892.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFingerprintMetric[4](testdata/picard/fingerprint/NA12892.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: WARNING 2024-07-02 11:50:59 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.fp.vcf going to read through it all. WARNING 2024-07-02 11:50:59 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.fp.vcf going to read through it all. Test: Test method testFingerprintMetric[4](testdata/picard/fingerprint/NA12892.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: INFO 2024-07-02 11:50:59 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:50:59 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testFingerprintMetric[4](testdata/picard/fingerprint/NA12892.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] picard.fingerprint.CalculateFingerprintMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:59 GMT+14:00 2024] picard.fingerprint.CalculateFingerprintMetrics done. Elapsed time: 0.00 minutes. Test: Test method testFingerprintMetric[4](testdata/picard/fingerprint/NA12892.fp.vcf)(picard.fingerprint.CalculateFingerprintMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testGetSingletonSample[0]([VC null @ 1:1 Q. of type=SNP alleles=[A*, C, G] attr={} GT=[[het A*/C]] filters=, het)(picard.vcf.CallingMetricAccumulatorTest) Running Test: Test method testGetSingletonSample[1]([VC null @ 1:1 Q. of type=SNP alleles=[A*, C, G] attr={} GT=[[het A*/C],[homref A*]] filters=, het)(picard.vcf.CallingMetricAccumulatorTest) Running Test: Test method testGetSingletonSample[2]([VC null @ 1:1 Q. of type=SNP alleles=[A*, C, G] attr={} GT=[[het A*/C],[homref A*],[homvar C]] filters=, null)(picard.vcf.CallingMetricAccumulatorTest) Running Test: Test method testGetSingletonSample[3]([VC null @ 1:1 Q. of type=SNP alleles=[A*, C, G] attr={} GT=[[het A*/C],[het2 A*/G],[homref A*]] filters=, null)(picard.vcf.CallingMetricAccumulatorTest) Running Test: Test method testGetSingletonSample[4]([VC null @ 1:1 Q. of type=SNP alleles=[A*, C, G] attr={} GT=[[homvar C]] filters=, null)(picard.vcf.CallingMetricAccumulatorTest) Running Test: Test method testGetSingletonSample[5]([VC null @ 1:1 Q. of type=SNP alleles=[A*, C, G] attr={} GT=[[homref A*],[homvar C]] filters=, null)(picard.vcf.CallingMetricAccumulatorTest) Running Test: Test method testGetSingletonSample[6]([VC null @ 1:1 Q. of type=SNP alleles=[A*, C, G] attr={} GT=[[homref A*],[homref2 A*]] filters=, null)(picard.vcf.CallingMetricAccumulatorTest) Running Test: Test method testEmptyTile(picard.illumina.parser.readers.CbclReaderTest) Test: Test method testEmptyTile(picard.illumina.parser.readers.CbclReaderTest) produced standard out/err: INFO 2024-07-02 11:50:59 CbclReader Processing tile 1101 Gradle suite > Gradle test > picard.illumina.parser.readers.CbclReaderTest.testEmptyTile STANDARD_ERROR INFO 2024-07-02 11:50:59 CbclReader Processing tile 1101 Test: Test method testEmptyTile(picard.illumina.parser.readers.CbclReaderTest) produced standard out/err: WARNING 2024-07-02 11:50:59 CbclReader Ignoring tile 1101 there are no PF reads. WARNING 2024-07-02 11:50:59 CbclReader Ignoring tile 1101 there are no PF reads. Running Test: Test method testMissingTile(picard.illumina.parser.readers.CbclReaderTest) Running Test: Test method testReadValidFile(picard.illumina.parser.readers.CbclReaderTest) Test: Test method testReadValidFile(picard.illumina.parser.readers.CbclReaderTest) produced standard out/err: INFO 2024-07-02 11:50:59 CbclReader Processing tile 1101 Gradle suite > Gradle test > picard.illumina.parser.readers.CbclReaderTest.testReadValidFile STANDARD_ERROR INFO 2024-07-02 11:50:59 CbclReader Processing tile 1101 Running Test: Test method testCheckDuplicateMarking[0](pass_queryname.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) Test: Test method testCheckDuplicateMarking[0](pass_queryname.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: INFO 2024-07-02 11:50:59 CheckDuplicateMarking Gradle suite > Gradle test > picard.sam.markduplicates.CheckDuplicateMarkingTest.testCheckDuplicateMarking[0](pass_queryname.sam, 0) STANDARD_ERROR INFO 2024-07-02 11:50:59 CheckDuplicateMarking Test: Test method testCheckDuplicateMarking[0](pass_queryname.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[0](pass_queryname.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckDuplicateMarking[0](pass_queryname.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[0](pass_queryname.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckDuplicateMarking[0](pass_queryname.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckDuplicateMarking[0](pass_queryname.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[0](pass_queryname.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckDuplicateMarking[0](pass_queryname.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[0](pass_queryname.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** CheckDuplicateMarking -I testdata/picard/sam/CheckDuplicateMarking/pass_queryname.sam ********** CheckDuplicateMarking -I testdata/picard/sam/CheckDuplicateMarking/pass_queryname.sam Test: Test method testCheckDuplicateMarking[0](pass_queryname.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[0](pass_queryname.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[0](pass_queryname.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[0](pass_queryname.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.689 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:59.689 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckDuplicateMarking[0](pass_queryname.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.689 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:59.689 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckDuplicateMarking[0](pass_queryname.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.690 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:59.690 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckDuplicateMarking[0](pass_queryname.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.690 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:59.690 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckDuplicateMarking[0](pass_queryname.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] CheckDuplicateMarking INPUT=testdata/picard/sam/CheckDuplicateMarking/pass_queryname.sam MODE=ALL VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:59 GMT+14:00 2024] CheckDuplicateMarking INPUT=testdata/picard/sam/CheckDuplicateMarking/pass_queryname.sam MODE=ALL VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckDuplicateMarking[0](pass_queryname.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckDuplicateMarking[0](pass_queryname.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: INFO 2024-07-02 11:50:59 CheckDuplicateMarking All records' duplicate markings agree. INFO 2024-07-02 11:50:59 CheckDuplicateMarking All records' duplicate markings agree. Test: Test method testCheckDuplicateMarking[0](pass_queryname.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:59 GMT+14:00 2024] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes. Test: Test method testCheckDuplicateMarking[0](pass_queryname.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testCheckDuplicateMarking[1](pass_coordinate.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) Test: Test method testCheckDuplicateMarking[1](pass_coordinate.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: INFO 2024-07-02 11:50:59 CheckDuplicateMarking Gradle suite > Gradle test > picard.sam.markduplicates.CheckDuplicateMarkingTest.testCheckDuplicateMarking[1](pass_coordinate.sam, 0) STANDARD_ERROR INFO 2024-07-02 11:50:59 CheckDuplicateMarking Test: Test method testCheckDuplicateMarking[1](pass_coordinate.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[1](pass_coordinate.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckDuplicateMarking[1](pass_coordinate.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[1](pass_coordinate.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckDuplicateMarking[1](pass_coordinate.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckDuplicateMarking[1](pass_coordinate.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[1](pass_coordinate.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckDuplicateMarking[1](pass_coordinate.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[1](pass_coordinate.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** CheckDuplicateMarking -I testdata/picard/sam/CheckDuplicateMarking/pass_coordinate.sam ********** CheckDuplicateMarking -I testdata/picard/sam/CheckDuplicateMarking/pass_coordinate.sam Test: Test method testCheckDuplicateMarking[1](pass_coordinate.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[1](pass_coordinate.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[1](pass_coordinate.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[1](pass_coordinate.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.700 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:59.700 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckDuplicateMarking[1](pass_coordinate.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.700 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:59.700 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckDuplicateMarking[1](pass_coordinate.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.700 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:59.700 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckDuplicateMarking[1](pass_coordinate.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.700 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:59.700 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckDuplicateMarking[1](pass_coordinate.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] CheckDuplicateMarking INPUT=testdata/picard/sam/CheckDuplicateMarking/pass_coordinate.sam MODE=ALL VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:59 GMT+14:00 2024] CheckDuplicateMarking INPUT=testdata/picard/sam/CheckDuplicateMarking/pass_coordinate.sam MODE=ALL VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckDuplicateMarking[1](pass_coordinate.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckDuplicateMarking[1](pass_coordinate.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: INFO 2024-07-02 11:50:59 CheckDuplicateMarking Input file isn't queryname sorted. Sorting into temp space. INFO 2024-07-02 11:50:59 CheckDuplicateMarking Input file isn't queryname sorted. Sorting into temp space. Test: Test method testCheckDuplicateMarking[1](pass_coordinate.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: INFO 2024-07-02 11:50:59 CheckDuplicateMarking All records' duplicate markings agree. INFO 2024-07-02 11:50:59 CheckDuplicateMarking All records' duplicate markings agree. Test: Test method testCheckDuplicateMarking[1](pass_coordinate.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:59 GMT+14:00 2024] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes. Test: Test method testCheckDuplicateMarking[1](pass_coordinate.sam, 0)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testCheckDuplicateMarking[2](fail_mate_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) Test: Test method testCheckDuplicateMarking[2](fail_mate_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: INFO 2024-07-02 11:50:59 CheckDuplicateMarking Gradle suite > Gradle test > picard.sam.markduplicates.CheckDuplicateMarkingTest.testCheckDuplicateMarking[2](fail_mate_queryname.sam, 1) STANDARD_ERROR INFO 2024-07-02 11:50:59 CheckDuplicateMarking Test: Test method testCheckDuplicateMarking[2](fail_mate_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[2](fail_mate_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckDuplicateMarking[2](fail_mate_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[2](fail_mate_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckDuplicateMarking[2](fail_mate_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckDuplicateMarking[2](fail_mate_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[2](fail_mate_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckDuplicateMarking[2](fail_mate_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[2](fail_mate_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** CheckDuplicateMarking -I testdata/picard/sam/CheckDuplicateMarking/fail_mate_queryname.sam ********** CheckDuplicateMarking -I testdata/picard/sam/CheckDuplicateMarking/fail_mate_queryname.sam Test: Test method testCheckDuplicateMarking[2](fail_mate_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[2](fail_mate_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[2](fail_mate_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[2](fail_mate_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.713 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:59.713 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckDuplicateMarking[2](fail_mate_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.713 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:59.713 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckDuplicateMarking[2](fail_mate_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.714 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:59.714 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckDuplicateMarking[2](fail_mate_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.714 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:59.714 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckDuplicateMarking[2](fail_mate_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] CheckDuplicateMarking INPUT=testdata/picard/sam/CheckDuplicateMarking/fail_mate_queryname.sam MODE=ALL VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:59 GMT+14:00 2024] CheckDuplicateMarking INPUT=testdata/picard/sam/CheckDuplicateMarking/fail_mate_queryname.sam MODE=ALL VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckDuplicateMarking[2](fail_mate_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckDuplicateMarking[2](fail_mate_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: WARNING 2024-07-02 11:50:59 CheckDuplicateMarking Reads with queryname read_28833_29006_6945 have different duplicate flags (at chr20:28993) WARNING 2024-07-02 11:50:59 CheckDuplicateMarking Reads with queryname read_28833_29006_6945 have different duplicate flags (at chr20:28993) Test: Test method testCheckDuplicateMarking[2](fail_mate_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ERROR 2024-07-02 11:50:59 CheckDuplicateMarking Found 1 records that do not agree on their duplicate flag. ERROR 2024-07-02 11:50:59 CheckDuplicateMarking Found 1 records that do not agree on their duplicate flag. Test: Test method testCheckDuplicateMarking[2](fail_mate_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:59 GMT+14:00 2024] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes. Test: Test method testCheckDuplicateMarking[2](fail_mate_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testCheckDuplicateMarking[2](fail_mate_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckDuplicateMarking[3](fail_mate_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) Test: Test method testCheckDuplicateMarking[3](fail_mate_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: INFO 2024-07-02 11:50:59 CheckDuplicateMarking Gradle suite > Gradle test > picard.sam.markduplicates.CheckDuplicateMarkingTest.testCheckDuplicateMarking[3](fail_mate_coordinate.sam, 1) STANDARD_ERROR INFO 2024-07-02 11:50:59 CheckDuplicateMarking Test: Test method testCheckDuplicateMarking[3](fail_mate_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[3](fail_mate_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckDuplicateMarking[3](fail_mate_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[3](fail_mate_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckDuplicateMarking[3](fail_mate_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckDuplicateMarking[3](fail_mate_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[3](fail_mate_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckDuplicateMarking[3](fail_mate_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[3](fail_mate_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** CheckDuplicateMarking -I testdata/picard/sam/CheckDuplicateMarking/fail_mate_coordinate.sam ********** CheckDuplicateMarking -I testdata/picard/sam/CheckDuplicateMarking/fail_mate_coordinate.sam Test: Test method testCheckDuplicateMarking[3](fail_mate_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[3](fail_mate_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[3](fail_mate_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[3](fail_mate_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.728 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:59.728 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckDuplicateMarking[3](fail_mate_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.733 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:59.733 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckDuplicateMarking[3](fail_mate_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.733 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:59.733 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckDuplicateMarking[3](fail_mate_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.733 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:59.733 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckDuplicateMarking[3](fail_mate_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] CheckDuplicateMarking INPUT=testdata/picard/sam/CheckDuplicateMarking/fail_mate_coordinate.sam MODE=ALL VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:59 GMT+14:00 2024] CheckDuplicateMarking INPUT=testdata/picard/sam/CheckDuplicateMarking/fail_mate_coordinate.sam MODE=ALL VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckDuplicateMarking[3](fail_mate_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckDuplicateMarking[3](fail_mate_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: INFO 2024-07-02 11:50:59 CheckDuplicateMarking Input file isn't queryname sorted. Sorting into temp space. INFO 2024-07-02 11:50:59 CheckDuplicateMarking Input file isn't queryname sorted. Sorting into temp space. Test: Test method testCheckDuplicateMarking[3](fail_mate_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: WARNING 2024-07-02 11:50:59 CheckDuplicateMarking Reads with queryname read_28833_29006_6945 have different duplicate flags (at chr20:28993) WARNING 2024-07-02 11:50:59 CheckDuplicateMarking Reads with queryname read_28833_29006_6945 have different duplicate flags (at chr20:28993) Test: Test method testCheckDuplicateMarking[3](fail_mate_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ERROR 2024-07-02 11:50:59 CheckDuplicateMarking Found 1 records that do not agree on their duplicate flag. ERROR 2024-07-02 11:50:59 CheckDuplicateMarking Found 1 records that do not agree on their duplicate flag. Test: Test method testCheckDuplicateMarking[3](fail_mate_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:59 GMT+14:00 2024] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes. Test: Test method testCheckDuplicateMarking[3](fail_mate_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testCheckDuplicateMarking[3](fail_mate_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckDuplicateMarking[4](fail_supplementary_queryname_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) Test: Test method testCheckDuplicateMarking[4](fail_supplementary_queryname_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: INFO 2024-07-02 11:50:59 CheckDuplicateMarking Gradle suite > Gradle test > picard.sam.markduplicates.CheckDuplicateMarkingTest.testCheckDuplicateMarking[4](fail_supplementary_queryname_1.sam, 1) STANDARD_ERROR INFO 2024-07-02 11:50:59 CheckDuplicateMarking Test: Test method testCheckDuplicateMarking[4](fail_supplementary_queryname_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[4](fail_supplementary_queryname_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckDuplicateMarking[4](fail_supplementary_queryname_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[4](fail_supplementary_queryname_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckDuplicateMarking[4](fail_supplementary_queryname_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckDuplicateMarking[4](fail_supplementary_queryname_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[4](fail_supplementary_queryname_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckDuplicateMarking[4](fail_supplementary_queryname_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[4](fail_supplementary_queryname_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** CheckDuplicateMarking -I testdata/picard/sam/CheckDuplicateMarking/fail_supplementary_queryname_1.sam ********** CheckDuplicateMarking -I testdata/picard/sam/CheckDuplicateMarking/fail_supplementary_queryname_1.sam Test: Test method testCheckDuplicateMarking[4](fail_supplementary_queryname_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[4](fail_supplementary_queryname_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[4](fail_supplementary_queryname_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[4](fail_supplementary_queryname_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.746 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:59.746 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckDuplicateMarking[4](fail_supplementary_queryname_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.746 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:59.746 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckDuplicateMarking[4](fail_supplementary_queryname_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.746 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:59.746 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckDuplicateMarking[4](fail_supplementary_queryname_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.746 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:59.746 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckDuplicateMarking[4](fail_supplementary_queryname_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] CheckDuplicateMarking INPUT=testdata/picard/sam/CheckDuplicateMarking/fail_supplementary_queryname_1.sam MODE=ALL VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:59 GMT+14:00 2024] CheckDuplicateMarking INPUT=testdata/picard/sam/CheckDuplicateMarking/fail_supplementary_queryname_1.sam MODE=ALL VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckDuplicateMarking[4](fail_supplementary_queryname_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckDuplicateMarking[4](fail_supplementary_queryname_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: WARNING 2024-07-02 11:50:59 CheckDuplicateMarking Reads with queryname read_28833_29006_6945 have different duplicate flags (at chr20:18935) WARNING 2024-07-02 11:50:59 CheckDuplicateMarking Reads with queryname read_28833_29006_6945 have different duplicate flags (at chr20:18935) Test: Test method testCheckDuplicateMarking[4](fail_supplementary_queryname_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ERROR 2024-07-02 11:50:59 CheckDuplicateMarking Found 1 records that do not agree on their duplicate flag. ERROR 2024-07-02 11:50:59 CheckDuplicateMarking Found 1 records that do not agree on their duplicate flag. Test: Test method testCheckDuplicateMarking[4](fail_supplementary_queryname_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:59 GMT+14:00 2024] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes. Test: Test method testCheckDuplicateMarking[4](fail_supplementary_queryname_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testCheckDuplicateMarking[4](fail_supplementary_queryname_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckDuplicateMarking[5](fail_supplementary_coordinate_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) Test: Test method testCheckDuplicateMarking[5](fail_supplementary_coordinate_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: INFO 2024-07-02 11:50:59 CheckDuplicateMarking Gradle suite > Gradle test > picard.sam.markduplicates.CheckDuplicateMarkingTest.testCheckDuplicateMarking[5](fail_supplementary_coordinate_1.sam, 1) STANDARD_ERROR INFO 2024-07-02 11:50:59 CheckDuplicateMarking Test: Test method testCheckDuplicateMarking[5](fail_supplementary_coordinate_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[5](fail_supplementary_coordinate_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckDuplicateMarking[5](fail_supplementary_coordinate_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[5](fail_supplementary_coordinate_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckDuplicateMarking[5](fail_supplementary_coordinate_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckDuplicateMarking[5](fail_supplementary_coordinate_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[5](fail_supplementary_coordinate_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckDuplicateMarking[5](fail_supplementary_coordinate_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[5](fail_supplementary_coordinate_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** CheckDuplicateMarking -I testdata/picard/sam/CheckDuplicateMarking/fail_supplementary_coordinate_1.sam ********** CheckDuplicateMarking -I testdata/picard/sam/CheckDuplicateMarking/fail_supplementary_coordinate_1.sam Test: Test method testCheckDuplicateMarking[5](fail_supplementary_coordinate_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[5](fail_supplementary_coordinate_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[5](fail_supplementary_coordinate_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[5](fail_supplementary_coordinate_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.750 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:59.750 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckDuplicateMarking[5](fail_supplementary_coordinate_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.750 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:59.750 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckDuplicateMarking[5](fail_supplementary_coordinate_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.750 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:59.750 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckDuplicateMarking[5](fail_supplementary_coordinate_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.750 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:59.750 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckDuplicateMarking[5](fail_supplementary_coordinate_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] CheckDuplicateMarking INPUT=testdata/picard/sam/CheckDuplicateMarking/fail_supplementary_coordinate_1.sam MODE=ALL VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:59 GMT+14:00 2024] CheckDuplicateMarking INPUT=testdata/picard/sam/CheckDuplicateMarking/fail_supplementary_coordinate_1.sam MODE=ALL VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckDuplicateMarking[5](fail_supplementary_coordinate_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckDuplicateMarking[5](fail_supplementary_coordinate_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: INFO 2024-07-02 11:50:59 CheckDuplicateMarking Input file isn't queryname sorted. Sorting into temp space. INFO 2024-07-02 11:50:59 CheckDuplicateMarking Input file isn't queryname sorted. Sorting into temp space. Test: Test method testCheckDuplicateMarking[5](fail_supplementary_coordinate_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: WARNING 2024-07-02 11:50:59 CheckDuplicateMarking Reads with queryname read_28833_29006_6945 have different duplicate flags (at chr20:18935) WARNING 2024-07-02 11:50:59 CheckDuplicateMarking Reads with queryname read_28833_29006_6945 have different duplicate flags (at chr20:18935) Test: Test method testCheckDuplicateMarking[5](fail_supplementary_coordinate_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ERROR 2024-07-02 11:50:59 CheckDuplicateMarking Found 1 records that do not agree on their duplicate flag. ERROR 2024-07-02 11:50:59 CheckDuplicateMarking Found 1 records that do not agree on their duplicate flag. Test: Test method testCheckDuplicateMarking[5](fail_supplementary_coordinate_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:59 GMT+14:00 2024] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes. Test: Test method testCheckDuplicateMarking[5](fail_supplementary_coordinate_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testCheckDuplicateMarking[5](fail_supplementary_coordinate_1.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckDuplicateMarking[6](fail_supplementary_queryname_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) Test: Test method testCheckDuplicateMarking[6](fail_supplementary_queryname_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: INFO 2024-07-02 11:50:59 CheckDuplicateMarking Gradle suite > Gradle test > picard.sam.markduplicates.CheckDuplicateMarkingTest.testCheckDuplicateMarking[6](fail_supplementary_queryname_2.sam, 1) STANDARD_ERROR INFO 2024-07-02 11:50:59 CheckDuplicateMarking Test: Test method testCheckDuplicateMarking[6](fail_supplementary_queryname_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[6](fail_supplementary_queryname_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckDuplicateMarking[6](fail_supplementary_queryname_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[6](fail_supplementary_queryname_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckDuplicateMarking[6](fail_supplementary_queryname_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckDuplicateMarking[6](fail_supplementary_queryname_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[6](fail_supplementary_queryname_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckDuplicateMarking[6](fail_supplementary_queryname_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[6](fail_supplementary_queryname_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** CheckDuplicateMarking -I testdata/picard/sam/CheckDuplicateMarking/fail_supplementary_queryname_2.sam ********** CheckDuplicateMarking -I testdata/picard/sam/CheckDuplicateMarking/fail_supplementary_queryname_2.sam Test: Test method testCheckDuplicateMarking[6](fail_supplementary_queryname_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[6](fail_supplementary_queryname_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[6](fail_supplementary_queryname_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[6](fail_supplementary_queryname_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.763 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:59.763 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckDuplicateMarking[6](fail_supplementary_queryname_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.764 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:59.764 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckDuplicateMarking[6](fail_supplementary_queryname_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.764 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:59.764 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckDuplicateMarking[6](fail_supplementary_queryname_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.764 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:59.764 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckDuplicateMarking[6](fail_supplementary_queryname_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] CheckDuplicateMarking INPUT=testdata/picard/sam/CheckDuplicateMarking/fail_supplementary_queryname_2.sam MODE=ALL VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:59 GMT+14:00 2024] CheckDuplicateMarking INPUT=testdata/picard/sam/CheckDuplicateMarking/fail_supplementary_queryname_2.sam MODE=ALL VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckDuplicateMarking[6](fail_supplementary_queryname_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckDuplicateMarking[6](fail_supplementary_queryname_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: WARNING 2024-07-02 11:50:59 CheckDuplicateMarking Reads with queryname read_28701_28881_323b have different duplicate flags (at chr20:19211) WARNING 2024-07-02 11:50:59 CheckDuplicateMarking Reads with queryname read_28701_28881_323b have different duplicate flags (at chr20:19211) Test: Test method testCheckDuplicateMarking[6](fail_supplementary_queryname_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ERROR 2024-07-02 11:50:59 CheckDuplicateMarking Found 1 records that do not agree on their duplicate flag. ERROR 2024-07-02 11:50:59 CheckDuplicateMarking Found 1 records that do not agree on their duplicate flag. Test: Test method testCheckDuplicateMarking[6](fail_supplementary_queryname_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:59 GMT+14:00 2024] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes. Test: Test method testCheckDuplicateMarking[6](fail_supplementary_queryname_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testCheckDuplicateMarking[6](fail_supplementary_queryname_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckDuplicateMarking[7](fail_supplementary_coordinate_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) Test: Test method testCheckDuplicateMarking[7](fail_supplementary_coordinate_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: INFO 2024-07-02 11:50:59 CheckDuplicateMarking Gradle suite > Gradle test > picard.sam.markduplicates.CheckDuplicateMarkingTest.testCheckDuplicateMarking[7](fail_supplementary_coordinate_2.sam, 1) STANDARD_ERROR INFO 2024-07-02 11:50:59 CheckDuplicateMarking Test: Test method testCheckDuplicateMarking[7](fail_supplementary_coordinate_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[7](fail_supplementary_coordinate_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckDuplicateMarking[7](fail_supplementary_coordinate_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[7](fail_supplementary_coordinate_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckDuplicateMarking[7](fail_supplementary_coordinate_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckDuplicateMarking[7](fail_supplementary_coordinate_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[7](fail_supplementary_coordinate_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckDuplicateMarking[7](fail_supplementary_coordinate_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[7](fail_supplementary_coordinate_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** CheckDuplicateMarking -I testdata/picard/sam/CheckDuplicateMarking/fail_supplementary_coordinate_2.sam ********** CheckDuplicateMarking -I testdata/picard/sam/CheckDuplicateMarking/fail_supplementary_coordinate_2.sam Test: Test method testCheckDuplicateMarking[7](fail_supplementary_coordinate_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[7](fail_supplementary_coordinate_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[7](fail_supplementary_coordinate_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[7](fail_supplementary_coordinate_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.779 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:59.779 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckDuplicateMarking[7](fail_supplementary_coordinate_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.779 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:59.779 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckDuplicateMarking[7](fail_supplementary_coordinate_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.780 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:59.780 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckDuplicateMarking[7](fail_supplementary_coordinate_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.780 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:59.780 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckDuplicateMarking[7](fail_supplementary_coordinate_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] CheckDuplicateMarking INPUT=testdata/picard/sam/CheckDuplicateMarking/fail_supplementary_coordinate_2.sam MODE=ALL VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:59 GMT+14:00 2024] CheckDuplicateMarking INPUT=testdata/picard/sam/CheckDuplicateMarking/fail_supplementary_coordinate_2.sam MODE=ALL VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckDuplicateMarking[7](fail_supplementary_coordinate_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckDuplicateMarking[7](fail_supplementary_coordinate_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: INFO 2024-07-02 11:50:59 CheckDuplicateMarking Input file isn't queryname sorted. Sorting into temp space. INFO 2024-07-02 11:50:59 CheckDuplicateMarking Input file isn't queryname sorted. Sorting into temp space. Test: Test method testCheckDuplicateMarking[7](fail_supplementary_coordinate_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: WARNING 2024-07-02 11:50:59 CheckDuplicateMarking Reads with queryname read_28701_28881_323b have different duplicate flags (at chr20:19211) WARNING 2024-07-02 11:50:59 CheckDuplicateMarking Reads with queryname read_28701_28881_323b have different duplicate flags (at chr20:19211) Test: Test method testCheckDuplicateMarking[7](fail_supplementary_coordinate_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ERROR 2024-07-02 11:50:59 CheckDuplicateMarking Found 1 records that do not agree on their duplicate flag. ERROR 2024-07-02 11:50:59 CheckDuplicateMarking Found 1 records that do not agree on their duplicate flag. Test: Test method testCheckDuplicateMarking[7](fail_supplementary_coordinate_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:59 GMT+14:00 2024] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes. Test: Test method testCheckDuplicateMarking[7](fail_supplementary_coordinate_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testCheckDuplicateMarking[7](fail_supplementary_coordinate_2.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckDuplicateMarking[8](fail_secondary_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) Test: Test method testCheckDuplicateMarking[8](fail_secondary_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: INFO 2024-07-02 11:50:59 CheckDuplicateMarking Gradle suite > Gradle test > picard.sam.markduplicates.CheckDuplicateMarkingTest.testCheckDuplicateMarking[8](fail_secondary_queryname.sam, 1) STANDARD_ERROR INFO 2024-07-02 11:50:59 CheckDuplicateMarking Test: Test method testCheckDuplicateMarking[8](fail_secondary_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[8](fail_secondary_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckDuplicateMarking[8](fail_secondary_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[8](fail_secondary_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckDuplicateMarking[8](fail_secondary_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckDuplicateMarking[8](fail_secondary_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[8](fail_secondary_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckDuplicateMarking[8](fail_secondary_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[8](fail_secondary_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** CheckDuplicateMarking -I testdata/picard/sam/CheckDuplicateMarking/fail_secondary_queryname.sam ********** CheckDuplicateMarking -I testdata/picard/sam/CheckDuplicateMarking/fail_secondary_queryname.sam Test: Test method testCheckDuplicateMarking[8](fail_secondary_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[8](fail_secondary_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[8](fail_secondary_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[8](fail_secondary_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.784 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:59.784 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckDuplicateMarking[8](fail_secondary_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.789 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:59.789 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckDuplicateMarking[8](fail_secondary_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.789 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:59.789 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckDuplicateMarking[8](fail_secondary_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.789 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:59.789 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckDuplicateMarking[8](fail_secondary_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] CheckDuplicateMarking INPUT=testdata/picard/sam/CheckDuplicateMarking/fail_secondary_queryname.sam MODE=ALL VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:59 GMT+14:00 2024] CheckDuplicateMarking INPUT=testdata/picard/sam/CheckDuplicateMarking/fail_secondary_queryname.sam MODE=ALL VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckDuplicateMarking[8](fail_secondary_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckDuplicateMarking[8](fail_secondary_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: WARNING 2024-07-02 11:50:59 CheckDuplicateMarking Reads with queryname read_28701_28881_323b have different duplicate flags (at chr20:19334) WARNING 2024-07-02 11:50:59 CheckDuplicateMarking Reads with queryname read_28701_28881_323b have different duplicate flags (at chr20:19334) Test: Test method testCheckDuplicateMarking[8](fail_secondary_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ERROR 2024-07-02 11:50:59 CheckDuplicateMarking Found 1 records that do not agree on their duplicate flag. ERROR 2024-07-02 11:50:59 CheckDuplicateMarking Found 1 records that do not agree on their duplicate flag. Test: Test method testCheckDuplicateMarking[8](fail_secondary_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:59 GMT+14:00 2024] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes. Test: Test method testCheckDuplicateMarking[8](fail_secondary_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testCheckDuplicateMarking[8](fail_secondary_queryname.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckDuplicateMarking[9](fail_secondary_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) Test: Test method testCheckDuplicateMarking[9](fail_secondary_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: INFO 2024-07-02 11:50:59 CheckDuplicateMarking Gradle suite > Gradle test > picard.sam.markduplicates.CheckDuplicateMarkingTest.testCheckDuplicateMarking[9](fail_secondary_coordinate.sam, 1) STANDARD_ERROR INFO 2024-07-02 11:50:59 CheckDuplicateMarking Test: Test method testCheckDuplicateMarking[9](fail_secondary_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[9](fail_secondary_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckDuplicateMarking[9](fail_secondary_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[9](fail_secondary_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckDuplicateMarking[9](fail_secondary_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckDuplicateMarking[9](fail_secondary_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[9](fail_secondary_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckDuplicateMarking[9](fail_secondary_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[9](fail_secondary_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** CheckDuplicateMarking -I testdata/picard/sam/CheckDuplicateMarking/fail_secondary_coordinate.sam ********** CheckDuplicateMarking -I testdata/picard/sam/CheckDuplicateMarking/fail_secondary_coordinate.sam Test: Test method testCheckDuplicateMarking[9](fail_secondary_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ********** ********** Test: Test method testCheckDuplicateMarking[9](fail_secondary_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[9](fail_secondary_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Test: Test method testCheckDuplicateMarking[9](fail_secondary_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.798 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:59.798 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckDuplicateMarking[9](fail_secondary_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.798 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:59.798 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckDuplicateMarking[9](fail_secondary_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.799 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:50:59.799 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckDuplicateMarking[9](fail_secondary_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: 11:50:59.799 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:50:59.799 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckDuplicateMarking[9](fail_secondary_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] CheckDuplicateMarking INPUT=testdata/picard/sam/CheckDuplicateMarking/fail_secondary_coordinate.sam MODE=ALL VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:50:59 GMT+14:00 2024] CheckDuplicateMarking INPUT=testdata/picard/sam/CheckDuplicateMarking/fail_secondary_coordinate.sam MODE=ALL VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckDuplicateMarking[9](fail_secondary_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:50:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckDuplicateMarking[9](fail_secondary_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: INFO 2024-07-02 11:50:59 CheckDuplicateMarking Input file isn't queryname sorted. Sorting into temp space. INFO 2024-07-02 11:50:59 CheckDuplicateMarking Input file isn't queryname sorted. Sorting into temp space. Test: Test method testCheckDuplicateMarking[9](fail_secondary_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: WARNING 2024-07-02 11:50:59 CheckDuplicateMarking Reads with queryname read_28701_28881_323b have different duplicate flags (at chr20:19334) WARNING 2024-07-02 11:50:59 CheckDuplicateMarking Reads with queryname read_28701_28881_323b have different duplicate flags (at chr20:19334) Test: Test method testCheckDuplicateMarking[9](fail_secondary_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: ERROR 2024-07-02 11:50:59 CheckDuplicateMarking Found 1 records that do not agree on their duplicate flag. ERROR 2024-07-02 11:50:59 CheckDuplicateMarking Found 1 records that do not agree on their duplicate flag. Test: Test method testCheckDuplicateMarking[9](fail_secondary_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: [Tue Jul 02 11:50:59 GMT+14:00 2024] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:50:59 GMT+14:00 2024] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes. Test: Test method testCheckDuplicateMarking[9](fail_secondary_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testCheckDuplicateMarking[9](fail_secondary_coordinate.sam, 1)(picard.sam.markduplicates.CheckDuplicateMarkingTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testBadData[0](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/void.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) Test: Test method testBadData[0](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/void.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Gradle suite > Gradle test > picard.fingerprint.CheckFingerprintTest.testBadData[0](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/void.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt) STANDARD_ERROR INFO 2024-07-02 11:51:00 CheckFingerprint Test: Test method testBadData[0](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/void.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testBadData[0](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/void.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadData[0](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/void.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testBadData[0](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/void.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadData[0](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/void.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadData[0](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/void.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testBadData[0](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/void.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadData[0](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/void.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testBadData[0](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/void.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** CheckFingerprint -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/void.vcf -O /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp -G /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt ********** CheckFingerprint -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/void.vcf -O /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp -G /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt Test: Test method testBadData[0](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/void.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testBadData[0](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/void.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testBadData[0](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/void.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testBadData[0](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/void.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.011 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:00.011 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadData[0](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/void.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.011 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:00.011 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadData[0](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/void.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.011 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:00.011 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadData[0](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/void.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.011 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:00.011 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadData[0](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/void.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:00 GMT+14:00 2024] CheckFingerprint INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/void.vcf OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp GENOTYPES=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt GENOTYPE_LOD_THRESHOLD=5.0 IGNORE_READ_GROUPS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:00 GMT+14:00 2024] CheckFingerprint INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/void.vcf OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp GENOTYPES=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt GENOTYPE_LOD_THRESHOLD=5.0 IGNORE_READ_GROUPS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBadData[0](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/void.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBadData[0](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/void.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:00 GMT+14:00 2024] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:00 GMT+14:00 2024] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes. Test: Test method testBadData[0](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/void.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testBadData[0](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/void.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testBadData[1](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) Test: Test method testBadData[1](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Gradle suite > Gradle test > picard.fingerprint.CheckFingerprintTest.testBadData[1](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt) STANDARD_ERROR INFO 2024-07-02 11:51:00 CheckFingerprint Test: Test method testBadData[1](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testBadData[1](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadData[1](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testBadData[1](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadData[1](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadData[1](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testBadData[1](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadData[1](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testBadData[1](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** CheckFingerprint -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf -O /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp -G /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt ********** CheckFingerprint -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf -O /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp -G /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt Test: Test method testBadData[1](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testBadData[1](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testBadData[1](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testBadData[1](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.040 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:00.040 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadData[1](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.040 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:00.040 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadData[1](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.040 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:00.040 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadData[1](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.040 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:00.040 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadData[1](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:00 GMT+14:00 2024] CheckFingerprint INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp GENOTYPES=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt GENOTYPE_LOD_THRESHOLD=5.0 IGNORE_READ_GROUPS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:00 GMT+14:00 2024] CheckFingerprint INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp GENOTYPES=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt GENOTYPE_LOD_THRESHOLD=5.0 IGNORE_READ_GROUPS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBadData[1](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBadData[1](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:00 GMT+14:00 2024] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:00 GMT+14:00 2024] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes. Test: Test method testBadData[1](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testBadData[1](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testBadData[2](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) Test: Test method testBadData[2](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Gradle suite > Gradle test > picard.fingerprint.CheckFingerprintTest.testBadData[2](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt) STANDARD_ERROR INFO 2024-07-02 11:51:00 CheckFingerprint Test: Test method testBadData[2](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testBadData[2](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadData[2](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testBadData[2](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadData[2](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadData[2](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testBadData[2](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadData[2](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testBadData[2](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** CheckFingerprint -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf -O /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp -G /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt ********** CheckFingerprint -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf -O /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp -G /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt Test: Test method testBadData[2](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testBadData[2](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testBadData[2](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testBadData[2](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.069 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:00.069 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadData[2](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.069 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:00.069 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadData[2](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.069 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:00.069 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadData[2](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.069 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:00.069 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadData[2](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:00 GMT+14:00 2024] CheckFingerprint INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp GENOTYPES=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt GENOTYPE_LOD_THRESHOLD=5.0 IGNORE_READ_GROUPS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:00 GMT+14:00 2024] CheckFingerprint INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp GENOTYPES=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt GENOTYPE_LOD_THRESHOLD=5.0 IGNORE_READ_GROUPS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBadData[2](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBadData[2](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:00 GMT+14:00 2024] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:00 GMT+14:00 2024] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes. Test: Test method testBadData[2](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testBadData[2](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testBadData[3](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) Test: Test method testBadData[3](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Gradle suite > Gradle test > picard.fingerprint.CheckFingerprintTest.testBadData[3](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt) STANDARD_ERROR INFO 2024-07-02 11:51:00 CheckFingerprint Test: Test method testBadData[3](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testBadData[3](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadData[3](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testBadData[3](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadData[3](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadData[3](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testBadData[3](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadData[3](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testBadData[3](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** CheckFingerprint -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf -O /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp -G /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt ********** CheckFingerprint -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf -O /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp -G /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt Test: Test method testBadData[3](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testBadData[3](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testBadData[3](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testBadData[3](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.100 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:00.100 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadData[3](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.100 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:00.100 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadData[3](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.101 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:00.101 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadData[3](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.101 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:00.101 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadData[3](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:00 GMT+14:00 2024] CheckFingerprint INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp GENOTYPES=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt GENOTYPE_LOD_THRESHOLD=5.0 IGNORE_READ_GROUPS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:00 GMT+14:00 2024] CheckFingerprint INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp GENOTYPES=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt GENOTYPE_LOD_THRESHOLD=5.0 IGNORE_READ_GROUPS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBadData[3](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBadData[3](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:00 GMT+14:00 2024] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:00 GMT+14:00 2024] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes. Test: Test method testBadData[3](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testBadData[3](/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.vcf, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/noFile.g.vcf, testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testBaseOutput(picard.fingerprint.CheckFingerprintTest) Test: Test method testBaseOutput(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Gradle suite > Gradle test > picard.fingerprint.CheckFingerprintTest.testBaseOutput STANDARD_ERROR INFO 2024-07-02 11:51:00 CheckFingerprint Test: Test method testBaseOutput(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testBaseOutput(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBaseOutput(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testBaseOutput(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBaseOutput(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBaseOutput(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testBaseOutput(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBaseOutput(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testBaseOutput(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** CheckFingerprint -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf -O /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp -G /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf -H testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt ********** CheckFingerprint -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf -O /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp -G /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf -H testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt Test: Test method testBaseOutput(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testBaseOutput(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testBaseOutput(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testBaseOutput(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.131 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:00.131 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBaseOutput(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.131 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:00.131 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBaseOutput(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.131 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:00.131 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBaseOutput(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.131 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:00.131 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBaseOutput(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:00 GMT+14:00 2024] CheckFingerprint INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp GENOTYPES=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt GENOTYPE_LOD_THRESHOLD=5.0 IGNORE_READ_GROUPS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:00 GMT+14:00 2024] CheckFingerprint INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp GENOTYPES=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt GENOTYPE_LOD_THRESHOLD=5.0 IGNORE_READ_GROUPS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBaseOutput(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBaseOutput(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:00 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf going to read through it all. WARNING 2024-07-02 11:51:00 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf going to read through it all. Test: Test method testBaseOutput(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:00 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf going to read through it all. WARNING 2024-07-02 11:51:00 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf going to read through it all. Test: Test method testBaseOutput(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: null / NA12892 vs. NA12892: LOD = 1.0699858771062327 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: null / NA12892 vs. NA12892: LOD = 1.0699858771062327 Test: Test method testBaseOutput(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:00 GMT+14:00 2024] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:00 GMT+14:00 2024] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes. Test: Test method testBaseOutput(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testCheckFingerprintNoRg[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) Test: Test method testCheckFingerprintNoRg[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Gradle suite > Gradle test > picard.fingerprint.CheckFingerprintTest.testCheckFingerprintNoRg[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0) STANDARD_ERROR INFO 2024-07-02 11:51:00 CheckFingerprint Test: Test method testCheckFingerprintNoRg[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testCheckFingerprintNoRg[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFingerprintNoRg[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintNoRg[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFingerprintNoRg[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFingerprintNoRg[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintNoRg[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFingerprintNoRg[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintNoRg[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** CheckFingerprint -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam -G /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf -IGNORE_RG true -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -SUMMARY_OUTPUT /tmp/fingerprint11650940498152648415summary_metrics -DETAIL_OUTPUT /tmp/fingerprint5285873308050383217detail_metrics ********** CheckFingerprint -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam -G /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf -IGNORE_RG true -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -SUMMARY_OUTPUT /tmp/fingerprint11650940498152648415summary_metrics -DETAIL_OUTPUT /tmp/fingerprint5285873308050383217detail_metrics Test: Test method testCheckFingerprintNoRg[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintNoRg[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testCheckFingerprintNoRg[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testCheckFingerprintNoRg[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.240 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:00.240 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintNoRg[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.240 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:00.240 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintNoRg[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.241 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:00.241 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintNoRg[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.241 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:00.241 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintNoRg[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:00 GMT+14:00 2024] CheckFingerprint INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam SUMMARY_OUTPUT=/tmp/fingerprint11650940498152648415summary_metrics DETAIL_OUTPUT=/tmp/fingerprint5285873308050383217detail_metrics GENOTYPES=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt IGNORE_READ_GROUPS=true GENOTYPE_LOD_THRESHOLD=5.0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:00 GMT+14:00 2024] CheckFingerprint INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam SUMMARY_OUTPUT=/tmp/fingerprint11650940498152648415summary_metrics DETAIL_OUTPUT=/tmp/fingerprint5285873308050383217detail_metrics GENOTYPES=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt IGNORE_READ_GROUPS=true GENOTYPE_LOD_THRESHOLD=5.0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFingerprintNoRg[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFingerprintNoRg[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:00 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf going to read through it all. WARNING 2024-07-02 11:51:00 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf going to read through it all. Test: Test method testCheckFingerprintNoRg[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:00 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam) WARNING 2024-07-02 11:51:00 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam) Test: Test method testCheckFingerprintNoRg[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: null / NA12891 vs. NA12891: LOD = 1.9575410308482257 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: null / NA12891 vs. NA12891: LOD = 1.9575410308482257 Test: Test method testCheckFingerprintNoRg[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:00 GMT+14:00 2024] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:00 GMT+14:00 2024] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes. Test: Test method testCheckFingerprintNoRg[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Gradle suite > Gradle test > picard.fingerprint.CheckFingerprintTest.testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1) STANDARD_ERROR INFO 2024-07-02 11:51:00 CheckFingerprint Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** CheckFingerprint -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -G /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf -IGNORE_RG true -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -SUMMARY_OUTPUT /tmp/fingerprint13145886583975585839summary_metrics -DETAIL_OUTPUT /tmp/fingerprint8037766562354171834detail_metrics ********** CheckFingerprint -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -G /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf -IGNORE_RG true -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -SUMMARY_OUTPUT /tmp/fingerprint13145886583975585839summary_metrics -DETAIL_OUTPUT /tmp/fingerprint8037766562354171834detail_metrics Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.475 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:00.475 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.475 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:00.475 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:00.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:00.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:00 GMT+14:00 2024] CheckFingerprint INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam SUMMARY_OUTPUT=/tmp/fingerprint13145886583975585839summary_metrics DETAIL_OUTPUT=/tmp/fingerprint8037766562354171834detail_metrics GENOTYPES=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt IGNORE_READ_GROUPS=true GENOTYPE_LOD_THRESHOLD=5.0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:00 GMT+14:00 2024] CheckFingerprint INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam SUMMARY_OUTPUT=/tmp/fingerprint13145886583975585839summary_metrics DETAIL_OUTPUT=/tmp/fingerprint8037766562354171834detail_metrics GENOTYPES=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt IGNORE_READ_GROUPS=true GENOTYPE_LOD_THRESHOLD=5.0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:00 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf going to read through it all. WARNING 2024-07-02 11:51:00 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf going to read through it all. Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:00 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf WARNING 2024-07-02 11:51:00 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Cannot find sample NA12892 in provided file. Cannot find sample NA12892 in provided file. Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: java.lang.IllegalArgumentException: Cannot find sample NA12892 in provided file. java.lang.IllegalArgumentException: Cannot find sample NA12892 in provided file. Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:96) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:96) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.tester(CheckFingerprintTest.java:285) at picard.fingerprint.CheckFingerprintTest.tester(CheckFingerprintTest.java:285) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.testCheckFingerprintNoRg(CheckFingerprintTest.java:266) at picard.fingerprint.CheckFingerprintTest.testCheckFingerprintNoRg(CheckFingerprintTest.java:266) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:00 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf WARNING 2024-07-02 11:51:00 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Cannot find sample NA12892 in provided file. Cannot find sample NA12892 in provided file. Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: java.lang.IllegalArgumentException: Cannot find sample NA12892 in provided file. java.lang.IllegalArgumentException: Cannot find sample NA12892 in provided file. Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:96) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:96) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.tester(CheckFingerprintTest.java:285) at picard.fingerprint.CheckFingerprintTest.tester(CheckFingerprintTest.java:285) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.testCheckFingerprintNoRg(CheckFingerprintTest.java:266) at picard.fingerprint.CheckFingerprintTest.testCheckFingerprintNoRg(CheckFingerprintTest.java:266) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:00 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf WARNING 2024-07-02 11:51:00 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Cannot find sample NA12892 in provided file. Cannot find sample NA12892 in provided file. Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: java.lang.IllegalArgumentException: Cannot find sample NA12892 in provided file. java.lang.IllegalArgumentException: Cannot find sample NA12892 in provided file. Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:96) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:96) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.tester(CheckFingerprintTest.java:285) at picard.fingerprint.CheckFingerprintTest.tester(CheckFingerprintTest.java:285) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.testCheckFingerprintNoRg(CheckFingerprintTest.java:266) at picard.fingerprint.CheckFingerprintTest.testCheckFingerprintNoRg(CheckFingerprintTest.java:266) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:00 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf WARNING 2024-07-02 11:51:00 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Cannot find sample NA12892 in provided file. Cannot find sample NA12892 in provided file. Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: java.lang.IllegalArgumentException: Cannot find sample NA12892 in provided file. java.lang.IllegalArgumentException: Cannot find sample NA12892 in provided file. Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:96) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:96) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.tester(CheckFingerprintTest.java:285) at picard.fingerprint.CheckFingerprintTest.tester(CheckFingerprintTest.java:285) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.testCheckFingerprintNoRg(CheckFingerprintTest.java:266) at picard.fingerprint.CheckFingerprintTest.testCheckFingerprintNoRg(CheckFingerprintTest.java:266) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:00 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf WARNING 2024-07-02 11:51:00 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Cannot find sample NA12892 in provided file. Cannot find sample NA12892 in provided file. Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: java.lang.IllegalArgumentException: Cannot find sample NA12892 in provided file. java.lang.IllegalArgumentException: Cannot find sample NA12892 in provided file. Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:96) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:96) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.tester(CheckFingerprintTest.java:285) at picard.fingerprint.CheckFingerprintTest.tester(CheckFingerprintTest.java:285) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.testCheckFingerprintNoRg(CheckFingerprintTest.java:266) at picard.fingerprint.CheckFingerprintTest.testCheckFingerprintNoRg(CheckFingerprintTest.java:266) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:00 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) WARNING 2024-07-02 11:51:00 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: null / NA12892 vs. NA12892: LOD = 0.0 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: null / NA12892 vs. NA12892: LOD = 0.0 Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ERROR 2024-07-02 11:51:00 CheckFingerprint No non-zero results found. This is likely an error. Probable cause: EXPECTED_SAMPLE (if provided) or the sample name from INPUT (if EXPECTED_SAMPLE isn't provided)isn't a sample in GENOTYPES file. ERROR 2024-07-02 11:51:00 CheckFingerprint No non-zero results found. This is likely an error. Probable cause: EXPECTED_SAMPLE (if provided) or the sample name from INPUT (if EXPECTED_SAMPLE isn't provided)isn't a sample in GENOTYPES file. Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:00 GMT+14:00 2024] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:00 GMT+14:00 2024] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes. Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testCheckFingerprintNoRg[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Gradle suite > Gradle test > picard.fingerprint.CheckFingerprintTest.testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0) STANDARD_ERROR INFO 2024-07-02 11:51:00 CheckFingerprint Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** CheckFingerprint -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam -G /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -SUMMARY_OUTPUT /tmp/fingerprint12997328375139855212summary_metrics -DETAIL_OUTPUT /tmp/fingerprint15324624956674349911detail_metrics ********** CheckFingerprint -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam -G /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -SUMMARY_OUTPUT /tmp/fingerprint12997328375139855212summary_metrics -DETAIL_OUTPUT /tmp/fingerprint15324624956674349911detail_metrics Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.715 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:00.715 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.715 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:00.715 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.715 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:00.715 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.715 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:00.715 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:00 GMT+14:00 2024] CheckFingerprint INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam SUMMARY_OUTPUT=/tmp/fingerprint12997328375139855212summary_metrics DETAIL_OUTPUT=/tmp/fingerprint15324624956674349911detail_metrics GENOTYPES=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt GENOTYPE_LOD_THRESHOLD=5.0 IGNORE_READ_GROUPS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:00 GMT+14:00 2024] CheckFingerprint INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam SUMMARY_OUTPUT=/tmp/fingerprint12997328375139855212summary_metrics DETAIL_OUTPUT=/tmp/fingerprint15324624956674349911detail_metrics GENOTYPES=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt GENOTYPE_LOD_THRESHOLD=5.0 IGNORE_READ_GROUPS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:00 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf going to read through it all. WARNING 2024-07-02 11:51:00 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf going to read through it all. Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:00 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam) WARNING 2024-07-02 11:51:00 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam) Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HJYN2CCXX160123.1.TATCCAGG / NA12891 vs. NA12891: LOD = 0.7515877715986727 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HJYN2CCXX160123.1.TATCCAGG / NA12891 vs. NA12891: LOD = 0.7515877715986727 Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK3T5CCXX160204.7.TATCCAGG / NA12891 vs. NA12891: LOD = 0.8813562283192153 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK3T5CCXX160204.7.TATCCAGG / NA12891 vs. NA12891: LOD = 0.8813562283192153 Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK3T5CCXX160204.1.TATCCAGG / NA12891 vs. NA12891: LOD = 0.5790017814227286 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK3T5CCXX160204.1.TATCCAGG / NA12891 vs. NA12891: LOD = 0.5790017814227286 Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK3T5CCXX160204.2.TATCCAGG / NA12891 vs. NA12891: LOD = 0.7368081322746325 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK3T5CCXX160204.2.TATCCAGG / NA12891 vs. NA12891: LOD = 0.7368081322746325 Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK3T5CCXX160204.3.TATCCAGG / NA12891 vs. NA12891: LOD = 0.4286259057547821 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK3T5CCXX160204.3.TATCCAGG / NA12891 vs. NA12891: LOD = 0.4286259057547821 Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK3T5CCXX160204.4.TATCCAGG / NA12891 vs. NA12891: LOD = 1.105755285701254 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK3T5CCXX160204.4.TATCCAGG / NA12891 vs. NA12891: LOD = 1.105755285701254 Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK3T5CCXX160204.5.TATCCAGG / NA12891 vs. NA12891: LOD = 0.21447953267151032 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK3T5CCXX160204.5.TATCCAGG / NA12891 vs. NA12891: LOD = 0.21447953267151032 Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK3T5CCXX160204.6.TATCCAGG / NA12891 vs. NA12891: LOD = 0.8376997076761636 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK3T5CCXX160204.6.TATCCAGG / NA12891 vs. NA12891: LOD = 0.8376997076761636 Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK3T5CCXX160204.8.TATCCAGG / NA12891 vs. NA12891: LOD = 0.9989888195257852 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK3T5CCXX160204.8.TATCCAGG / NA12891 vs. NA12891: LOD = 0.9989888195257852 Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HTL2KCCXX160412.5.TATCCAGG-GAAGTGGA / NA12891 vs. NA12891: LOD = 0.6821768525202883 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HTL2KCCXX160412.5.TATCCAGG-GAAGTGGA / NA12891 vs. NA12891: LOD = 0.6821768525202883 Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HTL2KCCXX160412.6.TATCCAGG-GAAGTGGA / NA12891 vs. NA12891: LOD = 1.5638358662469267 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HTL2KCCXX160412.6.TATCCAGG-GAAGTGGA / NA12891 vs. NA12891: LOD = 1.5638358662469267 Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK35NCCXX160204.1.TATCCAGG / NA12891 vs. NA12891: LOD = 0.6767828904844997 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK35NCCXX160204.1.TATCCAGG / NA12891 vs. NA12891: LOD = 0.6767828904844997 Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK35NCCXX160204.2.TATCCAGG / NA12891 vs. NA12891: LOD = -0.1777885789893492 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK35NCCXX160204.2.TATCCAGG / NA12891 vs. NA12891: LOD = -0.1777885789893492 Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HM3G2CCXX160308.2.TATCCAGG / NA12891 vs. NA12891: LOD = 1.9575145012761315 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HM3G2CCXX160308.2.TATCCAGG / NA12891 vs. NA12891: LOD = 1.9575145012761315 Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK35MCCXX160204.1.TATCCAGG / NA12891 vs. NA12891: LOD = 1.04405813553949 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK35MCCXX160204.1.TATCCAGG / NA12891 vs. NA12891: LOD = 1.04405813553949 Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK35MCCXX160204.2.TATCCAGG / NA12891 vs. NA12891: LOD = 0.5893772852178616 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK35MCCXX160204.2.TATCCAGG / NA12891 vs. NA12891: LOD = 0.5893772852178616 Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK35MCCXX160204.3.TATCCAGG / NA12891 vs. NA12891: LOD = 0.4593438456798795 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK35MCCXX160204.3.TATCCAGG / NA12891 vs. NA12891: LOD = 0.4593438456798795 Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK35MCCXX160204.4.TATCCAGG / NA12891 vs. NA12891: LOD = 1.1930705126333643 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK35MCCXX160204.4.TATCCAGG / NA12891 vs. NA12891: LOD = 1.1930705126333643 Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK35MCCXX160204.5.TATCCAGG / NA12891 vs. NA12891: LOD = 0.642675010900108 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK35MCCXX160204.5.TATCCAGG / NA12891 vs. NA12891: LOD = 0.642675010900108 Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK35MCCXX160204.6.TATCCAGG / NA12891 vs. NA12891: LOD = 0.1844134560992945 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK35MCCXX160204.6.TATCCAGG / NA12891 vs. NA12891: LOD = 0.1844134560992945 Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK35MCCXX160204.7.TATCCAGG / NA12891 vs. NA12891: LOD = 0.2934236641373207 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK35MCCXX160204.7.TATCCAGG / NA12891 vs. NA12891: LOD = 0.2934236641373207 Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK35MCCXX160204.8.TATCCAGG / NA12891 vs. NA12891: LOD = 0.3307277843999552 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HK35MCCXX160204.8.TATCCAGG / NA12891 vs. NA12891: LOD = 0.3307277843999552 Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HJYFJCCXX160204.4.TATCCAGG / NA12891 vs. NA12891: LOD = -0.016667966118423472 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HJYFJCCXX160204.4.TATCCAGG / NA12891 vs. NA12891: LOD = -0.016667966118423472 Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HJYFJCCXX160204.5.TATCCAGG / NA12891 vs. NA12891: LOD = 1.4949377033063986 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HJYFJCCXX160204.5.TATCCAGG / NA12891 vs. NA12891: LOD = 1.4949377033063986 Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HJYFJCCXX160204.6.TATCCAGG / NA12891 vs. NA12891: LOD = -0.09171156502005773 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HJYFJCCXX160204.6.TATCCAGG / NA12891 vs. NA12891: LOD = -0.09171156502005773 Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HJYFJCCXX160204.7.TATCCAGG / NA12891 vs. NA12891: LOD = -0.09768004672552877 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HJYFJCCXX160204.7.TATCCAGG / NA12891 vs. NA12891: LOD = -0.09768004672552877 Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HJYFJCCXX160204.8.TATCCAGG / NA12891 vs. NA12891: LOD = 0.7893729828153071 INFO 2024-07-02 11:51:00 CheckFingerprint Read Group: HJYFJCCXX160204.8.TATCCAGG / NA12891 vs. NA12891: LOD = 0.7893729828153071 Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:00 GMT+14:00 2024] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:00 GMT+14:00 2024] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes. Test: Test method testCheckFingerprintSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:00 CheckFingerprint Gradle suite > Gradle test > picard.fingerprint.CheckFingerprintTest.testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1) STANDARD_ERROR INFO 2024-07-02 11:51:00 CheckFingerprint Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** CheckFingerprint -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -G /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -SUMMARY_OUTPUT /tmp/fingerprint14790772453419949336summary_metrics -DETAIL_OUTPUT /tmp/fingerprint1183302273855567645detail_metrics ********** CheckFingerprint -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -G /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -SUMMARY_OUTPUT /tmp/fingerprint14790772453419949336summary_metrics -DETAIL_OUTPUT /tmp/fingerprint1183302273855567645detail_metrics Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.874 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:00.874 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.874 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:00.874 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.874 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:00.874 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:00.874 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:00.874 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:00 GMT+14:00 2024] CheckFingerprint INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam SUMMARY_OUTPUT=/tmp/fingerprint14790772453419949336summary_metrics DETAIL_OUTPUT=/tmp/fingerprint1183302273855567645detail_metrics GENOTYPES=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt GENOTYPE_LOD_THRESHOLD=5.0 IGNORE_READ_GROUPS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:00 GMT+14:00 2024] CheckFingerprint INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam SUMMARY_OUTPUT=/tmp/fingerprint14790772453419949336summary_metrics DETAIL_OUTPUT=/tmp/fingerprint1183302273855567645detail_metrics GENOTYPES=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt GENOTYPE_LOD_THRESHOLD=5.0 IGNORE_READ_GROUPS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:00 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf going to read through it all. WARNING 2024-07-02 11:51:00 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf going to read through it all. Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:00 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf WARNING 2024-07-02 11:51:00 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Cannot find sample NA12892 in provided file. Cannot find sample NA12892 in provided file. Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: java.lang.IllegalArgumentException: Cannot find sample NA12892 in provided file. java.lang.IllegalArgumentException: Cannot find sample NA12892 in provided file. Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:96) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:96) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.tester(CheckFingerprintTest.java:285) at picard.fingerprint.CheckFingerprintTest.tester(CheckFingerprintTest.java:285) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.testCheckFingerprintSam(CheckFingerprintTest.java:256) at picard.fingerprint.CheckFingerprintTest.testCheckFingerprintSam(CheckFingerprintTest.java:256) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:00 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf WARNING 2024-07-02 11:51:00 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Cannot find sample NA12892 in provided file. Cannot find sample NA12892 in provided file. Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: java.lang.IllegalArgumentException: Cannot find sample NA12892 in provided file. java.lang.IllegalArgumentException: Cannot find sample NA12892 in provided file. Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:96) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:96) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.tester(CheckFingerprintTest.java:285) at picard.fingerprint.CheckFingerprintTest.tester(CheckFingerprintTest.java:285) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.testCheckFingerprintSam(CheckFingerprintTest.java:256) at picard.fingerprint.CheckFingerprintTest.testCheckFingerprintSam(CheckFingerprintTest.java:256) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:00 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf WARNING 2024-07-02 11:51:00 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Cannot find sample NA12892 in provided file. Cannot find sample NA12892 in provided file. Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: java.lang.IllegalArgumentException: Cannot find sample NA12892 in provided file. java.lang.IllegalArgumentException: Cannot find sample NA12892 in provided file. Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:96) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:96) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.tester(CheckFingerprintTest.java:285) at picard.fingerprint.CheckFingerprintTest.tester(CheckFingerprintTest.java:285) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.testCheckFingerprintSam(CheckFingerprintTest.java:256) at picard.fingerprint.CheckFingerprintTest.testCheckFingerprintSam(CheckFingerprintTest.java:256) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:00 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf WARNING 2024-07-02 11:51:00 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Cannot find sample NA12892 in provided file. Cannot find sample NA12892 in provided file. Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: java.lang.IllegalArgumentException: Cannot find sample NA12892 in provided file. java.lang.IllegalArgumentException: Cannot find sample NA12892 in provided file. Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:96) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:96) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.tester(CheckFingerprintTest.java:285) at picard.fingerprint.CheckFingerprintTest.tester(CheckFingerprintTest.java:285) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.testCheckFingerprintSam(CheckFingerprintTest.java:256) at picard.fingerprint.CheckFingerprintTest.testCheckFingerprintSam(CheckFingerprintTest.java:256) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:00 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf WARNING 2024-07-02 11:51:00 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.fp.vcf Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Cannot find sample NA12892 in provided file. Cannot find sample NA12892 in provided file. Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: java.lang.IllegalArgumentException: Cannot find sample NA12892 in provided file. java.lang.IllegalArgumentException: Cannot find sample NA12892 in provided file. Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:96) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:96) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.tester(CheckFingerprintTest.java:285) at picard.fingerprint.CheckFingerprintTest.tester(CheckFingerprintTest.java:285) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.testCheckFingerprintSam(CheckFingerprintTest.java:256) at picard.fingerprint.CheckFingerprintTest.testCheckFingerprintSam(CheckFingerprintTest.java:256) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:00 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) WARNING 2024-07-02 11:51:00 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK35NCCXX160204.1.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK35NCCXX160204.1.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK35NCCXX160204.2.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK35NCCXX160204.2.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HJYN2CCXX160123.1.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HJYN2CCXX160123.1.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK35MCCXX160204.1.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK35MCCXX160204.1.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK35MCCXX160204.2.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK35MCCXX160204.2.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK35MCCXX160204.3.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK35MCCXX160204.3.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK35MCCXX160204.4.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK35MCCXX160204.4.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK35MCCXX160204.5.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK35MCCXX160204.5.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK35MCCXX160204.6.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK35MCCXX160204.6.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK35MCCXX160204.7.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK35MCCXX160204.7.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK35MCCXX160204.8.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK35MCCXX160204.8.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HJYFJCCXX160204.4.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HJYFJCCXX160204.4.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HJYFJCCXX160204.5.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HJYFJCCXX160204.5.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HJYFJCCXX160204.6.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HJYFJCCXX160204.6.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HJYFJCCXX160204.7.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HJYFJCCXX160204.7.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HJYFJCCXX160204.8.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HJYFJCCXX160204.8.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK3T5CCXX160204.1.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK3T5CCXX160204.1.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK3T5CCXX160204.2.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK3T5CCXX160204.2.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK3T5CCXX160204.3.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK3T5CCXX160204.3.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK3T5CCXX160204.4.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK3T5CCXX160204.4.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK3T5CCXX160204.5.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK3T5CCXX160204.5.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK3T5CCXX160204.6.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK3T5CCXX160204.6.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK3T5CCXX160204.7.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK3T5CCXX160204.7.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK3T5CCXX160204.8.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HK3T5CCXX160204.8.CGCTATGT / NA12892 vs. NA12892: LOD = 0.0 Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HT23WCCXX160402.3.CGCTATGT-TATGCGGA / NA12892 vs. NA12892: LOD = 0.0 INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: HT23WCCXX160402.3.CGCTATGT-TATGCGGA / NA12892 vs. NA12892: LOD = 0.0 Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ERROR 2024-07-02 11:51:01 CheckFingerprint No non-zero results found. This is likely an error. Probable cause: EXPECTED_SAMPLE (if provided) or the sample name from INPUT (if EXPECTED_SAMPLE isn't provided)isn't a sample in GENOTYPES file. ERROR 2024-07-02 11:51:01 CheckFingerprint No non-zero results found. This is likely an error. Probable cause: EXPECTED_SAMPLE (if provided) or the sample name from INPUT (if EXPECTED_SAMPLE isn't provided)isn't a sample in GENOTYPES file. Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:01 GMT+14:00 2024] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:01 GMT+14:00 2024] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes. Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testCheckFingerprintSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.fp.vcf, 1)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckFingerprintVcf[0](/tmp/fingerprint11943323503813140247.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) Test: Test method testCheckFingerprintVcf[0](/tmp/fingerprint11943323503813140247.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Gradle suite > Gradle test > picard.fingerprint.CheckFingerprintTest.testCheckFingerprintVcf[0](/tmp/fingerprint11943323503813140247.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0) STANDARD_ERROR INFO 2024-07-02 11:51:01 CheckFingerprint Test: Test method testCheckFingerprintVcf[0](/tmp/fingerprint11943323503813140247.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testCheckFingerprintVcf[0](/tmp/fingerprint11943323503813140247.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFingerprintVcf[0](/tmp/fingerprint11943323503813140247.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintVcf[0](/tmp/fingerprint11943323503813140247.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFingerprintVcf[0](/tmp/fingerprint11943323503813140247.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFingerprintVcf[0](/tmp/fingerprint11943323503813140247.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintVcf[0](/tmp/fingerprint11943323503813140247.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFingerprintVcf[0](/tmp/fingerprint11943323503813140247.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintVcf[0](/tmp/fingerprint11943323503813140247.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** CheckFingerprint -INPUT /tmp/fingerprint11943323503813140247.vcf -G /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.fp.vcf -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -SUMMARY_OUTPUT /tmp/fingerprint16181502237545937978summary_metrics -DETAIL_OUTPUT /tmp/fingerprint3035398899923551094detail_metrics ********** CheckFingerprint -INPUT /tmp/fingerprint11943323503813140247.vcf -G /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.fp.vcf -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -SUMMARY_OUTPUT /tmp/fingerprint16181502237545937978summary_metrics -DETAIL_OUTPUT /tmp/fingerprint3035398899923551094detail_metrics Test: Test method testCheckFingerprintVcf[0](/tmp/fingerprint11943323503813140247.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintVcf[0](/tmp/fingerprint11943323503813140247.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testCheckFingerprintVcf[0](/tmp/fingerprint11943323503813140247.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testCheckFingerprintVcf[0](/tmp/fingerprint11943323503813140247.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:01.157 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:01.157 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintVcf[0](/tmp/fingerprint11943323503813140247.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:01.157 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:01.157 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintVcf[0](/tmp/fingerprint11943323503813140247.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:01.157 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:01.157 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintVcf[0](/tmp/fingerprint11943323503813140247.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:01.157 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:01.157 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintVcf[0](/tmp/fingerprint11943323503813140247.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:01 GMT+14:00 2024] CheckFingerprint INPUT=/tmp/fingerprint11943323503813140247.vcf SUMMARY_OUTPUT=/tmp/fingerprint16181502237545937978summary_metrics DETAIL_OUTPUT=/tmp/fingerprint3035398899923551094detail_metrics GENOTYPES=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.fp.vcf HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt GENOTYPE_LOD_THRESHOLD=5.0 IGNORE_READ_GROUPS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:01 GMT+14:00 2024] CheckFingerprint INPUT=/tmp/fingerprint11943323503813140247.vcf SUMMARY_OUTPUT=/tmp/fingerprint16181502237545937978summary_metrics DETAIL_OUTPUT=/tmp/fingerprint3035398899923551094detail_metrics GENOTYPES=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.fp.vcf HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt GENOTYPE_LOD_THRESHOLD=5.0 IGNORE_READ_GROUPS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFingerprintVcf[0](/tmp/fingerprint11943323503813140247.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFingerprintVcf[0](/tmp/fingerprint11943323503813140247.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:01 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.fp.vcf going to read through it all. WARNING 2024-07-02 11:51:01 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.fp.vcf going to read through it all. Test: Test method testCheckFingerprintVcf[0](/tmp/fingerprint11943323503813140247.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: null / NA12892 vs. NA12892: LOD = -4.9149484155816 INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: null / NA12892 vs. NA12892: LOD = -4.9149484155816 Test: Test method testCheckFingerprintVcf[0](/tmp/fingerprint11943323503813140247.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:01 GMT+14:00 2024] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:01 GMT+14:00 2024] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes. Test: Test method testCheckFingerprintVcf[0](/tmp/fingerprint11943323503813140247.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testCheckFingerprintVcf[1](/tmp/fingerprint1312288342375720703.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) Test: Test method testCheckFingerprintVcf[1](/tmp/fingerprint1312288342375720703.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Gradle suite > Gradle test > picard.fingerprint.CheckFingerprintTest.testCheckFingerprintVcf[1](/tmp/fingerprint1312288342375720703.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0) STANDARD_ERROR INFO 2024-07-02 11:51:01 CheckFingerprint Test: Test method testCheckFingerprintVcf[1](/tmp/fingerprint1312288342375720703.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testCheckFingerprintVcf[1](/tmp/fingerprint1312288342375720703.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFingerprintVcf[1](/tmp/fingerprint1312288342375720703.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintVcf[1](/tmp/fingerprint1312288342375720703.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFingerprintVcf[1](/tmp/fingerprint1312288342375720703.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFingerprintVcf[1](/tmp/fingerprint1312288342375720703.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintVcf[1](/tmp/fingerprint1312288342375720703.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFingerprintVcf[1](/tmp/fingerprint1312288342375720703.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintVcf[1](/tmp/fingerprint1312288342375720703.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** CheckFingerprint -INPUT /tmp/fingerprint1312288342375720703.vcf -G /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.fp.vcf -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -SUMMARY_OUTPUT /tmp/fingerprint10188943399668549662summary_metrics -DETAIL_OUTPUT /tmp/fingerprint9283737956725928491detail_metrics ********** CheckFingerprint -INPUT /tmp/fingerprint1312288342375720703.vcf -G /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.fp.vcf -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -SUMMARY_OUTPUT /tmp/fingerprint10188943399668549662summary_metrics -DETAIL_OUTPUT /tmp/fingerprint9283737956725928491detail_metrics Test: Test method testCheckFingerprintVcf[1](/tmp/fingerprint1312288342375720703.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintVcf[1](/tmp/fingerprint1312288342375720703.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testCheckFingerprintVcf[1](/tmp/fingerprint1312288342375720703.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testCheckFingerprintVcf[1](/tmp/fingerprint1312288342375720703.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:01.257 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:01.257 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintVcf[1](/tmp/fingerprint1312288342375720703.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:01.257 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:01.257 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintVcf[1](/tmp/fingerprint1312288342375720703.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:01.257 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:01.257 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintVcf[1](/tmp/fingerprint1312288342375720703.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:01.257 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:01.257 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintVcf[1](/tmp/fingerprint1312288342375720703.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:01 GMT+14:00 2024] CheckFingerprint INPUT=/tmp/fingerprint1312288342375720703.vcf SUMMARY_OUTPUT=/tmp/fingerprint10188943399668549662summary_metrics DETAIL_OUTPUT=/tmp/fingerprint9283737956725928491detail_metrics GENOTYPES=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.fp.vcf HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt GENOTYPE_LOD_THRESHOLD=5.0 IGNORE_READ_GROUPS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:01 GMT+14:00 2024] CheckFingerprint INPUT=/tmp/fingerprint1312288342375720703.vcf SUMMARY_OUTPUT=/tmp/fingerprint10188943399668549662summary_metrics DETAIL_OUTPUT=/tmp/fingerprint9283737956725928491detail_metrics GENOTYPES=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.fp.vcf HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt GENOTYPE_LOD_THRESHOLD=5.0 IGNORE_READ_GROUPS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFingerprintVcf[1](/tmp/fingerprint1312288342375720703.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFingerprintVcf[1](/tmp/fingerprint1312288342375720703.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:01 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.fp.vcf going to read through it all. WARNING 2024-07-02 11:51:01 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.fp.vcf going to read through it all. Test: Test method testCheckFingerprintVcf[1](/tmp/fingerprint1312288342375720703.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: null / NA12892 vs. NA12892: LOD = 1.06113519110639 INFO 2024-07-02 11:51:01 CheckFingerprint Read Group: null / NA12892 vs. NA12892: LOD = 1.06113519110639 Test: Test method testCheckFingerprintVcf[1](/tmp/fingerprint1312288342375720703.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:01 GMT+14:00 2024] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:01 GMT+14:00 2024] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes. Test: Test method testCheckFingerprintVcf[1](/tmp/fingerprint1312288342375720703.vcf, testdata/picard/fingerprint/NA12892.fp.vcf, 0)(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testFPToVC(picard.fingerprint.CheckFingerprintTest) Test: Test method testFPToVC(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:01 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.shifted.for.crams.r1.sam) Gradle suite > Gradle test > picard.fingerprint.CheckFingerprintTest.testFPToVC STANDARD_ERROR WARNING 2024-07-02 11:51:01 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.shifted.for.crams.r1.sam) Test: Test method testFPToVC(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:51:01 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testFPToVC(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:01 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.shifted.for.crams.r1.sam) WARNING 2024-07-02 11:51:01 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.shifted.for.crams.r1.sam) Test: Test method testFPToVC(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 FingerprintChecker Processed files. 27 fingerprints found in map. INFO 2024-07-02 11:51:01 FingerprintChecker Processed files. 27 fingerprints found in map. Test: Test method testFPToVC(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:01 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.shifted.for.crams.r1.sam) WARNING 2024-07-02 11:51:01 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.shifted.for.crams.r1.sam) Test: Test method testFPToVC(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:01 FingerprintChecker Processed files. 25 fingerprints found in map. INFO 2024-07-02 11:51:01 FingerprintChecker Processed files. 25 fingerprints found in map. Running Test: Test method testIdentifyContaminant(picard.fingerprint.CheckFingerprintTest) Test: Test method testIdentifyContaminant(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:01 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA128791_in_NA12892.25_PCT.sam) Gradle suite > Gradle test > picard.fingerprint.CheckFingerprintTest.testIdentifyContaminant STANDARD_ERROR WARNING 2024-07-02 11:51:01 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA128791_in_NA12892.25_PCT.sam) Test: Test method testIdentifyContaminant(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:01 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) WARNING 2024-07-02 11:51:01 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) Test: Test method testIdentifyContaminant(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 FingerprintChecker Processed files. 26 fingerprints found in map. INFO 2024-07-02 11:51:02 FingerprintChecker Processed files. 26 fingerprints found in map. Test: Test method testIdentifyContaminant(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:02 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) WARNING 2024-07-02 11:51:02 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) Test: Test method testIdentifyContaminant(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 FingerprintChecker Processed files. 26 fingerprints found in map. INFO 2024-07-02 11:51:02 FingerprintChecker Processed files. 26 fingerprints found in map. Running Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Gradle suite > Gradle test > picard.fingerprint.CheckFingerprintTest.testMismatchingSamples STANDARD_ERROR INFO 2024-07-02 11:51:02 CheckFingerprint Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** CheckFingerprint -I testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam -O /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp -G /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf -H testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt ********** CheckFingerprint -I testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam -O /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp -G /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf -H testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:02.414 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:02.414 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:02.414 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:02.414 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:02.414 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:02.414 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:02.414 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:02.414 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:02 GMT+14:00 2024] CheckFingerprint INPUT=testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp GENOTYPES=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt GENOTYPE_LOD_THRESHOLD=5.0 IGNORE_READ_GROUPS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:02 GMT+14:00 2024] CheckFingerprint INPUT=testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp GENOTYPES=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt GENOTYPE_LOD_THRESHOLD=5.0 IGNORE_READ_GROUPS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:02 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf going to read through it all. WARNING 2024-07-02 11:51:02 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf going to read through it all. Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:02 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf WARNING 2024-07-02 11:51:02 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Cannot find sample NA12891 in provided file. Cannot find sample NA12891 in provided file. Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: java.lang.IllegalArgumentException: Cannot find sample NA12891 in provided file. java.lang.IllegalArgumentException: Cannot find sample NA12891 in provided file. Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.testMismatchingSamples(CheckFingerprintTest.java:112) at picard.fingerprint.CheckFingerprintTest.testMismatchingSamples(CheckFingerprintTest.java:112) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:02 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf WARNING 2024-07-02 11:51:02 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Cannot find sample NA12891 in provided file. Cannot find sample NA12891 in provided file. Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: java.lang.IllegalArgumentException: Cannot find sample NA12891 in provided file. java.lang.IllegalArgumentException: Cannot find sample NA12891 in provided file. Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.testMismatchingSamples(CheckFingerprintTest.java:112) at picard.fingerprint.CheckFingerprintTest.testMismatchingSamples(CheckFingerprintTest.java:112) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:02 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf WARNING 2024-07-02 11:51:02 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Cannot find sample NA12891 in provided file. Cannot find sample NA12891 in provided file. Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: java.lang.IllegalArgumentException: Cannot find sample NA12891 in provided file. java.lang.IllegalArgumentException: Cannot find sample NA12891 in provided file. Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.testMismatchingSamples(CheckFingerprintTest.java:112) at picard.fingerprint.CheckFingerprintTest.testMismatchingSamples(CheckFingerprintTest.java:112) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:02 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf WARNING 2024-07-02 11:51:02 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Cannot find sample NA12891 in provided file. Cannot find sample NA12891 in provided file. Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: java.lang.IllegalArgumentException: Cannot find sample NA12891 in provided file. java.lang.IllegalArgumentException: Cannot find sample NA12891 in provided file. Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.testMismatchingSamples(CheckFingerprintTest.java:112) at picard.fingerprint.CheckFingerprintTest.testMismatchingSamples(CheckFingerprintTest.java:112) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:02 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf WARNING 2024-07-02 11:51:02 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Cannot find sample NA12891 in provided file. Cannot find sample NA12891 in provided file. Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: java.lang.IllegalArgumentException: Cannot find sample NA12891 in provided file. java.lang.IllegalArgumentException: Cannot find sample NA12891 in provided file. Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) at picard.fingerprint.FingerprintChecker.checkFingerprints(FingerprintChecker.java:694) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:268) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.testMismatchingSamples(CheckFingerprintTest.java:112) at picard.fingerprint.CheckFingerprintTest.testMismatchingSamples(CheckFingerprintTest.java:112) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:02 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam) WARNING 2024-07-02 11:51:02 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam) Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HJYN2CCXX160123.1.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HJYN2CCXX160123.1.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK3T5CCXX160204.7.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK3T5CCXX160204.7.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK3T5CCXX160204.1.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK3T5CCXX160204.1.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK3T5CCXX160204.2.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK3T5CCXX160204.2.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK3T5CCXX160204.3.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK3T5CCXX160204.3.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK3T5CCXX160204.4.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK3T5CCXX160204.4.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK3T5CCXX160204.5.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK3T5CCXX160204.5.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK3T5CCXX160204.6.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK3T5CCXX160204.6.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK3T5CCXX160204.8.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK3T5CCXX160204.8.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HTL2KCCXX160412.5.TATCCAGG-GAAGTGGA / NA12891 vs. NA12891: LOD = 0.0 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HTL2KCCXX160412.5.TATCCAGG-GAAGTGGA / NA12891 vs. NA12891: LOD = 0.0 Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HTL2KCCXX160412.6.TATCCAGG-GAAGTGGA / NA12891 vs. NA12891: LOD = 0.0 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HTL2KCCXX160412.6.TATCCAGG-GAAGTGGA / NA12891 vs. NA12891: LOD = 0.0 Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK35NCCXX160204.1.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK35NCCXX160204.1.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK35NCCXX160204.2.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK35NCCXX160204.2.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HM3G2CCXX160308.2.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HM3G2CCXX160308.2.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK35MCCXX160204.1.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK35MCCXX160204.1.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK35MCCXX160204.2.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK35MCCXX160204.2.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK35MCCXX160204.3.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK35MCCXX160204.3.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK35MCCXX160204.4.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK35MCCXX160204.4.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK35MCCXX160204.5.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK35MCCXX160204.5.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK35MCCXX160204.6.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK35MCCXX160204.6.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK35MCCXX160204.7.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK35MCCXX160204.7.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK35MCCXX160204.8.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HK35MCCXX160204.8.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HJYFJCCXX160204.4.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HJYFJCCXX160204.4.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HJYFJCCXX160204.5.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HJYFJCCXX160204.5.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HJYFJCCXX160204.6.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HJYFJCCXX160204.6.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HJYFJCCXX160204.7.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HJYFJCCXX160204.7.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HJYFJCCXX160204.8.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: HJYFJCCXX160204.8.TATCCAGG / NA12891 vs. NA12891: LOD = 0.0 Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ERROR 2024-07-02 11:51:02 CheckFingerprint No non-zero results found. This is likely an error. Probable cause: EXPECTED_SAMPLE (if provided) or the sample name from INPUT (if EXPECTED_SAMPLE isn't provided)isn't a sample in GENOTYPES file. ERROR 2024-07-02 11:51:02 CheckFingerprint No non-zero results found. This is likely an error. Probable cause: EXPECTED_SAMPLE (if provided) or the sample name from INPUT (if EXPECTED_SAMPLE isn't provided)isn't a sample in GENOTYPES file. Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:02 GMT+14:00 2024] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:51:02 GMT+14:00 2024] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.01 minutes. Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testMismatchingSamples(picard.fingerprint.CheckFingerprintTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Gradle suite > Gradle test > picard.fingerprint.CheckFingerprintTest.testMismatchingSamples2 STANDARD_ERROR INFO 2024-07-02 11:51:02 CheckFingerprint Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** CheckFingerprint -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf -O /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp -G /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf -EXPECTED_SAMPLE_ALIAS TEST123 -H testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt ********** CheckFingerprint -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf -O /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp -G /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf -EXPECTED_SAMPLE_ALIAS TEST123 -H testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:02.807 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:02.807 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:02.807 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:02.807 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:02.807 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:02.807 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:02.807 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:02.807 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:02 GMT+14:00 2024] CheckFingerprint INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp GENOTYPES=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf EXPECTED_SAMPLE_ALIAS=TEST123 HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt GENOTYPE_LOD_THRESHOLD=5.0 IGNORE_READ_GROUPS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:02 GMT+14:00 2024] CheckFingerprint INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/tempCheckFPDir/otp.fp GENOTYPES=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf EXPECTED_SAMPLE_ALIAS=TEST123 HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt GENOTYPE_LOD_THRESHOLD=5.0 IGNORE_READ_GROUPS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:02 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf going to read through it all. WARNING 2024-07-02 11:51:02 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf going to read through it all. Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:02 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf WARNING 2024-07-02 11:51:02 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Cannot find sample TEST123 in provided file. Cannot find sample TEST123 in provided file. Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: java.lang.IllegalArgumentException: Cannot find sample TEST123 in provided file. java.lang.IllegalArgumentException: Cannot find sample TEST123 in provided file. Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.checkFingerprintsFromPaths(FingerprintChecker.java:752) at picard.fingerprint.FingerprintChecker.checkFingerprintsFromPaths(FingerprintChecker.java:752) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:303) at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:303) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.testMismatchingSamples2(CheckFingerprintTest.java:125) at picard.fingerprint.CheckFingerprintTest.testMismatchingSamples2(CheckFingerprintTest.java:125) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:02 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf WARNING 2024-07-02 11:51:02 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Cannot find sample TEST123 in provided file. Cannot find sample TEST123 in provided file. Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: java.lang.IllegalArgumentException: Cannot find sample TEST123 in provided file. java.lang.IllegalArgumentException: Cannot find sample TEST123 in provided file. Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.checkFingerprintsFromPaths(FingerprintChecker.java:752) at picard.fingerprint.FingerprintChecker.checkFingerprintsFromPaths(FingerprintChecker.java:752) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:303) at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:303) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.testMismatchingSamples2(CheckFingerprintTest.java:125) at picard.fingerprint.CheckFingerprintTest.testMismatchingSamples2(CheckFingerprintTest.java:125) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:02 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf WARNING 2024-07-02 11:51:02 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Cannot find sample TEST123 in provided file. Cannot find sample TEST123 in provided file. Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: java.lang.IllegalArgumentException: Cannot find sample TEST123 in provided file. java.lang.IllegalArgumentException: Cannot find sample TEST123 in provided file. Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.checkFingerprintsFromPaths(FingerprintChecker.java:752) at picard.fingerprint.FingerprintChecker.checkFingerprintsFromPaths(FingerprintChecker.java:752) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:303) at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:303) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.testMismatchingSamples2(CheckFingerprintTest.java:125) at picard.fingerprint.CheckFingerprintTest.testMismatchingSamples2(CheckFingerprintTest.java:125) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:02 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf WARNING 2024-07-02 11:51:02 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Cannot find sample TEST123 in provided file. Cannot find sample TEST123 in provided file. Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: java.lang.IllegalArgumentException: Cannot find sample TEST123 in provided file. java.lang.IllegalArgumentException: Cannot find sample TEST123 in provided file. Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.checkFingerprintsFromPaths(FingerprintChecker.java:752) at picard.fingerprint.FingerprintChecker.checkFingerprintsFromPaths(FingerprintChecker.java:752) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:303) at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:303) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.testMismatchingSamples2(CheckFingerprintTest.java:125) at picard.fingerprint.CheckFingerprintTest.testMismatchingSamples2(CheckFingerprintTest.java:125) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:02 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf WARNING 2024-07-02 11:51:02 FingerprintChecker There was a genotyping error in File: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Cannot find sample TEST123 in provided file. Cannot find sample TEST123 in provided file. Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: java.lang.IllegalArgumentException: Cannot find sample TEST123 in provided file. java.lang.IllegalArgumentException: Cannot find sample TEST123 in provided file. Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) at picard.fingerprint.FingerprintChecker.getFingerprintFromVc(FingerprintChecker.java:377) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) at picard.fingerprint.FingerprintChecker.loadFingerprintsFromVariantContexts(FingerprintChecker.java:280) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) at picard.fingerprint.FingerprintChecker.loadFingerprints(FingerprintChecker.java:197) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.FingerprintChecker.checkFingerprintsFromPaths(FingerprintChecker.java:752) at picard.fingerprint.FingerprintChecker.checkFingerprintsFromPaths(FingerprintChecker.java:752) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:303) at picard.fingerprint.CheckFingerprint.doWork(CheckFingerprint.java:303) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at picard.fingerprint.CheckFingerprintTest.testMismatchingSamples2(CheckFingerprintTest.java:125) at picard.fingerprint.CheckFingerprintTest.testMismatchingSamples2(CheckFingerprintTest.java:125) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:02 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf going to read through it all. WARNING 2024-07-02 11:51:02 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf going to read through it all. Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: null / NA12892 vs. TEST123: LOD = 0.0 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: null / NA12892 vs. TEST123: LOD = 0.0 Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ERROR 2024-07-02 11:51:02 CheckFingerprint No non-zero results found. This is likely an error. Probable cause: EXPECTED_SAMPLE (if provided) or the sample name from INPUT (if EXPECTED_SAMPLE isn't provided)isn't a sample in GENOTYPES file. ERROR 2024-07-02 11:51:02 CheckFingerprint No non-zero results found. This is likely an error. Probable cause: EXPECTED_SAMPLE (if provided) or the sample name from INPUT (if EXPECTED_SAMPLE isn't provided)isn't a sample in GENOTYPES file. Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:02 GMT+14:00 2024] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:02 GMT+14:00 2024] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes. Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testMismatchingSamples2(picard.fingerprint.CheckFingerprintTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testSummaryAndDetailOutputs(picard.fingerprint.CheckFingerprintTest) Test: Test method testSummaryAndDetailOutputs(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Gradle suite > Gradle test > picard.fingerprint.CheckFingerprintTest.testSummaryAndDetailOutputs STANDARD_ERROR INFO 2024-07-02 11:51:02 CheckFingerprint Test: Test method testSummaryAndDetailOutputs(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testSummaryAndDetailOutputs(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSummaryAndDetailOutputs(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testSummaryAndDetailOutputs(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSummaryAndDetailOutputs(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSummaryAndDetailOutputs(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testSummaryAndDetailOutputs(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSummaryAndDetailOutputs(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testSummaryAndDetailOutputs(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** CheckFingerprint -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf -S testdata/picard/fingerprint/tempCheckFPDir/summary -D testdata/picard/fingerprint/tempCheckFPDir/detail -G /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf -H testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt ********** CheckFingerprint -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf -S testdata/picard/fingerprint/tempCheckFPDir/summary -D testdata/picard/fingerprint/tempCheckFPDir/detail -G /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf -H testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt Test: Test method testSummaryAndDetailOutputs(picard.fingerprint.CheckFingerprintTest) produced standard out/err: ********** ********** Test: Test method testSummaryAndDetailOutputs(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testSummaryAndDetailOutputs(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Test: Test method testSummaryAndDetailOutputs(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:02.870 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:02.870 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSummaryAndDetailOutputs(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:02.870 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:02.870 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSummaryAndDetailOutputs(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:02.870 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:02.870 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSummaryAndDetailOutputs(picard.fingerprint.CheckFingerprintTest) produced standard out/err: 11:51:02.871 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:02.871 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSummaryAndDetailOutputs(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:02 GMT+14:00 2024] CheckFingerprint INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf SUMMARY_OUTPUT=testdata/picard/fingerprint/tempCheckFPDir/summary DETAIL_OUTPUT=testdata/picard/fingerprint/tempCheckFPDir/detail GENOTYPES=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt GENOTYPE_LOD_THRESHOLD=5.0 IGNORE_READ_GROUPS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:02 GMT+14:00 2024] CheckFingerprint INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf SUMMARY_OUTPUT=testdata/picard/fingerprint/tempCheckFPDir/summary DETAIL_OUTPUT=testdata/picard/fingerprint/tempCheckFPDir/detail GENOTYPES=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt GENOTYPE_LOD_THRESHOLD=5.0 IGNORE_READ_GROUPS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSummaryAndDetailOutputs(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSummaryAndDetailOutputs(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:02 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf going to read through it all. WARNING 2024-07-02 11:51:02 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.g.vcf going to read through it all. Test: Test method testSummaryAndDetailOutputs(picard.fingerprint.CheckFingerprintTest) produced standard out/err: WARNING 2024-07-02 11:51:02 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf going to read through it all. WARNING 2024-07-02 11:51:02 FingerprintChecker Couldn't find index for file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.vcf going to read through it all. Test: Test method testSummaryAndDetailOutputs(picard.fingerprint.CheckFingerprintTest) produced standard out/err: INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: null / NA12892 vs. NA12892: LOD = 1.0699858771062327 INFO 2024-07-02 11:51:02 CheckFingerprint Read Group: null / NA12892 vs. NA12892: LOD = 1.0699858771062327 Test: Test method testSummaryAndDetailOutputs(picard.fingerprint.CheckFingerprintTest) produced standard out/err: [Tue Jul 02 11:51:02 GMT+14:00 2024] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:02 GMT+14:00 2024] picard.fingerprint.CheckFingerprint done. Elapsed time: 0.00 minutes. Test: Test method testSummaryAndDetailOutputs(picard.fingerprint.CheckFingerprintTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method basedirDoesntExistTest(picard.illumina.CheckIlluminaDirectoryTest) Test: Test method basedirDoesntExistTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:03 CheckIlluminaDirectory Gradle suite > Gradle test > picard.illumina.CheckIlluminaDirectoryTest.basedirDoesntExistTest STANDARD_ERROR INFO 2024-07-02 11:51:03 CheckIlluminaDirectory Test: Test method basedirDoesntExistTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method basedirDoesntExistTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method basedirDoesntExistTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method basedirDoesntExistTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method basedirDoesntExistTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method basedirDoesntExistTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method basedirDoesntExistTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method basedirDoesntExistTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method basedirDoesntExistTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** CheckIlluminaDirectory -B a_made_up_file/in_some_weird_location -L 1 -RS 76T76T -F false -X false -DT Position ********** CheckIlluminaDirectory -B a_made_up_file/in_some_weird_location -L 1 -RS 76T76T -F false -X false -DT Position Test: Test method basedirDoesntExistTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method basedirDoesntExistTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method basedirDoesntExistTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Running Test: Test method cbclWithSkipsInReadStructureTest(picard.illumina.CheckIlluminaDirectoryTest) Test: Test method cbclWithSkipsInReadStructureTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:03 CheckIlluminaDirectory Gradle suite > Gradle test > picard.illumina.CheckIlluminaDirectoryTest.cbclWithSkipsInReadStructureTest STANDARD_ERROR INFO 2024-07-02 11:51:03 CheckIlluminaDirectory Test: Test method cbclWithSkipsInReadStructureTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method cbclWithSkipsInReadStructureTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method cbclWithSkipsInReadStructureTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method cbclWithSkipsInReadStructureTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method cbclWithSkipsInReadStructureTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method cbclWithSkipsInReadStructureTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method cbclWithSkipsInReadStructureTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method cbclWithSkipsInReadStructureTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method cbclWithSkipsInReadStructureTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** CheckIlluminaDirectory -B testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls -L 1 -RS 1S1T -F false -X false -DT BaseCalls ********** CheckIlluminaDirectory -B testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls -L 1 -RS 1S1T -F false -X false -DT BaseCalls Test: Test method cbclWithSkipsInReadStructureTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method cbclWithSkipsInReadStructureTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method cbclWithSkipsInReadStructureTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method cbclWithSkipsInReadStructureTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:03.383 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:03.383 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method cbclWithSkipsInReadStructureTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:03.383 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:03.383 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method cbclWithSkipsInReadStructureTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:03.383 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:03.383 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method cbclWithSkipsInReadStructureTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:03.383 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:03.383 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method cbclWithSkipsInReadStructureTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:03 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls] READ_STRUCTURE=1S1T LANES=[1] FAKE_FILES=false LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:03 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls] READ_STRUCTURE=1S1T LANES=[1] FAKE_FILES=false LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method cbclWithSkipsInReadStructureTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method cbclWithSkipsInReadStructureTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:03 CheckIlluminaDirectory Checking lanes(1 in basecalls directory (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls) INFO 2024-07-02 11:51:03 CheckIlluminaDirectory Checking lanes(1 in basecalls directory (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls) Test: Test method cbclWithSkipsInReadStructureTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method cbclWithSkipsInReadStructureTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:03 CheckIlluminaDirectory Expected cycles: 2 INFO 2024-07-02 11:51:03 CheckIlluminaDirectory Expected cycles: 2 Test: Test method cbclWithSkipsInReadStructureTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:03 CbclReader Processing tile 1101 INFO 2024-07-02 11:51:03 CbclReader Processing tile 1101 Test: Test method cbclWithSkipsInReadStructureTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:03 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty. INFO 2024-07-02 11:51:03 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty. Test: Test method cbclWithSkipsInReadStructureTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:03 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:51:03 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.01 minutes. Test: Test method cbclWithSkipsInReadStructureTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:04 CheckIlluminaDirectory Gradle suite > Gradle test > picard.illumina.CheckIlluminaDirectoryTest.differentSizedBclTest STANDARD_ERROR INFO 2024-07-02 11:51:04 CheckIlluminaDirectory Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** CheckIlluminaDirectory -B /tmp/ift_test13826404557139756508IlluminaDir/Data/Intensities/BaseCalls -L 5 -RS 50T -F false -X false -DT BaseCalls -DT QualityScores ********** CheckIlluminaDirectory -B /tmp/ift_test13826404557139756508IlluminaDir/Data/Intensities/BaseCalls -L 5 -RS 50T -F false -X false -DT BaseCalls -DT QualityScores Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:04.329 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:04.329 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:04.329 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:04.329 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:04.329 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:04.329 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:04.329 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:04.329 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:04 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test13826404557139756508IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores] READ_STRUCTURE=50T LANES=[5] FAKE_FILES=false LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:04 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test13826404557139756508IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores] READ_STRUCTURE=50T LANES=[5] FAKE_FILES=false LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:04 CheckIlluminaDirectory Checking lanes(5 in basecalls directory (/tmp/ift_test13826404557139756508IlluminaDir/Data/Intensities/BaseCalls) INFO 2024-07-02 11:51:04 CheckIlluminaDirectory Checking lanes(5 in basecalls directory (/tmp/ift_test13826404557139756508IlluminaDir/Data/Intensities/BaseCalls) Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:04 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 INFO 2024-07-02 11:51:04 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:04 CheckIlluminaDirectory Checking lane 5 INFO 2024-07-02 11:51:04 CheckIlluminaDirectory Checking lane 5 Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:04 CheckIlluminaDirectory Expected tiles: 1, 2, 3, 4 INFO 2024-07-02 11:51:04 CheckIlluminaDirectory Expected tiles: 1, 2, 3, 4 Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:04 CheckIlluminaDirectory File type .bcl has cycles files of different length. Current cycle (9) Length of first non-empty file (14) length of current cycle (56403) File(/tmp/ift_test13826404557139756508IlluminaDir/Data/Intensities/BaseCalls/L005/C9.1/s_5_3.bcl) INFO 2024-07-02 11:51:04 CheckIlluminaDirectory File type .bcl has cycles files of different length. Current cycle (9) Length of first non-empty file (14) length of current cycle (56403) File(/tmp/ift_test13826404557139756508IlluminaDir/Data/Intensities/BaseCalls/L005/C9.1/s_5_3.bcl) Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:04 CheckIlluminaDirectory Lane 5 FAILED Total Errors: 1 INFO 2024-07-02 11:51:04 CheckIlluminaDirectory Lane 5 FAILED Total Errors: 1 Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:04 CheckIlluminaDirectory FAILED! There were 1 in the following lanes: 5 INFO 2024-07-02 11:51:04 CheckIlluminaDirectory FAILED! There were 1 in the following lanes: 5 Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:04 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:04 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Test: Test method differentSizedBclTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:04 CheckIlluminaDirectory Gradle suite > Gradle test > picard.illumina.CheckIlluminaDirectoryTest.negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true) STANDARD_ERROR INFO 2024-07-02 11:51:04 CheckIlluminaDirectory Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** CheckIlluminaDirectory -B /tmp/ift_test13822209977492432153IlluminaDir/Data/Intensities/BaseCalls -L 2 -RS 68T8B68T -F true -X false -DT BaseCalls -DT QualityScores -DT PF -DT Position -DT Barcodes ********** CheckIlluminaDirectory -B /tmp/ift_test13822209977492432153IlluminaDir/Data/Intensities/BaseCalls -L 2 -RS 68T8B68T -F true -X false -DT BaseCalls -DT QualityScores -DT PF -DT Position -DT Barcodes Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:04.946 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:04.946 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:04.946 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:04.946 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:04.946 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:04.946 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:04.946 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:04.946 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:04 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test13822209977492432153IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position, BaseCalls, QualityScores, PF, Barcodes] READ_STRUCTURE=68T8B68T LANES=[2] FAKE_FILES=true LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:04 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test13822209977492432153IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position, BaseCalls, QualityScores, PF, Barcodes] READ_STRUCTURE=68T8B68T LANES=[2] FAKE_FILES=true LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:04 CheckIlluminaDirectory Checking lanes(2 in basecalls directory (/tmp/ift_test13822209977492432153IlluminaDir/Data/Intensities/BaseCalls) INFO 2024-07-02 11:51:04 CheckIlluminaDirectory Checking lanes(2 in basecalls directory (/tmp/ift_test13822209977492432153IlluminaDir/Data/Intensities/BaseCalls) Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:04 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144 INFO 2024-07-02 11:51:04 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144 Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:04 CheckIlluminaDirectory Checking lane 2 INFO 2024-07-02 11:51:04 CheckIlluminaDirectory Checking lane 2 Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:04 CheckIlluminaDirectory Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301 INFO 2024-07-02 11:51:04 CheckIlluminaDirectory Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301 Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:04 CheckIlluminaDirectory Faking files for Barcodes INFO 2024-07-02 11:51:04 CheckIlluminaDirectory Faking files for Barcodes Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:04 CheckIlluminaDirectory Faking files for Position INFO 2024-07-02 11:51:04 CheckIlluminaDirectory Faking files for Position Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:05 CheckIlluminaDirectory Could not find a format with available files for the following data types: Barcodes, Position INFO 2024-07-02 11:51:05 CheckIlluminaDirectory Could not find a format with available files for the following data types: Barcodes, Position Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:05 CheckIlluminaDirectory Lane 2 FAILED Total Errors: 2 INFO 2024-07-02 11:51:05 CheckIlluminaDirectory Lane 2 FAILED Total Errors: 2 Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:05 CheckIlluminaDirectory FAILED! There were 2 in the following lanes: 2 INFO 2024-07-02 11:51:05 CheckIlluminaDirectory FAILED! There were 2 in the following lanes: 2 Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:05 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:51:05 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.01 minutes. Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:05 CheckIlluminaDirectory INFO 2024-07-02 11:51:05 CheckIlluminaDirectory Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** CheckIlluminaDirectory -B /tmp/ift_test13822209977492432153IlluminaDir/Data/Intensities/BaseCalls -L 2 -RS 68T8B68T -F true -X false -DT BaseCalls -DT QualityScores -DT PF -DT Position -DT Barcodes ********** CheckIlluminaDirectory -B /tmp/ift_test13822209977492432153IlluminaDir/Data/Intensities/BaseCalls -L 2 -RS 68T8B68T -F true -X false -DT BaseCalls -DT QualityScores -DT PF -DT Position -DT Barcodes Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:05.896 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:05.896 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:05.896 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:05.896 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:05.897 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:05.897 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:05.897 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:05.897 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:05 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test13822209977492432153IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position, BaseCalls, QualityScores, PF, Barcodes] READ_STRUCTURE=68T8B68T LANES=[2] FAKE_FILES=true LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:05 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test13822209977492432153IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position, BaseCalls, QualityScores, PF, Barcodes] READ_STRUCTURE=68T8B68T LANES=[2] FAKE_FILES=true LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:05 CheckIlluminaDirectory Checking lanes(2 in basecalls directory (/tmp/ift_test13822209977492432153IlluminaDir/Data/Intensities/BaseCalls) INFO 2024-07-02 11:51:05 CheckIlluminaDirectory Checking lanes(2 in basecalls directory (/tmp/ift_test13822209977492432153IlluminaDir/Data/Intensities/BaseCalls) Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:05 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144 INFO 2024-07-02 11:51:05 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144 Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:05 CheckIlluminaDirectory Checking lane 2 INFO 2024-07-02 11:51:05 CheckIlluminaDirectory Checking lane 2 Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:05 CheckIlluminaDirectory Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301 INFO 2024-07-02 11:51:05 CheckIlluminaDirectory Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301 Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:05 CheckIlluminaDirectory Lane 2 SUCCEEDED INFO 2024-07-02 11:51:05 CheckIlluminaDirectory Lane 2 SUCCEEDED Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:05 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty. INFO 2024-07-02 11:51:05 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty. Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:05 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:05 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. Test: Test method negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@544fd89b, [Lpicard.illumina.parser.IlluminaDataType;@42e5d02d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@66eccd43, 68T8B68T, 2, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:06 CheckIlluminaDirectory Gradle suite > Gradle test > picard.illumina.CheckIlluminaDirectoryTest.negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true) STANDARD_ERROR INFO 2024-07-02 11:51:06 CheckIlluminaDirectory Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** CheckIlluminaDirectory -B /tmp/ift_test7098337622477089115IlluminaDir/Data/Intensities/BaseCalls -L 2 -RS 13T -F true -X false -DT BaseCalls -DT QualityScores -DT PF ********** CheckIlluminaDirectory -B /tmp/ift_test7098337622477089115IlluminaDir/Data/Intensities/BaseCalls -L 2 -RS 13T -F true -X false -DT BaseCalls -DT QualityScores -DT PF Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:06.531 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:06.531 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:06.531 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:06.531 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:06.531 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:06.531 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:06.531 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:06.531 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:06 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test7098337622477089115IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores, PF] READ_STRUCTURE=13T LANES=[2] FAKE_FILES=true LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:06 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test7098337622477089115IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores, PF] READ_STRUCTURE=13T LANES=[2] FAKE_FILES=true LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:06 CheckIlluminaDirectory Checking lanes(2 in basecalls directory (/tmp/ift_test7098337622477089115IlluminaDir/Data/Intensities/BaseCalls) INFO 2024-07-02 11:51:06 CheckIlluminaDirectory Checking lanes(2 in basecalls directory (/tmp/ift_test7098337622477089115IlluminaDir/Data/Intensities/BaseCalls) Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:06 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 INFO 2024-07-02 11:51:06 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:06 CheckIlluminaDirectory Checking lane 2 INFO 2024-07-02 11:51:06 CheckIlluminaDirectory Checking lane 2 Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:06 CheckIlluminaDirectory Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301 INFO 2024-07-02 11:51:06 CheckIlluminaDirectory Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301 Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:06 CheckIlluminaDirectory File type .bcl is missing a file for cycle 13 and tile 1201 INFO 2024-07-02 11:51:06 CheckIlluminaDirectory File type .bcl is missing a file for cycle 13 and tile 1201 Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:06 CheckIlluminaDirectory File type .bcl is missing a file for cycle 13 and tile 2101 INFO 2024-07-02 11:51:06 CheckIlluminaDirectory File type .bcl is missing a file for cycle 13 and tile 2101 Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:06 CheckIlluminaDirectory Missing tile [2101] for file type .filter. INFO 2024-07-02 11:51:06 CheckIlluminaDirectory Missing tile [2101] for file type .filter. Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:06 CheckIlluminaDirectory Lane 2 FAILED Total Errors: 3 INFO 2024-07-02 11:51:06 CheckIlluminaDirectory Lane 2 FAILED Total Errors: 3 Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:06 CheckIlluminaDirectory FAILED! There were 3 in the following lanes: 2 INFO 2024-07-02 11:51:06 CheckIlluminaDirectory FAILED! There were 3 in the following lanes: 2 Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:06 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:06 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:06 CheckIlluminaDirectory INFO 2024-07-02 11:51:06 CheckIlluminaDirectory Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** CheckIlluminaDirectory -B /tmp/ift_test7098337622477089115IlluminaDir/Data/Intensities/BaseCalls -L 2 -RS 13T -F true -X false -DT BaseCalls -DT QualityScores -DT PF ********** CheckIlluminaDirectory -B /tmp/ift_test7098337622477089115IlluminaDir/Data/Intensities/BaseCalls -L 2 -RS 13T -F true -X false -DT BaseCalls -DT QualityScores -DT PF Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:06.914 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:06.914 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:06.914 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:06.914 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:06.914 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:06.914 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:06.914 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:06.914 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:06 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test7098337622477089115IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores, PF] READ_STRUCTURE=13T LANES=[2] FAKE_FILES=true LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:06 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test7098337622477089115IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores, PF] READ_STRUCTURE=13T LANES=[2] FAKE_FILES=true LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:06 CheckIlluminaDirectory Checking lanes(2 in basecalls directory (/tmp/ift_test7098337622477089115IlluminaDir/Data/Intensities/BaseCalls) INFO 2024-07-02 11:51:06 CheckIlluminaDirectory Checking lanes(2 in basecalls directory (/tmp/ift_test7098337622477089115IlluminaDir/Data/Intensities/BaseCalls) Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:06 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 INFO 2024-07-02 11:51:06 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:06 CheckIlluminaDirectory Checking lane 2 INFO 2024-07-02 11:51:06 CheckIlluminaDirectory Checking lane 2 Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:06 CheckIlluminaDirectory Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301 INFO 2024-07-02 11:51:06 CheckIlluminaDirectory Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301 Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:06 CheckIlluminaDirectory Lane 2 SUCCEEDED INFO 2024-07-02 11:51:06 CheckIlluminaDirectory Lane 2 SUCCEEDED Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:06 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty. INFO 2024-07-02 11:51:06 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty. Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:06 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:06 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. Test: Test method negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@8a31f37, [Lpicard.illumina.parser.IlluminaDataType;@1a3434a7, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@7a188397, 13T, 3, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Gradle suite > Gradle test > picard.illumina.CheckIlluminaDirectoryTest.negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true) STANDARD_ERROR INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** CheckIlluminaDirectory -B /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls -L 5 -RS 250T -F true -X false -DT BaseCalls -DT QualityScores -DT PF ********** CheckIlluminaDirectory -B /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls -L 5 -RS 250T -F true -X false -DT BaseCalls -DT QualityScores -DT PF Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:07.652 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:07.652 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:07.652 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:07.652 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:07.655 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:07.655 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:07.655 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:07.655 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:07 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores, PF] READ_STRUCTURE=250T LANES=[5] FAKE_FILES=true LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:07 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores, PF] READ_STRUCTURE=250T LANES=[5] FAKE_FILES=true LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Checking lanes(5 in basecalls directory (/tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls) INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Checking lanes(5 in basecalls directory (/tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls) Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250 INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250 Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Checking lane 5 INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Checking lane 5 Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301 INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301 Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 153 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 153 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 154 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 154 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 155 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 155 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 156 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 156 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 157 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 157 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 158 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 158 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 159 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 159 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 160 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 160 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 161 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 161 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 162 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 162 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 163 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 163 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 164 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 164 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 165 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 165 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 166 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 166 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 167 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 167 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 168 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 168 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 169 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 169 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 170 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 170 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 171 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 171 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 172 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 172 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 173 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 173 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 174 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 174 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 175 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 175 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 176 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 176 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 177 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 177 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 178 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 178 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 179 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 179 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 180 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 180 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 181 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 181 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 182 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 182 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 183 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 183 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 184 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 184 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 185 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 185 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 186 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 186 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 187 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 187 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 188 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 188 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 189 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 189 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 190 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 190 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 191 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 191 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 192 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 192 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 193 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 193 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 194 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 194 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 195 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 195 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 196 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 196 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 197 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 197 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 198 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 198 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 199 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 199 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 200 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 200 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 201 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 201 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 202 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 202 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 203 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 203 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 204 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 204 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 205 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 205 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 206 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 206 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 207 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 207 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 208 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 208 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 209 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 209 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 210 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 210 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 211 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 211 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 212 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 212 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 213 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 213 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 214 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 214 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 215 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 215 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 216 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 216 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 217 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 217 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 218 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 218 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 219 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 219 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 220 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 220 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 221 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 221 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 222 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 222 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 223 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 223 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 224 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 224 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 225 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 225 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 226 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 226 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 227 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 227 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 228 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 228 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 229 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 229 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 230 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 230 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 231 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 231 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 232 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 232 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 233 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 233 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 234 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 234 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 235 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 235 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 236 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 236 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 237 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 237 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 238 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 238 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 239 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 239 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 240 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 240 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 241 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 241 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 242 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 242 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 243 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 243 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 244 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 244 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 245 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 245 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 246 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 246 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 247 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 247 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 248 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 248 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 249 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 249 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 250 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Missing file for cycle 250 in directory /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Lane 5 FAILED Total Errors: 98 INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Lane 5 FAILED Total Errors: 98 Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory FAILED! There were 98 in the following lanes: 5 INFO 2024-07-02 11:51:07 CheckIlluminaDirectory FAILED! There were 98 in the following lanes: 5 Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:07 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:07 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** CheckIlluminaDirectory -B /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls -L 5 -RS 250T -F true -X false -DT BaseCalls -DT QualityScores -DT PF ********** CheckIlluminaDirectory -B /tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls -L 5 -RS 250T -F true -X false -DT BaseCalls -DT QualityScores -DT PF Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:07.788 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:07.788 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:07.794 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:07.794 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:07.794 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:07.794 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:07.794 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:07.794 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:07 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores, PF] READ_STRUCTURE=250T LANES=[5] FAKE_FILES=true LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:07 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores, PF] READ_STRUCTURE=250T LANES=[5] FAKE_FILES=true LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Checking lanes(5 in basecalls directory (/tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls) INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Checking lanes(5 in basecalls directory (/tmp/ift_test18213916829162294857IlluminaDir/Data/Intensities/BaseCalls) Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250 INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250 Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Checking lane 5 INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Checking lane 5 Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301 INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301 Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Lane 5 SUCCEEDED INFO 2024-07-02 11:51:07 CheckIlluminaDirectory Lane 5 SUCCEEDED Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:07 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty. INFO 2024-07-02 11:51:07 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty. Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:07 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:07 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. Test: Test method negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4e0d0264, [Lpicard.illumina.parser.IlluminaDataType;@2f34f268, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@9b7c50f, 250T, 98, [], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Gradle suite > Gradle test > picard.illumina.CheckIlluminaDirectoryTest.negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true) STANDARD_ERROR INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** CheckIlluminaDirectory -B /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls -L 5 -RS 250T -F true -X false -DT BaseCalls -DT QualityScores -DT PF -T 1301 -T 2201 ********** CheckIlluminaDirectory -B /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls -L 5 -RS 250T -F true -X false -DT BaseCalls -DT QualityScores -DT PF -T 1301 -T 2201 Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:08.644 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:08.644 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:08.644 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:08.644 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:08.645 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:08.645 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:08.645 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:08.645 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:08 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores, PF] READ_STRUCTURE=250T LANES=[5] TILE_NUMBERS=[1301, 2201] FAKE_FILES=true LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:08 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores, PF] READ_STRUCTURE=250T LANES=[5] TILE_NUMBERS=[1301, 2201] FAKE_FILES=true LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Checking lanes(5 in basecalls directory (/tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls) INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Checking lanes(5 in basecalls directory (/tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls) Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250 INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250 Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Checking lane 5 INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Checking lane 5 Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Expected tiles: 1301, 2201 INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Expected tiles: 1301, 2201 Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 153 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 153 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 154 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 154 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 155 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 155 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 156 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 156 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 157 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 157 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 158 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 158 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 159 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 159 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 160 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 160 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 161 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 161 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 162 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 162 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 163 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 163 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 164 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 164 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 165 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 165 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 166 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 166 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 167 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 167 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 168 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 168 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 169 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 169 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 170 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 170 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 171 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 171 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 172 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 172 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 173 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 173 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 174 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 174 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 175 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 175 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 176 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 176 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 177 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 177 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 178 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 178 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 179 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 179 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 180 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 180 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 181 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 181 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 182 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 182 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 183 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 183 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 184 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 184 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 185 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 185 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 186 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 186 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 187 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 187 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 188 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 188 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 189 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 189 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 190 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 190 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 191 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 191 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 192 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 192 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 193 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 193 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 194 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 194 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 195 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 195 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 196 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 196 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 197 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 197 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 198 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 198 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 199 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 199 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 200 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 200 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 201 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 201 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 202 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 202 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 203 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 203 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 204 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 204 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 205 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 205 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 206 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 206 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 207 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 207 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 208 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 208 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 209 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 209 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 210 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 210 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 211 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 211 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 212 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 212 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 213 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 213 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 214 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 214 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 215 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 215 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 216 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 216 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 217 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 217 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 218 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 218 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 219 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 219 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 220 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 220 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 221 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 221 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 222 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 222 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 223 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 223 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 224 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 224 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 225 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 225 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 226 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 226 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 227 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 227 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 228 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 228 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 229 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 229 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 230 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 230 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 231 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 231 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 232 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 232 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 233 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 233 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 234 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 234 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 235 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 235 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 236 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 236 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 237 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 237 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 238 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 238 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 239 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 239 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 240 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 240 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 241 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 241 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 242 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 242 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 243 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 243 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 244 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 244 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 245 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 245 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 246 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 246 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 247 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 247 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 248 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 248 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 249 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 249 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 250 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Missing file for cycle 250 in directory /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Lane 5 FAILED Total Errors: 98 INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Lane 5 FAILED Total Errors: 98 Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory FAILED! There were 98 in the following lanes: 5 INFO 2024-07-02 11:51:08 CheckIlluminaDirectory FAILED! There were 98 in the following lanes: 5 Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:08 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:08 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** CheckIlluminaDirectory -B /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls -L 5 -RS 250T -F true -X false -DT BaseCalls -DT QualityScores -DT PF -T 1301 -T 2201 ********** CheckIlluminaDirectory -B /tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls -L 5 -RS 250T -F true -X false -DT BaseCalls -DT QualityScores -DT PF -T 1301 -T 2201 Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:08.751 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:08.751 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:08.751 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:08.751 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:08.751 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:08.751 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:08.751 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:08.751 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:08 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores, PF] READ_STRUCTURE=250T LANES=[5] TILE_NUMBERS=[1301, 2201] FAKE_FILES=true LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:08 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores, PF] READ_STRUCTURE=250T LANES=[5] TILE_NUMBERS=[1301, 2201] FAKE_FILES=true LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Checking lanes(5 in basecalls directory (/tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls) INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Checking lanes(5 in basecalls directory (/tmp/ift_test15553246092919987835IlluminaDir/Data/Intensities/BaseCalls) Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250 INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250 Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Checking lane 5 INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Checking lane 5 Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Expected tiles: 1301, 2201 INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Expected tiles: 1301, 2201 Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Lane 5 SUCCEEDED INFO 2024-07-02 11:51:08 CheckIlluminaDirectory Lane 5 SUCCEEDED Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:08 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty. INFO 2024-07-02 11:51:08 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty. Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:08 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:08 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. Test: Test method negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@59e83c95, [Lpicard.illumina.parser.IlluminaDataType;@20338b82, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@3e956d26, 250T, 98, [1301, 2201], true)(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Gradle suite > Gradle test > picard.illumina.CheckIlluminaDirectoryTest.noSymlinkLocsTest STANDARD_ERROR INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** CheckIlluminaDirectory -B /tmp/ift_test5194205330633580970IlluminaDir/Data/Intensities/BaseCalls -L 5 -RS 50T -F false -X false -DT Position ********** CheckIlluminaDirectory -B /tmp/ift_test5194205330633580970IlluminaDir/Data/Intensities/BaseCalls -L 5 -RS 50T -F false -X false -DT Position Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:09.567 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:09.567 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:09.567 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:09.567 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:09.567 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:09.567 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:09.567 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:09.567 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:09 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test5194205330633580970IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position] READ_STRUCTURE=50T LANES=[5] FAKE_FILES=false LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:09 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test5194205330633580970IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position] READ_STRUCTURE=50T LANES=[5] FAKE_FILES=false LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Checking lanes(5 in basecalls directory (/tmp/ift_test5194205330633580970IlluminaDir/Data/Intensities/BaseCalls) INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Checking lanes(5 in basecalls directory (/tmp/ift_test5194205330633580970IlluminaDir/Data/Intensities/BaseCalls) Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Checking lane 5 INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Checking lane 5 Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Expected tiles: 1101, 1102, 1103, 2101, 2102, 2103 INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Expected tiles: 1101, 1102, 1103, 2101, 2102, 2103 Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Lane 5 SUCCEEDED INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Lane 5 SUCCEEDED Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:09 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty. INFO 2024-07-02 11:51:09 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty. Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:09 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:09 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:09 CheckIlluminaDirectory INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** CheckIlluminaDirectory -B /tmp/ift_test5194205330633580970IlluminaDir/Data/Intensities/BaseCalls -L 5 -RS 50T -F false -X true -DT Position ********** CheckIlluminaDirectory -B /tmp/ift_test5194205330633580970IlluminaDir/Data/Intensities/BaseCalls -L 5 -RS 50T -F false -X true -DT Position Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:09.592 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:09.592 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:09.592 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:09.592 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:09.592 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:09.592 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:09.592 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:09.592 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:09 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test5194205330633580970IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position] READ_STRUCTURE=50T LANES=[5] FAKE_FILES=false LINK_LOCS=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:09 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test5194205330633580970IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position] READ_STRUCTURE=50T LANES=[5] FAKE_FILES=false LINK_LOCS=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Checking lanes(5 in basecalls directory (/tmp/ift_test5194205330633580970IlluminaDir/Data/Intensities/BaseCalls) INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Checking lanes(5 in basecalls directory (/tmp/ift_test5194205330633580970IlluminaDir/Data/Intensities/BaseCalls) Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Checking lane 5 INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Checking lane 5 Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Expected tiles: 1101, 1102, 1103, 2101, 2102, 2103 INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Expected tiles: 1101, 1102, 1103, 2101, 2102, 2103 Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Lane 5 SUCCEEDED INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Lane 5 SUCCEEDED Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:09 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty. INFO 2024-07-02 11:51:09 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty. Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:09 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:09 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. Test: Test method noSymlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Gradle suite > Gradle test > picard.illumina.CheckIlluminaDirectoryTest.positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, []) STANDARD_ERROR INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** CheckIlluminaDirectory -B /tmp/ift_test3325281147682946163IlluminaDir/Data/Intensities/BaseCalls -L 3 -RS 25T25T -F false -X false -DT BaseCalls -DT QualityScores -DT Position -DT PF ********** CheckIlluminaDirectory -B /tmp/ift_test3325281147682946163IlluminaDir/Data/Intensities/BaseCalls -L 3 -RS 25T25T -F false -X false -DT BaseCalls -DT QualityScores -DT Position -DT PF Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:09.883 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:09.883 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:09.883 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:09.883 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:09.883 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:09.883 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:09.883 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:09.883 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:09 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test3325281147682946163IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position, BaseCalls, QualityScores, PF] READ_STRUCTURE=25T25T LANES=[3] FAKE_FILES=false LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:09 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test3325281147682946163IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position, BaseCalls, QualityScores, PF] READ_STRUCTURE=25T25T LANES=[3] FAKE_FILES=false LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Checking lanes(3 in basecalls directory (/tmp/ift_test3325281147682946163IlluminaDir/Data/Intensities/BaseCalls) INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Checking lanes(3 in basecalls directory (/tmp/ift_test3325281147682946163IlluminaDir/Data/Intensities/BaseCalls) Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Checking lane 3 INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Checking lane 3 Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301 INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301 Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Lane 3 SUCCEEDED INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Lane 3 SUCCEEDED Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:09 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty. INFO 2024-07-02 11:51:09 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty. Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:09 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:09 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. Test: Test method positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@68c7fc09, [Lpicard.illumina.parser.IlluminaDataType;@364762d0, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@1e5959cc, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Gradle suite > Gradle test > picard.illumina.CheckIlluminaDirectoryTest.positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, []) STANDARD_ERROR INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** CheckIlluminaDirectory -B /tmp/ift_test2945691116266074086IlluminaDir/Data/Intensities/BaseCalls -L 2 -RS 8S15T8S -F false -X false -DT BaseCalls -DT QualityScores -DT Position -DT PF ********** CheckIlluminaDirectory -B /tmp/ift_test2945691116266074086IlluminaDir/Data/Intensities/BaseCalls -L 2 -RS 8S15T8S -F false -X false -DT BaseCalls -DT QualityScores -DT Position -DT PF Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:09.978 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:09.978 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:09.978 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:09.978 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:09.978 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:09.978 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:09.978 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:09.978 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:09 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test2945691116266074086IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position, BaseCalls, QualityScores, PF] READ_STRUCTURE=8S15T8S LANES=[2] FAKE_FILES=false LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:09 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test2945691116266074086IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position, BaseCalls, QualityScores, PF] READ_STRUCTURE=8S15T8S LANES=[2] FAKE_FILES=false LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Checking lanes(2 in basecalls directory (/tmp/ift_test2945691116266074086IlluminaDir/Data/Intensities/BaseCalls) INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Checking lanes(2 in basecalls directory (/tmp/ift_test2945691116266074086IlluminaDir/Data/Intensities/BaseCalls) Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Expected cycles: 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Expected cycles: 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Checking lane 2 INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Checking lane 2 Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301 INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301 Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Lane 2 SUCCEEDED INFO 2024-07-02 11:51:09 CheckIlluminaDirectory Lane 2 SUCCEEDED Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:09 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty. INFO 2024-07-02 11:51:09 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty. Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:09 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:09 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. Test: Test method positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@43536967, [Lpicard.illumina.parser.IlluminaDataType;@69bd527b, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1020966a, 8S15T8S, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Gradle suite > Gradle test > picard.illumina.CheckIlluminaDirectoryTest.positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, []) STANDARD_ERROR INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** CheckIlluminaDirectory -B /tmp/ift_test17719418720190964370IlluminaDir/Data/Intensities/BaseCalls -L 2 -RS 68T8B68T -F false -X false -DT BaseCalls -DT QualityScores -DT PF ********** CheckIlluminaDirectory -B /tmp/ift_test17719418720190964370IlluminaDir/Data/Intensities/BaseCalls -L 2 -RS 68T8B68T -F false -X false -DT BaseCalls -DT QualityScores -DT PF Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:10.127 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.127 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:10.127 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.127 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:10.127 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.127 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:10.127 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.127 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test17719418720190964370IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores, PF] READ_STRUCTURE=68T8B68T LANES=[2] FAKE_FILES=false LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:10 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test17719418720190964370IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores, PF] READ_STRUCTURE=68T8B68T LANES=[2] FAKE_FILES=false LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Checking lanes(2 in basecalls directory (/tmp/ift_test17719418720190964370IlluminaDir/Data/Intensities/BaseCalls) INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Checking lanes(2 in basecalls directory (/tmp/ift_test17719418720190964370IlluminaDir/Data/Intensities/BaseCalls) Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144 INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144 Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Checking lane 2 INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Checking lane 2 Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301 INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301 Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Lane 2 SUCCEEDED INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Lane 2 SUCCEEDED Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty. INFO 2024-07-02 11:51:10 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty. Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. Test: Test method positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4ee05274, [Lpicard.illumina.parser.IlluminaDataType;@18eeb1c1, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@1432a1d3, 68T8B68T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Gradle suite > Gradle test > picard.illumina.CheckIlluminaDirectoryTest.positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, []) STANDARD_ERROR INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** CheckIlluminaDirectory -B /tmp/ift_test4331301915678432003IlluminaDir/Data/Intensities/BaseCalls -L 5 -RS 25T25T -F false -X false -DT BaseCalls -DT QualityScores -DT Position -DT PF ********** CheckIlluminaDirectory -B /tmp/ift_test4331301915678432003IlluminaDir/Data/Intensities/BaseCalls -L 5 -RS 25T25T -F false -X false -DT BaseCalls -DT QualityScores -DT Position -DT PF Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:10.264 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.264 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:10.264 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.264 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:10.265 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.265 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:10.265 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.265 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test4331301915678432003IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position, BaseCalls, QualityScores, PF] READ_STRUCTURE=25T25T LANES=[5] FAKE_FILES=false LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:10 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test4331301915678432003IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position, BaseCalls, QualityScores, PF] READ_STRUCTURE=25T25T LANES=[5] FAKE_FILES=false LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Checking lanes(5 in basecalls directory (/tmp/ift_test4331301915678432003IlluminaDir/Data/Intensities/BaseCalls) INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Checking lanes(5 in basecalls directory (/tmp/ift_test4331301915678432003IlluminaDir/Data/Intensities/BaseCalls) Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Checking lane 5 INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Checking lane 5 Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301 INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301 Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Lane 5 SUCCEEDED INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Lane 5 SUCCEEDED Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty. INFO 2024-07-02 11:51:10 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty. Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. Test: Test method positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@66a9f57a, [Lpicard.illumina.parser.IlluminaDataType;@3b7d1d46, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@f850479, 25T25T, [])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Gradle suite > Gradle test > picard.illumina.CheckIlluminaDirectoryTest.positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101]) STANDARD_ERROR INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** CheckIlluminaDirectory -B /tmp/ift_test131464076872506377IlluminaDir/Data/Intensities/BaseCalls -L 5 -RS 25T25T -F false -X false -DT BaseCalls -DT QualityScores -DT Position -DT PF -T 1301 -T 2101 ********** CheckIlluminaDirectory -B /tmp/ift_test131464076872506377IlluminaDir/Data/Intensities/BaseCalls -L 5 -RS 25T25T -F false -X false -DT BaseCalls -DT QualityScores -DT Position -DT PF -T 1301 -T 2101 Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:10.357 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.357 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:10.357 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.357 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:10.357 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.357 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:10.357 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.357 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test131464076872506377IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position, BaseCalls, QualityScores, PF] READ_STRUCTURE=25T25T LANES=[5] TILE_NUMBERS=[1301, 2101] FAKE_FILES=false LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:10 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test131464076872506377IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position, BaseCalls, QualityScores, PF] READ_STRUCTURE=25T25T LANES=[5] TILE_NUMBERS=[1301, 2101] FAKE_FILES=false LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Checking lanes(5 in basecalls directory (/tmp/ift_test131464076872506377IlluminaDir/Data/Intensities/BaseCalls) INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Checking lanes(5 in basecalls directory (/tmp/ift_test131464076872506377IlluminaDir/Data/Intensities/BaseCalls) Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Checking lane 5 INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Checking lane 5 Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Expected tiles: 1301, 2101 INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Expected tiles: 1301, 2101 Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Lane 5 SUCCEEDED INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Lane 5 SUCCEEDED Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty. INFO 2024-07-02 11:51:10 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty. Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. Test: Test method positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@7aa78455, [Lpicard.illumina.parser.IlluminaDataType;@16e87d91, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@ae1acf9, 25T25T, [1301, 2101])(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Gradle suite > Gradle test > picard.illumina.CheckIlluminaDirectoryTest.symlinkLocsTest STANDARD_ERROR INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** CheckIlluminaDirectory -B /tmp/ift_test11535945361910481264IlluminaDir/Data/Intensities/BaseCalls -L 5 -RS 50T -F false -X true -DT Position ********** CheckIlluminaDirectory -B /tmp/ift_test11535945361910481264IlluminaDir/Data/Intensities/BaseCalls -L 5 -RS 50T -F false -X true -DT Position Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:10.441 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.441 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:10.441 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.441 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:10.441 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.441 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:10.441 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.441 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test11535945361910481264IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position] READ_STRUCTURE=50T LANES=[5] FAKE_FILES=false LINK_LOCS=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:10 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test11535945361910481264IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position] READ_STRUCTURE=50T LANES=[5] FAKE_FILES=false LINK_LOCS=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Checking lanes(5 in basecalls directory (/tmp/ift_test11535945361910481264IlluminaDir/Data/Intensities/BaseCalls) INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Checking lanes(5 in basecalls directory (/tmp/ift_test11535945361910481264IlluminaDir/Data/Intensities/BaseCalls) Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Checking lane 5 INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Checking lane 5 Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Expected tiles: 1101, 1102, 1103, 2101, 2102, 2103 INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Expected tiles: 1101, 1102, 1103, 2101, 2102, 2103 Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Lane 5 SUCCEEDED INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Lane 5 SUCCEEDED Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty. INFO 2024-07-02 11:51:10 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty. Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** CheckIlluminaDirectory -B /tmp/ift_test11535945361910481264IlluminaDir/Data/Intensities/BaseCalls -L 5 -RS 50T -F false -X true -DT Position ********** CheckIlluminaDirectory -B /tmp/ift_test11535945361910481264IlluminaDir/Data/Intensities/BaseCalls -L 5 -RS 50T -F false -X true -DT Position Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: ********** ********** Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:10.489 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.489 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:10.489 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.489 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:10.489 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.489 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: 11:51:10.489 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.489 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test11535945361910481264IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position] READ_STRUCTURE=50T LANES=[5] FAKE_FILES=false LINK_LOCS=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:10 GMT+14:00 2024] CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test11535945361910481264IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position] READ_STRUCTURE=50T LANES=[5] FAKE_FILES=false LINK_LOCS=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Checking lanes(5 in basecalls directory (/tmp/ift_test11535945361910481264IlluminaDir/Data/Intensities/BaseCalls) INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Checking lanes(5 in basecalls directory (/tmp/ift_test11535945361910481264IlluminaDir/Data/Intensities/BaseCalls) Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Checking lane 5 INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Checking lane 5 Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Expected tiles: 1101, 1102, 1103, 2101, 2102, 2103 INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Expected tiles: 1101, 1102, 1103, 2101, 2102, 2103 Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Lane 5 SUCCEEDED INFO 2024-07-02 11:51:10 CheckIlluminaDirectory Lane 5 SUCCEEDED Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: INFO 2024-07-02 11:51:10 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty. INFO 2024-07-02 11:51:10 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty. Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes. Test: Test method symlinkLocsTest(picard.illumina.CheckIlluminaDirectoryTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method testCleanSam[0](simple_fits.sam, 100M)(picard.sam.CleanSamTest) Test: Test method testCleanSam[0](simple_fits.sam, 100M)(picard.sam.CleanSamTest) produced standard out/err: INFO 2024-07-02 11:51:10 CleanSam Gradle suite > Gradle test > picard.sam.CleanSamTest.testCleanSam[0](simple_fits.sam, 100M) STANDARD_ERROR INFO 2024-07-02 11:51:10 CleanSam Test: Test method testCleanSam[0](simple_fits.sam, 100M)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSam[0](simple_fits.sam, 100M)(picard.sam.CleanSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCleanSam[0](simple_fits.sam, 100M)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSam[0](simple_fits.sam, 100M)(picard.sam.CleanSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCleanSam[0](simple_fits.sam, 100M)(picard.sam.CleanSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCleanSam[0](simple_fits.sam, 100M)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSam[0](simple_fits.sam, 100M)(picard.sam.CleanSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCleanSam[0](simple_fits.sam, 100M)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSam[0](simple_fits.sam, 100M)(picard.sam.CleanSamTest) produced standard out/err: ********** CleanSam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CleanSam/simple_fits.sam -OUTPUT /tmp/simple_fits.sam.10730080787076038872.sam ********** CleanSam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CleanSam/simple_fits.sam -OUTPUT /tmp/simple_fits.sam.10730080787076038872.sam Test: Test method testCleanSam[0](simple_fits.sam, 100M)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSam[0](simple_fits.sam, 100M)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSam[0](simple_fits.sam, 100M)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSam[0](simple_fits.sam, 100M)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.560 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.560 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCleanSam[0](simple_fits.sam, 100M)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.560 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.560 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCleanSam[0](simple_fits.sam, 100M)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.560 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.560 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCleanSam[0](simple_fits.sam, 100M)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.560 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.560 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCleanSam[0](simple_fits.sam, 100M)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] CleanSam INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CleanSam/simple_fits.sam OUTPUT=/tmp/simple_fits.sam.10730080787076038872.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:10 GMT+14:00 2024] CleanSam INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CleanSam/simple_fits.sam OUTPUT=/tmp/simple_fits.sam.10730080787076038872.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCleanSam[0](simple_fits.sam, 100M)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCleanSam[0](simple_fits.sam, 100M)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.sam.CleanSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.sam.CleanSam done. Elapsed time: 0.00 minutes. Test: Test method testCleanSam[0](simple_fits.sam, 100M)(picard.sam.CleanSamTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Test: Test method testCleanSam[0](simple_fits.sam, 100M)(picard.sam.CleanSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.CleanSamTest.testCleanSam[0](simple_fits.sam, 100M) STANDARD_OUT No errors found Running Test: Test method testCleanSam[1](simple_overhang.sam, 99M1S)(picard.sam.CleanSamTest) Test: Test method testCleanSam[1](simple_overhang.sam, 99M1S)(picard.sam.CleanSamTest) produced standard out/err: INFO 2024-07-02 11:51:10 CleanSam Gradle suite > Gradle test > picard.sam.CleanSamTest.testCleanSam[1](simple_overhang.sam, 99M1S) STANDARD_ERROR INFO 2024-07-02 11:51:10 CleanSam Test: Test method testCleanSam[1](simple_overhang.sam, 99M1S)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSam[1](simple_overhang.sam, 99M1S)(picard.sam.CleanSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCleanSam[1](simple_overhang.sam, 99M1S)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSam[1](simple_overhang.sam, 99M1S)(picard.sam.CleanSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCleanSam[1](simple_overhang.sam, 99M1S)(picard.sam.CleanSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCleanSam[1](simple_overhang.sam, 99M1S)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSam[1](simple_overhang.sam, 99M1S)(picard.sam.CleanSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCleanSam[1](simple_overhang.sam, 99M1S)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSam[1](simple_overhang.sam, 99M1S)(picard.sam.CleanSamTest) produced standard out/err: ********** CleanSam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CleanSam/simple_overhang.sam -OUTPUT /tmp/simple_overhang.sam.18093831834239423527.sam ********** CleanSam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CleanSam/simple_overhang.sam -OUTPUT /tmp/simple_overhang.sam.18093831834239423527.sam Test: Test method testCleanSam[1](simple_overhang.sam, 99M1S)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSam[1](simple_overhang.sam, 99M1S)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSam[1](simple_overhang.sam, 99M1S)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSam[1](simple_overhang.sam, 99M1S)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.593 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.593 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCleanSam[1](simple_overhang.sam, 99M1S)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.593 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.593 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCleanSam[1](simple_overhang.sam, 99M1S)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.593 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.593 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCleanSam[1](simple_overhang.sam, 99M1S)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.593 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.593 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCleanSam[1](simple_overhang.sam, 99M1S)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] CleanSam INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CleanSam/simple_overhang.sam OUTPUT=/tmp/simple_overhang.sam.18093831834239423527.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:10 GMT+14:00 2024] CleanSam INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CleanSam/simple_overhang.sam OUTPUT=/tmp/simple_overhang.sam.18093831834239423527.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCleanSam[1](simple_overhang.sam, 99M1S)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCleanSam[1](simple_overhang.sam, 99M1S)(picard.sam.CleanSamTest) produced standard out/err: Ignoring SAM validation error: ERROR::CIGAR_MAPS_OFF_REFERENCE:Read name simple_overhang, Read CIGAR M operator maps off end of reference Ignoring SAM validation error: ERROR::CIGAR_MAPS_OFF_REFERENCE:Read name simple_overhang, Read CIGAR M operator maps off end of reference Test: Test method testCleanSam[1](simple_overhang.sam, 99M1S)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.sam.CleanSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.sam.CleanSam done. Elapsed time: 0.00 minutes. Test: Test method testCleanSam[1](simple_overhang.sam, 99M1S)(picard.sam.CleanSamTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Test: Test method testCleanSam[1](simple_overhang.sam, 99M1S)(picard.sam.CleanSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.CleanSamTest.testCleanSam[1](simple_overhang.sam, 99M1S) STANDARD_OUT No errors found Running Test: Test method testCleanSam[2](fits_with_deletion.sam, 91M2D9M)(picard.sam.CleanSamTest) Test: Test method testCleanSam[2](fits_with_deletion.sam, 91M2D9M)(picard.sam.CleanSamTest) produced standard out/err: INFO 2024-07-02 11:51:10 CleanSam Gradle suite > Gradle test > picard.sam.CleanSamTest.testCleanSam[2](fits_with_deletion.sam, 91M2D9M) STANDARD_ERROR INFO 2024-07-02 11:51:10 CleanSam Test: Test method testCleanSam[2](fits_with_deletion.sam, 91M2D9M)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSam[2](fits_with_deletion.sam, 91M2D9M)(picard.sam.CleanSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCleanSam[2](fits_with_deletion.sam, 91M2D9M)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSam[2](fits_with_deletion.sam, 91M2D9M)(picard.sam.CleanSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCleanSam[2](fits_with_deletion.sam, 91M2D9M)(picard.sam.CleanSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCleanSam[2](fits_with_deletion.sam, 91M2D9M)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSam[2](fits_with_deletion.sam, 91M2D9M)(picard.sam.CleanSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCleanSam[2](fits_with_deletion.sam, 91M2D9M)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSam[2](fits_with_deletion.sam, 91M2D9M)(picard.sam.CleanSamTest) produced standard out/err: ********** CleanSam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CleanSam/fits_with_deletion.sam -OUTPUT /tmp/fits_with_deletion.sam.3536561644324526564.sam ********** CleanSam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CleanSam/fits_with_deletion.sam -OUTPUT /tmp/fits_with_deletion.sam.3536561644324526564.sam Test: Test method testCleanSam[2](fits_with_deletion.sam, 91M2D9M)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSam[2](fits_with_deletion.sam, 91M2D9M)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSam[2](fits_with_deletion.sam, 91M2D9M)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSam[2](fits_with_deletion.sam, 91M2D9M)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.613 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.613 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCleanSam[2](fits_with_deletion.sam, 91M2D9M)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.613 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.613 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCleanSam[2](fits_with_deletion.sam, 91M2D9M)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.613 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.613 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCleanSam[2](fits_with_deletion.sam, 91M2D9M)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.613 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.613 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCleanSam[2](fits_with_deletion.sam, 91M2D9M)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] CleanSam INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CleanSam/fits_with_deletion.sam OUTPUT=/tmp/fits_with_deletion.sam.3536561644324526564.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:10 GMT+14:00 2024] CleanSam INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CleanSam/fits_with_deletion.sam OUTPUT=/tmp/fits_with_deletion.sam.3536561644324526564.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCleanSam[2](fits_with_deletion.sam, 91M2D9M)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCleanSam[2](fits_with_deletion.sam, 91M2D9M)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.sam.CleanSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.sam.CleanSam done. Elapsed time: 0.00 minutes. Test: Test method testCleanSam[2](fits_with_deletion.sam, 91M2D9M)(picard.sam.CleanSamTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Test: Test method testCleanSam[2](fits_with_deletion.sam, 91M2D9M)(picard.sam.CleanSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.CleanSamTest.testCleanSam[2](fits_with_deletion.sam, 91M2D9M) STANDARD_OUT No errors found Running Test: Test method testCleanSam[3](overhang_with_deletion.sam, 91M2D8M1S)(picard.sam.CleanSamTest) Test: Test method testCleanSam[3](overhang_with_deletion.sam, 91M2D8M1S)(picard.sam.CleanSamTest) produced standard out/err: INFO 2024-07-02 11:51:10 CleanSam Gradle suite > Gradle test > picard.sam.CleanSamTest.testCleanSam[3](overhang_with_deletion.sam, 91M2D8M1S) STANDARD_ERROR INFO 2024-07-02 11:51:10 CleanSam Test: Test method testCleanSam[3](overhang_with_deletion.sam, 91M2D8M1S)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSam[3](overhang_with_deletion.sam, 91M2D8M1S)(picard.sam.CleanSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCleanSam[3](overhang_with_deletion.sam, 91M2D8M1S)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSam[3](overhang_with_deletion.sam, 91M2D8M1S)(picard.sam.CleanSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCleanSam[3](overhang_with_deletion.sam, 91M2D8M1S)(picard.sam.CleanSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCleanSam[3](overhang_with_deletion.sam, 91M2D8M1S)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSam[3](overhang_with_deletion.sam, 91M2D8M1S)(picard.sam.CleanSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCleanSam[3](overhang_with_deletion.sam, 91M2D8M1S)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSam[3](overhang_with_deletion.sam, 91M2D8M1S)(picard.sam.CleanSamTest) produced standard out/err: ********** CleanSam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CleanSam/overhang_with_deletion.sam -OUTPUT /tmp/overhang_with_deletion.sam.16576249448735592248.sam ********** CleanSam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CleanSam/overhang_with_deletion.sam -OUTPUT /tmp/overhang_with_deletion.sam.16576249448735592248.sam Test: Test method testCleanSam[3](overhang_with_deletion.sam, 91M2D8M1S)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSam[3](overhang_with_deletion.sam, 91M2D8M1S)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSam[3](overhang_with_deletion.sam, 91M2D8M1S)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSam[3](overhang_with_deletion.sam, 91M2D8M1S)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.633 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.633 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCleanSam[3](overhang_with_deletion.sam, 91M2D8M1S)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.633 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.633 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCleanSam[3](overhang_with_deletion.sam, 91M2D8M1S)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.633 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.633 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCleanSam[3](overhang_with_deletion.sam, 91M2D8M1S)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.633 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.633 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCleanSam[3](overhang_with_deletion.sam, 91M2D8M1S)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] CleanSam INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CleanSam/overhang_with_deletion.sam OUTPUT=/tmp/overhang_with_deletion.sam.16576249448735592248.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:10 GMT+14:00 2024] CleanSam INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CleanSam/overhang_with_deletion.sam OUTPUT=/tmp/overhang_with_deletion.sam.16576249448735592248.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCleanSam[3](overhang_with_deletion.sam, 91M2D8M1S)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCleanSam[3](overhang_with_deletion.sam, 91M2D8M1S)(picard.sam.CleanSamTest) produced standard out/err: Ignoring SAM validation error: ERROR::CIGAR_MAPS_OFF_REFERENCE:Read name overhang_with_deletion, Read CIGAR M operator maps off end of reference Ignoring SAM validation error: ERROR::CIGAR_MAPS_OFF_REFERENCE:Read name overhang_with_deletion, Read CIGAR M operator maps off end of reference Test: Test method testCleanSam[3](overhang_with_deletion.sam, 91M2D8M1S)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.sam.CleanSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.sam.CleanSam done. Elapsed time: 0.00 minutes. Test: Test method testCleanSam[3](overhang_with_deletion.sam, 91M2D8M1S)(picard.sam.CleanSamTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Test: Test method testCleanSam[3](overhang_with_deletion.sam, 91M2D8M1S)(picard.sam.CleanSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.CleanSamTest.testCleanSam[3](overhang_with_deletion.sam, 91M2D8M1S) STANDARD_OUT No errors found Running Test: Test method testCleanSam[4](trailing_insertion.sam, 99M1I)(picard.sam.CleanSamTest) Test: Test method testCleanSam[4](trailing_insertion.sam, 99M1I)(picard.sam.CleanSamTest) produced standard out/err: INFO 2024-07-02 11:51:10 CleanSam Gradle suite > Gradle test > picard.sam.CleanSamTest.testCleanSam[4](trailing_insertion.sam, 99M1I) STANDARD_ERROR INFO 2024-07-02 11:51:10 CleanSam Test: Test method testCleanSam[4](trailing_insertion.sam, 99M1I)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSam[4](trailing_insertion.sam, 99M1I)(picard.sam.CleanSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCleanSam[4](trailing_insertion.sam, 99M1I)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSam[4](trailing_insertion.sam, 99M1I)(picard.sam.CleanSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCleanSam[4](trailing_insertion.sam, 99M1I)(picard.sam.CleanSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCleanSam[4](trailing_insertion.sam, 99M1I)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSam[4](trailing_insertion.sam, 99M1I)(picard.sam.CleanSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCleanSam[4](trailing_insertion.sam, 99M1I)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSam[4](trailing_insertion.sam, 99M1I)(picard.sam.CleanSamTest) produced standard out/err: ********** CleanSam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CleanSam/trailing_insertion.sam -OUTPUT /tmp/trailing_insertion.sam.11191772055868707229.sam ********** CleanSam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CleanSam/trailing_insertion.sam -OUTPUT /tmp/trailing_insertion.sam.11191772055868707229.sam Test: Test method testCleanSam[4](trailing_insertion.sam, 99M1I)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSam[4](trailing_insertion.sam, 99M1I)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSam[4](trailing_insertion.sam, 99M1I)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSam[4](trailing_insertion.sam, 99M1I)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.652 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.652 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCleanSam[4](trailing_insertion.sam, 99M1I)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.652 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.652 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCleanSam[4](trailing_insertion.sam, 99M1I)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.652 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.652 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCleanSam[4](trailing_insertion.sam, 99M1I)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.652 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.652 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCleanSam[4](trailing_insertion.sam, 99M1I)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] CleanSam INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CleanSam/trailing_insertion.sam OUTPUT=/tmp/trailing_insertion.sam.11191772055868707229.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:10 GMT+14:00 2024] CleanSam INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CleanSam/trailing_insertion.sam OUTPUT=/tmp/trailing_insertion.sam.11191772055868707229.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCleanSam[4](trailing_insertion.sam, 99M1I)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCleanSam[4](trailing_insertion.sam, 99M1I)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.sam.CleanSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.sam.CleanSam done. Elapsed time: 0.00 minutes. Test: Test method testCleanSam[4](trailing_insertion.sam, 99M1I)(picard.sam.CleanSamTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Test: Test method testCleanSam[4](trailing_insertion.sam, 99M1I)(picard.sam.CleanSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.CleanSamTest.testCleanSam[4](trailing_insertion.sam, 99M1I) STANDARD_OUT No errors found Running Test: Test method testCleanSam[5](long_trailing_insertion.sam, 90M10I)(picard.sam.CleanSamTest) Test: Test method testCleanSam[5](long_trailing_insertion.sam, 90M10I)(picard.sam.CleanSamTest) produced standard out/err: INFO 2024-07-02 11:51:10 CleanSam Gradle suite > Gradle test > picard.sam.CleanSamTest.testCleanSam[5](long_trailing_insertion.sam, 90M10I) STANDARD_ERROR INFO 2024-07-02 11:51:10 CleanSam Test: Test method testCleanSam[5](long_trailing_insertion.sam, 90M10I)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSam[5](long_trailing_insertion.sam, 90M10I)(picard.sam.CleanSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCleanSam[5](long_trailing_insertion.sam, 90M10I)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSam[5](long_trailing_insertion.sam, 90M10I)(picard.sam.CleanSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCleanSam[5](long_trailing_insertion.sam, 90M10I)(picard.sam.CleanSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCleanSam[5](long_trailing_insertion.sam, 90M10I)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSam[5](long_trailing_insertion.sam, 90M10I)(picard.sam.CleanSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCleanSam[5](long_trailing_insertion.sam, 90M10I)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSam[5](long_trailing_insertion.sam, 90M10I)(picard.sam.CleanSamTest) produced standard out/err: ********** CleanSam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CleanSam/long_trailing_insertion.sam -OUTPUT /tmp/long_trailing_insertion.sam.13932560085960873020.sam ********** CleanSam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CleanSam/long_trailing_insertion.sam -OUTPUT /tmp/long_trailing_insertion.sam.13932560085960873020.sam Test: Test method testCleanSam[5](long_trailing_insertion.sam, 90M10I)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSam[5](long_trailing_insertion.sam, 90M10I)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSam[5](long_trailing_insertion.sam, 90M10I)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSam[5](long_trailing_insertion.sam, 90M10I)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.672 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.672 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCleanSam[5](long_trailing_insertion.sam, 90M10I)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.672 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.672 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCleanSam[5](long_trailing_insertion.sam, 90M10I)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.672 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.672 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCleanSam[5](long_trailing_insertion.sam, 90M10I)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.672 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.672 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCleanSam[5](long_trailing_insertion.sam, 90M10I)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] CleanSam INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CleanSam/long_trailing_insertion.sam OUTPUT=/tmp/long_trailing_insertion.sam.13932560085960873020.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:10 GMT+14:00 2024] CleanSam INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CleanSam/long_trailing_insertion.sam OUTPUT=/tmp/long_trailing_insertion.sam.13932560085960873020.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCleanSam[5](long_trailing_insertion.sam, 90M10I)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCleanSam[5](long_trailing_insertion.sam, 90M10I)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.sam.CleanSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.sam.CleanSam done. Elapsed time: 0.00 minutes. Test: Test method testCleanSam[5](long_trailing_insertion.sam, 90M10I)(picard.sam.CleanSamTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Test: Test method testCleanSam[5](long_trailing_insertion.sam, 90M10I)(picard.sam.CleanSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.CleanSamTest.testCleanSam[5](long_trailing_insertion.sam, 90M10I) STANDARD_OUT No errors found Running Test: Test method testCleanSamTester[0](100M, 100M, 101, 2)(picard.sam.CleanSamTest) Test: Test method testCleanSamTester[0](100M, 100M, 101, 2)(picard.sam.CleanSamTest) produced standard out/err: INFO 2024-07-02 11:51:10 CleanSam Gradle suite > Gradle test > picard.sam.CleanSamTest.testCleanSamTester[0](100M, 100M, 101, 2) STANDARD_ERROR INFO 2024-07-02 11:51:10 CleanSam Test: Test method testCleanSamTester[0](100M, 100M, 101, 2)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSamTester[0](100M, 100M, 101, 2)(picard.sam.CleanSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCleanSamTester[0](100M, 100M, 101, 2)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSamTester[0](100M, 100M, 101, 2)(picard.sam.CleanSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCleanSamTester[0](100M, 100M, 101, 2)(picard.sam.CleanSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCleanSamTester[0](100M, 100M, 101, 2)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSamTester[0](100M, 100M, 101, 2)(picard.sam.CleanSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCleanSamTester[0](100M, 100M, 101, 2)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSamTester[0](100M, 100M, 101, 2)(picard.sam.CleanSamTest) produced standard out/err: ********** CleanSam -INPUT /tmp/CleanSamTester.13578903960739889040.tmp/input.sam -OUTPUT /tmp/CleanSamTester.13578903960739889040.tmp/output.sam ********** CleanSam -INPUT /tmp/CleanSamTester.13578903960739889040.tmp/input.sam -OUTPUT /tmp/CleanSamTester.13578903960739889040.tmp/output.sam Test: Test method testCleanSamTester[0](100M, 100M, 101, 2)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSamTester[0](100M, 100M, 101, 2)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSamTester[0](100M, 100M, 101, 2)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSamTester[0](100M, 100M, 101, 2)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.692 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.692 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCleanSamTester[0](100M, 100M, 101, 2)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.692 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.692 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCleanSamTester[0](100M, 100M, 101, 2)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.692 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.692 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCleanSamTester[0](100M, 100M, 101, 2)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.692 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.692 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCleanSamTester[0](100M, 100M, 101, 2)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] CleanSam INPUT=/tmp/CleanSamTester.13578903960739889040.tmp/input.sam OUTPUT=/tmp/CleanSamTester.13578903960739889040.tmp/output.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:10 GMT+14:00 2024] CleanSam INPUT=/tmp/CleanSamTester.13578903960739889040.tmp/input.sam OUTPUT=/tmp/CleanSamTester.13578903960739889040.tmp/output.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCleanSamTester[0](100M, 100M, 101, 2)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCleanSamTester[0](100M, 100M, 101, 2)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.sam.CleanSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.sam.CleanSam done. Elapsed time: 0.00 minutes. Test: Test method testCleanSamTester[0](100M, 100M, 101, 2)(picard.sam.CleanSamTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Test: Test method testCleanSamTester[0](100M, 100M, 101, 2)(picard.sam.CleanSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.CleanSamTest.testCleanSamTester[0](100M, 100M, 101, 2) STANDARD_OUT No errors found Running Test: Test method testCleanSamTester[1](100M, 99M1S, 101, 3)(picard.sam.CleanSamTest) Test: Test method testCleanSamTester[1](100M, 99M1S, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: INFO 2024-07-02 11:51:10 CleanSam Gradle suite > Gradle test > picard.sam.CleanSamTest.testCleanSamTester[1](100M, 99M1S, 101, 3) STANDARD_ERROR INFO 2024-07-02 11:51:10 CleanSam Test: Test method testCleanSamTester[1](100M, 99M1S, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSamTester[1](100M, 99M1S, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCleanSamTester[1](100M, 99M1S, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSamTester[1](100M, 99M1S, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCleanSamTester[1](100M, 99M1S, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCleanSamTester[1](100M, 99M1S, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSamTester[1](100M, 99M1S, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCleanSamTester[1](100M, 99M1S, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSamTester[1](100M, 99M1S, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: ********** CleanSam -INPUT /tmp/CleanSamTester.985992136977072441.tmp/input.sam -OUTPUT /tmp/CleanSamTester.985992136977072441.tmp/output.sam ********** CleanSam -INPUT /tmp/CleanSamTester.985992136977072441.tmp/input.sam -OUTPUT /tmp/CleanSamTester.985992136977072441.tmp/output.sam Test: Test method testCleanSamTester[1](100M, 99M1S, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSamTester[1](100M, 99M1S, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSamTester[1](100M, 99M1S, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSamTester[1](100M, 99M1S, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.715 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.715 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCleanSamTester[1](100M, 99M1S, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.715 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.715 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCleanSamTester[1](100M, 99M1S, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.715 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.715 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCleanSamTester[1](100M, 99M1S, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.715 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.715 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCleanSamTester[1](100M, 99M1S, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] CleanSam INPUT=/tmp/CleanSamTester.985992136977072441.tmp/input.sam OUTPUT=/tmp/CleanSamTester.985992136977072441.tmp/output.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:10 GMT+14:00 2024] CleanSam INPUT=/tmp/CleanSamTester.985992136977072441.tmp/input.sam OUTPUT=/tmp/CleanSamTester.985992136977072441.tmp/output.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCleanSamTester[1](100M, 99M1S, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCleanSamTester[1](100M, 99M1S, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: Ignoring SAM validation error: ERROR::CIGAR_MAPS_OFF_REFERENCE:Read name READ0, Read CIGAR M operator maps off end of reference Ignoring SAM validation error: ERROR::CIGAR_MAPS_OFF_REFERENCE:Read name READ0, Read CIGAR M operator maps off end of reference Test: Test method testCleanSamTester[1](100M, 99M1S, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: Ignoring SAM validation error: ERROR::CIGAR_MAPS_OFF_REFERENCE:Read name READ0, Read CIGAR M operator maps off end of reference Ignoring SAM validation error: ERROR::CIGAR_MAPS_OFF_REFERENCE:Read name READ0, Read CIGAR M operator maps off end of reference Test: Test method testCleanSamTester[1](100M, 99M1S, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.sam.CleanSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.sam.CleanSam done. Elapsed time: 0.00 minutes. Test: Test method testCleanSamTester[1](100M, 99M1S, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Test: Test method testCleanSamTester[1](100M, 99M1S, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.CleanSamTest.testCleanSamTester[1](100M, 99M1S, 101, 3) STANDARD_OUT No errors found Running Test: Test method testCleanSamTester[2](91M2D9M, 91M2D9M, 102, 1)(picard.sam.CleanSamTest) Test: Test method testCleanSamTester[2](91M2D9M, 91M2D9M, 102, 1)(picard.sam.CleanSamTest) produced standard out/err: INFO 2024-07-02 11:51:10 CleanSam Gradle suite > Gradle test > picard.sam.CleanSamTest.testCleanSamTester[2](91M2D9M, 91M2D9M, 102, 1) STANDARD_ERROR INFO 2024-07-02 11:51:10 CleanSam Test: Test method testCleanSamTester[2](91M2D9M, 91M2D9M, 102, 1)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSamTester[2](91M2D9M, 91M2D9M, 102, 1)(picard.sam.CleanSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCleanSamTester[2](91M2D9M, 91M2D9M, 102, 1)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSamTester[2](91M2D9M, 91M2D9M, 102, 1)(picard.sam.CleanSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCleanSamTester[2](91M2D9M, 91M2D9M, 102, 1)(picard.sam.CleanSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCleanSamTester[2](91M2D9M, 91M2D9M, 102, 1)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSamTester[2](91M2D9M, 91M2D9M, 102, 1)(picard.sam.CleanSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCleanSamTester[2](91M2D9M, 91M2D9M, 102, 1)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSamTester[2](91M2D9M, 91M2D9M, 102, 1)(picard.sam.CleanSamTest) produced standard out/err: ********** CleanSam -INPUT /tmp/CleanSamTester.15019539775046973946.tmp/input.sam -OUTPUT /tmp/CleanSamTester.15019539775046973946.tmp/output.sam ********** CleanSam -INPUT /tmp/CleanSamTester.15019539775046973946.tmp/input.sam -OUTPUT /tmp/CleanSamTester.15019539775046973946.tmp/output.sam Test: Test method testCleanSamTester[2](91M2D9M, 91M2D9M, 102, 1)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSamTester[2](91M2D9M, 91M2D9M, 102, 1)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSamTester[2](91M2D9M, 91M2D9M, 102, 1)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSamTester[2](91M2D9M, 91M2D9M, 102, 1)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.736 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.736 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCleanSamTester[2](91M2D9M, 91M2D9M, 102, 1)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.736 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.736 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCleanSamTester[2](91M2D9M, 91M2D9M, 102, 1)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.736 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.736 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCleanSamTester[2](91M2D9M, 91M2D9M, 102, 1)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.736 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.736 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCleanSamTester[2](91M2D9M, 91M2D9M, 102, 1)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] CleanSam INPUT=/tmp/CleanSamTester.15019539775046973946.tmp/input.sam OUTPUT=/tmp/CleanSamTester.15019539775046973946.tmp/output.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:10 GMT+14:00 2024] CleanSam INPUT=/tmp/CleanSamTester.15019539775046973946.tmp/input.sam OUTPUT=/tmp/CleanSamTester.15019539775046973946.tmp/output.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCleanSamTester[2](91M2D9M, 91M2D9M, 102, 1)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCleanSamTester[2](91M2D9M, 91M2D9M, 102, 1)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.sam.CleanSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.sam.CleanSam done. Elapsed time: 0.00 minutes. Test: Test method testCleanSamTester[2](91M2D9M, 91M2D9M, 102, 1)(picard.sam.CleanSamTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Test: Test method testCleanSamTester[2](91M2D9M, 91M2D9M, 102, 1)(picard.sam.CleanSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.CleanSamTest.testCleanSamTester[2](91M2D9M, 91M2D9M, 102, 1) STANDARD_OUT No errors found Running Test: Test method testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1)(picard.sam.CleanSamTest) Test: Test method testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1)(picard.sam.CleanSamTest) produced standard out/err: INFO 2024-07-02 11:51:10 CleanSam Gradle suite > Gradle test > picard.sam.CleanSamTest.testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1) STANDARD_ERROR INFO 2024-07-02 11:51:10 CleanSam Test: Test method testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1)(picard.sam.CleanSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1)(picard.sam.CleanSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1)(picard.sam.CleanSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1)(picard.sam.CleanSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1)(picard.sam.CleanSamTest) produced standard out/err: ********** CleanSam -INPUT /tmp/CleanSamTester.12193330399357015493.tmp/input.sam -OUTPUT /tmp/CleanSamTester.12193330399357015493.tmp/output.sam ********** CleanSam -INPUT /tmp/CleanSamTester.12193330399357015493.tmp/input.sam -OUTPUT /tmp/CleanSamTester.12193330399357015493.tmp/output.sam Test: Test method testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.756 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.756 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.756 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.756 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.756 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.756 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.756 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.756 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] CleanSam INPUT=/tmp/CleanSamTester.12193330399357015493.tmp/input.sam OUTPUT=/tmp/CleanSamTester.12193330399357015493.tmp/output.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:10 GMT+14:00 2024] CleanSam INPUT=/tmp/CleanSamTester.12193330399357015493.tmp/input.sam OUTPUT=/tmp/CleanSamTester.12193330399357015493.tmp/output.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1)(picard.sam.CleanSamTest) produced standard out/err: Ignoring SAM validation error: ERROR::CIGAR_MAPS_OFF_REFERENCE:Read name READ0, Read CIGAR M operator maps off end of reference Ignoring SAM validation error: ERROR::CIGAR_MAPS_OFF_REFERENCE:Read name READ0, Read CIGAR M operator maps off end of reference Test: Test method testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1)(picard.sam.CleanSamTest) produced standard out/err: Ignoring SAM validation error: ERROR::CIGAR_MAPS_OFF_REFERENCE:Read name READ0, Read CIGAR M operator maps off end of reference Ignoring SAM validation error: ERROR::CIGAR_MAPS_OFF_REFERENCE:Read name READ0, Read CIGAR M operator maps off end of reference Test: Test method testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.sam.CleanSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.sam.CleanSam done. Elapsed time: 0.00 minutes. Test: Test method testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1)(picard.sam.CleanSamTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Test: Test method testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1)(picard.sam.CleanSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.CleanSamTest.testCleanSamTester[3](91M2D9M, 91M2D8M1S, 101, 1) STANDARD_OUT No errors found Running Test: Test method testCleanSamTester[4](99M1I, 99M1I, 101, 3)(picard.sam.CleanSamTest) Test: Test method testCleanSamTester[4](99M1I, 99M1I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: INFO 2024-07-02 11:51:10 CleanSam Gradle suite > Gradle test > picard.sam.CleanSamTest.testCleanSamTester[4](99M1I, 99M1I, 101, 3) STANDARD_ERROR INFO 2024-07-02 11:51:10 CleanSam Test: Test method testCleanSamTester[4](99M1I, 99M1I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSamTester[4](99M1I, 99M1I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCleanSamTester[4](99M1I, 99M1I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSamTester[4](99M1I, 99M1I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCleanSamTester[4](99M1I, 99M1I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCleanSamTester[4](99M1I, 99M1I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSamTester[4](99M1I, 99M1I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCleanSamTester[4](99M1I, 99M1I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSamTester[4](99M1I, 99M1I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: ********** CleanSam -INPUT /tmp/CleanSamTester.6208153359783140118.tmp/input.sam -OUTPUT /tmp/CleanSamTester.6208153359783140118.tmp/output.sam ********** CleanSam -INPUT /tmp/CleanSamTester.6208153359783140118.tmp/input.sam -OUTPUT /tmp/CleanSamTester.6208153359783140118.tmp/output.sam Test: Test method testCleanSamTester[4](99M1I, 99M1I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSamTester[4](99M1I, 99M1I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSamTester[4](99M1I, 99M1I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSamTester[4](99M1I, 99M1I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.777 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.777 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCleanSamTester[4](99M1I, 99M1I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.777 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.777 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCleanSamTester[4](99M1I, 99M1I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.777 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.777 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCleanSamTester[4](99M1I, 99M1I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.777 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.777 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCleanSamTester[4](99M1I, 99M1I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] CleanSam INPUT=/tmp/CleanSamTester.6208153359783140118.tmp/input.sam OUTPUT=/tmp/CleanSamTester.6208153359783140118.tmp/output.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:10 GMT+14:00 2024] CleanSam INPUT=/tmp/CleanSamTester.6208153359783140118.tmp/input.sam OUTPUT=/tmp/CleanSamTester.6208153359783140118.tmp/output.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCleanSamTester[4](99M1I, 99M1I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCleanSamTester[4](99M1I, 99M1I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.sam.CleanSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.sam.CleanSam done. Elapsed time: 0.00 minutes. Test: Test method testCleanSamTester[4](99M1I, 99M1I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Test: Test method testCleanSamTester[4](99M1I, 99M1I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.CleanSamTest.testCleanSamTester[4](99M1I, 99M1I, 101, 3) STANDARD_OUT No errors found Running Test: Test method testCleanSamTester[5](90M10I, 90M10I, 101, 3)(picard.sam.CleanSamTest) Test: Test method testCleanSamTester[5](90M10I, 90M10I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: INFO 2024-07-02 11:51:10 CleanSam Gradle suite > Gradle test > picard.sam.CleanSamTest.testCleanSamTester[5](90M10I, 90M10I, 101, 3) STANDARD_ERROR INFO 2024-07-02 11:51:10 CleanSam Test: Test method testCleanSamTester[5](90M10I, 90M10I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSamTester[5](90M10I, 90M10I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCleanSamTester[5](90M10I, 90M10I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSamTester[5](90M10I, 90M10I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCleanSamTester[5](90M10I, 90M10I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCleanSamTester[5](90M10I, 90M10I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSamTester[5](90M10I, 90M10I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCleanSamTester[5](90M10I, 90M10I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSamTester[5](90M10I, 90M10I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: ********** CleanSam -INPUT /tmp/CleanSamTester.15000478306604827348.tmp/input.sam -OUTPUT /tmp/CleanSamTester.15000478306604827348.tmp/output.sam ********** CleanSam -INPUT /tmp/CleanSamTester.15000478306604827348.tmp/input.sam -OUTPUT /tmp/CleanSamTester.15000478306604827348.tmp/output.sam Test: Test method testCleanSamTester[5](90M10I, 90M10I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: ********** ********** Test: Test method testCleanSamTester[5](90M10I, 90M10I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSamTester[5](90M10I, 90M10I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: Test: Test method testCleanSamTester[5](90M10I, 90M10I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.798 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.798 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCleanSamTester[5](90M10I, 90M10I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.798 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.798 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCleanSamTester[5](90M10I, 90M10I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.798 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.798 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCleanSamTester[5](90M10I, 90M10I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: 11:51:10.798 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.798 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCleanSamTester[5](90M10I, 90M10I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] CleanSam INPUT=/tmp/CleanSamTester.15000478306604827348.tmp/input.sam OUTPUT=/tmp/CleanSamTester.15000478306604827348.tmp/output.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:10 GMT+14:00 2024] CleanSam INPUT=/tmp/CleanSamTester.15000478306604827348.tmp/input.sam OUTPUT=/tmp/CleanSamTester.15000478306604827348.tmp/output.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCleanSamTester[5](90M10I, 90M10I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCleanSamTester[5](90M10I, 90M10I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.sam.CleanSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:10 GMT+14:00 2024] picard.sam.CleanSam done. Elapsed time: 0.00 minutes. Test: Test method testCleanSamTester[5](90M10I, 90M10I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Test: Test method testCleanSamTester[5](90M10I, 90M10I, 101, 3)(picard.sam.CleanSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.CleanSamTest.testCleanSamTester[5](90M10I, 90M10I, 101, 3) STANDARD_OUT No errors found Running Test: Test method testAdapterInAllReadPositions[0](100)(picard.util.ClippingUtilityTest) Running Test: Test method testAdapterInAllReadPositions[1](36)(picard.util.ClippingUtilityTest) Running Test: Test method testAdapterListTruncation[0](PAIRED_END)(picard.util.ClippingUtilityTest) Running Test: Test method testAdapterListTruncation[1](INDEXED)(picard.util.ClippingUtilityTest) Running Test: Test method testAdapterListTruncation[2](SINGLE_END)(picard.util.ClippingUtilityTest) Running Test: Test method testAdapterListTruncation[3](NEXTERA_V1)(picard.util.ClippingUtilityTest) Running Test: Test method testAdapterListTruncation[4](NEXTERA_V2)(picard.util.ClippingUtilityTest) Running Test: Test method testAdapterListTruncation[5](DUAL_INDEXED)(picard.util.ClippingUtilityTest) Running Test: Test method testAdapterListTruncation[6](FLUIDIGM)(picard.util.ClippingUtilityTest) Running Test: Test method testAdapterListTruncation[7](TRUSEQ_SMALLRNA)(picard.util.ClippingUtilityTest) Running Test: Test method testAdapterListTruncation[8](ALTERNATIVE_SINGLE_END)(picard.util.ClippingUtilityTest) Running Test: Test method testAdapterTruncation(picard.util.ClippingUtilityTest) Running Test: Test method testBasicClip[0](Simple test 1, AAAAACCCCCAGATCGGAAGAGCA, AGATCGGAAGAGCG, 14, 0.15, 10)(picard.util.ClippingUtilityTest) Running Test: Test method testBasicClip[1](Simple test 2, AAAAACCCCCGGGGGAGATCGGAAGAGCA, AGATCGGAAGAGCG, 14, 0.15, 15)(picard.util.ClippingUtilityTest) Running Test: Test method testBasicClip[2](No adapter, AAAAACCCCCGGGGGTTTTT, AGATCGGAAGAGCG, 6, 0.15, -1)(picard.util.ClippingUtilityTest) Running Test: Test method testBasicClip[3](Partial adapter, AAAAACCCCCTGATCGGAA, AGATCGGAAGAGCG, 9, 0.15, 10)(picard.util.ClippingUtilityTest) Running Test: Test method testBasicClip[4](No sequence, null, AGATCGGAAGAGCG, 6, 0.15, -1)(picard.util.ClippingUtilityTest) Running Test: Test method testBasicClip[5](Read too short, AGATCGGAAG, AGATCGGAAGAGCG, 11, 0.15, -1)(picard.util.ClippingUtilityTest) Running Test: Test method testBasicClip[6](All No Calls, AAACCCNNNNNNNNNNNNNNNNNNNN, AGATCGGAAGAGCG, 6, 0.15, -1)(picard.util.ClippingUtilityTest) Running Test: Test method testBasicClip[7](From Test Data1, CGGCATTCCTGCTGAACCGAGATCGGAAGAGCGTCGTGTAGGGAAAGGGGGTGGATCTCGGTGGGCGGCGTGTTGT, AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT, 57, 0.15, 19)(picard.util.ClippingUtilityTest) Running Test: Test method testBasicClip[8](From Test Data2a, CGGAAGAGCGGTTCAGCAGGAATGCCGAGATCCGAA, AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT, 9, 0.14, 27)(picard.util.ClippingUtilityTest) Running Test: Test method testBasicClip[9](From Test Data2b, CGGAAGAGCGGTTCAGCAGGAATGCCGAGATCGGAA, AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT, 10, 0.14, -1)(picard.util.ClippingUtilityTest) Running Test: Test method testBasicClip[10](From PE Test Data1, CGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGGT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, 17, 0.14, 19)(picard.util.ClippingUtilityTest) Running Test: Test method testBasicClip[11](From PE Test Data2, CGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGGT, AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT, 5, 0.14, -1)(picard.util.ClippingUtilityTest) Running Test: Test method testBasicClip[12](From Test 8-clipped, TGGGGTGGTTATTGTTGATTTTTGTTTGTGTGTTAGGTTGTTTGTGTTAGTTTTTTATTTTATTTTCGAGATCGAA, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, 8, 0.14, 68)(picard.util.ClippingUtilityTest) Running Test: Test method testBasicClip[13](50% can be bad, AAAAACCCCCAGGTCGGAAGAGCG, AGATCGGAAGAGCG, 5, 0.5, 18)(picard.util.ClippingUtilityTest) Running Test: Test method testBasicClip[14](From 30E54AAXX.5.a, ATATCTGAAGATCTCGTATGCCGTCTTCTGCTTG, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, 34, 0.14, 0)(picard.util.ClippingUtilityTest) Running Test: Test method testBasicClip[15](From 30E54AAXX.5.b, ATATCTGAAGATCTCGTATGCCGTCTTCTGCTTG, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, 34, 0.14, 0)(picard.util.ClippingUtilityTest) Running Test: Test method testOneSidedMatchSupersededByTwoSidedMatch(picard.util.ClippingUtilityTest) Running Test: Test method testPairedEndClip[0](Basic positive paired test matching, CTACTGGCGCTGAAACTGAGCAGCCAAGCAGATCGG, GCTTGGCTGCTCAGTTTCAGCGCCAGTAGAGATCGG, INDEXED)(picard.util.ClippingUtilityTest) Running Test: Test method testPairedEndClip[1](Basic positive first end one-sided test matching, CTACTGGCGCTGAAAAGATCGGAAGAGCGGTTCAGC, AAAAAATTTTTTCCCCCCGGGGGGAAAAAATTTTTT, PAIRED_END)(picard.util.ClippingUtilityTest) Running Test: Test method testPairedEndClip[2](Basic positive second end one-sided test matching, AAAAAATTTTTTCCCCCCGGGGGGAAAAAATTTTTT, AAAAAATTTTTTCCCAGATCGGAAGAGCGTCGTGTA, PAIRED_END)(picard.util.ClippingUtilityTest) Running Test: Test method testPairedEndClip[3](Basic negative one-sided test matching, GGCGCTGAAACTACTGGCGCTGAAAAGATCGGAAGA, AAAAAATTTTTTCCCCCCGGGGGGAAAAAATTTTTT, null)(picard.util.ClippingUtilityTest) Running Test: Test method testPairedEndClip[4](Mis-match paired test matching, CTACTGGCGCTGAAACTGAGCAGCCAAGCAGATCGG, AGCTTGGCTGCTCAGTTTCAGCGCCAGTAGAGATCG, null)(picard.util.ClippingUtilityTest) Running Test: Test method testSingleEndSamRecordClip[0](Simple test 1, AAAAACCCCCAGATCGGAAGAGCA, AGATCGGAAGAGCG, 14, 0.15, 10)(picard.util.ClippingUtilityTest) Running Test: Test method testSingleEndSamRecordClip[1](Simple test 2, AAAAACCCCCGGGGGAGATCGGAAGAGCA, AGATCGGAAGAGCG, 14, 0.15, 15)(picard.util.ClippingUtilityTest) Running Test: Test method testSingleEndSamRecordClip[2](No adapter, AAAAACCCCCGGGGGTTTTT, AGATCGGAAGAGCG, 6, 0.15, -1)(picard.util.ClippingUtilityTest) Running Test: Test method testSingleEndSamRecordClip[3](Partial adapter, AAAAACCCCCTGATCGGAA, AGATCGGAAGAGCG, 9, 0.15, 10)(picard.util.ClippingUtilityTest) Running Test: Test method testSingleEndSamRecordClip[4](No sequence, null, AGATCGGAAGAGCG, 6, 0.15, -1)(picard.util.ClippingUtilityTest) Running Test: Test method testSingleEndSamRecordClip[5](Read too short, AGATCGGAAG, AGATCGGAAGAGCG, 11, 0.15, -1)(picard.util.ClippingUtilityTest) Running Test: Test method testSingleEndSamRecordClip[6](All No Calls, AAACCCNNNNNNNNNNNNNNNNNNNN, AGATCGGAAGAGCG, 6, 0.15, -1)(picard.util.ClippingUtilityTest) Running Test: Test method testSingleEndSamRecordClip[7](From Test Data1, CGGCATTCCTGCTGAACCGAGATCGGAAGAGCGTCGTGTAGGGAAAGGGGGTGGATCTCGGTGGGCGGCGTGTTGT, AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT, 57, 0.15, 19)(picard.util.ClippingUtilityTest) Running Test: Test method testSingleEndSamRecordClip[8](From Test Data2a, CGGAAGAGCGGTTCAGCAGGAATGCCGAGATCCGAA, AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT, 9, 0.14, 27)(picard.util.ClippingUtilityTest) Running Test: Test method testSingleEndSamRecordClip[9](From Test Data2b, CGGAAGAGCGGTTCAGCAGGAATGCCGAGATCGGAA, AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT, 10, 0.14, -1)(picard.util.ClippingUtilityTest) Running Test: Test method testSingleEndSamRecordClip[10](From PE Test Data1, CGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGGT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, 17, 0.14, 19)(picard.util.ClippingUtilityTest) Running Test: Test method testSingleEndSamRecordClip[11](From PE Test Data2, CGGTTCAGCAGGAATGCCGAGATCGGAAGAGCGGGT, AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT, 5, 0.14, -1)(picard.util.ClippingUtilityTest) Running Test: Test method testSingleEndSamRecordClip[12](From Test 8-clipped, TGGGGTGGTTATTGTTGATTTTTGTTTGTGTGTTAGGTTGTTTGTGTTAGTTTTTTATTTTATTTTCGAGATCGAA, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, 8, 0.14, 68)(picard.util.ClippingUtilityTest) Running Test: Test method testSingleEndSamRecordClip[13](50% can be bad, AAAAACCCCCAGGTCGGAAGAGCG, AGATCGGAAGAGCG, 5, 0.5, 18)(picard.util.ClippingUtilityTest) Running Test: Test method testSingleEndSamRecordClip[14](From 30E54AAXX.5.a, ATATCTGAAGATCTCGTATGCCGTCTTCTGCTTG, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, 34, 0.14, 0)(picard.util.ClippingUtilityTest) Running Test: Test method testSingleEndSamRecordClip[15](From 30E54AAXX.5.b, ATATCTGAAGATCTCGTATGCCGTCTTCTGCTTG, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, 34, 0.14, 0)(picard.util.ClippingUtilityTest) Running Test: Test method multiBinMixedEmptyBinTest(picard.illumina.parser.readers.ClocsFileReaderTest) Running Test: Test method multiBinTest[0](testdata/picard/illumina/readerTests/s_3_2102.clocs, 0, 2102)(picard.illumina.parser.readers.ClocsFileReaderTest) Running Test: Test method multiBinTest[1](testdata/picard/illumina/readerTests/s_3_2103.clocs, 2, 2103)(picard.illumina.parser.readers.ClocsFileReaderTest) Running Test: Test method multiBinTest[2](testdata/picard/illumina/readerTests/s_3_2104.clocs, 0, 2104)(picard.illumina.parser.readers.ClocsFileReaderTest) Running Test: Test method multiRowFileTest(picard.illumina.parser.readers.ClocsFileReaderTest) Running Test: Test method singleBinTest(picard.illumina.parser.readers.ClocsFileReaderTest) Running Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:10 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.ClusterCrosscheckMetricsTest.testSimpleCluster STANDARD_ERROR INFO 2024-07-02 11:51:10 CrosscheckFingerprints Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: ********** ********** Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: ********** ********** Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: ********** ********** Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam -OUTPUT /tmp/Fingerprinting8715544843321534001NA1291_and_NA12892.RG.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -2.0 -CROSSCHECK_BY FILE -EXPECT_ALL_GROUPS_TO_MATCH false ********** CrosscheckFingerprints -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam -OUTPUT /tmp/Fingerprinting8715544843321534001NA1291_and_NA12892.RG.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -2.0 -CROSSCHECK_BY FILE -EXPECT_ALL_GROUPS_TO_MATCH false Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: ********** ********** Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: 11:51:10.942 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:51:10.942 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: 11:51:10.944 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:51:10.944 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: 11:51:10.945 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.945 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: 11:51:10.945 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.945 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: 11:51:10.945 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:10.945 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: 11:51:10.945 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:10.945 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam] OUTPUT=/tmp/Fingerprinting8715544843321534001NA1291_and_NA12892.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 CROSSCHECK_BY=FILE EXPECT_ALL_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:10 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam] OUTPUT=/tmp/Fingerprinting8715544843321534001NA1291_and_NA12892.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 CROSSCHECK_BY=FILE EXPECT_ALL_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:10 CrosscheckFingerprints Fingerprinting 4 INPUT files. INFO 2024-07-02 11:51:10 CrosscheckFingerprints Fingerprinting 4 INPUT files. Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: WARNING 2024-07-02 11:51:10 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam) WARNING 2024-07-02 11:51:10 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam) Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: WARNING 2024-07-02 11:51:11 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) WARNING 2024-07-02 11:51:11 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: WARNING 2024-07-02 11:51:11 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) WARNING 2024-07-02 11:51:11 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: WARNING 2024-07-02 11:51:11 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) WARNING 2024-07-02 11:51:11 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:11 FingerprintChecker Processed files. 104 fingerprints found in map. INFO 2024-07-02 11:51:11 FingerprintChecker Processed files. 104 fingerprints found in map. Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:11 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:51:11 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:11 CrosscheckFingerprints All FILEs are related as expected. INFO 2024-07-02 11:51:11 CrosscheckFingerprints All FILEs are related as expected. Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: [Tue Jul 02 11:51:11 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:11 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:11 ClusterCrosscheckMetrics INFO 2024-07-02 11:51:11 ClusterCrosscheckMetrics Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: ********** ********** Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: ********** ********** Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: ********** ********** Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: ********** ClusterCrosscheckMetrics -INPUT /tmp/Fingerprinting8715544843321534001NA1291_and_NA12892.RG.crosscheck_metrics -OUTPUT /tmp/Fingerprinting6250461236325628900NA1291_and_NA12892.RG.clustered_crosscheck_metrics -LOD_THRESHOLD 1.5 ********** ClusterCrosscheckMetrics -INPUT /tmp/Fingerprinting8715544843321534001NA1291_and_NA12892.RG.crosscheck_metrics -OUTPUT /tmp/Fingerprinting6250461236325628900NA1291_and_NA12892.RG.clustered_crosscheck_metrics -LOD_THRESHOLD 1.5 Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: ********** ********** Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: 11:51:11.228 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:11.228 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: 11:51:11.228 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:11.228 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: 11:51:11.228 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:11.228 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: 11:51:11.228 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:11.228 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: [Tue Jul 02 11:51:11 GMT+14:00 2024] ClusterCrosscheckMetrics INPUT=/tmp/Fingerprinting8715544843321534001NA1291_and_NA12892.RG.crosscheck_metrics OUTPUT=/tmp/Fingerprinting6250461236325628900NA1291_and_NA12892.RG.clustered_crosscheck_metrics LOD_THRESHOLD=1.5 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:11 GMT+14:00 2024] ClusterCrosscheckMetrics INPUT=/tmp/Fingerprinting8715544843321534001NA1291_and_NA12892.RG.crosscheck_metrics OUTPUT=/tmp/Fingerprinting6250461236325628900NA1291_and_NA12892.RG.clustered_crosscheck_metrics LOD_THRESHOLD=1.5 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: [Tue Jul 02 11:51:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: [Tue Jul 02 11:51:11 GMT+14:00 2024] picard.fingerprint.ClusterCrosscheckMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:11 GMT+14:00 2024] picard.fingerprint.ClusterCrosscheckMetrics done. Elapsed time: 0.00 minutes. Test: Test method testSimpleCluster(picard.fingerprint.ClusterCrosscheckMetricsTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method test(picard.analysis.CollectAlignmentSummaryMetricsTest) Test: Test method test(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:11 CollectAlignmentSummaryMetrics Gradle suite > Gradle test > picard.analysis.CollectAlignmentSummaryMetricsTest.test STANDARD_ERROR INFO 2024-07-02 11:51:11 CollectAlignmentSummaryMetrics Test: Test method test(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method test(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method test(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method test(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method test(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method test(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method test(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method test(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method test(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** CollectAlignmentSummaryMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/test13935909767586949159.txt -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta ********** CollectAlignmentSummaryMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/test13935909767586949159.txt -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta Test: Test method test(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method test(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method test(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method test(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.254 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:11.254 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method test(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.254 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:11.254 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method test(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.254 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:11.254 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method test(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.254 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:11.254 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method test(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:11 GMT+14:00 2024] CollectAlignmentSummaryMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/test13935909767586949159.txt REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false COLLECT_ALIGNMENT_INFORMATION=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:11 GMT+14:00 2024] CollectAlignmentSummaryMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/test13935909767586949159.txt REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false COLLECT_ALIGNMENT_INFORMATION=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method test(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method test(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:11 GMT+14:00 2024] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:11 GMT+14:00 2024] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes. Test: Test method test(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method testAdapterReads(picard.analysis.CollectAlignmentSummaryMetricsTest) Test: Test method testAdapterReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:11 CollectAlignmentSummaryMetrics Gradle suite > Gradle test > picard.analysis.CollectAlignmentSummaryMetricsTest.testAdapterReads STANDARD_ERROR INFO 2024-07-02 11:51:11 CollectAlignmentSummaryMetrics Test: Test method testAdapterReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testAdapterReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testAdapterReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testAdapterReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testAdapterReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testAdapterReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testAdapterReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testAdapterReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testAdapterReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** CollectAlignmentSummaryMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test_adapter_reads.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testAdapterReads16817723578033892143.txt -MAX_INSERT_SIZE 200 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta ********** CollectAlignmentSummaryMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test_adapter_reads.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testAdapterReads16817723578033892143.txt -MAX_INSERT_SIZE 200 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta Test: Test method testAdapterReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testAdapterReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testAdapterReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testAdapterReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.283 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:11.283 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAdapterReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.283 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:11.283 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAdapterReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.283 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:11.283 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAdapterReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.283 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:11.283 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAdapterReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:11 GMT+14:00 2024] CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=200 INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test_adapter_reads.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testAdapterReads16817723578033892143.txt REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false COLLECT_ALIGNMENT_INFORMATION=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:11 GMT+14:00 2024] CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=200 INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test_adapter_reads.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testAdapterReads16817723578033892143.txt REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false COLLECT_ALIGNMENT_INFORMATION=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testAdapterReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testAdapterReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: WARNING 2024-07-02 11:51:11 SinglePassSamProgram File reports sort order 'unsorted', assuming it's coordinate sorted anyway. WARNING 2024-07-02 11:51:11 SinglePassSamProgram File reports sort order 'unsorted', assuming it's coordinate sorted anyway. Test: Test method testAdapterReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:11 GMT+14:00 2024] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:11 GMT+14:00 2024] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes. Test: Test method testAdapterReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method testBisulfite(picard.analysis.CollectAlignmentSummaryMetricsTest) Test: Test method testBisulfite(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:11 CollectAlignmentSummaryMetrics Gradle suite > Gradle test > picard.analysis.CollectAlignmentSummaryMetricsTest.testBisulfite STANDARD_ERROR INFO 2024-07-02 11:51:11 CollectAlignmentSummaryMetrics Test: Test method testBisulfite(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testBisulfite(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBisulfite(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testBisulfite(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBisulfite(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBisulfite(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testBisulfite(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBisulfite(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testBisulfite(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** CollectAlignmentSummaryMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_bisulfite_test.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testBisulfite5610661962832091205.txt -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta -IS_BISULFITE_SEQUENCED true ********** CollectAlignmentSummaryMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_bisulfite_test.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testBisulfite5610661962832091205.txt -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta -IS_BISULFITE_SEQUENCED true Test: Test method testBisulfite(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testBisulfite(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testBisulfite(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testBisulfite(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.306 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:11.306 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBisulfite(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.306 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:11.306 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBisulfite(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.306 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:11.306 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBisulfite(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.306 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:11.306 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBisulfite(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:11 GMT+14:00 2024] CollectAlignmentSummaryMetrics IS_BISULFITE_SEQUENCED=true INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_bisulfite_test.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testBisulfite5610661962832091205.txt REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] COLLECT_ALIGNMENT_INFORMATION=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:11 GMT+14:00 2024] CollectAlignmentSummaryMetrics IS_BISULFITE_SEQUENCED=true INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_bisulfite_test.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testBisulfite5610661962832091205.txt REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] COLLECT_ALIGNMENT_INFORMATION=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBisulfite(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBisulfite(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:11 GMT+14:00 2024] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:11 GMT+14:00 2024] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes. Test: Test method testBisulfite(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method testBisulfiteButNot(picard.analysis.CollectAlignmentSummaryMetricsTest) Test: Test method testBisulfiteButNot(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:11 CollectAlignmentSummaryMetrics Gradle suite > Gradle test > picard.analysis.CollectAlignmentSummaryMetricsTest.testBisulfiteButNot STANDARD_ERROR INFO 2024-07-02 11:51:11 CollectAlignmentSummaryMetrics Test: Test method testBisulfiteButNot(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testBisulfiteButNot(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBisulfiteButNot(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testBisulfiteButNot(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBisulfiteButNot(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBisulfiteButNot(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testBisulfiteButNot(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBisulfiteButNot(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testBisulfiteButNot(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** CollectAlignmentSummaryMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_bisulfite_test.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testBisulfiteButNot6491890580888310090.txt -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta -IS_BISULFITE_SEQUENCED false ********** CollectAlignmentSummaryMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_bisulfite_test.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testBisulfiteButNot6491890580888310090.txt -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta -IS_BISULFITE_SEQUENCED false Test: Test method testBisulfiteButNot(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testBisulfiteButNot(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testBisulfiteButNot(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testBisulfiteButNot(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.327 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:11.327 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBisulfiteButNot(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.328 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:11.328 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBisulfiteButNot(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.328 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:11.328 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBisulfiteButNot(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.328 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:11.328 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBisulfiteButNot(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:11 GMT+14:00 2024] CollectAlignmentSummaryMetrics IS_BISULFITE_SEQUENCED=false INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_bisulfite_test.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testBisulfiteButNot6491890580888310090.txt REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] COLLECT_ALIGNMENT_INFORMATION=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:11 GMT+14:00 2024] CollectAlignmentSummaryMetrics IS_BISULFITE_SEQUENCED=false INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_bisulfite_test.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testBisulfiteButNot6491890580888310090.txt REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] COLLECT_ALIGNMENT_INFORMATION=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBisulfiteButNot(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBisulfiteButNot(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:11 GMT+14:00 2024] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:11 GMT+14:00 2024] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes. Test: Test method testBisulfiteButNot(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method testChimeras(picard.analysis.CollectAlignmentSummaryMetricsTest) Test: Test method testChimeras(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:11 CollectAlignmentSummaryMetrics Gradle suite > Gradle test > picard.analysis.CollectAlignmentSummaryMetricsTest.testChimeras STANDARD_ERROR INFO 2024-07-02 11:51:11 CollectAlignmentSummaryMetrics Test: Test method testChimeras(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testChimeras(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testChimeras(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testChimeras(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testChimeras(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testChimeras(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testChimeras(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testChimeras(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testChimeras(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** CollectAlignmentSummaryMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test_chimeras.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testChimeras10428059226092083565.txt -MAX_INSERT_SIZE 20 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta ********** CollectAlignmentSummaryMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test_chimeras.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testChimeras10428059226092083565.txt -MAX_INSERT_SIZE 20 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta Test: Test method testChimeras(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testChimeras(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testChimeras(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testChimeras(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.351 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:11.351 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testChimeras(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.351 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:11.351 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testChimeras(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.351 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:11.351 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testChimeras(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.351 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:11.351 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testChimeras(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:11 GMT+14:00 2024] CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=20 INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test_chimeras.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testChimeras10428059226092083565.txt REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false COLLECT_ALIGNMENT_INFORMATION=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:11 GMT+14:00 2024] CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=20 INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test_chimeras.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testChimeras10428059226092083565.txt REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false COLLECT_ALIGNMENT_INFORMATION=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testChimeras(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testChimeras(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:11 GMT+14:00 2024] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:11 GMT+14:00 2024] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes. Test: Test method testChimeras(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method testMultipleLevelsOfMetrics(picard.analysis.CollectAlignmentSummaryMetricsTest) Test: Test method testMultipleLevelsOfMetrics(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:11 CollectAlignmentSummaryMetrics Gradle suite > Gradle test > picard.analysis.CollectAlignmentSummaryMetricsTest.testMultipleLevelsOfMetrics STANDARD_ERROR INFO 2024-07-02 11:51:11 CollectAlignmentSummaryMetrics Test: Test method testMultipleLevelsOfMetrics(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testMultipleLevelsOfMetrics(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMultipleLevelsOfMetrics(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleLevelsOfMetrics(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMultipleLevelsOfMetrics(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMultipleLevelsOfMetrics(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleLevelsOfMetrics(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMultipleLevelsOfMetrics(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleLevelsOfMetrics(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** CollectAlignmentSummaryMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test_multiple.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testMultipleLevelsOfMetrics14340386973897376839.txt -METRIC_ACCUMULATION_LEVEL ALL_READS -METRIC_ACCUMULATION_LEVEL SAMPLE -METRIC_ACCUMULATION_LEVEL LIBRARY -METRIC_ACCUMULATION_LEVEL READ_GROUP -COLLECT_ALIGNMENT_INFORMATION false ********** CollectAlignmentSummaryMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test_multiple.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testMultipleLevelsOfMetrics14340386973897376839.txt -METRIC_ACCUMULATION_LEVEL ALL_READS -METRIC_ACCUMULATION_LEVEL SAMPLE -METRIC_ACCUMULATION_LEVEL LIBRARY -METRIC_ACCUMULATION_LEVEL READ_GROUP -COLLECT_ALIGNMENT_INFORMATION false Test: Test method testMultipleLevelsOfMetrics(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleLevelsOfMetrics(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testMultipleLevelsOfMetrics(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testMultipleLevelsOfMetrics(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.375 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:11.375 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleLevelsOfMetrics(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.375 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:11.375 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleLevelsOfMetrics(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.375 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:11.375 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleLevelsOfMetrics(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.375 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:11.375 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleLevelsOfMetrics(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:11 GMT+14:00 2024] CollectAlignmentSummaryMetrics METRIC_ACCUMULATION_LEVEL=[READ_GROUP, LIBRARY, SAMPLE, ALL_READS] COLLECT_ALIGNMENT_INFORMATION=false INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test_multiple.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testMultipleLevelsOfMetrics14340386973897376839.txt MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] IS_BISULFITE_SEQUENCED=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:11 GMT+14:00 2024] CollectAlignmentSummaryMetrics METRIC_ACCUMULATION_LEVEL=[READ_GROUP, LIBRARY, SAMPLE, ALL_READS] COLLECT_ALIGNMENT_INFORMATION=false INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test_multiple.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testMultipleLevelsOfMetrics14340386973897376839.txt MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] IS_BISULFITE_SEQUENCED=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMultipleLevelsOfMetrics(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMultipleLevelsOfMetrics(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:11 GMT+14:00 2024] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:11 GMT+14:00 2024] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes. Test: Test method testMultipleLevelsOfMetrics(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method testNoReference(picard.analysis.CollectAlignmentSummaryMetricsTest) Test: Test method testNoReference(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:11 CollectAlignmentSummaryMetrics Gradle suite > Gradle test > picard.analysis.CollectAlignmentSummaryMetricsTest.testNoReference STANDARD_ERROR INFO 2024-07-02 11:51:11 CollectAlignmentSummaryMetrics Test: Test method testNoReference(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testNoReference(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testNoReference(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testNoReference(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testNoReference(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testNoReference(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testNoReference(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testNoReference(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testNoReference(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** CollectAlignmentSummaryMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testNoReference16818142105108246094.txt -COLLECT_ALIGNMENT_INFORMATION false ********** CollectAlignmentSummaryMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testNoReference16818142105108246094.txt -COLLECT_ALIGNMENT_INFORMATION false Test: Test method testNoReference(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testNoReference(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testNoReference(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testNoReference(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.406 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:11.406 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoReference(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.406 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:11.406 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoReference(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.406 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:11.406 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoReference(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.406 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:11.406 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoReference(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:11 GMT+14:00 2024] CollectAlignmentSummaryMetrics COLLECT_ALIGNMENT_INFORMATION=false INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testNoReference16818142105108246094.txt MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:11 GMT+14:00 2024] CollectAlignmentSummaryMetrics COLLECT_ALIGNMENT_INFORMATION=false INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testNoReference16818142105108246094.txt MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testNoReference(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testNoReference(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:11 GMT+14:00 2024] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:11 GMT+14:00 2024] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes. Test: Test method testNoReference(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method testReadLengthHistogram[0](true)(picard.analysis.CollectAlignmentSummaryMetricsTest) Test: Test method testReadLengthHistogram[0](true)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:11 CollectAlignmentSummaryMetrics Gradle suite > Gradle test > picard.analysis.CollectAlignmentSummaryMetricsTest.testReadLengthHistogram[0](true) STANDARD_ERROR INFO 2024-07-02 11:51:11 CollectAlignmentSummaryMetrics Test: Test method testReadLengthHistogram[0](true)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testReadLengthHistogram[0](true)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testReadLengthHistogram[0](true)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testReadLengthHistogram[0](true)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testReadLengthHistogram[0](true)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testReadLengthHistogram[0](true)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testReadLengthHistogram[0](true)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testReadLengthHistogram[0](true)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testReadLengthHistogram[0](true)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** CollectAlignmentSummaryMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test3.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram362130143235998138.txt -HISTOGRAM_FILE /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram16657560627795002349.pdf ********** CollectAlignmentSummaryMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test3.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram362130143235998138.txt -HISTOGRAM_FILE /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram16657560627795002349.pdf Test: Test method testReadLengthHistogram[0](true)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testReadLengthHistogram[0](true)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testReadLengthHistogram[0](true)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testReadLengthHistogram[0](true)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:11 RExecutor Executing R script via command: Rscript /tmp/script441140086220925347.R INFO 2024-07-02 11:51:11 RExecutor Executing R script via command: Rscript /tmp/script441140086220925347.R Test: Test method testReadLengthHistogram[0](true)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:11 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:51:11 ProcessExecutor [1] "Checking if R is installed" Test: Test method testReadLengthHistogram[0](true)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.835 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:11.835 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testReadLengthHistogram[0](true)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.835 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:11.835 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testReadLengthHistogram[0](true)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.835 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:11.835 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testReadLengthHistogram[0](true)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:11.835 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:11.835 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testReadLengthHistogram[0](true)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:11 GMT+14:00 2024] CollectAlignmentSummaryMetrics HISTOGRAM_FILE=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram16657560627795002349.pdf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test3.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram362130143235998138.txt MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false COLLECT_ALIGNMENT_INFORMATION=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:11 GMT+14:00 2024] CollectAlignmentSummaryMetrics HISTOGRAM_FILE=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram16657560627795002349.pdf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test3.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram362130143235998138.txt MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false COLLECT_ALIGNMENT_INFORMATION=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testReadLengthHistogram[0](true)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testReadLengthHistogram[0](true)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: WARNING 2024-07-02 11:51:11 CollectAlignmentSummaryMetrics Without a REFERENCE_SEQUENCE, metrics pertaining to mismatch rates will not be collected! WARNING 2024-07-02 11:51:11 CollectAlignmentSummaryMetrics Without a REFERENCE_SEQUENCE, metrics pertaining to mismatch rates will not be collected! Test: Test method testReadLengthHistogram[0](true)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:11 RExecutor Executing R script via command: Rscript /tmp/script12979680596181997566.R /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram362130143235998138.txt /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram16657560627795002349.pdf summary_alignment_stats_test3.sam INFO 2024-07-02 11:51:11 RExecutor Executing R script via command: Rscript /tmp/script12979680596181997566.R /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram362130143235998138.txt /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram16657560627795002349.pdf summary_alignment_stats_test3.sam Test: Test method testReadLengthHistogram[0](true)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:12 ProcessExecutor null device INFO 2024-07-02 11:51:12 ProcessExecutor null device Test: Test method testReadLengthHistogram[0](true)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:12 ProcessExecutor 1 INFO 2024-07-02 11:51:12 ProcessExecutor 1 Test: Test method testReadLengthHistogram[0](true)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:12 GMT+14:00 2024] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:51:12 GMT+14:00 2024] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.01 minutes. Test: Test method testReadLengthHistogram[0](true)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method testReadLengthHistogram[1](false)(picard.analysis.CollectAlignmentSummaryMetricsTest) Test: Test method testReadLengthHistogram[1](false)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:12 CollectAlignmentSummaryMetrics Gradle suite > Gradle test > picard.analysis.CollectAlignmentSummaryMetricsTest.testReadLengthHistogram[1](false) STANDARD_ERROR INFO 2024-07-02 11:51:12 CollectAlignmentSummaryMetrics Test: Test method testReadLengthHistogram[1](false)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testReadLengthHistogram[1](false)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testReadLengthHistogram[1](false)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testReadLengthHistogram[1](false)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testReadLengthHistogram[1](false)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testReadLengthHistogram[1](false)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testReadLengthHistogram[1](false)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testReadLengthHistogram[1](false)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testReadLengthHistogram[1](false)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** CollectAlignmentSummaryMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test3.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram10081899431491943154.txt ********** CollectAlignmentSummaryMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test3.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram10081899431491943154.txt Test: Test method testReadLengthHistogram[1](false)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testReadLengthHistogram[1](false)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testReadLengthHistogram[1](false)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testReadLengthHistogram[1](false)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:12.427 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:12.427 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testReadLengthHistogram[1](false)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:12.427 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:12.427 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testReadLengthHistogram[1](false)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:12.427 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:12.427 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testReadLengthHistogram[1](false)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:12.427 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:12.427 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testReadLengthHistogram[1](false)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:12 GMT+14:00 2024] CollectAlignmentSummaryMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test3.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram10081899431491943154.txt MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false COLLECT_ALIGNMENT_INFORMATION=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:12 GMT+14:00 2024] CollectAlignmentSummaryMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test3.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram10081899431491943154.txt MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false COLLECT_ALIGNMENT_INFORMATION=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testReadLengthHistogram[1](false)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testReadLengthHistogram[1](false)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: WARNING 2024-07-02 11:51:12 CollectAlignmentSummaryMetrics Without a REFERENCE_SEQUENCE, metrics pertaining to mismatch rates will not be collected! WARNING 2024-07-02 11:51:12 CollectAlignmentSummaryMetrics Without a REFERENCE_SEQUENCE, metrics pertaining to mismatch rates will not be collected! Test: Test method testReadLengthHistogram[1](false)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:12 GMT+14:00 2024] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:12 GMT+14:00 2024] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes. Test: Test method testReadLengthHistogram[1](false)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method testReadLengthHistogram[0](summary_alignment_stats_test.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) Test: Test method testReadLengthHistogram[0](summary_alignment_stats_test.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:12 CollectAlignmentSummaryMetrics Gradle suite > Gradle test > picard.analysis.CollectAlignmentSummaryMetricsTest.testReadLengthHistogram[0](summary_alignment_stats_test.sam) STANDARD_ERROR INFO 2024-07-02 11:51:12 CollectAlignmentSummaryMetrics Test: Test method testReadLengthHistogram[0](summary_alignment_stats_test.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testReadLengthHistogram[0](summary_alignment_stats_test.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testReadLengthHistogram[0](summary_alignment_stats_test.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testReadLengthHistogram[0](summary_alignment_stats_test.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testReadLengthHistogram[0](summary_alignment_stats_test.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testReadLengthHistogram[0](summary_alignment_stats_test.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testReadLengthHistogram[0](summary_alignment_stats_test.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testReadLengthHistogram[0](summary_alignment_stats_test.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testReadLengthHistogram[0](summary_alignment_stats_test.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** CollectAlignmentSummaryMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram17913440134379748939.txt -HISTOGRAM_FILE /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram594526351809848081.pdf ********** CollectAlignmentSummaryMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram17913440134379748939.txt -HISTOGRAM_FILE /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram594526351809848081.pdf Test: Test method testReadLengthHistogram[0](summary_alignment_stats_test.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testReadLengthHistogram[0](summary_alignment_stats_test.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testReadLengthHistogram[0](summary_alignment_stats_test.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testReadLengthHistogram[0](summary_alignment_stats_test.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:12 RExecutor Executing R script via command: Rscript /tmp/script12106980038600933299.R INFO 2024-07-02 11:51:12 RExecutor Executing R script via command: Rscript /tmp/script12106980038600933299.R Test: Test method testReadLengthHistogram[0](summary_alignment_stats_test.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:12 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:51:12 ProcessExecutor [1] "Checking if R is installed" Test: Test method testReadLengthHistogram[0](summary_alignment_stats_test.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:12.739 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:12.739 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testReadLengthHistogram[0](summary_alignment_stats_test.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:12.739 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:12.739 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testReadLengthHistogram[0](summary_alignment_stats_test.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:12.739 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:12.739 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testReadLengthHistogram[0](summary_alignment_stats_test.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:12.739 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:12.739 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testReadLengthHistogram[0](summary_alignment_stats_test.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:12 GMT+14:00 2024] CollectAlignmentSummaryMetrics HISTOGRAM_FILE=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram594526351809848081.pdf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram17913440134379748939.txt MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false COLLECT_ALIGNMENT_INFORMATION=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:12 GMT+14:00 2024] CollectAlignmentSummaryMetrics HISTOGRAM_FILE=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram594526351809848081.pdf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram17913440134379748939.txt MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false COLLECT_ALIGNMENT_INFORMATION=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testReadLengthHistogram[0](summary_alignment_stats_test.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testReadLengthHistogram[0](summary_alignment_stats_test.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: WARNING 2024-07-02 11:51:12 CollectAlignmentSummaryMetrics Without a REFERENCE_SEQUENCE, metrics pertaining to mismatch rates will not be collected! WARNING 2024-07-02 11:51:12 CollectAlignmentSummaryMetrics Without a REFERENCE_SEQUENCE, metrics pertaining to mismatch rates will not be collected! Test: Test method testReadLengthHistogram[0](summary_alignment_stats_test.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:12 RExecutor Executing R script via command: Rscript /tmp/script17740975330557811285.R /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram17913440134379748939.txt /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram594526351809848081.pdf summary_alignment_stats_test.sam INFO 2024-07-02 11:51:12 RExecutor Executing R script via command: Rscript /tmp/script17740975330557811285.R /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram17913440134379748939.txt /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram594526351809848081.pdf summary_alignment_stats_test.sam Test: Test method testReadLengthHistogram[0](summary_alignment_stats_test.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:13 ProcessExecutor null device INFO 2024-07-02 11:51:13 ProcessExecutor null device Test: Test method testReadLengthHistogram[0](summary_alignment_stats_test.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:13 ProcessExecutor 1 INFO 2024-07-02 11:51:13 ProcessExecutor 1 Test: Test method testReadLengthHistogram[0](summary_alignment_stats_test.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:13 GMT+14:00 2024] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:51:13 GMT+14:00 2024] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.01 minutes. Test: Test method testReadLengthHistogram[0](summary_alignment_stats_test.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method testReadLengthHistogram[1](summary_alignment_stats_test2.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) Test: Test method testReadLengthHistogram[1](summary_alignment_stats_test2.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:13 CollectAlignmentSummaryMetrics Gradle suite > Gradle test > picard.analysis.CollectAlignmentSummaryMetricsTest.testReadLengthHistogram[1](summary_alignment_stats_test2.sam) STANDARD_ERROR INFO 2024-07-02 11:51:13 CollectAlignmentSummaryMetrics Test: Test method testReadLengthHistogram[1](summary_alignment_stats_test2.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testReadLengthHistogram[1](summary_alignment_stats_test2.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testReadLengthHistogram[1](summary_alignment_stats_test2.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testReadLengthHistogram[1](summary_alignment_stats_test2.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testReadLengthHistogram[1](summary_alignment_stats_test2.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testReadLengthHistogram[1](summary_alignment_stats_test2.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testReadLengthHistogram[1](summary_alignment_stats_test2.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testReadLengthHistogram[1](summary_alignment_stats_test2.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testReadLengthHistogram[1](summary_alignment_stats_test2.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** CollectAlignmentSummaryMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test2.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram17615859372813705161.txt -HISTOGRAM_FILE /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram13897361998925178687.pdf ********** CollectAlignmentSummaryMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test2.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram17615859372813705161.txt -HISTOGRAM_FILE /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram13897361998925178687.pdf Test: Test method testReadLengthHistogram[1](summary_alignment_stats_test2.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testReadLengthHistogram[1](summary_alignment_stats_test2.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testReadLengthHistogram[1](summary_alignment_stats_test2.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testReadLengthHistogram[1](summary_alignment_stats_test2.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:13 RExecutor Executing R script via command: Rscript /tmp/script15398774496022622253.R INFO 2024-07-02 11:51:13 RExecutor Executing R script via command: Rscript /tmp/script15398774496022622253.R Test: Test method testReadLengthHistogram[1](summary_alignment_stats_test2.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:13 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:51:13 ProcessExecutor [1] "Checking if R is installed" Test: Test method testReadLengthHistogram[1](summary_alignment_stats_test2.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:13.570 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:13.570 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testReadLengthHistogram[1](summary_alignment_stats_test2.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:13.570 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:13.570 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testReadLengthHistogram[1](summary_alignment_stats_test2.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:13.570 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:13.570 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testReadLengthHistogram[1](summary_alignment_stats_test2.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:13.570 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:13.570 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testReadLengthHistogram[1](summary_alignment_stats_test2.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:13 GMT+14:00 2024] CollectAlignmentSummaryMetrics HISTOGRAM_FILE=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram13897361998925178687.pdf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test2.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram17615859372813705161.txt MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false COLLECT_ALIGNMENT_INFORMATION=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:13 GMT+14:00 2024] CollectAlignmentSummaryMetrics HISTOGRAM_FILE=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram13897361998925178687.pdf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test2.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram17615859372813705161.txt MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false COLLECT_ALIGNMENT_INFORMATION=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testReadLengthHistogram[1](summary_alignment_stats_test2.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testReadLengthHistogram[1](summary_alignment_stats_test2.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: WARNING 2024-07-02 11:51:13 CollectAlignmentSummaryMetrics Without a REFERENCE_SEQUENCE, metrics pertaining to mismatch rates will not be collected! WARNING 2024-07-02 11:51:13 CollectAlignmentSummaryMetrics Without a REFERENCE_SEQUENCE, metrics pertaining to mismatch rates will not be collected! Test: Test method testReadLengthHistogram[1](summary_alignment_stats_test2.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:13 RExecutor Executing R script via command: Rscript /tmp/script12784852811772085853.R /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram17615859372813705161.txt /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram13897361998925178687.pdf summary_alignment_stats_test2.sam INFO 2024-07-02 11:51:13 RExecutor Executing R script via command: Rscript /tmp/script12784852811772085853.R /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram17615859372813705161.txt /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram13897361998925178687.pdf summary_alignment_stats_test2.sam Test: Test method testReadLengthHistogram[1](summary_alignment_stats_test2.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:14 ProcessExecutor null device INFO 2024-07-02 11:51:14 ProcessExecutor null device Test: Test method testReadLengthHistogram[1](summary_alignment_stats_test2.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:14 ProcessExecutor 1 INFO 2024-07-02 11:51:14 ProcessExecutor 1 Test: Test method testReadLengthHistogram[1](summary_alignment_stats_test2.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:14 GMT+14:00 2024] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:51:14 GMT+14:00 2024] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.01 minutes. Test: Test method testReadLengthHistogram[1](summary_alignment_stats_test2.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method testReadLengthHistogram[2](summary_alignment_stats_test3.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) Test: Test method testReadLengthHistogram[2](summary_alignment_stats_test3.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:14 CollectAlignmentSummaryMetrics Gradle suite > Gradle test > picard.analysis.CollectAlignmentSummaryMetricsTest.testReadLengthHistogram[2](summary_alignment_stats_test3.sam) STANDARD_ERROR INFO 2024-07-02 11:51:14 CollectAlignmentSummaryMetrics Test: Test method testReadLengthHistogram[2](summary_alignment_stats_test3.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testReadLengthHistogram[2](summary_alignment_stats_test3.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testReadLengthHistogram[2](summary_alignment_stats_test3.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testReadLengthHistogram[2](summary_alignment_stats_test3.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testReadLengthHistogram[2](summary_alignment_stats_test3.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testReadLengthHistogram[2](summary_alignment_stats_test3.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testReadLengthHistogram[2](summary_alignment_stats_test3.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testReadLengthHistogram[2](summary_alignment_stats_test3.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testReadLengthHistogram[2](summary_alignment_stats_test3.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** CollectAlignmentSummaryMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test3.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram17030145315466703920.txt -HISTOGRAM_FILE /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram10971354147812176455.pdf ********** CollectAlignmentSummaryMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test3.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram17030145315466703920.txt -HISTOGRAM_FILE /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram10971354147812176455.pdf Test: Test method testReadLengthHistogram[2](summary_alignment_stats_test3.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testReadLengthHistogram[2](summary_alignment_stats_test3.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testReadLengthHistogram[2](summary_alignment_stats_test3.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testReadLengthHistogram[2](summary_alignment_stats_test3.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:14 RExecutor Executing R script via command: Rscript /tmp/script15410067709032331892.R INFO 2024-07-02 11:51:14 RExecutor Executing R script via command: Rscript /tmp/script15410067709032331892.R Test: Test method testReadLengthHistogram[2](summary_alignment_stats_test3.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:14 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:51:14 ProcessExecutor [1] "Checking if R is installed" Test: Test method testReadLengthHistogram[2](summary_alignment_stats_test3.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:14.541 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:14.541 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testReadLengthHistogram[2](summary_alignment_stats_test3.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:14.541 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:14.541 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testReadLengthHistogram[2](summary_alignment_stats_test3.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:14.541 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:14.541 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testReadLengthHistogram[2](summary_alignment_stats_test3.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:14.541 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:14.541 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testReadLengthHistogram[2](summary_alignment_stats_test3.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:14 GMT+14:00 2024] CollectAlignmentSummaryMetrics HISTOGRAM_FILE=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram10971354147812176455.pdf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test3.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram17030145315466703920.txt MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false COLLECT_ALIGNMENT_INFORMATION=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:14 GMT+14:00 2024] CollectAlignmentSummaryMetrics HISTOGRAM_FILE=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram10971354147812176455.pdf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test3.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram17030145315466703920.txt MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false COLLECT_ALIGNMENT_INFORMATION=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testReadLengthHistogram[2](summary_alignment_stats_test3.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testReadLengthHistogram[2](summary_alignment_stats_test3.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: WARNING 2024-07-02 11:51:14 CollectAlignmentSummaryMetrics Without a REFERENCE_SEQUENCE, metrics pertaining to mismatch rates will not be collected! WARNING 2024-07-02 11:51:14 CollectAlignmentSummaryMetrics Without a REFERENCE_SEQUENCE, metrics pertaining to mismatch rates will not be collected! Test: Test method testReadLengthHistogram[2](summary_alignment_stats_test3.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:14 RExecutor Executing R script via command: Rscript /tmp/script205900148946609083.R /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram17030145315466703920.txt /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram10971354147812176455.pdf summary_alignment_stats_test3.sam INFO 2024-07-02 11:51:14 RExecutor Executing R script via command: Rscript /tmp/script205900148946609083.R /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram17030145315466703920.txt /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testReadLengthHistogram10971354147812176455.pdf summary_alignment_stats_test3.sam Test: Test method testReadLengthHistogram[2](summary_alignment_stats_test3.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:14 ProcessExecutor null device INFO 2024-07-02 11:51:14 ProcessExecutor null device Test: Test method testReadLengthHistogram[2](summary_alignment_stats_test3.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:14 ProcessExecutor 1 INFO 2024-07-02 11:51:14 ProcessExecutor 1 Test: Test method testReadLengthHistogram[2](summary_alignment_stats_test3.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:15 GMT+14:00 2024] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:51:15 GMT+14:00 2024] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.01 minutes. Test: Test method testReadLengthHistogram[2](summary_alignment_stats_test3.sam)(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method testZeroLengthReads(picard.analysis.CollectAlignmentSummaryMetricsTest) Test: Test method testZeroLengthReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:15 CollectAlignmentSummaryMetrics Gradle suite > Gradle test > picard.analysis.CollectAlignmentSummaryMetricsTest.testZeroLengthReads STANDARD_ERROR INFO 2024-07-02 11:51:15 CollectAlignmentSummaryMetrics Test: Test method testZeroLengthReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testZeroLengthReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testZeroLengthReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testZeroLengthReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testZeroLengthReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testZeroLengthReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testZeroLengthReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testZeroLengthReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testZeroLengthReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** CollectAlignmentSummaryMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test2.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testZeroLengthReads16039595152710989461.txt -COLLECT_ALIGNMENT_INFORMATION false ********** CollectAlignmentSummaryMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test2.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testZeroLengthReads16039595152710989461.txt -COLLECT_ALIGNMENT_INFORMATION false Test: Test method testZeroLengthReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: ********** ********** Test: Test method testZeroLengthReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testZeroLengthReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Test: Test method testZeroLengthReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:15.032 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:15.032 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testZeroLengthReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:15.032 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:15.032 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testZeroLengthReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:15.032 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:15.032 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testZeroLengthReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: 11:51:15.032 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:15.032 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testZeroLengthReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:15 GMT+14:00 2024] CollectAlignmentSummaryMetrics COLLECT_ALIGNMENT_INFORMATION=false INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test2.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testZeroLengthReads16039595152710989461.txt MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:15 GMT+14:00 2024] CollectAlignmentSummaryMetrics COLLECT_ALIGNMENT_INFORMATION=false INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test2.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectAlignmentSummaryMetricsTest11656522459179551928/testZeroLengthReads16039595152710989461.txt MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testZeroLengthReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testZeroLengthReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:15 GMT+14:00 2024] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:15 GMT+14:00 2024] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes. Test: Test method testZeroLengthReads(picard.analysis.CollectAlignmentSummaryMetricsTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method testCollectArraysVariantCallingMetricsOverkillTest[0](7991775143_R01C01, 636, 1, true, F, F, true, 3.0.0, 1.0.0.0, IlluminaGenotypingArray_v1.5, 0.999)(picard.arrays.CollectArraysVariantCallingMetricsTest) Test: Test method testCollectArraysVariantCallingMetricsOverkillTest[0](7991775143_R01C01, 636, 1, true, F, F, true, 3.0.0, 1.0.0.0, IlluminaGenotypingArray_v1.5, 0.999)(picard.arrays.CollectArraysVariantCallingMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:15 CollectArraysVariantCallingMetrics Loading dbSNP file. Gradle suite > Gradle test > picard.arrays.CollectArraysVariantCallingMetricsTest.testCollectArraysVariantCallingMetricsOverkillTest[0](7991775143_R01C01, 636, 1, true, F, F, true, 3.0.0, 1.0.0.0, IlluminaGenotypingArray_v1.5, 0.999) STANDARD_ERROR INFO 2024-07-02 11:51:15 CollectArraysVariantCallingMetrics Loading dbSNP file. Test: Test method testCollectArraysVariantCallingMetricsOverkillTest[0](7991775143_R01C01, 636, 1, true, F, F, true, 3.0.0, 1.0.0.0, IlluminaGenotypingArray_v1.5, 0.999)(picard.arrays.CollectArraysVariantCallingMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:15 CollectArraysVariantCallingMetrics Starting iteration of variants. INFO 2024-07-02 11:51:15 CollectArraysVariantCallingMetrics Starting iteration of variants. Running Test: Test method testCollectArraysVariantCallingMetricsOverkillTest[1](7991775143_R01C01_wo_optional_fields, 631, null, false, M, N, false, 2.0.0.137, null, null, null)(picard.arrays.CollectArraysVariantCallingMetricsTest) Test: Test method testCollectArraysVariantCallingMetricsOverkillTest[1](7991775143_R01C01_wo_optional_fields, 631, null, false, M, N, false, 2.0.0.137, null, null, null)(picard.arrays.CollectArraysVariantCallingMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:15 CollectArraysVariantCallingMetrics Loading dbSNP file. Gradle suite > Gradle test > picard.arrays.CollectArraysVariantCallingMetricsTest.testCollectArraysVariantCallingMetricsOverkillTest[1](7991775143_R01C01_wo_optional_fields, 631, null, false, M, N, false, 2.0.0.137, null, null, null) STANDARD_ERROR INFO 2024-07-02 11:51:15 CollectArraysVariantCallingMetrics Loading dbSNP file. Test: Test method testCollectArraysVariantCallingMetricsOverkillTest[1](7991775143_R01C01_wo_optional_fields, 631, null, false, M, N, false, 2.0.0.137, null, null, null)(picard.arrays.CollectArraysVariantCallingMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:15 CollectArraysVariantCallingMetrics Starting iteration of variants. INFO 2024-07-02 11:51:15 CollectArraysVariantCallingMetrics Starting iteration of variants. Running Test: Test method testCollectArraysVariantCallingMetricsTwoSamples(picard.arrays.CollectArraysVariantCallingMetricsTest) Test: Test method testCollectArraysVariantCallingMetricsTwoSamples(picard.arrays.CollectArraysVariantCallingMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:15 CollectArraysVariantCallingMetrics Loading dbSNP file. Gradle suite > Gradle test > picard.arrays.CollectArraysVariantCallingMetricsTest.testCollectArraysVariantCallingMetricsTwoSamples STANDARD_ERROR INFO 2024-07-02 11:51:15 CollectArraysVariantCallingMetrics Loading dbSNP file. Test: Test method testCollectArraysVariantCallingMetricsTwoSamples(picard.arrays.CollectArraysVariantCallingMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:15 CollectArraysVariantCallingMetrics Starting iteration of variants. INFO 2024-07-02 11:51:15 CollectArraysVariantCallingMetrics Starting iteration of variants. Running Test: Test method testSexConcordance[0](Male, Male, Male, true)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[1](Male, Male, Female, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[2](Male, Male, Unknown, true)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[3](Male, Male, NotReported, true)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[4](Male, Female, Male, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[5](Male, Female, Female, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[6](Male, Female, Unknown, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[7](Male, Female, NotReported, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[8](Male, Unknown, Male, true)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[9](Male, Unknown, Female, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[10](Male, Unknown, Unknown, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[11](Male, Unknown, NotReported, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[12](Male, NotReported, Male, true)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[13](Male, NotReported, Female, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[14](Male, NotReported, Unknown, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[15](Male, NotReported, NotReported, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[16](Female, Male, Male, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[17](Female, Male, Female, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[18](Female, Male, Unknown, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[19](Female, Male, NotReported, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[20](Female, Female, Male, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[21](Female, Female, Female, true)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[22](Female, Female, Unknown, true)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[23](Female, Female, NotReported, true)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[24](Female, Unknown, Male, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[25](Female, Unknown, Female, true)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[26](Female, Unknown, Unknown, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[27](Female, Unknown, NotReported, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[28](Female, NotReported, Male, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[29](Female, NotReported, Female, true)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[30](Female, NotReported, Unknown, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[31](Female, NotReported, NotReported, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[32](Unknown, Male, Male, true)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[33](Unknown, Male, Female, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[34](Unknown, Male, Unknown, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[35](Unknown, Male, NotReported, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[36](Unknown, Female, Male, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[37](Unknown, Female, Female, true)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[38](Unknown, Female, Unknown, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[39](Unknown, Female, NotReported, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[40](Unknown, Unknown, Male, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[41](Unknown, Unknown, Female, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[42](Unknown, Unknown, Unknown, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[43](Unknown, Unknown, NotReported, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[44](Unknown, NotReported, Male, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[45](Unknown, NotReported, Female, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[46](Unknown, NotReported, Unknown, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[47](Unknown, NotReported, NotReported, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[48](NotReported, Male, Male, true)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[49](NotReported, Male, Female, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[50](NotReported, Male, Unknown, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[51](NotReported, Male, NotReported, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[52](NotReported, Female, Male, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[53](NotReported, Female, Female, true)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[54](NotReported, Female, Unknown, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[55](NotReported, Female, NotReported, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[56](NotReported, Unknown, Male, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[57](NotReported, Unknown, Female, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[58](NotReported, Unknown, Unknown, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[59](NotReported, Unknown, NotReported, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[60](NotReported, NotReported, Male, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[61](NotReported, NotReported, Female, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[62](NotReported, NotReported, Unknown, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method testSexConcordance[63](NotReported, NotReported, NotReported, false)(picard.arrays.CollectArraysVariantCallingMetricsTest) Running Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:15 CollectGcBiasMetrics Gradle suite > Gradle test > picard.analysis.CollectGcBiasMetricsTest.runCheckingNoSEQTest STANDARD_ERROR INFO 2024-07-02 11:51:15 CollectGcBiasMetrics Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** ********** Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** ********** Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** ********** Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** CollectGcBiasMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/metrics/chrM_NO_SEQ.sam -OUTPUT /tmp/test3865833659892562660.gc_bias.detail_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -SUMMARY_OUTPUT /tmp/test2017122183936713296.gc_bias.summary_metrics -CHART_OUTPUT /tmp/test6760984481453897312.pdf -SCAN_WINDOW_SIZE 100 -MINIMUM_GENOME_FRACTION 1.0E-5 -IS_BISULFITE_SEQUENCED false -LEVEL ALL_READS -LEVEL SAMPLE -LEVEL READ_GROUP -ASSUME_SORTED false -ALSO_IGNORE_DUPLICATES false ********** CollectGcBiasMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/metrics/chrM_NO_SEQ.sam -OUTPUT /tmp/test3865833659892562660.gc_bias.detail_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -SUMMARY_OUTPUT /tmp/test2017122183936713296.gc_bias.summary_metrics -CHART_OUTPUT /tmp/test6760984481453897312.pdf -SCAN_WINDOW_SIZE 100 -MINIMUM_GENOME_FRACTION 1.0E-5 -IS_BISULFITE_SEQUENCED false -LEVEL ALL_READS -LEVEL SAMPLE -LEVEL READ_GROUP -ASSUME_SORTED false -ALSO_IGNORE_DUPLICATES false Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** ********** Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:15 RExecutor Executing R script via command: Rscript /tmp/script13152590403137804920.R INFO 2024-07-02 11:51:15 RExecutor Executing R script via command: Rscript /tmp/script13152590403137804920.R Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:16 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:51:16 ProcessExecutor [1] "Checking if R is installed" Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: 11:51:16.024 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:16.024 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: 11:51:16.024 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:16.024 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: 11:51:16.025 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:16.025 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: 11:51:16.025 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:16.025 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: [Tue Jul 02 11:51:16 GMT+14:00 2024] CollectGcBiasMetrics CHART_OUTPUT=/tmp/test6760984481453897312.pdf SUMMARY_OUTPUT=/tmp/test2017122183936713296.gc_bias.summary_metrics SCAN_WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=1.0E-5 IS_BISULFITE_SEQUENCED=false METRIC_ACCUMULATION_LEVEL=[READ_GROUP, SAMPLE, ALL_READS] ALSO_IGNORE_DUPLICATES=false INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/metrics/chrM_NO_SEQ.sam OUTPUT=/tmp/test3865833659892562660.gc_bias.detail_metrics ASSUME_SORTED=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:16 GMT+14:00 2024] CollectGcBiasMetrics CHART_OUTPUT=/tmp/test6760984481453897312.pdf SUMMARY_OUTPUT=/tmp/test2017122183936713296.gc_bias.summary_metrics SCAN_WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=1.0E-5 IS_BISULFITE_SEQUENCED=false METRIC_ACCUMULATION_LEVEL=[READ_GROUP, SAMPLE, ALL_READS] ALSO_IGNORE_DUPLICATES=false INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/metrics/chrM_NO_SEQ.sam OUTPUT=/tmp/test3865833659892562660.gc_bias.detail_metrics ASSUME_SORTED=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: [Tue Jul 02 11:51:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: WARNING 2024-07-02 11:51:16 GcBiasMetricsCollector Omitting read NRUSCA-WDL30341:66:000000000-ABTGC:1:2111:13507:4770 with '*' in SEQ field. WARNING 2024-07-02 11:51:16 GcBiasMetricsCollector Omitting read NRUSCA-WDL30341:66:000000000-ABTGC:1:2111:13507:4770 with '*' in SEQ field. Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: WARNING 2024-07-02 11:51:16 GcBiasMetricsCollector Omitting read NRUSCA-WDL30341:66:000000000-ABTGC:1:2111:13507:4770 with '*' in SEQ field. WARNING 2024-07-02 11:51:16 GcBiasMetricsCollector Omitting read NRUSCA-WDL30341:66:000000000-ABTGC:1:2111:13507:4770 with '*' in SEQ field. Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: WARNING 2024-07-02 11:51:16 GcBiasMetricsCollector Omitting read NRUSCA-WDL30341:66:000000000-ABTGC:1:2111:13507:4770 with '*' in SEQ field. WARNING 2024-07-02 11:51:16 GcBiasMetricsCollector Omitting read NRUSCA-WDL30341:66:000000000-ABTGC:1:2111:13507:4770 with '*' in SEQ field. Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:16 RExecutor Executing R script via command: Rscript /tmp/script14430108355352908696.R /tmp/test3865833659892562660.gc_bias.detail_metrics /tmp/test2017122183936713296.gc_bias.summary_metrics /tmp/test6760984481453897312.pdf 100 INFO 2024-07-02 11:51:16 RExecutor Executing R script via command: Rscript /tmp/script14430108355352908696.R /tmp/test3865833659892562660.gc_bias.detail_metrics /tmp/test2017122183936713296.gc_bias.summary_metrics /tmp/test6760984481453897312.pdf 100 Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:16 ProcessExecutor Total clusters: 0 , Aligned reads: 1Total clusters: 0 , Aligned reads: 1Total clusters: 0 , Aligned reads: 1 INFO 2024-07-02 11:51:16 ProcessExecutor Total clusters: 0 , Aligned reads: 1Total clusters: 0 , Aligned reads: 1Total clusters: 0 , Aligned reads: 1 Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: [Tue Jul 02 11:51:16 GMT+14:00 2024] picard.analysis.CollectGcBiasMetrics done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:51:16 GMT+14:00 2024] picard.analysis.CollectGcBiasMetrics done. Elapsed time: 0.01 minutes. Test: Test method runCheckingNoSEQTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method runGcBiasMultiLevelTest(picard.analysis.CollectGcBiasMetricsTest) Test: Test method runGcBiasMultiLevelTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:16 CollectGcBiasMetrics Gradle suite > Gradle test > picard.analysis.CollectGcBiasMetricsTest.runGcBiasMultiLevelTest STANDARD_ERROR INFO 2024-07-02 11:51:16 CollectGcBiasMetrics Test: Test method runGcBiasMultiLevelTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: Test: Test method runGcBiasMultiLevelTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method runGcBiasMultiLevelTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** ********** Test: Test method runGcBiasMultiLevelTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method runGcBiasMultiLevelTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method runGcBiasMultiLevelTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** ********** Test: Test method runGcBiasMultiLevelTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method runGcBiasMultiLevelTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** ********** Test: Test method runGcBiasMultiLevelTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** CollectGcBiasMetrics -INPUT /tmp/CollectGcBias18028020853166826936.bam -OUTPUT /tmp/test3448324265100105138.gc_bias.detail_metrics -REFERENCE_SEQUENCE testdata/picard/metrics/chrMNO.reference.fasta -SUMMARY_OUTPUT /tmp/test1390245289389205636.gc_bias.summary_metrics -CHART_OUTPUT /tmp/test4946491071912170144.pdf -SCAN_WINDOW_SIZE 100 -MINIMUM_GENOME_FRACTION 1.0E-5 -IS_BISULFITE_SEQUENCED false -LEVEL ALL_READS -LEVEL SAMPLE -LEVEL READ_GROUP -ASSUME_SORTED false -ALSO_IGNORE_DUPLICATES false ********** CollectGcBiasMetrics -INPUT /tmp/CollectGcBias18028020853166826936.bam -OUTPUT /tmp/test3448324265100105138.gc_bias.detail_metrics -REFERENCE_SEQUENCE testdata/picard/metrics/chrMNO.reference.fasta -SUMMARY_OUTPUT /tmp/test1390245289389205636.gc_bias.summary_metrics -CHART_OUTPUT /tmp/test4946491071912170144.pdf -SCAN_WINDOW_SIZE 100 -MINIMUM_GENOME_FRACTION 1.0E-5 -IS_BISULFITE_SEQUENCED false -LEVEL ALL_READS -LEVEL SAMPLE -LEVEL READ_GROUP -ASSUME_SORTED false -ALSO_IGNORE_DUPLICATES false Test: Test method runGcBiasMultiLevelTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** ********** Test: Test method runGcBiasMultiLevelTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: Test: Test method runGcBiasMultiLevelTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: Test: Test method runGcBiasMultiLevelTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:16 RExecutor Executing R script via command: Rscript /tmp/script9523507956290414582.R INFO 2024-07-02 11:51:16 RExecutor Executing R script via command: Rscript /tmp/script9523507956290414582.R Test: Test method runGcBiasMultiLevelTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:17 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:51:17 ProcessExecutor [1] "Checking if R is installed" Test: Test method runGcBiasMultiLevelTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: 11:51:17.045 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:17.045 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method runGcBiasMultiLevelTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: 11:51:17.045 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:17.045 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method runGcBiasMultiLevelTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: 11:51:17.045 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:17.045 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method runGcBiasMultiLevelTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: 11:51:17.045 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:17.045 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method runGcBiasMultiLevelTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: [Tue Jul 02 11:51:17 GMT+14:00 2024] CollectGcBiasMetrics CHART_OUTPUT=/tmp/test4946491071912170144.pdf SUMMARY_OUTPUT=/tmp/test1390245289389205636.gc_bias.summary_metrics SCAN_WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=1.0E-5 IS_BISULFITE_SEQUENCED=false METRIC_ACCUMULATION_LEVEL=[READ_GROUP, SAMPLE, ALL_READS] ALSO_IGNORE_DUPLICATES=false INPUT=/tmp/CollectGcBias18028020853166826936.bam OUTPUT=/tmp/test3448324265100105138.gc_bias.detail_metrics ASSUME_SORTED=false REFERENCE_SEQUENCE=testdata/picard/metrics/chrMNO.reference.fasta STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:17 GMT+14:00 2024] CollectGcBiasMetrics CHART_OUTPUT=/tmp/test4946491071912170144.pdf SUMMARY_OUTPUT=/tmp/test1390245289389205636.gc_bias.summary_metrics SCAN_WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=1.0E-5 IS_BISULFITE_SEQUENCED=false METRIC_ACCUMULATION_LEVEL=[READ_GROUP, SAMPLE, ALL_READS] ALSO_IGNORE_DUPLICATES=false INPUT=/tmp/CollectGcBias18028020853166826936.bam OUTPUT=/tmp/test3448324265100105138.gc_bias.detail_metrics ASSUME_SORTED=false REFERENCE_SEQUENCE=testdata/picard/metrics/chrMNO.reference.fasta STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method runGcBiasMultiLevelTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: [Tue Jul 02 11:51:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method runGcBiasMultiLevelTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:17 RExecutor Executing R script via command: Rscript /tmp/script14027862810670892789.R /tmp/test3448324265100105138.gc_bias.detail_metrics /tmp/test1390245289389205636.gc_bias.summary_metrics /tmp/test4946491071912170144.pdf 100 INFO 2024-07-02 11:51:17 RExecutor Executing R script via command: Rscript /tmp/script14027862810670892789.R /tmp/test3448324265100105138.gc_bias.detail_metrics /tmp/test1390245289389205636.gc_bias.summary_metrics /tmp/test4946491071912170144.pdf 100 Test: Test method runGcBiasMultiLevelTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:17 ProcessExecutor Total clusters: 300 , Aligned reads: 600Total clusters: 200 , Aligned reads: 400Total clusters: 100 , Aligned reads: 200Total clusters: 100 , Aligned reads: 200Total clusters: 100 , Aligned reads: 200Total clusters: 100 , Aligned reads: 200 INFO 2024-07-02 11:51:17 ProcessExecutor Total clusters: 300 , Aligned reads: 600Total clusters: 200 , Aligned reads: 400Total clusters: 100 , Aligned reads: 200Total clusters: 100 , Aligned reads: 200Total clusters: 100 , Aligned reads: 200Total clusters: 100 , Aligned reads: 200 Test: Test method runGcBiasMultiLevelTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: [Tue Jul 02 11:51:17 GMT+14:00 2024] picard.analysis.CollectGcBiasMetrics done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:51:17 GMT+14:00 2024] picard.analysis.CollectGcBiasMetrics done. Elapsed time: 0.01 minutes. Test: Test method runGcBiasMultiLevelTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method runNonDupsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) Test: Test method runNonDupsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:17 CollectGcBiasMetrics Gradle suite > Gradle test > picard.analysis.CollectGcBiasMetricsTest.runNonDupsComparisonTest STANDARD_ERROR INFO 2024-07-02 11:51:17 CollectGcBiasMetrics Test: Test method runNonDupsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: Test: Test method runNonDupsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method runNonDupsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** ********** Test: Test method runNonDupsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method runNonDupsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method runNonDupsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** ********** Test: Test method runNonDupsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method runNonDupsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** ********** Test: Test method runNonDupsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** CollectGcBiasMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/metrics/chrMReads.sam -OUTPUT /tmp/test12302684058849772540.gc_bias_detail_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -SUMMARY_OUTPUT /tmp/test17418971575939812197.gc_bias_summary_metrics -CHART_OUTPUT /tmp/test9071066001758849807.pdf -SCAN_WINDOW_SIZE 100 -MINIMUM_GENOME_FRACTION 1.0E-5 -IS_BISULFITE_SEQUENCED false -LEVEL ALL_READS -LEVEL SAMPLE -LEVEL READ_GROUP -ASSUME_SORTED false -ALSO_IGNORE_DUPLICATES true ********** CollectGcBiasMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/metrics/chrMReads.sam -OUTPUT /tmp/test12302684058849772540.gc_bias_detail_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -SUMMARY_OUTPUT /tmp/test17418971575939812197.gc_bias_summary_metrics -CHART_OUTPUT /tmp/test9071066001758849807.pdf -SCAN_WINDOW_SIZE 100 -MINIMUM_GENOME_FRACTION 1.0E-5 -IS_BISULFITE_SEQUENCED false -LEVEL ALL_READS -LEVEL SAMPLE -LEVEL READ_GROUP -ASSUME_SORTED false -ALSO_IGNORE_DUPLICATES true Test: Test method runNonDupsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** ********** Test: Test method runNonDupsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: Test: Test method runNonDupsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: Test: Test method runNonDupsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:17 RExecutor Executing R script via command: Rscript /tmp/script3512569064855552306.R INFO 2024-07-02 11:51:17 RExecutor Executing R script via command: Rscript /tmp/script3512569064855552306.R Test: Test method runNonDupsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:17 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:51:17 ProcessExecutor [1] "Checking if R is installed" Test: Test method runNonDupsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: 11:51:18.008 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:18.008 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method runNonDupsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: 11:51:18.009 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:18.009 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method runNonDupsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: 11:51:18.009 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:18.009 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method runNonDupsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: 11:51:18.009 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:18.009 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method runNonDupsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: [Tue Jul 02 11:51:18 GMT+14:00 2024] CollectGcBiasMetrics CHART_OUTPUT=/tmp/test9071066001758849807.pdf SUMMARY_OUTPUT=/tmp/test17418971575939812197.gc_bias_summary_metrics SCAN_WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=1.0E-5 IS_BISULFITE_SEQUENCED=false METRIC_ACCUMULATION_LEVEL=[READ_GROUP, SAMPLE, ALL_READS] ALSO_IGNORE_DUPLICATES=true INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/metrics/chrMReads.sam OUTPUT=/tmp/test12302684058849772540.gc_bias_detail_metrics ASSUME_SORTED=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:18 GMT+14:00 2024] CollectGcBiasMetrics CHART_OUTPUT=/tmp/test9071066001758849807.pdf SUMMARY_OUTPUT=/tmp/test17418971575939812197.gc_bias_summary_metrics SCAN_WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=1.0E-5 IS_BISULFITE_SEQUENCED=false METRIC_ACCUMULATION_LEVEL=[READ_GROUP, SAMPLE, ALL_READS] ALSO_IGNORE_DUPLICATES=true INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/metrics/chrMReads.sam OUTPUT=/tmp/test12302684058849772540.gc_bias_detail_metrics ASSUME_SORTED=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method runNonDupsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: [Tue Jul 02 11:51:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method runNonDupsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:18 RExecutor Executing R script via command: Rscript /tmp/script8538212751412538174.R /tmp/test12302684058849772540.gc_bias_detail_metrics /tmp/test17418971575939812197.gc_bias_summary_metrics /tmp/test9071066001758849807.pdf 100 INFO 2024-07-02 11:51:18 RExecutor Executing R script via command: Rscript /tmp/script8538212751412538174.R /tmp/test12302684058849772540.gc_bias_detail_metrics /tmp/test17418971575939812197.gc_bias_summary_metrics /tmp/test9071066001758849807.pdf 100 Test: Test method runNonDupsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:18 ProcessExecutor Total clusters: 5 , Aligned reads: 5Total clusters: 3 , Aligned reads: 3Total clusters: 5 , Aligned reads: 5Total clusters: 3 , Aligned reads: 3Total clusters: 5 , Aligned reads: 5Total clusters: 3 , Aligned reads: 3 INFO 2024-07-02 11:51:18 ProcessExecutor Total clusters: 5 , Aligned reads: 5Total clusters: 3 , Aligned reads: 3Total clusters: 5 , Aligned reads: 5Total clusters: 3 , Aligned reads: 3Total clusters: 5 , Aligned reads: 5Total clusters: 3 , Aligned reads: 3 Test: Test method runNonDupsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: [Tue Jul 02 11:51:18 GMT+14:00 2024] picard.analysis.CollectGcBiasMetrics done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:51:18 GMT+14:00 2024] picard.analysis.CollectGcBiasMetrics done. Elapsed time: 0.01 minutes. Test: Test method runNonDupsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:18 CollectGcBiasMetrics Gradle suite > Gradle test > picard.analysis.CollectGcBiasMetricsTest.runWindowsComparisonTest STANDARD_ERROR INFO 2024-07-02 11:51:18 CollectGcBiasMetrics Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** ********** Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** ********** Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** ********** Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** CollectGcBiasMetrics -INPUT /tmp/CollectGcBias18028020853166826936.bam -OUTPUT /tmp/test4886916216998781269.gc_bias_detail_metrics -REFERENCE_SEQUENCE testdata/picard/metrics/chrMNO.reference.fasta -SUMMARY_OUTPUT /tmp/test12824516104406877188.gc_bias_summary_metrics -CHART_OUTPUT /tmp/test11752592808999335267.pdf -SCAN_WINDOW_SIZE 100 -MINIMUM_GENOME_FRACTION 1.0E-5 -IS_BISULFITE_SEQUENCED false -LEVEL ALL_READS -LEVEL SAMPLE -LEVEL READ_GROUP -ASSUME_SORTED false -ALSO_IGNORE_DUPLICATES false ********** CollectGcBiasMetrics -INPUT /tmp/CollectGcBias18028020853166826936.bam -OUTPUT /tmp/test4886916216998781269.gc_bias_detail_metrics -REFERENCE_SEQUENCE testdata/picard/metrics/chrMNO.reference.fasta -SUMMARY_OUTPUT /tmp/test12824516104406877188.gc_bias_summary_metrics -CHART_OUTPUT /tmp/test11752592808999335267.pdf -SCAN_WINDOW_SIZE 100 -MINIMUM_GENOME_FRACTION 1.0E-5 -IS_BISULFITE_SEQUENCED false -LEVEL ALL_READS -LEVEL SAMPLE -LEVEL READ_GROUP -ASSUME_SORTED false -ALSO_IGNORE_DUPLICATES false Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** ********** Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:18 RExecutor Executing R script via command: Rscript /tmp/script8905141910980798130.R INFO 2024-07-02 11:51:18 RExecutor Executing R script via command: Rscript /tmp/script8905141910980798130.R Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:19 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:51:19 ProcessExecutor [1] "Checking if R is installed" Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: 11:51:19.094 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:19.094 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: 11:51:19.094 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:19.094 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: 11:51:19.094 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:19.094 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: 11:51:19.094 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:19.094 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: [Tue Jul 02 11:51:19 GMT+14:00 2024] CollectGcBiasMetrics CHART_OUTPUT=/tmp/test11752592808999335267.pdf SUMMARY_OUTPUT=/tmp/test12824516104406877188.gc_bias_summary_metrics SCAN_WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=1.0E-5 IS_BISULFITE_SEQUENCED=false METRIC_ACCUMULATION_LEVEL=[READ_GROUP, SAMPLE, ALL_READS] ALSO_IGNORE_DUPLICATES=false INPUT=/tmp/CollectGcBias18028020853166826936.bam OUTPUT=/tmp/test4886916216998781269.gc_bias_detail_metrics ASSUME_SORTED=false REFERENCE_SEQUENCE=testdata/picard/metrics/chrMNO.reference.fasta STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:19 GMT+14:00 2024] CollectGcBiasMetrics CHART_OUTPUT=/tmp/test11752592808999335267.pdf SUMMARY_OUTPUT=/tmp/test12824516104406877188.gc_bias_summary_metrics SCAN_WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=1.0E-5 IS_BISULFITE_SEQUENCED=false METRIC_ACCUMULATION_LEVEL=[READ_GROUP, SAMPLE, ALL_READS] ALSO_IGNORE_DUPLICATES=false INPUT=/tmp/CollectGcBias18028020853166826936.bam OUTPUT=/tmp/test4886916216998781269.gc_bias_detail_metrics ASSUME_SORTED=false REFERENCE_SEQUENCE=testdata/picard/metrics/chrMNO.reference.fasta STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: [Tue Jul 02 11:51:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:19 RExecutor Executing R script via command: Rscript /tmp/script15694823707141338179.R /tmp/test4886916216998781269.gc_bias_detail_metrics /tmp/test12824516104406877188.gc_bias_summary_metrics /tmp/test11752592808999335267.pdf 100 INFO 2024-07-02 11:51:19 RExecutor Executing R script via command: Rscript /tmp/script15694823707141338179.R /tmp/test4886916216998781269.gc_bias_detail_metrics /tmp/test12824516104406877188.gc_bias_summary_metrics /tmp/test11752592808999335267.pdf 100 Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:19 ProcessExecutor Total clusters: 300 , Aligned reads: 600Total clusters: 200 , Aligned reads: 400Total clusters: 100 , Aligned reads: 200Total clusters: 100 , Aligned reads: 200Total clusters: 100 , Aligned reads: 200Total clusters: 100 , Aligned reads: 200 INFO 2024-07-02 11:51:19 ProcessExecutor Total clusters: 300 , Aligned reads: 600Total clusters: 200 , Aligned reads: 400Total clusters: 100 , Aligned reads: 200Total clusters: 100 , Aligned reads: 200Total clusters: 100 , Aligned reads: 200Total clusters: 100 , Aligned reads: 200 Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: [Tue Jul 02 11:51:19 GMT+14:00 2024] picard.analysis.CollectGcBiasMetrics done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:51:19 GMT+14:00 2024] picard.analysis.CollectGcBiasMetrics done. Elapsed time: 0.01 minutes. Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:19 CollectGcBiasMetrics INFO 2024-07-02 11:51:19 CollectGcBiasMetrics Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** ********** Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** ********** Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** ********** Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** CollectGcBiasMetrics -INPUT /tmp/CollectGcBias13823779816851466163.bam -OUTPUT /tmp/testAllChrDetails1546016460150666037.gc_bias_detail_metrics -REFERENCE_SEQUENCE testdata/picard/metrics/chrMNO.reference.fasta -SUMMARY_OUTPUT /tmp/testAllChr11593184944798037039.gc_bias_summary_metrics -CHART_OUTPUT /tmp/test7620850762333890674.pdf -SCAN_WINDOW_SIZE 100 -MINIMUM_GENOME_FRACTION 1.0E-5 -IS_BISULFITE_SEQUENCED false -LEVEL ALL_READS -LEVEL SAMPLE -LEVEL READ_GROUP -ASSUME_SORTED false -ALSO_IGNORE_DUPLICATES false ********** CollectGcBiasMetrics -INPUT /tmp/CollectGcBias13823779816851466163.bam -OUTPUT /tmp/testAllChrDetails1546016460150666037.gc_bias_detail_metrics -REFERENCE_SEQUENCE testdata/picard/metrics/chrMNO.reference.fasta -SUMMARY_OUTPUT /tmp/testAllChr11593184944798037039.gc_bias_summary_metrics -CHART_OUTPUT /tmp/test7620850762333890674.pdf -SCAN_WINDOW_SIZE 100 -MINIMUM_GENOME_FRACTION 1.0E-5 -IS_BISULFITE_SEQUENCED false -LEVEL ALL_READS -LEVEL SAMPLE -LEVEL READ_GROUP -ASSUME_SORTED false -ALSO_IGNORE_DUPLICATES false Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: ********** ********** Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:19 RExecutor Executing R script via command: Rscript /tmp/script6927548659497843723.R INFO 2024-07-02 11:51:19 RExecutor Executing R script via command: Rscript /tmp/script6927548659497843723.R Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:20 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:51:20 ProcessExecutor [1] "Checking if R is installed" Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: 11:51:20.172 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:20.172 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: 11:51:20.172 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:20.172 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: 11:51:20.172 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:20.172 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: 11:51:20.172 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:20.172 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: [Tue Jul 02 11:51:20 GMT+14:00 2024] CollectGcBiasMetrics CHART_OUTPUT=/tmp/test7620850762333890674.pdf SUMMARY_OUTPUT=/tmp/testAllChr11593184944798037039.gc_bias_summary_metrics SCAN_WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=1.0E-5 IS_BISULFITE_SEQUENCED=false METRIC_ACCUMULATION_LEVEL=[READ_GROUP, SAMPLE, ALL_READS] ALSO_IGNORE_DUPLICATES=false INPUT=/tmp/CollectGcBias13823779816851466163.bam OUTPUT=/tmp/testAllChrDetails1546016460150666037.gc_bias_detail_metrics ASSUME_SORTED=false REFERENCE_SEQUENCE=testdata/picard/metrics/chrMNO.reference.fasta STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:20 GMT+14:00 2024] CollectGcBiasMetrics CHART_OUTPUT=/tmp/test7620850762333890674.pdf SUMMARY_OUTPUT=/tmp/testAllChr11593184944798037039.gc_bias_summary_metrics SCAN_WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=1.0E-5 IS_BISULFITE_SEQUENCED=false METRIC_ACCUMULATION_LEVEL=[READ_GROUP, SAMPLE, ALL_READS] ALSO_IGNORE_DUPLICATES=false INPUT=/tmp/CollectGcBias13823779816851466163.bam OUTPUT=/tmp/testAllChrDetails1546016460150666037.gc_bias_detail_metrics ASSUME_SORTED=false REFERENCE_SEQUENCE=testdata/picard/metrics/chrMNO.reference.fasta STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: [Tue Jul 02 11:51:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:20 RExecutor Executing R script via command: Rscript /tmp/script2160493787402870744.R /tmp/testAllChrDetails1546016460150666037.gc_bias_detail_metrics /tmp/testAllChr11593184944798037039.gc_bias_summary_metrics /tmp/test7620850762333890674.pdf 100 INFO 2024-07-02 11:51:20 RExecutor Executing R script via command: Rscript /tmp/script2160493787402870744.R /tmp/testAllChrDetails1546016460150666037.gc_bias_detail_metrics /tmp/testAllChr11593184944798037039.gc_bias_summary_metrics /tmp/test7620850762333890674.pdf 100 Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:20 ProcessExecutor Total clusters: 100 , Aligned reads: 200Total clusters: 100 , Aligned reads: 200Total clusters: 100 , Aligned reads: 200 INFO 2024-07-02 11:51:20 ProcessExecutor Total clusters: 100 , Aligned reads: 200Total clusters: 100 , Aligned reads: 200Total clusters: 100 , Aligned reads: 200 Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: [Tue Jul 02 11:51:20 GMT+14:00 2024] picard.analysis.CollectGcBiasMetrics done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:51:20 GMT+14:00 2024] picard.analysis.CollectGcBiasMetrics done. Elapsed time: 0.01 minutes. Test: Test method runWindowsComparisonTest(picard.analysis.CollectGcBiasMetricsTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method testCoverageHistogram(picard.analysis.directed.CollectHsMetricsTest) Test: Test method testCoverageHistogram(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:20 CollectHsMetrics Gradle suite > Gradle test > picard.analysis.directed.CollectHsMetricsTest.testCoverageHistogram STANDARD_ERROR INFO 2024-07-02 11:51:20 CollectHsMetrics Test: Test method testCoverageHistogram(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: Test: Test method testCoverageHistogram(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCoverageHistogram(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** ********** Test: Test method testCoverageHistogram(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCoverageHistogram(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCoverageHistogram(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** ********** Test: Test method testCoverageHistogram(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCoverageHistogram(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** ********** Test: Test method testCoverageHistogram(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** CollectHsMetrics -TARGET_INTERVALS /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/directed/CollectHsMetrics/two-small.interval_list -BAIT_INTERVALS /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/directed/CollectHsMetrics/two-small.interval_list -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/directed/CollectHsMetrics/single-short-read.sam -OUTPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/directed/CollectHsMetrics/testCoverageHistogram7065752832740537661.hs_metrics -MINIMUM_MAPPING_QUALITY 20 -MINIMUM_BASE_QUALITY 20 -CLIP_OVERLAPPING_READS true -SAMPLE_SIZE 10 ********** CollectHsMetrics -TARGET_INTERVALS /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/directed/CollectHsMetrics/two-small.interval_list -BAIT_INTERVALS /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/directed/CollectHsMetrics/two-small.interval_list -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/directed/CollectHsMetrics/single-short-read.sam -OUTPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/directed/CollectHsMetrics/testCoverageHistogram7065752832740537661.hs_metrics -MINIMUM_MAPPING_QUALITY 20 -MINIMUM_BASE_QUALITY 20 -CLIP_OVERLAPPING_READS true -SAMPLE_SIZE 10 Test: Test method testCoverageHistogram(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** ********** Test: Test method testCoverageHistogram(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: Test: Test method testCoverageHistogram(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: Test: Test method testCoverageHistogram(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: 11:51:20.786 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:20.786 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCoverageHistogram(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: 11:51:20.787 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:20.787 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCoverageHistogram(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: 11:51:20.787 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:20.787 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCoverageHistogram(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: 11:51:20.787 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:20.787 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCoverageHistogram(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: [Tue Jul 02 11:51:20 GMT+14:00 2024] CollectHsMetrics BAIT_INTERVALS=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/directed/CollectHsMetrics/two-small.interval_list] TARGET_INTERVALS=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/directed/CollectHsMetrics/two-small.interval_list] INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/directed/CollectHsMetrics/single-short-read.sam OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/directed/CollectHsMetrics/testCoverageHistogram7065752832740537661.hs_metrics MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 CLIP_OVERLAPPING_READS=true SAMPLE_SIZE=10 METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 INCLUDE_INDELS=false COVERAGE_CAP=200 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:20 GMT+14:00 2024] CollectHsMetrics BAIT_INTERVALS=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/directed/CollectHsMetrics/two-small.interval_list] TARGET_INTERVALS=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/directed/CollectHsMetrics/two-small.interval_list] INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/directed/CollectHsMetrics/single-short-read.sam OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/directed/CollectHsMetrics/testCoverageHistogram7065752832740537661.hs_metrics MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 CLIP_OVERLAPPING_READS=true SAMPLE_SIZE=10 METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 INCLUDE_INDELS=false COVERAGE_CAP=200 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCoverageHistogram(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: [Tue Jul 02 11:51:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCoverageHistogram(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:20 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:51:20 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testCoverageHistogram(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:20 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:51:20 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testCoverageHistogram(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:20 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 11:51:20 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testCoverageHistogram(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:20 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:51:20 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testCoverageHistogram(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: [Tue Jul 02 11:51:20 GMT+14:00 2024] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:20 GMT+14:00 2024] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.00 minutes. Test: Test method testCoverageHistogram(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:20 CollectHsMetrics Gradle suite > Gradle test > picard.analysis.directed.CollectHsMetricsTest.testHsMetricsHandlesIndelsAppropriately STANDARD_ERROR INFO 2024-07-02 11:51:20 CollectHsMetrics Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** ********** Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** ********** Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** ********** Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** CollectHsMetrics -INCLUDE_INDELS false -SAMPLE_SIZE 0 -TI /tmp/hsmetrics.6607580604821614100.test/targets.interval_list -BI /tmp/hsmetrics.6607580604821614100.test/baits.interval_list -O /tmp/pbuilder2/hsmetrics.5814739245647050600.txt -I /tmp/hsmetrics.6607580604821614100.test/with_del.bam ********** CollectHsMetrics -INCLUDE_INDELS false -SAMPLE_SIZE 0 -TI /tmp/hsmetrics.6607580604821614100.test/targets.interval_list -BI /tmp/hsmetrics.6607580604821614100.test/baits.interval_list -O /tmp/pbuilder2/hsmetrics.5814739245647050600.txt -I /tmp/hsmetrics.6607580604821614100.test/with_del.bam Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** ********** Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: 11:51:20.892 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:20.892 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: 11:51:20.892 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:20.892 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: 11:51:20.892 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:20.892 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: 11:51:20.892 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:20.892 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: [Tue Jul 02 11:51:20 GMT+14:00 2024] CollectHsMetrics BAIT_INTERVALS=[/tmp/hsmetrics.6607580604821614100.test/baits.interval_list] TARGET_INTERVALS=[/tmp/hsmetrics.6607580604821614100.test/targets.interval_list] INPUT=/tmp/hsmetrics.6607580604821614100.test/with_del.bam OUTPUT=/tmp/pbuilder2/hsmetrics.5814739245647050600.txt INCLUDE_INDELS=false SAMPLE_SIZE=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 CLIP_OVERLAPPING_READS=true COVERAGE_CAP=200 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:20 GMT+14:00 2024] CollectHsMetrics BAIT_INTERVALS=[/tmp/hsmetrics.6607580604821614100.test/baits.interval_list] TARGET_INTERVALS=[/tmp/hsmetrics.6607580604821614100.test/targets.interval_list] INPUT=/tmp/hsmetrics.6607580604821614100.test/with_del.bam OUTPUT=/tmp/pbuilder2/hsmetrics.5814739245647050600.txt INCLUDE_INDELS=false SAMPLE_SIZE=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 CLIP_OVERLAPPING_READS=true COVERAGE_CAP=200 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: [Tue Jul 02 11:51:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:20 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:51:20 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:20 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:51:20 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:20 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:51:20 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: [Tue Jul 02 11:51:20 GMT+14:00 2024] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:20 GMT+14:00 2024] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.00 minutes. Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:20 CollectHsMetrics INFO 2024-07-02 11:51:20 CollectHsMetrics Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** ********** Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** ********** Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** ********** Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** CollectHsMetrics -INCLUDE_INDELS true -SAMPLE_SIZE 0 -TI /tmp/hsmetrics.6607580604821614100.test/targets.interval_list -BI /tmp/hsmetrics.6607580604821614100.test/baits.interval_list -O /tmp/pbuilder2/hsmetrics.5814739245647050600.txt -I /tmp/hsmetrics.6607580604821614100.test/with_del.bam ********** CollectHsMetrics -INCLUDE_INDELS true -SAMPLE_SIZE 0 -TI /tmp/hsmetrics.6607580604821614100.test/targets.interval_list -BI /tmp/hsmetrics.6607580604821614100.test/baits.interval_list -O /tmp/pbuilder2/hsmetrics.5814739245647050600.txt -I /tmp/hsmetrics.6607580604821614100.test/with_del.bam Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** ********** Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: 11:51:20.967 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:20.967 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: 11:51:20.967 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:20.967 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: 11:51:20.968 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:20.968 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: 11:51:20.968 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:20.968 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: [Tue Jul 02 11:51:20 GMT+14:00 2024] CollectHsMetrics BAIT_INTERVALS=[/tmp/hsmetrics.6607580604821614100.test/baits.interval_list] TARGET_INTERVALS=[/tmp/hsmetrics.6607580604821614100.test/targets.interval_list] INPUT=/tmp/hsmetrics.6607580604821614100.test/with_del.bam OUTPUT=/tmp/pbuilder2/hsmetrics.5814739245647050600.txt INCLUDE_INDELS=true SAMPLE_SIZE=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 CLIP_OVERLAPPING_READS=true COVERAGE_CAP=200 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:20 GMT+14:00 2024] CollectHsMetrics BAIT_INTERVALS=[/tmp/hsmetrics.6607580604821614100.test/baits.interval_list] TARGET_INTERVALS=[/tmp/hsmetrics.6607580604821614100.test/targets.interval_list] INPUT=/tmp/hsmetrics.6607580604821614100.test/with_del.bam OUTPUT=/tmp/pbuilder2/hsmetrics.5814739245647050600.txt INCLUDE_INDELS=true SAMPLE_SIZE=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 CLIP_OVERLAPPING_READS=true COVERAGE_CAP=200 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: [Tue Jul 02 11:51:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:20 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:51:20 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:20 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:51:20 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:20 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:51:20 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: [Tue Jul 02 11:51:20 GMT+14:00 2024] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:20 GMT+14:00 2024] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.00 minutes. Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:21 CollectHsMetrics INFO 2024-07-02 11:51:21 CollectHsMetrics Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** ********** Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** ********** Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** ********** Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** CollectHsMetrics -INCLUDE_INDELS false -SAMPLE_SIZE 0 -TI /tmp/hsmetrics.6607580604821614100.test/targets.interval_list -BI /tmp/hsmetrics.6607580604821614100.test/baits.interval_list -O /tmp/pbuilder2/hsmetrics.5814739245647050600.txt -I /tmp/hsmetrics.6607580604821614100.test/with_ins.bam ********** CollectHsMetrics -INCLUDE_INDELS false -SAMPLE_SIZE 0 -TI /tmp/hsmetrics.6607580604821614100.test/targets.interval_list -BI /tmp/hsmetrics.6607580604821614100.test/baits.interval_list -O /tmp/pbuilder2/hsmetrics.5814739245647050600.txt -I /tmp/hsmetrics.6607580604821614100.test/with_ins.bam Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** ********** Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: 11:51:21.014 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:21.014 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: 11:51:21.014 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:21.014 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: 11:51:21.014 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:21.014 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: 11:51:21.014 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:21.014 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: [Tue Jul 02 11:51:21 GMT+14:00 2024] CollectHsMetrics BAIT_INTERVALS=[/tmp/hsmetrics.6607580604821614100.test/baits.interval_list] TARGET_INTERVALS=[/tmp/hsmetrics.6607580604821614100.test/targets.interval_list] INPUT=/tmp/hsmetrics.6607580604821614100.test/with_ins.bam OUTPUT=/tmp/pbuilder2/hsmetrics.5814739245647050600.txt INCLUDE_INDELS=false SAMPLE_SIZE=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 CLIP_OVERLAPPING_READS=true COVERAGE_CAP=200 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:21 GMT+14:00 2024] CollectHsMetrics BAIT_INTERVALS=[/tmp/hsmetrics.6607580604821614100.test/baits.interval_list] TARGET_INTERVALS=[/tmp/hsmetrics.6607580604821614100.test/targets.interval_list] INPUT=/tmp/hsmetrics.6607580604821614100.test/with_ins.bam OUTPUT=/tmp/pbuilder2/hsmetrics.5814739245647050600.txt INCLUDE_INDELS=false SAMPLE_SIZE=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 CLIP_OVERLAPPING_READS=true COVERAGE_CAP=200 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: [Tue Jul 02 11:51:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:21 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:51:21 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:21 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:51:21 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:21 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:51:21 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: [Tue Jul 02 11:51:21 GMT+14:00 2024] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:21 GMT+14:00 2024] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.00 minutes. Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:21 CollectHsMetrics INFO 2024-07-02 11:51:21 CollectHsMetrics Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** ********** Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** ********** Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** ********** Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** CollectHsMetrics -INCLUDE_INDELS true -SAMPLE_SIZE 0 -TI /tmp/hsmetrics.6607580604821614100.test/targets.interval_list -BI /tmp/hsmetrics.6607580604821614100.test/baits.interval_list -O /tmp/pbuilder2/hsmetrics.5814739245647050600.txt -I /tmp/hsmetrics.6607580604821614100.test/with_ins.bam ********** CollectHsMetrics -INCLUDE_INDELS true -SAMPLE_SIZE 0 -TI /tmp/hsmetrics.6607580604821614100.test/targets.interval_list -BI /tmp/hsmetrics.6607580604821614100.test/baits.interval_list -O /tmp/pbuilder2/hsmetrics.5814739245647050600.txt -I /tmp/hsmetrics.6607580604821614100.test/with_ins.bam Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** ********** Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: 11:51:21.059 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:21.059 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: 11:51:21.059 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:21.059 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: 11:51:21.060 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:21.060 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: 11:51:21.060 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:21.060 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: [Tue Jul 02 11:51:21 GMT+14:00 2024] CollectHsMetrics BAIT_INTERVALS=[/tmp/hsmetrics.6607580604821614100.test/baits.interval_list] TARGET_INTERVALS=[/tmp/hsmetrics.6607580604821614100.test/targets.interval_list] INPUT=/tmp/hsmetrics.6607580604821614100.test/with_ins.bam OUTPUT=/tmp/pbuilder2/hsmetrics.5814739245647050600.txt INCLUDE_INDELS=true SAMPLE_SIZE=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 CLIP_OVERLAPPING_READS=true COVERAGE_CAP=200 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:21 GMT+14:00 2024] CollectHsMetrics BAIT_INTERVALS=[/tmp/hsmetrics.6607580604821614100.test/baits.interval_list] TARGET_INTERVALS=[/tmp/hsmetrics.6607580604821614100.test/targets.interval_list] INPUT=/tmp/hsmetrics.6607580604821614100.test/with_ins.bam OUTPUT=/tmp/pbuilder2/hsmetrics.5814739245647050600.txt INCLUDE_INDELS=true SAMPLE_SIZE=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 CLIP_OVERLAPPING_READS=true COVERAGE_CAP=200 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: [Tue Jul 02 11:51:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:21 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:51:21 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:21 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:51:21 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:21 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:51:21 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: [Tue Jul 02 11:51:21 GMT+14:00 2024] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:21 GMT+14:00 2024] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.00 minutes. Test: Test method testHsMetricsHandlesIndelsAppropriately(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: Runtime.totalMemory()=1084227584 Runtime.totalMemory()=1084227584 Running Test: Test method testHsMetricsHighTargetCoverage(picard.analysis.directed.CollectHsMetricsTest) Test: Test method testHsMetricsHighTargetCoverage(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:24 CollectHsMetrics Gradle suite > Gradle test > picard.analysis.directed.CollectHsMetricsTest.testHsMetricsHighTargetCoverage STANDARD_ERROR INFO 2024-07-02 11:51:24 CollectHsMetrics Test: Test method testHsMetricsHighTargetCoverage(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: Test: Test method testHsMetricsHighTargetCoverage(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testHsMetricsHighTargetCoverage(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** ********** Test: Test method testHsMetricsHighTargetCoverage(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testHsMetricsHighTargetCoverage(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testHsMetricsHighTargetCoverage(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** ********** Test: Test method testHsMetricsHighTargetCoverage(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testHsMetricsHighTargetCoverage(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** ********** Test: Test method testHsMetricsHighTargetCoverage(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** CollectHsMetrics -SAMPLE_SIZE 0 -TI /tmp/hsmetrics.17270460970141367393.test/targets.interval_list -BI /tmp/hsmetrics.17270460970141367393.test/baits.interval_list -O /tmp/pbuilder2/hsmetrics_high_coverage.1476764833194785231.txt -I /tmp/hsmetrics.17270460970141367393.test/high_coverage.bam ********** CollectHsMetrics -SAMPLE_SIZE 0 -TI /tmp/hsmetrics.17270460970141367393.test/targets.interval_list -BI /tmp/hsmetrics.17270460970141367393.test/baits.interval_list -O /tmp/pbuilder2/hsmetrics_high_coverage.1476764833194785231.txt -I /tmp/hsmetrics.17270460970141367393.test/high_coverage.bam Test: Test method testHsMetricsHighTargetCoverage(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: ********** ********** Test: Test method testHsMetricsHighTargetCoverage(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: Test: Test method testHsMetricsHighTargetCoverage(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: Test: Test method testHsMetricsHighTargetCoverage(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: 11:51:24.460 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:24.460 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testHsMetricsHighTargetCoverage(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: 11:51:24.460 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:24.460 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testHsMetricsHighTargetCoverage(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: 11:51:24.460 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:24.460 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testHsMetricsHighTargetCoverage(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: 11:51:24.460 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:24.460 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testHsMetricsHighTargetCoverage(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: [Tue Jul 02 11:51:24 GMT+14:00 2024] CollectHsMetrics BAIT_INTERVALS=[/tmp/hsmetrics.17270460970141367393.test/baits.interval_list] TARGET_INTERVALS=[/tmp/hsmetrics.17270460970141367393.test/targets.interval_list] INPUT=/tmp/hsmetrics.17270460970141367393.test/high_coverage.bam OUTPUT=/tmp/pbuilder2/hsmetrics_high_coverage.1476764833194785231.txt SAMPLE_SIZE=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 CLIP_OVERLAPPING_READS=true INCLUDE_INDELS=false COVERAGE_CAP=200 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:24 GMT+14:00 2024] CollectHsMetrics BAIT_INTERVALS=[/tmp/hsmetrics.17270460970141367393.test/baits.interval_list] TARGET_INTERVALS=[/tmp/hsmetrics.17270460970141367393.test/targets.interval_list] INPUT=/tmp/hsmetrics.17270460970141367393.test/high_coverage.bam OUTPUT=/tmp/pbuilder2/hsmetrics_high_coverage.1476764833194785231.txt SAMPLE_SIZE=0 METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 CLIP_OVERLAPPING_READS=true INCLUDE_INDELS=false COVERAGE_CAP=200 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testHsMetricsHighTargetCoverage(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: [Tue Jul 02 11:51:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testHsMetricsHighTargetCoverage(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:30 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:51:30 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testHsMetricsHighTargetCoverage(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:30 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:51:30 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testHsMetricsHighTargetCoverage(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:30 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:51:30 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testHsMetricsHighTargetCoverage(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: [Tue Jul 02 11:51:30 GMT+14:00 2024] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.11 minutes. [Tue Jul 02 11:51:30 GMT+14:00 2024] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.11 minutes. Test: Test method testHsMetricsHighTargetCoverage(picard.analysis.directed.CollectHsMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndexedRunLane1[0](true)(picard.illumina.CollectIlluminaBasecallingMetricsTest) Test: Test method testIndexedRunLane1[0](true)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:30 CollectIlluminaBasecallingMetrics Gradle suite > Gradle test > picard.illumina.CollectIlluminaBasecallingMetricsTest.testIndexedRunLane1[0](true) STANDARD_ERROR INFO 2024-07-02 11:51:30 CollectIlluminaBasecallingMetrics Test: Test method testIndexedRunLane1[0](true)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: Test: Test method testIndexedRunLane1[0](true)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndexedRunLane1[0](true)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndexedRunLane1[0](true)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndexedRunLane1[0](true)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndexedRunLane1[0](true)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndexedRunLane1[0](true)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndexedRunLane1[0](true)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndexedRunLane1[0](true)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** CollectIlluminaBasecallingMetrics -BASECALLS_DIR /tmp/cibm.4615651916577689834.tmp/25T8B25T/Data/Intensities/BaseCalls -BARCODES_DIR /tmp/cibm.4615651916577689834.tmp/25T8B25T/barcodes_dir -LANE 1 -OUTPUT /tmp/cibm.18234945307402643048.metrics -READ_STRUCTURE 25T8B25T -INPUT /tmp/cibm.4615651916577689834.tmp/25T8B25T/Data/Intensities/BaseCalls/barcodeData.1 ********** CollectIlluminaBasecallingMetrics -BASECALLS_DIR /tmp/cibm.4615651916577689834.tmp/25T8B25T/Data/Intensities/BaseCalls -BARCODES_DIR /tmp/cibm.4615651916577689834.tmp/25T8B25T/barcodes_dir -LANE 1 -OUTPUT /tmp/cibm.18234945307402643048.metrics -READ_STRUCTURE 25T8B25T -INPUT /tmp/cibm.4615651916577689834.tmp/25T8B25T/Data/Intensities/BaseCalls/barcodeData.1 Test: Test method testIndexedRunLane1[0](true)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndexedRunLane1[0](true)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: Test: Test method testIndexedRunLane1[0](true)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: Test: Test method testIndexedRunLane1[0](true)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: 11:51:30.798 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:30.798 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndexedRunLane1[0](true)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: 11:51:30.798 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:30.798 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndexedRunLane1[0](true)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: 11:51:30.798 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:30.798 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndexedRunLane1[0](true)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: 11:51:30.798 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:30.798 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndexedRunLane1[0](true)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: [Tue Jul 02 11:51:30 GMT+14:00 2024] CollectIlluminaBasecallingMetrics BASECALLS_DIR=/tmp/cibm.4615651916577689834.tmp/25T8B25T/Data/Intensities/BaseCalls BARCODES_DIR=/tmp/cibm.4615651916577689834.tmp/25T8B25T/barcodes_dir LANE=1 INPUT=/tmp/cibm.4615651916577689834.tmp/25T8B25T/Data/Intensities/BaseCalls/barcodeData.1 READ_STRUCTURE=25T8B25T OUTPUT=/tmp/cibm.18234945307402643048.metrics VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:30 GMT+14:00 2024] CollectIlluminaBasecallingMetrics BASECALLS_DIR=/tmp/cibm.4615651916577689834.tmp/25T8B25T/Data/Intensities/BaseCalls BARCODES_DIR=/tmp/cibm.4615651916577689834.tmp/25T8B25T/barcodes_dir LANE=1 INPUT=/tmp/cibm.4615651916577689834.tmp/25T8B25T/Data/Intensities/BaseCalls/barcodeData.1 READ_STRUCTURE=25T8B25T OUTPUT=/tmp/cibm.18234945307402643048.metrics VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndexedRunLane1[0](true)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: [Tue Jul 02 11:51:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndexedRunLane1[0](true)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: [Tue Jul 02 11:51:30 GMT+14:00 2024] picard.illumina.CollectIlluminaBasecallingMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:30 GMT+14:00 2024] picard.illumina.CollectIlluminaBasecallingMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndexedRunLane1[0](true)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndexedRunLane1[1](false)(picard.illumina.CollectIlluminaBasecallingMetricsTest) Test: Test method testIndexedRunLane1[1](false)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:30 CollectIlluminaBasecallingMetrics Gradle suite > Gradle test > picard.illumina.CollectIlluminaBasecallingMetricsTest.testIndexedRunLane1[1](false) STANDARD_ERROR INFO 2024-07-02 11:51:30 CollectIlluminaBasecallingMetrics Test: Test method testIndexedRunLane1[1](false)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: Test: Test method testIndexedRunLane1[1](false)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndexedRunLane1[1](false)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndexedRunLane1[1](false)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndexedRunLane1[1](false)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndexedRunLane1[1](false)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndexedRunLane1[1](false)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndexedRunLane1[1](false)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndexedRunLane1[1](false)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** CollectIlluminaBasecallingMetrics -BASECALLS_DIR /tmp/cibm.4615651916577689834.tmp/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -OUTPUT /tmp/cibm.7128031027316168072.metrics -READ_STRUCTURE 25T8B25T -INPUT /tmp/cibm.4615651916577689834.tmp/25T8B25T/Data/Intensities/BaseCalls/barcodeData.1 ********** CollectIlluminaBasecallingMetrics -BASECALLS_DIR /tmp/cibm.4615651916577689834.tmp/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -OUTPUT /tmp/cibm.7128031027316168072.metrics -READ_STRUCTURE 25T8B25T -INPUT /tmp/cibm.4615651916577689834.tmp/25T8B25T/Data/Intensities/BaseCalls/barcodeData.1 Test: Test method testIndexedRunLane1[1](false)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndexedRunLane1[1](false)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: Test: Test method testIndexedRunLane1[1](false)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: Test: Test method testIndexedRunLane1[1](false)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: 11:51:30.857 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:30.857 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndexedRunLane1[1](false)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: 11:51:30.857 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:30.857 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndexedRunLane1[1](false)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: 11:51:30.858 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:30.858 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndexedRunLane1[1](false)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: 11:51:30.858 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:30.858 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndexedRunLane1[1](false)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: [Tue Jul 02 11:51:30 GMT+14:00 2024] CollectIlluminaBasecallingMetrics BASECALLS_DIR=/tmp/cibm.4615651916577689834.tmp/25T8B25T/Data/Intensities/BaseCalls LANE=1 INPUT=/tmp/cibm.4615651916577689834.tmp/25T8B25T/Data/Intensities/BaseCalls/barcodeData.1 READ_STRUCTURE=25T8B25T OUTPUT=/tmp/cibm.7128031027316168072.metrics VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:30 GMT+14:00 2024] CollectIlluminaBasecallingMetrics BASECALLS_DIR=/tmp/cibm.4615651916577689834.tmp/25T8B25T/Data/Intensities/BaseCalls LANE=1 INPUT=/tmp/cibm.4615651916577689834.tmp/25T8B25T/Data/Intensities/BaseCalls/barcodeData.1 READ_STRUCTURE=25T8B25T OUTPUT=/tmp/cibm.7128031027316168072.metrics VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndexedRunLane1[1](false)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: [Tue Jul 02 11:51:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndexedRunLane1[1](false)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: [Tue Jul 02 11:51:30 GMT+14:00 2024] picard.illumina.CollectIlluminaBasecallingMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:30 GMT+14:00 2024] picard.illumina.CollectIlluminaBasecallingMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndexedRunLane1[1](false)(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testNonIndexedRunLane1(picard.illumina.CollectIlluminaBasecallingMetricsTest) Test: Test method testNonIndexedRunLane1(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:30 CollectIlluminaBasecallingMetrics Gradle suite > Gradle test > picard.illumina.CollectIlluminaBasecallingMetricsTest.testNonIndexedRunLane1 STANDARD_ERROR INFO 2024-07-02 11:51:30 CollectIlluminaBasecallingMetrics Test: Test method testNonIndexedRunLane1(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: Test: Test method testNonIndexedRunLane1(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testNonIndexedRunLane1(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** ********** Test: Test method testNonIndexedRunLane1(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testNonIndexedRunLane1(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testNonIndexedRunLane1(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** ********** Test: Test method testNonIndexedRunLane1(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testNonIndexedRunLane1(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** ********** Test: Test method testNonIndexedRunLane1(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** CollectIlluminaBasecallingMetrics -BASECALLS_DIR /tmp/cibm.4615651916577689834.tmp/125T125T/Data/Intensities/BaseCalls -LANE 1 -OUTPUT /tmp/cibm.15791942032223910051.metrics -READ_STRUCTURE 125T125T ********** CollectIlluminaBasecallingMetrics -BASECALLS_DIR /tmp/cibm.4615651916577689834.tmp/125T125T/Data/Intensities/BaseCalls -LANE 1 -OUTPUT /tmp/cibm.15791942032223910051.metrics -READ_STRUCTURE 125T125T Test: Test method testNonIndexedRunLane1(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** ********** Test: Test method testNonIndexedRunLane1(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: Test: Test method testNonIndexedRunLane1(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: Test: Test method testNonIndexedRunLane1(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: 11:51:30.897 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:30.897 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNonIndexedRunLane1(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: 11:51:30.897 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:30.897 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNonIndexedRunLane1(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: 11:51:30.897 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:30.897 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNonIndexedRunLane1(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: 11:51:30.897 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:30.897 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNonIndexedRunLane1(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: [Tue Jul 02 11:51:30 GMT+14:00 2024] CollectIlluminaBasecallingMetrics BASECALLS_DIR=/tmp/cibm.4615651916577689834.tmp/125T125T/Data/Intensities/BaseCalls LANE=1 READ_STRUCTURE=125T125T OUTPUT=/tmp/cibm.15791942032223910051.metrics VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:30 GMT+14:00 2024] CollectIlluminaBasecallingMetrics BASECALLS_DIR=/tmp/cibm.4615651916577689834.tmp/125T125T/Data/Intensities/BaseCalls LANE=1 READ_STRUCTURE=125T125T OUTPUT=/tmp/cibm.15791942032223910051.metrics VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testNonIndexedRunLane1(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: [Tue Jul 02 11:51:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testNonIndexedRunLane1(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: [Tue Jul 02 11:51:30 GMT+14:00 2024] picard.illumina.CollectIlluminaBasecallingMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:30 GMT+14:00 2024] picard.illumina.CollectIlluminaBasecallingMetrics done. Elapsed time: 0.00 minutes. Test: Test method testNonIndexedRunLane1(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testNovaseqIndexedRun(picard.illumina.CollectIlluminaBasecallingMetricsTest) Test: Test method testNovaseqIndexedRun(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:30 CollectIlluminaBasecallingMetrics Gradle suite > Gradle test > picard.illumina.CollectIlluminaBasecallingMetricsTest.testNovaseqIndexedRun STANDARD_ERROR INFO 2024-07-02 11:51:30 CollectIlluminaBasecallingMetrics Test: Test method testNovaseqIndexedRun(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: Test: Test method testNovaseqIndexedRun(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testNovaseqIndexedRun(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** ********** Test: Test method testNovaseqIndexedRun(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testNovaseqIndexedRun(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testNovaseqIndexedRun(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** ********** Test: Test method testNovaseqIndexedRun(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testNovaseqIndexedRun(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** ********** Test: Test method testNovaseqIndexedRun(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** CollectIlluminaBasecallingMetrics -BASECALLS_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls -LANE 1 -OUTPUT /tmp/cibm.17266332632226253129.metrics -READ_STRUCTURE 151T8B8B151T -INPUT testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/barcodeData.1 ********** CollectIlluminaBasecallingMetrics -BASECALLS_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls -LANE 1 -OUTPUT /tmp/cibm.17266332632226253129.metrics -READ_STRUCTURE 151T8B8B151T -INPUT testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/barcodeData.1 Test: Test method testNovaseqIndexedRun(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: ********** ********** Test: Test method testNovaseqIndexedRun(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: Test: Test method testNovaseqIndexedRun(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: Test: Test method testNovaseqIndexedRun(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: 11:51:30.978 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:30.978 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNovaseqIndexedRun(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: 11:51:30.978 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:30.978 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNovaseqIndexedRun(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: 11:51:30.978 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:30.978 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNovaseqIndexedRun(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: 11:51:30.978 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:30.978 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNovaseqIndexedRun(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: [Tue Jul 02 11:51:30 GMT+14:00 2024] CollectIlluminaBasecallingMetrics BASECALLS_DIR=testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls LANE=1 INPUT=testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/barcodeData.1 READ_STRUCTURE=151T8B8B151T OUTPUT=/tmp/cibm.17266332632226253129.metrics VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:30 GMT+14:00 2024] CollectIlluminaBasecallingMetrics BASECALLS_DIR=testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls LANE=1 INPUT=testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls/barcodeData.1 READ_STRUCTURE=151T8B8B151T OUTPUT=/tmp/cibm.17266332632226253129.metrics VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testNovaseqIndexedRun(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: [Tue Jul 02 11:51:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testNovaseqIndexedRun(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:32 CbclReader Processing tile 1101 INFO 2024-07-02 11:51:32 CbclReader Processing tile 1101 Test: Test method testNovaseqIndexedRun(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:32 CbclReader Processing tile 1102 INFO 2024-07-02 11:51:32 CbclReader Processing tile 1102 Test: Test method testNovaseqIndexedRun(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: [Tue Jul 02 11:51:32 GMT+14:00 2024] picard.illumina.CollectIlluminaBasecallingMetrics done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:51:32 GMT+14:00 2024] picard.illumina.CollectIlluminaBasecallingMetrics done. Elapsed time: 0.03 minutes. Test: Test method testNovaseqIndexedRun(picard.illumina.CollectIlluminaBasecallingMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method simpleTest[0](multipleContigs.vcf, twopairsWithUMIsMultipleOrientations, {nSites=3, nDuplicateSets=3, nMismatchingUMIsInCoOrientedBiDups=2, nMismatchingUMIsInContraOrientedBiDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) Test: Test method simpleTest[0](multipleContigs.vcf, twopairsWithUMIsMultipleOrientations, {nSites=3, nDuplicateSets=3, nMismatchingUMIsInCoOrientedBiDups=2, nMismatchingUMIsInContraOrientedBiDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:32 CollectIndependentReplicateMetrics Found 5 heterozygous sites in VCF. Gradle suite > Gradle test > picard.analysis.replicates.CollectIndependentReplicatesMetricTest.simpleTest[0](multipleContigs.vcf, twopairsWithUMIsMultipleOrientations, {nSites=3, nDuplicateSets=3, nMismatchingUMIsInCoOrientedBiDups=2, nMismatchingUMIsInContraOrientedBiDups=1}) STANDARD_ERROR INFO 2024-07-02 11:51:32 CollectIndependentReplicateMetrics Found 5 heterozygous sites in VCF. Test: Test method simpleTest[0](multipleContigs.vcf, twopairsWithUMIsMultipleOrientations, {nSites=3, nDuplicateSets=3, nMismatchingUMIsInCoOrientedBiDups=2, nMismatchingUMIsInContraOrientedBiDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:32 CollectIndependentReplicateMetrics Querying BAM for sites. INFO 2024-07-02 11:51:32 CollectIndependentReplicateMetrics Querying BAM for sites. Test: Test method simpleTest[0](multipleContigs.vcf, twopairsWithUMIsMultipleOrientations, {nSites=3, nDuplicateSets=3, nMismatchingUMIsInCoOrientedBiDups=2, nMismatchingUMIsInContraOrientedBiDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. Test: Test method simpleTest[0](multipleContigs.vcf, twopairsWithUMIsMultipleOrientations, {nSites=3, nDuplicateSets=3, nMismatchingUMIsInCoOrientedBiDups=2, nMismatchingUMIsInContraOrientedBiDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initializing. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initializing. Test: Test method simpleTest[0](multipleContigs.vcf, twopairsWithUMIsMultipleOrientations, {nSites=3, nDuplicateSets=3, nMismatchingUMIsInCoOrientedBiDups=2, nMismatchingUMIsInContraOrientedBiDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initialized. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initialized. Test: Test method simpleTest[0](multipleContigs.vcf, twopairsWithUMIsMultipleOrientations, {nSites=3, nDuplicateSets=3, nMismatchingUMIsInCoOrientedBiDups=2, nMismatchingUMIsInContraOrientedBiDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Starting iteration on reads INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Starting iteration on reads Test: Test method simpleTest[0](multipleContigs.vcf, twopairsWithUMIsMultipleOrientations, {nSites=3, nDuplicateSets=3, nMismatchingUMIsInCoOrientedBiDups=2, nMismatchingUMIsInContraOrientedBiDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. Running Test: Test method simpleTest[1](hets.vcf, twoPairs, {nSites=1, nDuplicateSets=1, nDifferentAllelesTriDups=0, nDifferentAllelesBiDups=1, nReferenceAllelesBiDups=0, nAlternateAllelesBiDups=0, biSiteHeterogeneityRate=1.0, biSiteHomogeneityRate=0.0, nAlternateReads=1, nReferenceReads=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) Test: Test method simpleTest[1](hets.vcf, twoPairs, {nSites=1, nDuplicateSets=1, nDifferentAllelesTriDups=0, nDifferentAllelesBiDups=1, nReferenceAllelesBiDups=0, nAlternateAllelesBiDups=0, biSiteHeterogeneityRate=1.0, biSiteHomogeneityRate=0.0, nAlternateReads=1, nReferenceReads=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Found 1 heterozygous sites in VCF. Gradle suite > Gradle test > picard.analysis.replicates.CollectIndependentReplicatesMetricTest.simpleTest[1](hets.vcf, twoPairs, {nSites=1, nDuplicateSets=1, nDifferentAllelesTriDups=0, nDifferentAllelesBiDups=1, nReferenceAllelesBiDups=0, nAlternateAllelesBiDups=0, biSiteHeterogeneityRate=1.0, biSiteHomogeneityRate=0.0, nAlternateReads=1, nReferenceReads=1}) STANDARD_ERROR INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Found 1 heterozygous sites in VCF. Test: Test method simpleTest[1](hets.vcf, twoPairs, {nSites=1, nDuplicateSets=1, nDifferentAllelesTriDups=0, nDifferentAllelesBiDups=1, nReferenceAllelesBiDups=0, nAlternateAllelesBiDups=0, biSiteHeterogeneityRate=1.0, biSiteHomogeneityRate=0.0, nAlternateReads=1, nReferenceReads=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Querying BAM for sites. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Querying BAM for sites. Test: Test method simpleTest[1](hets.vcf, twoPairs, {nSites=1, nDuplicateSets=1, nDifferentAllelesTriDups=0, nDifferentAllelesBiDups=1, nReferenceAllelesBiDups=0, nAlternateAllelesBiDups=0, biSiteHeterogeneityRate=1.0, biSiteHomogeneityRate=0.0, nAlternateReads=1, nReferenceReads=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. Test: Test method simpleTest[1](hets.vcf, twoPairs, {nSites=1, nDuplicateSets=1, nDifferentAllelesTriDups=0, nDifferentAllelesBiDups=1, nReferenceAllelesBiDups=0, nAlternateAllelesBiDups=0, biSiteHeterogeneityRate=1.0, biSiteHomogeneityRate=0.0, nAlternateReads=1, nReferenceReads=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initializing. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initializing. Test: Test method simpleTest[1](hets.vcf, twoPairs, {nSites=1, nDuplicateSets=1, nDifferentAllelesTriDups=0, nDifferentAllelesBiDups=1, nReferenceAllelesBiDups=0, nAlternateAllelesBiDups=0, biSiteHeterogeneityRate=1.0, biSiteHomogeneityRate=0.0, nAlternateReads=1, nReferenceReads=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initialized. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initialized. Test: Test method simpleTest[1](hets.vcf, twoPairs, {nSites=1, nDuplicateSets=1, nDifferentAllelesTriDups=0, nDifferentAllelesBiDups=1, nReferenceAllelesBiDups=0, nAlternateAllelesBiDups=0, biSiteHeterogeneityRate=1.0, biSiteHomogeneityRate=0.0, nAlternateReads=1, nReferenceReads=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Starting iteration on reads INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Starting iteration on reads Test: Test method simpleTest[1](hets.vcf, twoPairs, {nSites=1, nDuplicateSets=1, nDifferentAllelesTriDups=0, nDifferentAllelesBiDups=1, nReferenceAllelesBiDups=0, nAlternateAllelesBiDups=0, biSiteHeterogeneityRate=1.0, biSiteHomogeneityRate=0.0, nAlternateReads=1, nReferenceReads=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. Running Test: Test method simpleTest[2](twoSamplesHet.vcf, twoPairs, {nDifferentAllelesBiDups=1, biSiteHeterogeneityRate=1.0, biSiteHomogeneityRate=0.0, nDifferentAllelesTriDups=0, nSites=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) Test: Test method simpleTest[2](twoSamplesHet.vcf, twoPairs, {nDifferentAllelesBiDups=1, biSiteHeterogeneityRate=1.0, biSiteHomogeneityRate=0.0, nDifferentAllelesTriDups=0, nSites=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Found 1 heterozygous sites in VCF. Gradle suite > Gradle test > picard.analysis.replicates.CollectIndependentReplicatesMetricTest.simpleTest[2](twoSamplesHet.vcf, twoPairs, {nDifferentAllelesBiDups=1, biSiteHeterogeneityRate=1.0, biSiteHomogeneityRate=0.0, nDifferentAllelesTriDups=0, nSites=1}) STANDARD_ERROR INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Found 1 heterozygous sites in VCF. Test: Test method simpleTest[2](twoSamplesHet.vcf, twoPairs, {nDifferentAllelesBiDups=1, biSiteHeterogeneityRate=1.0, biSiteHomogeneityRate=0.0, nDifferentAllelesTriDups=0, nSites=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Querying BAM for sites. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Querying BAM for sites. Test: Test method simpleTest[2](twoSamplesHet.vcf, twoPairs, {nDifferentAllelesBiDups=1, biSiteHeterogeneityRate=1.0, biSiteHomogeneityRate=0.0, nDifferentAllelesTriDups=0, nSites=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. Test: Test method simpleTest[2](twoSamplesHet.vcf, twoPairs, {nDifferentAllelesBiDups=1, biSiteHeterogeneityRate=1.0, biSiteHomogeneityRate=0.0, nDifferentAllelesTriDups=0, nSites=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initializing. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initializing. Test: Test method simpleTest[2](twoSamplesHet.vcf, twoPairs, {nDifferentAllelesBiDups=1, biSiteHeterogeneityRate=1.0, biSiteHomogeneityRate=0.0, nDifferentAllelesTriDups=0, nSites=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initialized. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initialized. Test: Test method simpleTest[2](twoSamplesHet.vcf, twoPairs, {nDifferentAllelesBiDups=1, biSiteHeterogeneityRate=1.0, biSiteHomogeneityRate=0.0, nDifferentAllelesTriDups=0, nSites=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Starting iteration on reads INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Starting iteration on reads Test: Test method simpleTest[2](twoSamplesHet.vcf, twoPairs, {nDifferentAllelesBiDups=1, biSiteHeterogeneityRate=1.0, biSiteHomogeneityRate=0.0, nDifferentAllelesTriDups=0, nSites=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. Running Test: Test method simpleTest[3](hets.vcf, aTriple, {nExactlyTriple=1, nExactlyDouble=1, nDuplicateSets=2, nAlternateReads=2, nReferenceReads=3})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) Test: Test method simpleTest[3](hets.vcf, aTriple, {nExactlyTriple=1, nExactlyDouble=1, nDuplicateSets=2, nAlternateReads=2, nReferenceReads=3})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Found 1 heterozygous sites in VCF. Gradle suite > Gradle test > picard.analysis.replicates.CollectIndependentReplicatesMetricTest.simpleTest[3](hets.vcf, aTriple, {nExactlyTriple=1, nExactlyDouble=1, nDuplicateSets=2, nAlternateReads=2, nReferenceReads=3}) STANDARD_ERROR INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Found 1 heterozygous sites in VCF. Test: Test method simpleTest[3](hets.vcf, aTriple, {nExactlyTriple=1, nExactlyDouble=1, nDuplicateSets=2, nAlternateReads=2, nReferenceReads=3})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Querying BAM for sites. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Querying BAM for sites. Test: Test method simpleTest[3](hets.vcf, aTriple, {nExactlyTriple=1, nExactlyDouble=1, nDuplicateSets=2, nAlternateReads=2, nReferenceReads=3})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. Test: Test method simpleTest[3](hets.vcf, aTriple, {nExactlyTriple=1, nExactlyDouble=1, nDuplicateSets=2, nAlternateReads=2, nReferenceReads=3})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initializing. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initializing. Test: Test method simpleTest[3](hets.vcf, aTriple, {nExactlyTriple=1, nExactlyDouble=1, nDuplicateSets=2, nAlternateReads=2, nReferenceReads=3})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initialized. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initialized. Test: Test method simpleTest[3](hets.vcf, aTriple, {nExactlyTriple=1, nExactlyDouble=1, nDuplicateSets=2, nAlternateReads=2, nReferenceReads=3})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Starting iteration on reads INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Starting iteration on reads Test: Test method simpleTest[3](hets.vcf, aTriple, {nExactlyTriple=1, nExactlyDouble=1, nDuplicateSets=2, nAlternateReads=2, nReferenceReads=3})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. Running Test: Test method simpleTest[4](multipleContigs.vcf, multipleContigs, {nDuplicateSets=8, nSites=4, nTotalReads=20})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) Test: Test method simpleTest[4](multipleContigs.vcf, multipleContigs, {nDuplicateSets=8, nSites=4, nTotalReads=20})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Found 5 heterozygous sites in VCF. Gradle suite > Gradle test > picard.analysis.replicates.CollectIndependentReplicatesMetricTest.simpleTest[4](multipleContigs.vcf, multipleContigs, {nDuplicateSets=8, nSites=4, nTotalReads=20}) STANDARD_ERROR INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Found 5 heterozygous sites in VCF. Test: Test method simpleTest[4](multipleContigs.vcf, multipleContigs, {nDuplicateSets=8, nSites=4, nTotalReads=20})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Querying BAM for sites. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Querying BAM for sites. Test: Test method simpleTest[4](multipleContigs.vcf, multipleContigs, {nDuplicateSets=8, nSites=4, nTotalReads=20})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. Test: Test method simpleTest[4](multipleContigs.vcf, multipleContigs, {nDuplicateSets=8, nSites=4, nTotalReads=20})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initializing. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initializing. Test: Test method simpleTest[4](multipleContigs.vcf, multipleContigs, {nDuplicateSets=8, nSites=4, nTotalReads=20})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initialized. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initialized. Test: Test method simpleTest[4](multipleContigs.vcf, multipleContigs, {nDuplicateSets=8, nSites=4, nTotalReads=20})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Starting iteration on reads INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Starting iteration on reads Test: Test method simpleTest[4](multipleContigs.vcf, multipleContigs, {nDuplicateSets=8, nSites=4, nTotalReads=20})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. Running Test: Test method simpleTest[5](hets_pos20.vcf, aTriple, {nAlternateAllelesTriDups=1, nMismatchingAllelesBiDups=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) Test: Test method simpleTest[5](hets_pos20.vcf, aTriple, {nAlternateAllelesTriDups=1, nMismatchingAllelesBiDups=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Found 1 heterozygous sites in VCF. Gradle suite > Gradle test > picard.analysis.replicates.CollectIndependentReplicatesMetricTest.simpleTest[5](hets_pos20.vcf, aTriple, {nAlternateAllelesTriDups=1, nMismatchingAllelesBiDups=0}) STANDARD_ERROR INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Found 1 heterozygous sites in VCF. Test: Test method simpleTest[5](hets_pos20.vcf, aTriple, {nAlternateAllelesTriDups=1, nMismatchingAllelesBiDups=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Querying BAM for sites. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Querying BAM for sites. Test: Test method simpleTest[5](hets_pos20.vcf, aTriple, {nAlternateAllelesTriDups=1, nMismatchingAllelesBiDups=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. Test: Test method simpleTest[5](hets_pos20.vcf, aTriple, {nAlternateAllelesTriDups=1, nMismatchingAllelesBiDups=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initializing. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initializing. Test: Test method simpleTest[5](hets_pos20.vcf, aTriple, {nAlternateAllelesTriDups=1, nMismatchingAllelesBiDups=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initialized. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initialized. Test: Test method simpleTest[5](hets_pos20.vcf, aTriple, {nAlternateAllelesTriDups=1, nMismatchingAllelesBiDups=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Starting iteration on reads INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Starting iteration on reads Test: Test method simpleTest[5](hets_pos20.vcf, aTriple, {nAlternateAllelesTriDups=1, nMismatchingAllelesBiDups=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. Running Test: Test method simpleTest[6](hets_pos21_HOMREF_G.vcf, aTriple, {nReferenceAllelesTriDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) Test: Test method simpleTest[6](hets_pos21_HOMREF_G.vcf, aTriple, {nReferenceAllelesTriDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Found 1 heterozygous sites in VCF. Gradle suite > Gradle test > picard.analysis.replicates.CollectIndependentReplicatesMetricTest.simpleTest[6](hets_pos21_HOMREF_G.vcf, aTriple, {nReferenceAllelesTriDups=1}) STANDARD_ERROR INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Found 1 heterozygous sites in VCF. Test: Test method simpleTest[6](hets_pos21_HOMREF_G.vcf, aTriple, {nReferenceAllelesTriDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Querying BAM for sites. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Querying BAM for sites. Test: Test method simpleTest[6](hets_pos21_HOMREF_G.vcf, aTriple, {nReferenceAllelesTriDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. Test: Test method simpleTest[6](hets_pos21_HOMREF_G.vcf, aTriple, {nReferenceAllelesTriDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initializing. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initializing. Test: Test method simpleTest[6](hets_pos21_HOMREF_G.vcf, aTriple, {nReferenceAllelesTriDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initialized. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initialized. Test: Test method simpleTest[6](hets_pos21_HOMREF_G.vcf, aTriple, {nReferenceAllelesTriDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Starting iteration on reads INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Starting iteration on reads Test: Test method simpleTest[6](hets_pos21_HOMREF_G.vcf, aTriple, {nReferenceAllelesTriDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. Running Test: Test method simpleTest[7](hets_pos20.vcf, twoPairs, {nAlternateAllelesBiDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) Test: Test method simpleTest[7](hets_pos20.vcf, twoPairs, {nAlternateAllelesBiDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Found 1 heterozygous sites in VCF. Gradle suite > Gradle test > picard.analysis.replicates.CollectIndependentReplicatesMetricTest.simpleTest[7](hets_pos20.vcf, twoPairs, {nAlternateAllelesBiDups=1}) STANDARD_ERROR INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Found 1 heterozygous sites in VCF. Test: Test method simpleTest[7](hets_pos20.vcf, twoPairs, {nAlternateAllelesBiDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Querying BAM for sites. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Querying BAM for sites. Test: Test method simpleTest[7](hets_pos20.vcf, twoPairs, {nAlternateAllelesBiDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. Test: Test method simpleTest[7](hets_pos20.vcf, twoPairs, {nAlternateAllelesBiDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initializing. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initializing. Test: Test method simpleTest[7](hets_pos20.vcf, twoPairs, {nAlternateAllelesBiDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initialized. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initialized. Test: Test method simpleTest[7](hets_pos20.vcf, twoPairs, {nAlternateAllelesBiDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Starting iteration on reads INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Starting iteration on reads Test: Test method simpleTest[7](hets_pos20.vcf, twoPairs, {nAlternateAllelesBiDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. Running Test: Test method simpleTest[8](hets_pos21_HOMREF_G.vcf, twoPairs, {nReferenceAllelesBiDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) Test: Test method simpleTest[8](hets_pos21_HOMREF_G.vcf, twoPairs, {nReferenceAllelesBiDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Found 1 heterozygous sites in VCF. Gradle suite > Gradle test > picard.analysis.replicates.CollectIndependentReplicatesMetricTest.simpleTest[8](hets_pos21_HOMREF_G.vcf, twoPairs, {nReferenceAllelesBiDups=1}) STANDARD_ERROR INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Found 1 heterozygous sites in VCF. Test: Test method simpleTest[8](hets_pos21_HOMREF_G.vcf, twoPairs, {nReferenceAllelesBiDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Querying BAM for sites. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Querying BAM for sites. Test: Test method simpleTest[8](hets_pos21_HOMREF_G.vcf, twoPairs, {nReferenceAllelesBiDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. Test: Test method simpleTest[8](hets_pos21_HOMREF_G.vcf, twoPairs, {nReferenceAllelesBiDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initializing. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initializing. Test: Test method simpleTest[8](hets_pos21_HOMREF_G.vcf, twoPairs, {nReferenceAllelesBiDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initialized. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initialized. Test: Test method simpleTest[8](hets_pos21_HOMREF_G.vcf, twoPairs, {nReferenceAllelesBiDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Starting iteration on reads INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Starting iteration on reads Test: Test method simpleTest[8](hets_pos21_HOMREF_G.vcf, twoPairs, {nReferenceAllelesBiDups=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. Running Test: Test method simpleTest[9](hets_pos22_IncorrectAlleles.vcf, twoPairs, {nSites=1, nThreeAllelesSites=1, nAlternateAllelesTriDups=0, nMismatchingAllelesBiDups=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) Test: Test method simpleTest[9](hets_pos22_IncorrectAlleles.vcf, twoPairs, {nSites=1, nThreeAllelesSites=1, nAlternateAllelesTriDups=0, nMismatchingAllelesBiDups=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Found 2 heterozygous sites in VCF. Gradle suite > Gradle test > picard.analysis.replicates.CollectIndependentReplicatesMetricTest.simpleTest[9](hets_pos22_IncorrectAlleles.vcf, twoPairs, {nSites=1, nThreeAllelesSites=1, nAlternateAllelesTriDups=0, nMismatchingAllelesBiDups=0}) STANDARD_ERROR INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Found 2 heterozygous sites in VCF. Test: Test method simpleTest[9](hets_pos22_IncorrectAlleles.vcf, twoPairs, {nSites=1, nThreeAllelesSites=1, nAlternateAllelesTriDups=0, nMismatchingAllelesBiDups=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Querying BAM for sites. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Querying BAM for sites. Test: Test method simpleTest[9](hets_pos22_IncorrectAlleles.vcf, twoPairs, {nSites=1, nThreeAllelesSites=1, nAlternateAllelesTriDups=0, nMismatchingAllelesBiDups=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. Test: Test method simpleTest[9](hets_pos22_IncorrectAlleles.vcf, twoPairs, {nSites=1, nThreeAllelesSites=1, nAlternateAllelesTriDups=0, nMismatchingAllelesBiDups=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initializing. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initializing. Test: Test method simpleTest[9](hets_pos22_IncorrectAlleles.vcf, twoPairs, {nSites=1, nThreeAllelesSites=1, nAlternateAllelesTriDups=0, nMismatchingAllelesBiDups=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initialized. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initialized. Test: Test method simpleTest[9](hets_pos22_IncorrectAlleles.vcf, twoPairs, {nSites=1, nThreeAllelesSites=1, nAlternateAllelesTriDups=0, nMismatchingAllelesBiDups=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Starting iteration on reads INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Starting iteration on reads Test: Test method simpleTest[9](hets_pos22_IncorrectAlleles.vcf, twoPairs, {nSites=1, nThreeAllelesSites=1, nAlternateAllelesTriDups=0, nMismatchingAllelesBiDups=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. Running Test: Test method simpleTest[10](hets_pos22_IncorrectAlleles.vcf, aTriple, {nMismatchingAllelesTriDups=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) Test: Test method simpleTest[10](hets_pos22_IncorrectAlleles.vcf, aTriple, {nMismatchingAllelesTriDups=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Found 2 heterozygous sites in VCF. Gradle suite > Gradle test > picard.analysis.replicates.CollectIndependentReplicatesMetricTest.simpleTest[10](hets_pos22_IncorrectAlleles.vcf, aTriple, {nMismatchingAllelesTriDups=0}) STANDARD_ERROR INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Found 2 heterozygous sites in VCF. Test: Test method simpleTest[10](hets_pos22_IncorrectAlleles.vcf, aTriple, {nMismatchingAllelesTriDups=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Querying BAM for sites. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Querying BAM for sites. Test: Test method simpleTest[10](hets_pos22_IncorrectAlleles.vcf, aTriple, {nMismatchingAllelesTriDups=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. Test: Test method simpleTest[10](hets_pos22_IncorrectAlleles.vcf, aTriple, {nMismatchingAllelesTriDups=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initializing. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initializing. Test: Test method simpleTest[10](hets_pos22_IncorrectAlleles.vcf, aTriple, {nMismatchingAllelesTriDups=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initialized. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initialized. Test: Test method simpleTest[10](hets_pos22_IncorrectAlleles.vcf, aTriple, {nMismatchingAllelesTriDups=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Starting iteration on reads INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Starting iteration on reads Test: Test method simpleTest[10](hets_pos22_IncorrectAlleles.vcf, aTriple, {nMismatchingAllelesTriDups=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. Running Test: Test method simpleTest[11](hets.vcf, twoPairsWithUMIs, {nSites=1, nMismatchingUMIsInDiffBiDups=1, nMatchingUMIsInDiffBiDups=0, nMismatchingUMIsInSameBiDups=0, nMatchingUMIsInSameBiDups=0, nGoodBarcodes=1, nBadBarcodes=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) Test: Test method simpleTest[11](hets.vcf, twoPairsWithUMIs, {nSites=1, nMismatchingUMIsInDiffBiDups=1, nMatchingUMIsInDiffBiDups=0, nMismatchingUMIsInSameBiDups=0, nMatchingUMIsInSameBiDups=0, nGoodBarcodes=1, nBadBarcodes=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Found 1 heterozygous sites in VCF. Gradle suite > Gradle test > picard.analysis.replicates.CollectIndependentReplicatesMetricTest.simpleTest[11](hets.vcf, twoPairsWithUMIs, {nSites=1, nMismatchingUMIsInDiffBiDups=1, nMatchingUMIsInDiffBiDups=0, nMismatchingUMIsInSameBiDups=0, nMatchingUMIsInSameBiDups=0, nGoodBarcodes=1, nBadBarcodes=0}) STANDARD_ERROR INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Found 1 heterozygous sites in VCF. Test: Test method simpleTest[11](hets.vcf, twoPairsWithUMIs, {nSites=1, nMismatchingUMIsInDiffBiDups=1, nMatchingUMIsInDiffBiDups=0, nMismatchingUMIsInSameBiDups=0, nMatchingUMIsInSameBiDups=0, nGoodBarcodes=1, nBadBarcodes=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Querying BAM for sites. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Querying BAM for sites. Test: Test method simpleTest[11](hets.vcf, twoPairsWithUMIs, {nSites=1, nMismatchingUMIsInDiffBiDups=1, nMatchingUMIsInDiffBiDups=0, nMismatchingUMIsInSameBiDups=0, nMatchingUMIsInSameBiDups=0, nGoodBarcodes=1, nBadBarcodes=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. Test: Test method simpleTest[11](hets.vcf, twoPairsWithUMIs, {nSites=1, nMismatchingUMIsInDiffBiDups=1, nMatchingUMIsInDiffBiDups=0, nMismatchingUMIsInSameBiDups=0, nMatchingUMIsInSameBiDups=0, nGoodBarcodes=1, nBadBarcodes=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initializing. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initializing. Test: Test method simpleTest[11](hets.vcf, twoPairsWithUMIs, {nSites=1, nMismatchingUMIsInDiffBiDups=1, nMatchingUMIsInDiffBiDups=0, nMismatchingUMIsInSameBiDups=0, nMatchingUMIsInSameBiDups=0, nGoodBarcodes=1, nBadBarcodes=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initialized. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initialized. Test: Test method simpleTest[11](hets.vcf, twoPairsWithUMIs, {nSites=1, nMismatchingUMIsInDiffBiDups=1, nMatchingUMIsInDiffBiDups=0, nMismatchingUMIsInSameBiDups=0, nMatchingUMIsInSameBiDups=0, nGoodBarcodes=1, nBadBarcodes=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Starting iteration on reads INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Starting iteration on reads Test: Test method simpleTest[11](hets.vcf, twoPairsWithUMIs, {nSites=1, nMismatchingUMIsInDiffBiDups=1, nMatchingUMIsInDiffBiDups=0, nMismatchingUMIsInSameBiDups=0, nMatchingUMIsInSameBiDups=0, nGoodBarcodes=1, nBadBarcodes=0})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. Running Test: Test method simpleTest[12](hets.vcf, twoPairsWithBadUMIs, {nSites=1, nMismatchingUMIsInDiffBiDups=0, nMatchingUMIsInDiffBiDups=0, nMismatchingUMIsInSameBiDups=0, nMatchingUMIsInSameBiDups=0, nGoodBarcodes=0, nBadBarcodes=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) Test: Test method simpleTest[12](hets.vcf, twoPairsWithBadUMIs, {nSites=1, nMismatchingUMIsInDiffBiDups=0, nMatchingUMIsInDiffBiDups=0, nMismatchingUMIsInSameBiDups=0, nMatchingUMIsInSameBiDups=0, nGoodBarcodes=0, nBadBarcodes=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Found 1 heterozygous sites in VCF. Gradle suite > Gradle test > picard.analysis.replicates.CollectIndependentReplicatesMetricTest.simpleTest[12](hets.vcf, twoPairsWithBadUMIs, {nSites=1, nMismatchingUMIsInDiffBiDups=0, nMatchingUMIsInDiffBiDups=0, nMismatchingUMIsInSameBiDups=0, nMatchingUMIsInSameBiDups=0, nGoodBarcodes=0, nBadBarcodes=1}) STANDARD_ERROR INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Found 1 heterozygous sites in VCF. Test: Test method simpleTest[12](hets.vcf, twoPairsWithBadUMIs, {nSites=1, nMismatchingUMIsInDiffBiDups=0, nMatchingUMIsInDiffBiDups=0, nMismatchingUMIsInSameBiDups=0, nMatchingUMIsInSameBiDups=0, nGoodBarcodes=0, nBadBarcodes=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Querying BAM for sites. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Querying BAM for sites. Test: Test method simpleTest[12](hets.vcf, twoPairsWithBadUMIs, {nSites=1, nMismatchingUMIsInDiffBiDups=0, nMatchingUMIsInDiffBiDups=0, nMismatchingUMIsInSameBiDups=0, nMatchingUMIsInSameBiDups=0, nGoodBarcodes=0, nBadBarcodes=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Queried BAM, getting duplicate sets. Test: Test method simpleTest[12](hets.vcf, twoPairsWithBadUMIs, {nSites=1, nMismatchingUMIsInDiffBiDups=0, nMatchingUMIsInDiffBiDups=0, nMismatchingUMIsInSameBiDups=0, nMatchingUMIsInSameBiDups=0, nGoodBarcodes=0, nBadBarcodes=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initializing. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initializing. Test: Test method simpleTest[12](hets.vcf, twoPairsWithBadUMIs, {nSites=1, nMismatchingUMIsInDiffBiDups=0, nMatchingUMIsInDiffBiDups=0, nMismatchingUMIsInSameBiDups=0, nMatchingUMIsInSameBiDups=0, nGoodBarcodes=0, nBadBarcodes=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initialized. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Duplicate set iterator initialized. Test: Test method simpleTest[12](hets.vcf, twoPairsWithBadUMIs, {nSites=1, nMismatchingUMIsInDiffBiDups=0, nMatchingUMIsInDiffBiDups=0, nMismatchingUMIsInSameBiDups=0, nMatchingUMIsInSameBiDups=0, nGoodBarcodes=0, nBadBarcodes=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Starting iteration on reads INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Starting iteration on reads Test: Test method simpleTest[12](hets.vcf, twoPairsWithBadUMIs, {nSites=1, nMismatchingUMIsInDiffBiDups=0, nMatchingUMIsInDiffBiDups=0, nMismatchingUMIsInSameBiDups=0, nMatchingUMIsInSameBiDups=0, nGoodBarcodes=0, nBadBarcodes=1})(picard.analysis.replicates.CollectIndependentReplicatesMetricTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. INFO 2024-07-02 11:51:33 CollectIndependentReplicateMetrics Iteration done. Emitting metrics. Running Test: Test method test(picard.analysis.CollectInsertSizeMetricsTest) Test: Test method test(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:33 CollectInsertSizeMetrics Gradle suite > Gradle test > picard.analysis.CollectInsertSizeMetricsTest.test STANDARD_ERROR INFO 2024-07-02 11:51:33 CollectInsertSizeMetrics Test: Test method test(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: Test: Test method test(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method test(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: ********** ********** Test: Test method test(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method test(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method test(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: ********** ********** Test: Test method test(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method test(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: ********** ********** Test: Test method test(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: ********** CollectInsertSizeMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/insert_size_metrics_test.sam -OUTPUT /tmp/test17923180758993789939.insert_size_metrics -Histogram_FILE /tmp/test15548606803037939493.pdf -LEVEL SAMPLE -LEVEL LIBRARY -LEVEL READ_GROUP ********** CollectInsertSizeMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/insert_size_metrics_test.sam -OUTPUT /tmp/test17923180758993789939.insert_size_metrics -Histogram_FILE /tmp/test15548606803037939493.pdf -LEVEL SAMPLE -LEVEL LIBRARY -LEVEL READ_GROUP Test: Test method test(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: ********** ********** Test: Test method test(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: Test: Test method test(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: Test: Test method test(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:33 RExecutor Executing R script via command: Rscript /tmp/script1833765290924790062.R INFO 2024-07-02 11:51:33 RExecutor Executing R script via command: Rscript /tmp/script1833765290924790062.R Test: Test method test(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:33 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:51:33 ProcessExecutor [1] "Checking if R is installed" Test: Test method test(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: 11:51:33.873 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:33.873 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method test(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: 11:51:33.873 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:33.873 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method test(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: 11:51:33.874 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:33.874 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method test(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: 11:51:33.874 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:33.874 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method test(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: [Tue Jul 02 11:51:33 GMT+14:00 2024] CollectInsertSizeMetrics HISTOGRAM_FILE=/tmp/test15548606803037939493.pdf METRIC_ACCUMULATION_LEVEL=[READ_GROUP, LIBRARY, SAMPLE, ALL_READS] INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/insert_size_metrics_test.sam OUTPUT=/tmp/test17923180758993789939.insert_size_metrics DEVIATIONS=10.0 MINIMUM_PCT=0.05 INCLUDE_DUPLICATES=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:33 GMT+14:00 2024] CollectInsertSizeMetrics HISTOGRAM_FILE=/tmp/test15548606803037939493.pdf METRIC_ACCUMULATION_LEVEL=[READ_GROUP, LIBRARY, SAMPLE, ALL_READS] INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/insert_size_metrics_test.sam OUTPUT=/tmp/test17923180758993789939.insert_size_metrics DEVIATIONS=10.0 MINIMUM_PCT=0.05 INCLUDE_DUPLICATES=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method test(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: [Tue Jul 02 11:51:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method test(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:33 RExecutor Executing R script via command: Rscript /tmp/script7698862728962938066.R /tmp/test17923180758993789939.insert_size_metrics /tmp/test15548606803037939493.pdf insert_size_metrics_test.sam INFO 2024-07-02 11:51:33 RExecutor Executing R script via command: Rscript /tmp/script7698862728962938066.R /tmp/test17923180758993789939.insert_size_metrics /tmp/test15548606803037939493.pdf insert_size_metrics_test.sam Test: Test method test(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:35 ProcessExecutor null device INFO 2024-07-02 11:51:35 ProcessExecutor null device Test: Test method test(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:35 ProcessExecutor 1 INFO 2024-07-02 11:51:35 ProcessExecutor 1 Test: Test method test(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: [Tue Jul 02 11:51:35 GMT+14:00 2024] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:51:35 GMT+14:00 2024] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 0.03 minutes. Test: Test method test(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testHistogramWidthIsSetProperly(picard.analysis.CollectInsertSizeMetricsTest) Test: Test method testHistogramWidthIsSetProperly(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:35 CollectInsertSizeMetrics Gradle suite > Gradle test > picard.analysis.CollectInsertSizeMetricsTest.testHistogramWidthIsSetProperly STANDARD_ERROR INFO 2024-07-02 11:51:35 CollectInsertSizeMetrics Test: Test method testHistogramWidthIsSetProperly(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: Test: Test method testHistogramWidthIsSetProperly(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testHistogramWidthIsSetProperly(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: ********** ********** Test: Test method testHistogramWidthIsSetProperly(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testHistogramWidthIsSetProperly(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testHistogramWidthIsSetProperly(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: ********** ********** Test: Test method testHistogramWidthIsSetProperly(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testHistogramWidthIsSetProperly(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: ********** ********** Test: Test method testHistogramWidthIsSetProperly(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: ********** CollectInsertSizeMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/insert_size_metrics_test.sam -OUTPUT /tmp/test5302918809976807017.insert_size_metrics -Histogram_FILE /tmp/test718202677032351567.pdf -LEVEL null -LEVEL READ_GROUP ********** CollectInsertSizeMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/insert_size_metrics_test.sam -OUTPUT /tmp/test5302918809976807017.insert_size_metrics -Histogram_FILE /tmp/test718202677032351567.pdf -LEVEL null -LEVEL READ_GROUP Test: Test method testHistogramWidthIsSetProperly(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: ********** ********** Test: Test method testHistogramWidthIsSetProperly(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: Test: Test method testHistogramWidthIsSetProperly(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: Test: Test method testHistogramWidthIsSetProperly(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:35 RExecutor Executing R script via command: Rscript /tmp/script8575192447262486357.R INFO 2024-07-02 11:51:35 RExecutor Executing R script via command: Rscript /tmp/script8575192447262486357.R Test: Test method testHistogramWidthIsSetProperly(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:36 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:51:36 ProcessExecutor [1] "Checking if R is installed" Test: Test method testHistogramWidthIsSetProperly(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: 11:51:36.773 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:36.773 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testHistogramWidthIsSetProperly(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: 11:51:36.773 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:36.773 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testHistogramWidthIsSetProperly(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: 11:51:36.774 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:36.774 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testHistogramWidthIsSetProperly(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: 11:51:36.774 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:36.774 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testHistogramWidthIsSetProperly(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: [Tue Jul 02 11:51:36 GMT+14:00 2024] CollectInsertSizeMetrics HISTOGRAM_FILE=/tmp/test718202677032351567.pdf METRIC_ACCUMULATION_LEVEL=[READ_GROUP] INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/insert_size_metrics_test.sam OUTPUT=/tmp/test5302918809976807017.insert_size_metrics DEVIATIONS=10.0 MINIMUM_PCT=0.05 INCLUDE_DUPLICATES=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:36 GMT+14:00 2024] CollectInsertSizeMetrics HISTOGRAM_FILE=/tmp/test718202677032351567.pdf METRIC_ACCUMULATION_LEVEL=[READ_GROUP] INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/insert_size_metrics_test.sam OUTPUT=/tmp/test5302918809976807017.insert_size_metrics DEVIATIONS=10.0 MINIMUM_PCT=0.05 INCLUDE_DUPLICATES=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testHistogramWidthIsSetProperly(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: [Tue Jul 02 11:51:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testHistogramWidthIsSetProperly(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:36 RExecutor Executing R script via command: Rscript /tmp/script1366090538785652673.R /tmp/test5302918809976807017.insert_size_metrics /tmp/test718202677032351567.pdf insert_size_metrics_test.sam INFO 2024-07-02 11:51:36 RExecutor Executing R script via command: Rscript /tmp/script1366090538785652673.R /tmp/test5302918809976807017.insert_size_metrics /tmp/test718202677032351567.pdf insert_size_metrics_test.sam Test: Test method testHistogramWidthIsSetProperly(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:38 ProcessExecutor null device INFO 2024-07-02 11:51:38 ProcessExecutor null device Test: Test method testHistogramWidthIsSetProperly(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:38 ProcessExecutor 1 INFO 2024-07-02 11:51:38 ProcessExecutor 1 Test: Test method testHistogramWidthIsSetProperly(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: [Tue Jul 02 11:51:38 GMT+14:00 2024] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:51:38 GMT+14:00 2024] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 0.03 minutes. Test: Test method testHistogramWidthIsSetProperly(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMultipleOrientationsForHistogram(picard.analysis.CollectInsertSizeMetricsTest) Test: Test method testMultipleOrientationsForHistogram(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:38 RExecutor Executing R script via command: Rscript /tmp/script92354506742962283.R /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/directed/CollectInsertSizeMetrics/multiple_orientation.sam.insert_size_metrics /tmp/test7151591376308372401.pdf Flags of Chad and Romania Gradle suite > Gradle test > picard.analysis.CollectInsertSizeMetricsTest.testMultipleOrientationsForHistogram STANDARD_ERROR INFO 2024-07-02 11:51:38 RExecutor Executing R script via command: Rscript /tmp/script92354506742962283.R /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/directed/CollectInsertSizeMetrics/multiple_orientation.sam.insert_size_metrics /tmp/test7151591376308372401.pdf Flags of Chad and Romania Test: Test method testMultipleOrientationsForHistogram(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:40 ProcessExecutor null device INFO 2024-07-02 11:51:40 ProcessExecutor null device Test: Test method testMultipleOrientationsForHistogram(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:40 ProcessExecutor 1 INFO 2024-07-02 11:51:40 ProcessExecutor 1 Running Test: Test method testWidthOfMetrics(picard.analysis.CollectInsertSizeMetricsTest) Test: Test method testWidthOfMetrics(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:40 CollectInsertSizeMetrics Gradle suite > Gradle test > picard.analysis.CollectInsertSizeMetricsTest.testWidthOfMetrics STANDARD_ERROR INFO 2024-07-02 11:51:40 CollectInsertSizeMetrics Test: Test method testWidthOfMetrics(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: Test: Test method testWidthOfMetrics(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWidthOfMetrics(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: ********** ********** Test: Test method testWidthOfMetrics(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWidthOfMetrics(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWidthOfMetrics(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: ********** ********** Test: Test method testWidthOfMetrics(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWidthOfMetrics(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: ********** ********** Test: Test method testWidthOfMetrics(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: ********** CollectInsertSizeMetrics -INPUT /tmp/CollectInsertSizeMetrics17253219495343620376.bam -OUTPUT /tmp/test11308716323923991083.insert_size_metrics -Histogram_FILE /tmp/test13842242185185688815.pdf ********** CollectInsertSizeMetrics -INPUT /tmp/CollectInsertSizeMetrics17253219495343620376.bam -OUTPUT /tmp/test11308716323923991083.insert_size_metrics -Histogram_FILE /tmp/test13842242185185688815.pdf Test: Test method testWidthOfMetrics(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: ********** ********** Test: Test method testWidthOfMetrics(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: Test: Test method testWidthOfMetrics(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: Test: Test method testWidthOfMetrics(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:40 RExecutor Executing R script via command: Rscript /tmp/script912623138687033076.R INFO 2024-07-02 11:51:40 RExecutor Executing R script via command: Rscript /tmp/script912623138687033076.R Test: Test method testWidthOfMetrics(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:41 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:51:41 ProcessExecutor [1] "Checking if R is installed" Test: Test method testWidthOfMetrics(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: 11:51:41.346 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:41.346 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWidthOfMetrics(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: 11:51:41.346 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:41.346 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWidthOfMetrics(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: 11:51:41.346 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:41.346 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWidthOfMetrics(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: 11:51:41.346 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:41.346 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWidthOfMetrics(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: [Tue Jul 02 11:51:41 GMT+14:00 2024] CollectInsertSizeMetrics HISTOGRAM_FILE=/tmp/test13842242185185688815.pdf INPUT=/tmp/CollectInsertSizeMetrics17253219495343620376.bam OUTPUT=/tmp/test11308716323923991083.insert_size_metrics DEVIATIONS=10.0 MINIMUM_PCT=0.05 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INCLUDE_DUPLICATES=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:41 GMT+14:00 2024] CollectInsertSizeMetrics HISTOGRAM_FILE=/tmp/test13842242185185688815.pdf INPUT=/tmp/CollectInsertSizeMetrics17253219495343620376.bam OUTPUT=/tmp/test11308716323923991083.insert_size_metrics DEVIATIONS=10.0 MINIMUM_PCT=0.05 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INCLUDE_DUPLICATES=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWidthOfMetrics(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: [Tue Jul 02 11:51:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWidthOfMetrics(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:41 RExecutor Executing R script via command: Rscript /tmp/script2329515237785751006.R /tmp/test11308716323923991083.insert_size_metrics /tmp/test13842242185185688815.pdf CollectInsertSizeMetrics17253219495343620376.bam INFO 2024-07-02 11:51:41 RExecutor Executing R script via command: Rscript /tmp/script2329515237785751006.R /tmp/test11308716323923991083.insert_size_metrics /tmp/test13842242185185688815.pdf CollectInsertSizeMetrics17253219495343620376.bam Test: Test method testWidthOfMetrics(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:42 ProcessExecutor null device INFO 2024-07-02 11:51:42 ProcessExecutor null device Test: Test method testWidthOfMetrics(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:42 ProcessExecutor 1 INFO 2024-07-02 11:51:42 ProcessExecutor 1 Test: Test method testWidthOfMetrics(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: [Tue Jul 02 11:51:42 GMT+14:00 2024] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:51:42 GMT+14:00 2024] picard.analysis.CollectInsertSizeMetrics done. Elapsed time: 0.01 minutes. Test: Test method testWidthOfMetrics(picard.analysis.CollectInsertSizeMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testCollectJumpingLibraryMetrics(picard.analysis.CollectJumpingLibraryMetricsTest) Test: Test method testCollectJumpingLibraryMetrics(picard.analysis.CollectJumpingLibraryMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:42 CollectJumpingLibraryMetrics Gradle suite > Gradle test > picard.analysis.CollectJumpingLibraryMetricsTest.testCollectJumpingLibraryMetrics STANDARD_ERROR INFO 2024-07-02 11:51:42 CollectJumpingLibraryMetrics Test: Test method testCollectJumpingLibraryMetrics(picard.analysis.CollectJumpingLibraryMetricsTest) produced standard out/err: Test: Test method testCollectJumpingLibraryMetrics(picard.analysis.CollectJumpingLibraryMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCollectJumpingLibraryMetrics(picard.analysis.CollectJumpingLibraryMetricsTest) produced standard out/err: ********** ********** Test: Test method testCollectJumpingLibraryMetrics(picard.analysis.CollectJumpingLibraryMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCollectJumpingLibraryMetrics(picard.analysis.CollectJumpingLibraryMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCollectJumpingLibraryMetrics(picard.analysis.CollectJumpingLibraryMetricsTest) produced standard out/err: ********** ********** Test: Test method testCollectJumpingLibraryMetrics(picard.analysis.CollectJumpingLibraryMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCollectJumpingLibraryMetrics(picard.analysis.CollectJumpingLibraryMetricsTest) produced standard out/err: ********** ********** Test: Test method testCollectJumpingLibraryMetrics(picard.analysis.CollectJumpingLibraryMetricsTest) produced standard out/err: ********** CollectJumpingLibraryMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/forMetrics.sam -OUTPUT /tmp/CollectJumpingLibraryMetricsTest6209877252824852290.txt ********** CollectJumpingLibraryMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/forMetrics.sam -OUTPUT /tmp/CollectJumpingLibraryMetricsTest6209877252824852290.txt Test: Test method testCollectJumpingLibraryMetrics(picard.analysis.CollectJumpingLibraryMetricsTest) produced standard out/err: ********** ********** Test: Test method testCollectJumpingLibraryMetrics(picard.analysis.CollectJumpingLibraryMetricsTest) produced standard out/err: Test: Test method testCollectJumpingLibraryMetrics(picard.analysis.CollectJumpingLibraryMetricsTest) produced standard out/err: Test: Test method testCollectJumpingLibraryMetrics(picard.analysis.CollectJumpingLibraryMetricsTest) produced standard out/err: 11:51:42.193 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:42.193 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCollectJumpingLibraryMetrics(picard.analysis.CollectJumpingLibraryMetricsTest) produced standard out/err: 11:51:42.194 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:42.194 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCollectJumpingLibraryMetrics(picard.analysis.CollectJumpingLibraryMetricsTest) produced standard out/err: 11:51:42.194 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:42.194 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCollectJumpingLibraryMetrics(picard.analysis.CollectJumpingLibraryMetricsTest) produced standard out/err: 11:51:42.194 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:42.194 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCollectJumpingLibraryMetrics(picard.analysis.CollectJumpingLibraryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:42 GMT+14:00 2024] CollectJumpingLibraryMetrics INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/forMetrics.sam] OUTPUT=/tmp/CollectJumpingLibraryMetricsTest6209877252824852290.txt MINIMUM_MAPPING_QUALITY=0 TAIL_LIMIT=10000 CHIMERA_KB_MIN=100000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:42 GMT+14:00 2024] CollectJumpingLibraryMetrics INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/forMetrics.sam] OUTPUT=/tmp/CollectJumpingLibraryMetricsTest6209877252824852290.txt MINIMUM_MAPPING_QUALITY=0 TAIL_LIMIT=10000 CHIMERA_KB_MIN=100000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCollectJumpingLibraryMetrics(picard.analysis.CollectJumpingLibraryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCollectJumpingLibraryMetrics(picard.analysis.CollectJumpingLibraryMetricsTest) produced standard out/err: [Tue Jul 02 11:51:42 GMT+14:00 2024] picard.analysis.CollectJumpingLibraryMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:42 GMT+14:00 2024] picard.analysis.CollectJumpingLibraryMetrics done. Elapsed time: 0.00 minutes. Test: Test method testCollectJumpingLibraryMetrics(picard.analysis.CollectJumpingLibraryMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:42 CollectMultipleMetrics Gradle suite > Gradle test > picard.analysis.CollectMultipleMetricsTest.testAlignmentSummaryViaMultipleMetrics STANDARD_ERROR INFO 2024-07-02 11:51:42 CollectMultipleMetrics Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** CollectMultipleMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam -OUTPUT /tmp/alignmentMetrics16078701636610821446 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta -METRIC_ACCUMULATION_LEVEL ALL_READS -PROGRAM null -PROGRAM CollectAlignmentSummaryMetrics -PROGRAM CollectInsertSizeMetrics -EXTRA_ARGUMENT CollectInsertSizeMetrics::--HISTOGRAM_WIDTH 58 -EXTRA_ARGUMENT CollectInsertSizeMetrics::--METRIC_ACCUMULATION_LEVEL LIBRARY -EXTRA_ARGUMENT CollectInsertSizeMetrics::--METRIC_ACCUMULATION_LEVEL READ_GROUP ********** CollectMultipleMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam -OUTPUT /tmp/alignmentMetrics16078701636610821446 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta -METRIC_ACCUMULATION_LEVEL ALL_READS -PROGRAM null -PROGRAM CollectAlignmentSummaryMetrics -PROGRAM CollectInsertSizeMetrics -EXTRA_ARGUMENT CollectInsertSizeMetrics::--HISTOGRAM_WIDTH 58 -EXTRA_ARGUMENT CollectInsertSizeMetrics::--METRIC_ACCUMULATION_LEVEL LIBRARY -EXTRA_ARGUMENT CollectInsertSizeMetrics::--METRIC_ACCUMULATION_LEVEL READ_GROUP Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:42 RExecutor Executing R script via command: Rscript /tmp/script12809111184702858489.R INFO 2024-07-02 11:51:42 RExecutor Executing R script via command: Rscript /tmp/script12809111184702858489.R Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:42 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:51:42 ProcessExecutor [1] "Checking if R is installed" Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:51:42.805 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:42.805 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:51:42.805 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:42.805 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:51:42.806 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:42.806 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:51:42.806 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:42.806 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:51:42 GMT+14:00 2024] CollectMultipleMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam OUTPUT=/tmp/alignmentMetrics16078701636610821446 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] EXTRA_ARGUMENT=[CollectInsertSizeMetrics::HISTOGRAM_WIDTH= 58, CollectInsertSizeMetrics::METRIC_ACCUMULATION_LEVEL=LIBRARY, CollectInsertSizeMetrics::METRIC_ACCUMULATION_LEVEL=READ_GROUP] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:42 GMT+14:00 2024] CollectMultipleMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam OUTPUT=/tmp/alignmentMetrics16078701636610821446 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] EXTRA_ARGUMENT=[CollectInsertSizeMetrics::HISTOGRAM_WIDTH= 58, CollectInsertSizeMetrics::METRIC_ACCUMULATION_LEVEL=LIBRARY, CollectInsertSizeMetrics::METRIC_ACCUMULATION_LEVEL=READ_GROUP] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:51:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:42 RExecutor Executing R script via command: Rscript /tmp/script15712127265436993579.R /tmp/alignmentMetrics16078701636610821446.alignment_summary_metrics /tmp/alignmentMetrics16078701636610821446.read_length_histogram.pdf summary_alignment_stats_test.sam INFO 2024-07-02 11:51:42 RExecutor Executing R script via command: Rscript /tmp/script15712127265436993579.R /tmp/alignmentMetrics16078701636610821446.alignment_summary_metrics /tmp/alignmentMetrics16078701636610821446.read_length_histogram.pdf summary_alignment_stats_test.sam Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:44 ProcessExecutor null device INFO 2024-07-02 11:51:44 ProcessExecutor null device Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:44 ProcessExecutor 1 INFO 2024-07-02 11:51:44 ProcessExecutor 1 Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:44 RExecutor Executing R script via command: Rscript /tmp/script11765866992871675790.R /tmp/alignmentMetrics16078701636610821446.insert_size_metrics /tmp/alignmentMetrics16078701636610821446.insert_size_histogram.pdf summary_alignment_stats_test.sam 58 INFO 2024-07-02 11:51:44 RExecutor Executing R script via command: Rscript /tmp/script11765866992871675790.R /tmp/alignmentMetrics16078701636610821446.insert_size_metrics /tmp/alignmentMetrics16078701636610821446.insert_size_histogram.pdf summary_alignment_stats_test.sam 58 Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:46 ProcessExecutor null device INFO 2024-07-02 11:51:46 ProcessExecutor null device Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:46 ProcessExecutor 1 INFO 2024-07-02 11:51:46 ProcessExecutor 1 Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:51:46 GMT+14:00 2024] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:51:46 GMT+14:00 2024] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.06 minutes. Test: Test method testAlignmentSummaryViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:46 CollectMultipleMetrics Gradle suite > Gradle test > picard.analysis.CollectMultipleMetricsTest.testGcBiasMetrics STANDARD_ERROR INFO 2024-07-02 11:51:46 CollectMultipleMetrics Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** CollectMultipleMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias16671323870963296687.bam -OUTPUT /tmp/test816307657183105647 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -METRIC_ACCUMULATION_LEVEL ALL_READS -PROGRAM null -PROGRAM CollectAlignmentSummaryMetrics -PROGRAM CollectInsertSizeMetrics -PROGRAM CollectGcBiasMetrics ********** CollectMultipleMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias16671323870963296687.bam -OUTPUT /tmp/test816307657183105647 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -METRIC_ACCUMULATION_LEVEL ALL_READS -PROGRAM null -PROGRAM CollectAlignmentSummaryMetrics -PROGRAM CollectInsertSizeMetrics -PROGRAM CollectGcBiasMetrics Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:46 RExecutor Executing R script via command: Rscript /tmp/script1415729544575745292.R INFO 2024-07-02 11:51:46 RExecutor Executing R script via command: Rscript /tmp/script1415729544575745292.R Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:47 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:51:47 ProcessExecutor [1] "Checking if R is installed" Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:51:47.473 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:47.473 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:51:47.473 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:47.473 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:51:47.474 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:47.474 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:51:47.474 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:47.474 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:51:47 GMT+14:00 2024] CollectMultipleMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias16671323870963296687.bam OUTPUT=/tmp/test816307657183105647 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics, CollectGcBiasMetrics] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:47 GMT+14:00 2024] CollectMultipleMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias16671323870963296687.bam OUTPUT=/tmp/test816307657183105647 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics, CollectGcBiasMetrics] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:51:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:47 RExecutor Executing R script via command: Rscript /tmp/script9727155356315421332.R /tmp/test816307657183105647.alignment_summary_metrics /tmp/test816307657183105647.read_length_histogram.pdf CollectGcBias16671323870963296687.bam INFO 2024-07-02 11:51:47 RExecutor Executing R script via command: Rscript /tmp/script9727155356315421332.R /tmp/test816307657183105647.alignment_summary_metrics /tmp/test816307657183105647.read_length_histogram.pdf CollectGcBias16671323870963296687.bam Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:48 ProcessExecutor null device INFO 2024-07-02 11:51:48 ProcessExecutor null device Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:48 ProcessExecutor 1 INFO 2024-07-02 11:51:48 ProcessExecutor 1 Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:48 RExecutor Executing R script via command: Rscript /tmp/script3252586274843036957.R /tmp/test816307657183105647.insert_size_metrics /tmp/test816307657183105647.insert_size_histogram.pdf CollectGcBias16671323870963296687.bam INFO 2024-07-02 11:51:48 RExecutor Executing R script via command: Rscript /tmp/script3252586274843036957.R /tmp/test816307657183105647.insert_size_metrics /tmp/test816307657183105647.insert_size_histogram.pdf CollectGcBias16671323870963296687.bam Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:50 ProcessExecutor null device INFO 2024-07-02 11:51:50 ProcessExecutor null device Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:50 ProcessExecutor 1 INFO 2024-07-02 11:51:50 ProcessExecutor 1 Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:50 RExecutor Executing R script via command: Rscript /tmp/script17624205794859791989.R /tmp/test816307657183105647.gc_bias.detail_metrics /tmp/test816307657183105647.gc_bias.summary_metrics /tmp/test816307657183105647.gc_bias.pdf 100 INFO 2024-07-02 11:51:50 RExecutor Executing R script via command: Rscript /tmp/script17624205794859791989.R /tmp/test816307657183105647.gc_bias.detail_metrics /tmp/test816307657183105647.gc_bias.summary_metrics /tmp/test816307657183105647.gc_bias.pdf 100 Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:51 ProcessExecutor Total clusters: 300 , Aligned reads: 600 INFO 2024-07-02 11:51:51 ProcessExecutor Total clusters: 300 , Aligned reads: 600 Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:51:51 GMT+14:00 2024] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.07 minutes. [Tue Jul 02 11:51:51 GMT+14:00 2024] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.07 minutes. Test: Test method testGcBiasMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:52 CollectMultipleMetrics Gradle suite > Gradle test > picard.analysis.CollectMultipleMetricsTest.testInsertSize STANDARD_ERROR INFO 2024-07-02 11:51:52 CollectMultipleMetrics Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** CollectMultipleMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/insert_size_metrics_test.sam -OUTPUT /tmp/test14081611626515873644 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta -METRIC_ACCUMULATION_LEVEL ALL_READS -PROGRAM null -PROGRAM CollectAlignmentSummaryMetrics -PROGRAM CollectInsertSizeMetrics ********** CollectMultipleMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/insert_size_metrics_test.sam -OUTPUT /tmp/test14081611626515873644 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta -METRIC_ACCUMULATION_LEVEL ALL_READS -PROGRAM null -PROGRAM CollectAlignmentSummaryMetrics -PROGRAM CollectInsertSizeMetrics Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:52 RExecutor Executing R script via command: Rscript /tmp/script10596498020896324253.R INFO 2024-07-02 11:51:52 RExecutor Executing R script via command: Rscript /tmp/script10596498020896324253.R Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:52 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:51:52 ProcessExecutor [1] "Checking if R is installed" Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:51:52.990 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:52.990 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:51:52.990 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:52.990 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:51:52.990 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:52.990 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:51:52.990 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:52.990 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:51:52 GMT+14:00 2024] CollectMultipleMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/insert_size_metrics_test.sam OUTPUT=/tmp/test14081611626515873644 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:52 GMT+14:00 2024] CollectMultipleMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/insert_size_metrics_test.sam OUTPUT=/tmp/test14081611626515873644 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:51:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:53 RExecutor Executing R script via command: Rscript /tmp/script2004836594506478599.R /tmp/test14081611626515873644.alignment_summary_metrics /tmp/test14081611626515873644.read_length_histogram.pdf insert_size_metrics_test.sam INFO 2024-07-02 11:51:53 RExecutor Executing R script via command: Rscript /tmp/script2004836594506478599.R /tmp/test14081611626515873644.alignment_summary_metrics /tmp/test14081611626515873644.read_length_histogram.pdf insert_size_metrics_test.sam Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:54 ProcessExecutor null device INFO 2024-07-02 11:51:54 ProcessExecutor null device Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:54 ProcessExecutor 1 INFO 2024-07-02 11:51:54 ProcessExecutor 1 Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:54 RExecutor Executing R script via command: Rscript /tmp/script18196458453834417731.R /tmp/test14081611626515873644.insert_size_metrics /tmp/test14081611626515873644.insert_size_histogram.pdf insert_size_metrics_test.sam INFO 2024-07-02 11:51:54 RExecutor Executing R script via command: Rscript /tmp/script18196458453834417731.R /tmp/test14081611626515873644.insert_size_metrics /tmp/test14081611626515873644.insert_size_histogram.pdf insert_size_metrics_test.sam Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:55 ProcessExecutor null device INFO 2024-07-02 11:51:55 ProcessExecutor null device Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:55 ProcessExecutor 1 INFO 2024-07-02 11:51:55 ProcessExecutor 1 Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:51:55 GMT+14:00 2024] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:51:55 GMT+14:00 2024] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.04 minutes. Test: Test method testInsertSize(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:55 CollectMultipleMetrics Gradle suite > Gradle test > picard.analysis.CollectMultipleMetricsTest.testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out) STANDARD_ERROR INFO 2024-07-02 11:51:55 CollectMultipleMetrics Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** CollectMultipleMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam -OUTPUT /tmp/alignmentMetrics8896670735993061337 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta -METRIC_ACCUMULATION_LEVEL ALL_READS -PROGRAM null -PROGRAM CollectAlignmentSummaryMetrics -PROGRAM CollectInsertSizeMetrics -EXTRA_ARGUMENT CollectInsertSizeMetrics::--OUTPUT hi.out ********** CollectMultipleMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam -OUTPUT /tmp/alignmentMetrics8896670735993061337 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta -METRIC_ACCUMULATION_LEVEL ALL_READS -PROGRAM null -PROGRAM CollectAlignmentSummaryMetrics -PROGRAM CollectInsertSizeMetrics -EXTRA_ARGUMENT CollectInsertSizeMetrics::--OUTPUT hi.out Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:55 RExecutor Executing R script via command: Rscript /tmp/script7840352681354071007.R INFO 2024-07-02 11:51:55 RExecutor Executing R script via command: Rscript /tmp/script7840352681354071007.R Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:56 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:51:56 ProcessExecutor [1] "Checking if R is installed" Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:51:56.165 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:56.165 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:51:56.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:56.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:51:56.166 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:56.166 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:51:56.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:56.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:51:56 GMT+14:00 2024] CollectMultipleMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=/tmp/alignmentMetrics8896670735993061337 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] EXTRA_ARGUMENT=[CollectInsertSizeMetrics::OUTPUT =hi.out] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:56 GMT+14:00 2024] CollectMultipleMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=/tmp/alignmentMetrics8896670735993061337 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] EXTRA_ARGUMENT=[CollectInsertSizeMetrics::OUTPUT =hi.out] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:51:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ERROR: Invalid argument 'OUTPUT'. ERROR: Invalid argument 'OUTPUT'. Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: USAGE: CollectInsertSizeMetrics [options] USAGE: CollectInsertSizeMetrics [options] Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CollectInsertSizeMetrics Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CollectInsertSizeMetrics Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Collect metrics about the insert size distribution of a paired-end library. This tool provides useful metrics for Collect metrics about the insert size distribution of a paired-end library. This tool provides useful metrics for Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: validating library construction including the insert size distribution and read orientation of paired-end libraries. validating library construction including the insert size distribution and read orientation of paired-end libraries. Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: The expected proportions of these metrics vary depending on the type of library preparation used, resulting from The expected proportions of these metrics vary depending on the type of library preparation used, resulting from Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: technical differences between pair-end libraries and mate-pair libraries. For a brief primer on paired-end sequencing technical differences between pair-end libraries and mate-pair libraries. For a brief primer on paired-end sequencing Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: and mate-pair reads, see the GATK Dictionary (https://www.broadinstitute.org/gatk/guide/article?id=6327). and mate-pair reads, see the GATK Dictionary (https://www.broadinstitute.org/gatk/guide/article?id=6327). Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: The CollectInsertSizeMetrics tool outputs the percentages of read pairs in each of the three orientations (FR, RF, and The CollectInsertSizeMetrics tool outputs the percentages of read pairs in each of the three orientations (FR, RF, and Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: TANDEM) as a histogram. In addition, the insert size distribution is output as both a histogram TANDEM) as a histogram. In addition, the insert size distribution is output as both a histogram Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: (.insert_size_Histogram.pdf) and as a data table (.insert_size_metrics.txt). (.insert_size_Histogram.pdf) and as a data table (.insert_size_metrics.txt). Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Note: Metrics labeled as percentages are actually expressed as fractions! Note: Metrics labeled as percentages are actually expressed as fractions! Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Usage example: Usage example: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: java -jar picard.jar CollectInsertSizeMetrics \ java -jar picard.jar CollectInsertSizeMetrics \ Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: O=insert_size_metrics.txt \ O=insert_size_metrics.txt \ Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: H=insert_size_histogram.pdf \ H=insert_size_histogram.pdf \ Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: M=0.5 M=0.5 Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Note: If processing a small file, set the minimum percentage option (M) to 0.5, otherwise an error may occur. Note: If processing a small file, set the minimum percentage option (M) to 0.5, otherwise an error may occur. Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Please see InsertSizeMetrics (https://broadinstitute.github.io/picard/picard-metric-definitions.html#InsertSizeMetrics) Please see InsertSizeMetrics (https://broadinstitute.github.io/picard/picard-metric-definitions.html#InsertSizeMetrics) Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: for detailed explanations of each metric. for detailed explanations of each metric. Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Version: null Version: null Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Options: Options: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: --help --help Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: tools. tools. Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: HISTOGRAM_FILE=File HISTOGRAM_FILE=File Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: H=File File to write insert size Histogram chart to. Default value: H=File File to write insert size Histogram chart to. Default value: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: /tmp/alignmentMetrics8896670735993061337.insert_size_histogram.pdf. This option can be set /tmp/alignmentMetrics8896670735993061337.insert_size_histogram.pdf. This option can be set Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: to 'null' to clear the default value. to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: DEVIATIONS=Double Generate mean, sd and plots by trimming the data down to MEDIAN + DEVIATIONS=Double Generate mean, sd and plots by trimming the data down to MEDIAN + Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: includes enough anomalous values from chimeras and other artifacts to make the mean and sd includes enough anomalous values from chimeras and other artifacts to make the mean and sd Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: grossly misleading regarding the real distribution. Default value: 10.0. This option can grossly misleading regarding the real distribution. Default value: 10.0. This option can Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: be set to 'null' to clear the default value. be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: HISTOGRAM_WIDTH=Integer HISTOGRAM_WIDTH=Integer Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: W=Integer Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail. W=Integer Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail. Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Also, when calculating mean and standard deviation, only bins <= Histogram_WIDTH will be Also, when calculating mean and standard deviation, only bins <= Histogram_WIDTH will be Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: included. Default value: null. included. Default value: null. Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: MIN_HISTOGRAM_WIDTH=Integer MIN_HISTOGRAM_WIDTH=Integer Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: MW=Integer Minimum width of histogram plots. In the case when the histogram would otherwise MW=Integer Minimum width of histogram plots. In the case when the histogram would otherwise Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: betruncated to a shorter range of sizes, the MIN_HISTOGRAM_WIDTH will enforce a minimum betruncated to a shorter range of sizes, the MIN_HISTOGRAM_WIDTH will enforce a minimum Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: range. Default value: null. range. Default value: null. Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: MINIMUM_PCT=Float MINIMUM_PCT=Float Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: M=Float When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that M=Float When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: have fewer than this percentage of overall reads. (Range: 0 to 1). Default value: 0.05. have fewer than this percentage of overall reads. (Range: 0 to 1). Default value: 0.05. Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Default value: [ALL_READS]. This option LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Default value: [ALL_READS]. This option Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: can be set to 'null' to clear the default value. Possible values: {ALL_READS, SAMPLE, can be set to 'null' to clear the default value. Possible values: {ALL_READS, SAMPLE, Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: LIBRARY, READ_GROUP} This option may be specified 0 or more times. This option can be set LIBRARY, READ_GROUP} This option may be specified 0 or more times. This option can be set Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: to 'null' to clear the default list. to 'null' to clear the default list. Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INCLUDE_DUPLICATES=Boolean If true, also include reads marked as duplicates in the insert size histogram. Default INCLUDE_DUPLICATES=Boolean If true, also include reads marked as duplicates in the insert size histogram. Default Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: value: false. This option can be set to 'null' to clear the default value. Possible value: false. This option can be set to 'null' to clear the default value. Possible Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: values: {true, false} values: {true, false} Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: I=File Input SAM or BAM file. Default value: I=File Input SAM or BAM file. Default value: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam. /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam. Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: O=File The file to write the output to. Default value: O=File The file to write the output to. Default value: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: /tmp/alignmentMetrics8896670735993061337.insert_size_metrics. This option can be set to /tmp/alignmentMetrics8896670735993061337.insert_size_metrics. This option can be set to Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 'null' to clear the default value. 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ASSUME_SORTED=Boolean ASSUME_SORTED=Boolean Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: AS=Boolean If true (default), then the sort order in the header file will be ignored. Default value: AS=Boolean If true (default), then the sort order in the header file will be ignored. Default value: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: true. This option can be set to 'null' to clear the default value. Possible values: {true, true. This option can be set to 'null' to clear the default value. Possible values: {true, Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: false} false} Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: 0. This option can be STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: 0. This option can be Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: set to 'null' to clear the default value. set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:51:56 GMT+14:00 2024] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:56 GMT+14:00 2024] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes. Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testMultipleMetricsFailing[0](CollectInsertSizeMetrics::OUTPUT =hi.out)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMultipleMetricsFailing[1](BLAH::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) Test: Test method testMultipleMetricsFailing[1](BLAH::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:56 CollectMultipleMetrics Gradle suite > Gradle test > picard.analysis.CollectMultipleMetricsTest.testMultipleMetricsFailing[1](BLAH::HISTOGRAM_WIDTH=58) STANDARD_ERROR INFO 2024-07-02 11:51:56 CollectMultipleMetrics Test: Test method testMultipleMetricsFailing[1](BLAH::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[1](BLAH::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMultipleMetricsFailing[1](BLAH::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[1](BLAH::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMultipleMetricsFailing[1](BLAH::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMultipleMetricsFailing[1](BLAH::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[1](BLAH::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMultipleMetricsFailing[1](BLAH::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[1](BLAH::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** CollectMultipleMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam -OUTPUT /tmp/alignmentMetrics15295167071806496111 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta -METRIC_ACCUMULATION_LEVEL ALL_READS -PROGRAM null -PROGRAM CollectAlignmentSummaryMetrics -PROGRAM CollectInsertSizeMetrics -EXTRA_ARGUMENT BLAH::--HISTOGRAM_WIDTH 58 ********** CollectMultipleMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam -OUTPUT /tmp/alignmentMetrics15295167071806496111 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta -METRIC_ACCUMULATION_LEVEL ALL_READS -PROGRAM null -PROGRAM CollectAlignmentSummaryMetrics -PROGRAM CollectInsertSizeMetrics -EXTRA_ARGUMENT BLAH::--HISTOGRAM_WIDTH 58 Test: Test method testMultipleMetricsFailing[1](BLAH::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[1](BLAH::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[1](BLAH::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[1](BLAH::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:56 RExecutor Executing R script via command: Rscript /tmp/script7800873838797615631.R INFO 2024-07-02 11:51:56 RExecutor Executing R script via command: Rscript /tmp/script7800873838797615631.R Test: Test method testMultipleMetricsFailing[1](BLAH::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:56 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:51:56 ProcessExecutor [1] "Checking if R is installed" Test: Test method testMultipleMetricsFailing[1](BLAH::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:51:56.871 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:56.871 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleMetricsFailing[1](BLAH::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:51:56.871 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:56.871 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleMetricsFailing[1](BLAH::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:51:56.871 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:56.871 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleMetricsFailing[1](BLAH::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:51:56.871 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:56.871 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleMetricsFailing[1](BLAH::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:51:56 GMT+14:00 2024] CollectMultipleMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=/tmp/alignmentMetrics15295167071806496111 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] EXTRA_ARGUMENT=[BLAH::HISTOGRAM_WIDTH=58] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:56 GMT+14:00 2024] CollectMultipleMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=/tmp/alignmentMetrics15295167071806496111 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] EXTRA_ARGUMENT=[BLAH::HISTOGRAM_WIDTH=58] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMultipleMetricsFailing[1](BLAH::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:51:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMultipleMetricsFailing[1](BLAH::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:51:56 GMT+14:00 2024] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:56 GMT+14:00 2024] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes. Test: Test method testMultipleMetricsFailing[1](BLAH::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testMultipleMetricsFailing[1](BLAH::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMultipleMetricsFailing[2](QualityScoreDistribution::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) Test: Test method testMultipleMetricsFailing[2](QualityScoreDistribution::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:56 CollectMultipleMetrics Gradle suite > Gradle test > picard.analysis.CollectMultipleMetricsTest.testMultipleMetricsFailing[2](QualityScoreDistribution::HISTOGRAM_WIDTH=58) STANDARD_ERROR INFO 2024-07-02 11:51:56 CollectMultipleMetrics Test: Test method testMultipleMetricsFailing[2](QualityScoreDistribution::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[2](QualityScoreDistribution::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMultipleMetricsFailing[2](QualityScoreDistribution::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[2](QualityScoreDistribution::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMultipleMetricsFailing[2](QualityScoreDistribution::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMultipleMetricsFailing[2](QualityScoreDistribution::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[2](QualityScoreDistribution::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMultipleMetricsFailing[2](QualityScoreDistribution::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[2](QualityScoreDistribution::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** CollectMultipleMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam -OUTPUT /tmp/alignmentMetrics2197056521423113035 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta -METRIC_ACCUMULATION_LEVEL ALL_READS -PROGRAM null -PROGRAM CollectAlignmentSummaryMetrics -PROGRAM CollectInsertSizeMetrics -EXTRA_ARGUMENT QualityScoreDistribution::--HISTOGRAM_WIDTH 58 ********** CollectMultipleMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam -OUTPUT /tmp/alignmentMetrics2197056521423113035 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta -METRIC_ACCUMULATION_LEVEL ALL_READS -PROGRAM null -PROGRAM CollectAlignmentSummaryMetrics -PROGRAM CollectInsertSizeMetrics -EXTRA_ARGUMENT QualityScoreDistribution::--HISTOGRAM_WIDTH 58 Test: Test method testMultipleMetricsFailing[2](QualityScoreDistribution::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[2](QualityScoreDistribution::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[2](QualityScoreDistribution::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[2](QualityScoreDistribution::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:56 RExecutor Executing R script via command: Rscript /tmp/script16532983928592740046.R INFO 2024-07-02 11:51:56 RExecutor Executing R script via command: Rscript /tmp/script16532983928592740046.R Test: Test method testMultipleMetricsFailing[2](QualityScoreDistribution::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:57 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:51:57 ProcessExecutor [1] "Checking if R is installed" Test: Test method testMultipleMetricsFailing[2](QualityScoreDistribution::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:51:58.037 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:58.037 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleMetricsFailing[2](QualityScoreDistribution::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:51:58.038 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:58.038 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleMetricsFailing[2](QualityScoreDistribution::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:51:58.038 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:58.038 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleMetricsFailing[2](QualityScoreDistribution::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:51:58.038 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:58.038 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleMetricsFailing[2](QualityScoreDistribution::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:51:58 GMT+14:00 2024] CollectMultipleMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=/tmp/alignmentMetrics2197056521423113035 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] EXTRA_ARGUMENT=[QualityScoreDistribution::HISTOGRAM_WIDTH=58] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:58 GMT+14:00 2024] CollectMultipleMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=/tmp/alignmentMetrics2197056521423113035 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] EXTRA_ARGUMENT=[QualityScoreDistribution::HISTOGRAM_WIDTH=58] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMultipleMetricsFailing[2](QualityScoreDistribution::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:51:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMultipleMetricsFailing[2](QualityScoreDistribution::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:51:58 GMT+14:00 2024] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:58 GMT+14:00 2024] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes. Test: Test method testMultipleMetricsFailing[2](QualityScoreDistribution::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testMultipleMetricsFailing[2](QualityScoreDistribution::HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:58 CollectMultipleMetrics Gradle suite > Gradle test > picard.analysis.CollectMultipleMetricsTest.testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58) STANDARD_ERROR INFO 2024-07-02 11:51:58 CollectMultipleMetrics Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** CollectMultipleMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam -OUTPUT /tmp/alignmentMetrics4319994569360903348 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta -METRIC_ACCUMULATION_LEVEL ALL_READS -PROGRAM null -PROGRAM CollectAlignmentSummaryMetrics -PROGRAM CollectInsertSizeMetrics -EXTRA_ARGUMENT CollectInsertSizeMetrics::--BLAH 58 ********** CollectMultipleMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam -OUTPUT /tmp/alignmentMetrics4319994569360903348 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta -METRIC_ACCUMULATION_LEVEL ALL_READS -PROGRAM null -PROGRAM CollectAlignmentSummaryMetrics -PROGRAM CollectInsertSizeMetrics -EXTRA_ARGUMENT CollectInsertSizeMetrics::--BLAH 58 Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:58 RExecutor Executing R script via command: Rscript /tmp/script7760002489452860807.R INFO 2024-07-02 11:51:58 RExecutor Executing R script via command: Rscript /tmp/script7760002489452860807.R Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:59 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:51:59 ProcessExecutor [1] "Checking if R is installed" Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:51:59.055 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:59.055 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:51:59.055 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:59.055 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:51:59.055 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:51:59.055 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:51:59.055 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:51:59.055 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:51:59 GMT+14:00 2024] CollectMultipleMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=/tmp/alignmentMetrics4319994569360903348 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] EXTRA_ARGUMENT=[CollectInsertSizeMetrics::BLAH=58] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:51:59 GMT+14:00 2024] CollectMultipleMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=/tmp/alignmentMetrics4319994569360903348 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] EXTRA_ARGUMENT=[CollectInsertSizeMetrics::BLAH=58] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:51:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:51:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ERROR: Unrecognized option: BLAH ERROR: Unrecognized option: BLAH Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: USAGE: CollectInsertSizeMetrics [options] USAGE: CollectInsertSizeMetrics [options] Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CollectInsertSizeMetrics Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CollectInsertSizeMetrics Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Collect metrics about the insert size distribution of a paired-end library. This tool provides useful metrics for Collect metrics about the insert size distribution of a paired-end library. This tool provides useful metrics for Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: validating library construction including the insert size distribution and read orientation of paired-end libraries. validating library construction including the insert size distribution and read orientation of paired-end libraries. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: The expected proportions of these metrics vary depending on the type of library preparation used, resulting from The expected proportions of these metrics vary depending on the type of library preparation used, resulting from Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: technical differences between pair-end libraries and mate-pair libraries. For a brief primer on paired-end sequencing technical differences between pair-end libraries and mate-pair libraries. For a brief primer on paired-end sequencing Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: and mate-pair reads, see the GATK Dictionary (https://www.broadinstitute.org/gatk/guide/article?id=6327). and mate-pair reads, see the GATK Dictionary (https://www.broadinstitute.org/gatk/guide/article?id=6327). Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: The CollectInsertSizeMetrics tool outputs the percentages of read pairs in each of the three orientations (FR, RF, and The CollectInsertSizeMetrics tool outputs the percentages of read pairs in each of the three orientations (FR, RF, and Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: TANDEM) as a histogram. In addition, the insert size distribution is output as both a histogram TANDEM) as a histogram. In addition, the insert size distribution is output as both a histogram Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: (.insert_size_Histogram.pdf) and as a data table (.insert_size_metrics.txt). (.insert_size_Histogram.pdf) and as a data table (.insert_size_metrics.txt). Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Note: Metrics labeled as percentages are actually expressed as fractions! Note: Metrics labeled as percentages are actually expressed as fractions! Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Usage example: Usage example: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: java -jar picard.jar CollectInsertSizeMetrics \ java -jar picard.jar CollectInsertSizeMetrics \ Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: O=insert_size_metrics.txt \ O=insert_size_metrics.txt \ Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: H=insert_size_histogram.pdf \ H=insert_size_histogram.pdf \ Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: M=0.5 M=0.5 Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Note: If processing a small file, set the minimum percentage option (M) to 0.5, otherwise an error may occur. Note: If processing a small file, set the minimum percentage option (M) to 0.5, otherwise an error may occur. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Please see InsertSizeMetrics (https://broadinstitute.github.io/picard/picard-metric-definitions.html#InsertSizeMetrics) Please see InsertSizeMetrics (https://broadinstitute.github.io/picard/picard-metric-definitions.html#InsertSizeMetrics) Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: for detailed explanations of each metric. for detailed explanations of each metric. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Version: null Version: null Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Options: Options: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: --help --help Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: tools. tools. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: HISTOGRAM_FILE=File HISTOGRAM_FILE=File Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: H=File File to write insert size Histogram chart to. Default value: H=File File to write insert size Histogram chart to. Default value: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: /tmp/alignmentMetrics4319994569360903348.insert_size_histogram.pdf. This option can be set /tmp/alignmentMetrics4319994569360903348.insert_size_histogram.pdf. This option can be set Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: to 'null' to clear the default value. to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: DEVIATIONS=Double Generate mean, sd and plots by trimming the data down to MEDIAN + DEVIATIONS=Double Generate mean, sd and plots by trimming the data down to MEDIAN + Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: includes enough anomalous values from chimeras and other artifacts to make the mean and sd includes enough anomalous values from chimeras and other artifacts to make the mean and sd Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: grossly misleading regarding the real distribution. Default value: 10.0. This option can grossly misleading regarding the real distribution. Default value: 10.0. This option can Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: be set to 'null' to clear the default value. be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: HISTOGRAM_WIDTH=Integer HISTOGRAM_WIDTH=Integer Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: W=Integer Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail. W=Integer Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Also, when calculating mean and standard deviation, only bins <= Histogram_WIDTH will be Also, when calculating mean and standard deviation, only bins <= Histogram_WIDTH will be Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: included. Default value: null. included. Default value: null. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: MIN_HISTOGRAM_WIDTH=Integer MIN_HISTOGRAM_WIDTH=Integer Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: MW=Integer Minimum width of histogram plots. In the case when the histogram would otherwise MW=Integer Minimum width of histogram plots. In the case when the histogram would otherwise Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: betruncated to a shorter range of sizes, the MIN_HISTOGRAM_WIDTH will enforce a minimum betruncated to a shorter range of sizes, the MIN_HISTOGRAM_WIDTH will enforce a minimum Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: range. Default value: null. range. Default value: null. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: MINIMUM_PCT=Float MINIMUM_PCT=Float Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: M=Float When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that M=Float When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: have fewer than this percentage of overall reads. (Range: 0 to 1). Default value: 0.05. have fewer than this percentage of overall reads. (Range: 0 to 1). Default value: 0.05. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Default value: [ALL_READS]. This option LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Default value: [ALL_READS]. This option Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: can be set to 'null' to clear the default value. Possible values: {ALL_READS, SAMPLE, can be set to 'null' to clear the default value. Possible values: {ALL_READS, SAMPLE, Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: LIBRARY, READ_GROUP} This option may be specified 0 or more times. This option can be set LIBRARY, READ_GROUP} This option may be specified 0 or more times. This option can be set Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: to 'null' to clear the default list. to 'null' to clear the default list. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INCLUDE_DUPLICATES=Boolean If true, also include reads marked as duplicates in the insert size histogram. Default INCLUDE_DUPLICATES=Boolean If true, also include reads marked as duplicates in the insert size histogram. Default Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: value: false. This option can be set to 'null' to clear the default value. Possible value: false. This option can be set to 'null' to clear the default value. Possible Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: values: {true, false} values: {true, false} Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: I=File Input SAM or BAM file. Default value: I=File Input SAM or BAM file. Default value: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam. /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: O=File The file to write the output to. Default value: O=File The file to write the output to. Default value: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: /tmp/alignmentMetrics4319994569360903348.insert_size_metrics. This option can be set to /tmp/alignmentMetrics4319994569360903348.insert_size_metrics. This option can be set to Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 'null' to clear the default value. 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ASSUME_SORTED=Boolean ASSUME_SORTED=Boolean Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: AS=Boolean If true (default), then the sort order in the header file will be ignored. Default value: AS=Boolean If true (default), then the sort order in the header file will be ignored. Default value: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: true. This option can be set to 'null' to clear the default value. Possible values: {true, true. This option can be set to 'null' to clear the default value. Possible values: {true, Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: false} false} Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: 0. This option can be STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: 0. This option can be Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: set to 'null' to clear the default value. set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: TMP_DIR=File One or more directories with space available to be used by this program for temporary TMP_DIR=File One or more directories with space available to be used by this program for temporary Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: storage of working files Default value: null. This option may be specified 0 or more storage of working files Default value: null. This option may be specified 0 or more Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: times. times. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: VERBOSITY=LogLevel Control verbosity of logging. Default value: INFO. This option can be set to 'null' to VERBOSITY=LogLevel Control verbosity of logging. Default value: INFO. This option can be set to 'null' to Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: clear the default value. Possible values: {ERROR, WARNING, INFO, DEBUG} clear the default value. Possible values: {ERROR, WARNING, INFO, DEBUG} Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: QUIET=Boolean Whether to suppress job-summary info on System.err. Default value: false. This option can QUIET=Boolean Whether to suppress job-summary info on System.err. Default value: false. This option can Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: be set to 'null' to clear the default value. Possible values: {true, false} be set to 'null' to clear the default value. Possible values: {true, false} Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: VALIDATION_STRINGENCY=ValidationStringency VALIDATION_STRINGENCY=ValidationStringency Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Validation stringency for all SAM files read by this program. Setting stringency to Validation stringency for all SAM files read by this program. Setting stringency to Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: SILENT can improve performance when processing a BAM file in which variable-length data SILENT can improve performance when processing a BAM file in which variable-length data Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: (read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT. This (read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT. This Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: option can be set to 'null' to clear the default value. Possible values: {STRICT, LENIENT, option can be set to 'null' to clear the default value. Possible values: {STRICT, LENIENT, Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: SILENT} SILENT} Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: COMPRESSION_LEVEL=Integer Compression level for all compressed files created (e.g. BAM and VCF). Default value: 5. COMPRESSION_LEVEL=Integer Compression level for all compressed files created (e.g. BAM and VCF). Default value: 5. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: MAX_RECORDS_IN_RAM=Integer When writing files that need to be sorted, this will specify the number of records stored MAX_RECORDS_IN_RAM=Integer When writing files that need to be sorted, this will specify the number of records stored Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: in RAM before spilling to disk. Increasing this number reduces the number of file handles in RAM before spilling to disk. Increasing this number reduces the number of file handles Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: needed to sort the file, and increases the amount of RAM needed. Default value: 1000. needed to sort the file, and increases the amount of RAM needed. Default value: 1000. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: CREATE_INDEX=Boolean Whether to create an index when writing VCF or coordinate sorted BAM output. Default CREATE_INDEX=Boolean Whether to create an index when writing VCF or coordinate sorted BAM output. Default Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: value: false. This option can be set to 'null' to clear the default value. Possible value: false. This option can be set to 'null' to clear the default value. Possible Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: values: {true, false} values: {true, false} Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: CREATE_MD5_FILE=Boolean Whether to create an MD5 digest for any BAM or FASTQ files created. Default value: CREATE_MD5_FILE=Boolean Whether to create an MD5 digest for any BAM or FASTQ files created. Default value: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: false. This option can be set to 'null' to clear the default value. Possible values: false. This option can be set to 'null' to clear the default value. Possible values: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: {true, false} {true, false} Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: REFERENCE_SEQUENCE=File REFERENCE_SEQUENCE=File Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: R=File Reference sequence file. Default value: null. R=File Reference sequence file. Default value: null. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: GA4GH_CLIENT_SECRETS=String Google Genomics API client_secrets.json file path. Default value: client_secrets.json. GA4GH_CLIENT_SECRETS=String Google Genomics API client_secrets.json file path. Default value: client_secrets.json. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: USE_JDK_DEFLATER=Boolean USE_JDK_DEFLATER=Boolean Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: USE_JDK_DEFLATER=Boolean Use the JDK Deflater instead of the Intel Deflater for writing compressed output Default USE_JDK_DEFLATER=Boolean Use the JDK Deflater instead of the Intel Deflater for writing compressed output Default Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: value: false. This option can be set to 'null' to clear the default value. Possible value: false. This option can be set to 'null' to clear the default value. Possible Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: values: {true, false} values: {true, false} Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: USE_JDK_INFLATER=Boolean USE_JDK_INFLATER=Boolean Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: USE_JDK_INFLATER=Boolean Use the JDK Inflater instead of the Intel Inflater for reading compressed input Default USE_JDK_INFLATER=Boolean Use the JDK Inflater instead of the Intel Inflater for reading compressed input Default Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: value: false. This option can be set to 'null' to clear the default value. Possible value: false. This option can be set to 'null' to clear the default value. Possible Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: values: {true, false} values: {true, false} Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: options, unrecognized options are ignored. A single-valued option set in an options file options, unrecognized options are ignored. A single-valued option set in an options file Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: may be overridden by a subsequent command-line option. A line starting with '#' is may be overridden by a subsequent command-line option. A line starting with '#' is Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: considered a comment. Required. considered a comment. Required. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:51:59 GMT+14:00 2024] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:51:59 GMT+14:00 2024] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes. Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testMultipleMetricsFailing[3](CollectInsertSizeMetrics::BLAH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMultipleMetricsFailing[4](CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) Test: Test method testMultipleMetricsFailing[4](CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:59 CollectMultipleMetrics Gradle suite > Gradle test > picard.analysis.CollectMultipleMetricsTest.testMultipleMetricsFailing[4](CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58) STANDARD_ERROR INFO 2024-07-02 11:51:59 CollectMultipleMetrics Test: Test method testMultipleMetricsFailing[4](CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[4](CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMultipleMetricsFailing[4](CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[4](CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMultipleMetricsFailing[4](CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMultipleMetricsFailing[4](CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[4](CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMultipleMetricsFailing[4](CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[4](CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** CollectMultipleMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam -OUTPUT /tmp/alignmentMetrics2360829557776922742 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta -METRIC_ACCUMULATION_LEVEL ALL_READS -PROGRAM null -PROGRAM CollectAlignmentSummaryMetrics -PROGRAM CollectInsertSizeMetrics -EXTRA_ARGUMENT CollectInsertSizeMetrics:HISTOGRAM_WIDTH 58 ********** CollectMultipleMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam -OUTPUT /tmp/alignmentMetrics2360829557776922742 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta -METRIC_ACCUMULATION_LEVEL ALL_READS -PROGRAM null -PROGRAM CollectAlignmentSummaryMetrics -PROGRAM CollectInsertSizeMetrics -EXTRA_ARGUMENT CollectInsertSizeMetrics:HISTOGRAM_WIDTH 58 Test: Test method testMultipleMetricsFailing[4](CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[4](CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[4](CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[4](CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:51:59 RExecutor Executing R script via command: Rscript /tmp/script3150767681037907145.R INFO 2024-07-02 11:51:59 RExecutor Executing R script via command: Rscript /tmp/script3150767681037907145.R Test: Test method testMultipleMetricsFailing[4](CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:00 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:52:00 ProcessExecutor [1] "Checking if R is installed" Test: Test method testMultipleMetricsFailing[4](CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:52:00.233 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:00.233 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleMetricsFailing[4](CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:52:00.233 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:00.233 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleMetricsFailing[4](CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:52:00.234 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:00.234 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleMetricsFailing[4](CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:52:00.234 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:00.234 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleMetricsFailing[4](CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:52:00 GMT+14:00 2024] CollectMultipleMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=/tmp/alignmentMetrics2360829557776922742 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] EXTRA_ARGUMENT=[CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:00 GMT+14:00 2024] CollectMultipleMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=/tmp/alignmentMetrics2360829557776922742 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] EXTRA_ARGUMENT=[CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMultipleMetricsFailing[4](CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:52:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMultipleMetricsFailing[4](CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:52:00 GMT+14:00 2024] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:00 GMT+14:00 2024] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes. Test: Test method testMultipleMetricsFailing[4](CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testMultipleMetricsFailing[4](CollectInsertSizeMetrics:HISTOGRAM_WIDTH=58)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:00 CollectMultipleMetrics Gradle suite > Gradle test > picard.analysis.CollectMultipleMetricsTest.testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8) STANDARD_ERROR INFO 2024-07-02 11:52:00 CollectMultipleMetrics Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** CollectMultipleMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam -OUTPUT /tmp/alignmentMetrics5621842099241671533 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta -METRIC_ACCUMULATION_LEVEL ALL_READS -PROGRAM null -PROGRAM CollectAlignmentSummaryMetrics -PROGRAM CollectInsertSizeMetrics -EXTRA_ARGUMENT CollectInsertSizeMetrics::--HISTOGRAM_WIDTH 5a8 ********** CollectMultipleMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam -OUTPUT /tmp/alignmentMetrics5621842099241671533 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta -METRIC_ACCUMULATION_LEVEL ALL_READS -PROGRAM null -PROGRAM CollectAlignmentSummaryMetrics -PROGRAM CollectInsertSizeMetrics -EXTRA_ARGUMENT CollectInsertSizeMetrics::--HISTOGRAM_WIDTH 5a8 Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:00 RExecutor Executing R script via command: Rscript /tmp/script2225567766730163282.R INFO 2024-07-02 11:52:00 RExecutor Executing R script via command: Rscript /tmp/script2225567766730163282.R Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:01 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:52:01 ProcessExecutor [1] "Checking if R is installed" Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:52:01.137 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:01.137 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:52:01.138 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:01.138 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:52:01.138 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:01.138 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:52:01.138 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:01.138 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:52:01 GMT+14:00 2024] CollectMultipleMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=/tmp/alignmentMetrics5621842099241671533 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] EXTRA_ARGUMENT=[CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:01 GMT+14:00 2024] CollectMultipleMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=/tmp/alignmentMetrics5621842099241671533 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] EXTRA_ARGUMENT=[CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:52:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ERROR: Problem constructing Integer from the string '5a8'. ERROR: Problem constructing Integer from the string '5a8'. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: USAGE: CollectInsertSizeMetrics [options] USAGE: CollectInsertSizeMetrics [options] Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CollectInsertSizeMetrics Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CollectInsertSizeMetrics Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Collect metrics about the insert size distribution of a paired-end library. This tool provides useful metrics for Collect metrics about the insert size distribution of a paired-end library. This tool provides useful metrics for Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: validating library construction including the insert size distribution and read orientation of paired-end libraries. validating library construction including the insert size distribution and read orientation of paired-end libraries. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: The expected proportions of these metrics vary depending on the type of library preparation used, resulting from The expected proportions of these metrics vary depending on the type of library preparation used, resulting from Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: technical differences between pair-end libraries and mate-pair libraries. For a brief primer on paired-end sequencing technical differences between pair-end libraries and mate-pair libraries. For a brief primer on paired-end sequencing Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: and mate-pair reads, see the GATK Dictionary (https://www.broadinstitute.org/gatk/guide/article?id=6327). and mate-pair reads, see the GATK Dictionary (https://www.broadinstitute.org/gatk/guide/article?id=6327). Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: The CollectInsertSizeMetrics tool outputs the percentages of read pairs in each of the three orientations (FR, RF, and The CollectInsertSizeMetrics tool outputs the percentages of read pairs in each of the three orientations (FR, RF, and Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: TANDEM) as a histogram. In addition, the insert size distribution is output as both a histogram TANDEM) as a histogram. In addition, the insert size distribution is output as both a histogram Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: (.insert_size_Histogram.pdf) and as a data table (.insert_size_metrics.txt). (.insert_size_Histogram.pdf) and as a data table (.insert_size_metrics.txt). Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Note: Metrics labeled as percentages are actually expressed as fractions! Note: Metrics labeled as percentages are actually expressed as fractions! Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Usage example: Usage example: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: java -jar picard.jar CollectInsertSizeMetrics \ java -jar picard.jar CollectInsertSizeMetrics \ Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: O=insert_size_metrics.txt \ O=insert_size_metrics.txt \ Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: H=insert_size_histogram.pdf \ H=insert_size_histogram.pdf \ Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: M=0.5 M=0.5 Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Note: If processing a small file, set the minimum percentage option (M) to 0.5, otherwise an error may occur. Note: If processing a small file, set the minimum percentage option (M) to 0.5, otherwise an error may occur. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Please see InsertSizeMetrics (https://broadinstitute.github.io/picard/picard-metric-definitions.html#InsertSizeMetrics) Please see InsertSizeMetrics (https://broadinstitute.github.io/picard/picard-metric-definitions.html#InsertSizeMetrics) Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: for detailed explanations of each metric. for detailed explanations of each metric. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Version: null Version: null Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Options: Options: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: --help --help Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: tools. tools. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: HISTOGRAM_FILE=File HISTOGRAM_FILE=File Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: H=File File to write insert size Histogram chart to. Default value: H=File File to write insert size Histogram chart to. Default value: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: /tmp/alignmentMetrics5621842099241671533.insert_size_histogram.pdf. This option can be set /tmp/alignmentMetrics5621842099241671533.insert_size_histogram.pdf. This option can be set Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: to 'null' to clear the default value. to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: DEVIATIONS=Double Generate mean, sd and plots by trimming the data down to MEDIAN + DEVIATIONS=Double Generate mean, sd and plots by trimming the data down to MEDIAN + Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: includes enough anomalous values from chimeras and other artifacts to make the mean and sd includes enough anomalous values from chimeras and other artifacts to make the mean and sd Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: grossly misleading regarding the real distribution. Default value: 10.0. This option can grossly misleading regarding the real distribution. Default value: 10.0. This option can Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: be set to 'null' to clear the default value. be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: HISTOGRAM_WIDTH=Integer HISTOGRAM_WIDTH=Integer Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: W=Integer Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail. W=Integer Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Also, when calculating mean and standard deviation, only bins <= Histogram_WIDTH will be Also, when calculating mean and standard deviation, only bins <= Histogram_WIDTH will be Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: included. Default value: null. included. Default value: null. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: MIN_HISTOGRAM_WIDTH=Integer MIN_HISTOGRAM_WIDTH=Integer Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: MW=Integer Minimum width of histogram plots. In the case when the histogram would otherwise MW=Integer Minimum width of histogram plots. In the case when the histogram would otherwise Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: betruncated to a shorter range of sizes, the MIN_HISTOGRAM_WIDTH will enforce a minimum betruncated to a shorter range of sizes, the MIN_HISTOGRAM_WIDTH will enforce a minimum Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: range. Default value: null. range. Default value: null. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: MINIMUM_PCT=Float MINIMUM_PCT=Float Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: M=Float When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that M=Float When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: have fewer than this percentage of overall reads. (Range: 0 to 1). Default value: 0.05. have fewer than this percentage of overall reads. (Range: 0 to 1). Default value: 0.05. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Default value: [ALL_READS]. This option LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Default value: [ALL_READS]. This option Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: can be set to 'null' to clear the default value. Possible values: {ALL_READS, SAMPLE, can be set to 'null' to clear the default value. Possible values: {ALL_READS, SAMPLE, Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: LIBRARY, READ_GROUP} This option may be specified 0 or more times. This option can be set LIBRARY, READ_GROUP} This option may be specified 0 or more times. This option can be set Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: to 'null' to clear the default list. to 'null' to clear the default list. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INCLUDE_DUPLICATES=Boolean If true, also include reads marked as duplicates in the insert size histogram. Default INCLUDE_DUPLICATES=Boolean If true, also include reads marked as duplicates in the insert size histogram. Default Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: value: false. This option can be set to 'null' to clear the default value. Possible value: false. This option can be set to 'null' to clear the default value. Possible Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: values: {true, false} values: {true, false} Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: I=File Input SAM or BAM file. Default value: I=File Input SAM or BAM file. Default value: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam. /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: O=File The file to write the output to. Default value: O=File The file to write the output to. Default value: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: /tmp/alignmentMetrics5621842099241671533.insert_size_metrics. This option can be set to /tmp/alignmentMetrics5621842099241671533.insert_size_metrics. This option can be set to Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 'null' to clear the default value. 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ASSUME_SORTED=Boolean ASSUME_SORTED=Boolean Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: AS=Boolean If true (default), then the sort order in the header file will be ignored. Default value: AS=Boolean If true (default), then the sort order in the header file will be ignored. Default value: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: true. This option can be set to 'null' to clear the default value. Possible values: {true, true. This option can be set to 'null' to clear the default value. Possible values: {true, Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: false} false} Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: 0. This option can be STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: 0. This option can be Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: set to 'null' to clear the default value. set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: TMP_DIR=File One or more directories with space available to be used by this program for temporary TMP_DIR=File One or more directories with space available to be used by this program for temporary Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: storage of working files Default value: null. This option may be specified 0 or more storage of working files Default value: null. This option may be specified 0 or more Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: times. times. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: VERBOSITY=LogLevel Control verbosity of logging. Default value: INFO. This option can be set to 'null' to VERBOSITY=LogLevel Control verbosity of logging. Default value: INFO. This option can be set to 'null' to Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: clear the default value. Possible values: {ERROR, WARNING, INFO, DEBUG} clear the default value. Possible values: {ERROR, WARNING, INFO, DEBUG} Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: QUIET=Boolean Whether to suppress job-summary info on System.err. Default value: false. This option can QUIET=Boolean Whether to suppress job-summary info on System.err. Default value: false. This option can Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: be set to 'null' to clear the default value. Possible values: {true, false} be set to 'null' to clear the default value. Possible values: {true, false} Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: VALIDATION_STRINGENCY=ValidationStringency VALIDATION_STRINGENCY=ValidationStringency Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Validation stringency for all SAM files read by this program. Setting stringency to Validation stringency for all SAM files read by this program. Setting stringency to Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: SILENT can improve performance when processing a BAM file in which variable-length data SILENT can improve performance when processing a BAM file in which variable-length data Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: (read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT. This (read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT. This Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: option can be set to 'null' to clear the default value. Possible values: {STRICT, LENIENT, option can be set to 'null' to clear the default value. Possible values: {STRICT, LENIENT, Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: SILENT} SILENT} Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: COMPRESSION_LEVEL=Integer Compression level for all compressed files created (e.g. BAM and VCF). Default value: 5. COMPRESSION_LEVEL=Integer Compression level for all compressed files created (e.g. BAM and VCF). Default value: 5. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: MAX_RECORDS_IN_RAM=Integer When writing files that need to be sorted, this will specify the number of records stored MAX_RECORDS_IN_RAM=Integer When writing files that need to be sorted, this will specify the number of records stored Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: in RAM before spilling to disk. Increasing this number reduces the number of file handles in RAM before spilling to disk. Increasing this number reduces the number of file handles Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: needed to sort the file, and increases the amount of RAM needed. Default value: 1000. needed to sort the file, and increases the amount of RAM needed. Default value: 1000. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: CREATE_INDEX=Boolean Whether to create an index when writing VCF or coordinate sorted BAM output. Default CREATE_INDEX=Boolean Whether to create an index when writing VCF or coordinate sorted BAM output. Default Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: value: false. This option can be set to 'null' to clear the default value. Possible value: false. This option can be set to 'null' to clear the default value. Possible Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: values: {true, false} values: {true, false} Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: CREATE_MD5_FILE=Boolean Whether to create an MD5 digest for any BAM or FASTQ files created. Default value: CREATE_MD5_FILE=Boolean Whether to create an MD5 digest for any BAM or FASTQ files created. Default value: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: false. This option can be set to 'null' to clear the default value. Possible values: false. This option can be set to 'null' to clear the default value. Possible values: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: {true, false} {true, false} Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: REFERENCE_SEQUENCE=File REFERENCE_SEQUENCE=File Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: R=File Reference sequence file. Default value: null. R=File Reference sequence file. Default value: null. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: GA4GH_CLIENT_SECRETS=String Google Genomics API client_secrets.json file path. Default value: client_secrets.json. GA4GH_CLIENT_SECRETS=String Google Genomics API client_secrets.json file path. Default value: client_secrets.json. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: USE_JDK_DEFLATER=Boolean USE_JDK_DEFLATER=Boolean Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: USE_JDK_DEFLATER=Boolean Use the JDK Deflater instead of the Intel Deflater for writing compressed output Default USE_JDK_DEFLATER=Boolean Use the JDK Deflater instead of the Intel Deflater for writing compressed output Default Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: value: false. This option can be set to 'null' to clear the default value. Possible value: false. This option can be set to 'null' to clear the default value. Possible Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: values: {true, false} values: {true, false} Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: USE_JDK_INFLATER=Boolean USE_JDK_INFLATER=Boolean Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: USE_JDK_INFLATER=Boolean Use the JDK Inflater instead of the Intel Inflater for reading compressed input Default USE_JDK_INFLATER=Boolean Use the JDK Inflater instead of the Intel Inflater for reading compressed input Default Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: value: false. This option can be set to 'null' to clear the default value. Possible value: false. This option can be set to 'null' to clear the default value. Possible Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: values: {true, false} values: {true, false} Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: options, unrecognized options are ignored. A single-valued option set in an options file options, unrecognized options are ignored. A single-valued option set in an options file Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: may be overridden by a subsequent command-line option. A line starting with '#' is may be overridden by a subsequent command-line option. A line starting with '#' is Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: considered a comment. Required. considered a comment. Required. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:52:01 GMT+14:00 2024] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:01 GMT+14:00 2024] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes. Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testMultipleMetricsFailing[5](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=5a8)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:01 CollectMultipleMetrics Gradle suite > Gradle test > picard.analysis.CollectMultipleMetricsTest.testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=) STANDARD_ERROR INFO 2024-07-02 11:52:01 CollectMultipleMetrics Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** CollectMultipleMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam -OUTPUT /tmp/alignmentMetrics14525890671093742022 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta -METRIC_ACCUMULATION_LEVEL ALL_READS -PROGRAM null -PROGRAM CollectAlignmentSummaryMetrics -PROGRAM CollectInsertSizeMetrics -EXTRA_ARGUMENT CollectInsertSizeMetrics::--HISTOGRAM_WIDTH ********** CollectMultipleMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam -OUTPUT /tmp/alignmentMetrics14525890671093742022 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta -METRIC_ACCUMULATION_LEVEL ALL_READS -PROGRAM null -PROGRAM CollectAlignmentSummaryMetrics -PROGRAM CollectInsertSizeMetrics -EXTRA_ARGUMENT CollectInsertSizeMetrics::--HISTOGRAM_WIDTH Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:01 RExecutor Executing R script via command: Rscript /tmp/script12505275559100313209.R INFO 2024-07-02 11:52:01 RExecutor Executing R script via command: Rscript /tmp/script12505275559100313209.R Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:02 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:52:02 ProcessExecutor [1] "Checking if R is installed" Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:52:02.105 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:02.105 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:52:02.106 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:02.106 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:52:02.106 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:02.106 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:52:02.106 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:02.106 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:52:02 GMT+14:00 2024] CollectMultipleMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=/tmp/alignmentMetrics14525890671093742022 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] EXTRA_ARGUMENT=[CollectInsertSizeMetrics::HISTOGRAM_WIDTH=] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:02 GMT+14:00 2024] CollectMultipleMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=/tmp/alignmentMetrics14525890671093742022 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] EXTRA_ARGUMENT=[CollectInsertSizeMetrics::HISTOGRAM_WIDTH=] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:52:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ERROR: Problem constructing Integer from the string ''. ERROR: Problem constructing Integer from the string ''. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: USAGE: CollectInsertSizeMetrics [options] USAGE: CollectInsertSizeMetrics [options] Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CollectInsertSizeMetrics Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CollectInsertSizeMetrics Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Collect metrics about the insert size distribution of a paired-end library. This tool provides useful metrics for Collect metrics about the insert size distribution of a paired-end library. This tool provides useful metrics for Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: validating library construction including the insert size distribution and read orientation of paired-end libraries. validating library construction including the insert size distribution and read orientation of paired-end libraries. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: The expected proportions of these metrics vary depending on the type of library preparation used, resulting from The expected proportions of these metrics vary depending on the type of library preparation used, resulting from Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: technical differences between pair-end libraries and mate-pair libraries. For a brief primer on paired-end sequencing technical differences between pair-end libraries and mate-pair libraries. For a brief primer on paired-end sequencing Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: and mate-pair reads, see the GATK Dictionary (https://www.broadinstitute.org/gatk/guide/article?id=6327). and mate-pair reads, see the GATK Dictionary (https://www.broadinstitute.org/gatk/guide/article?id=6327). Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: The CollectInsertSizeMetrics tool outputs the percentages of read pairs in each of the three orientations (FR, RF, and The CollectInsertSizeMetrics tool outputs the percentages of read pairs in each of the three orientations (FR, RF, and Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: TANDEM) as a histogram. In addition, the insert size distribution is output as both a histogram TANDEM) as a histogram. In addition, the insert size distribution is output as both a histogram Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: (.insert_size_Histogram.pdf) and as a data table (.insert_size_metrics.txt). (.insert_size_Histogram.pdf) and as a data table (.insert_size_metrics.txt). Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Note: Metrics labeled as percentages are actually expressed as fractions! Note: Metrics labeled as percentages are actually expressed as fractions! Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Usage example: Usage example: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: java -jar picard.jar CollectInsertSizeMetrics \ java -jar picard.jar CollectInsertSizeMetrics \ Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: O=insert_size_metrics.txt \ O=insert_size_metrics.txt \ Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: H=insert_size_histogram.pdf \ H=insert_size_histogram.pdf \ Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: M=0.5 M=0.5 Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Note: If processing a small file, set the minimum percentage option (M) to 0.5, otherwise an error may occur. Note: If processing a small file, set the minimum percentage option (M) to 0.5, otherwise an error may occur. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Please see InsertSizeMetrics (https://broadinstitute.github.io/picard/picard-metric-definitions.html#InsertSizeMetrics) Please see InsertSizeMetrics (https://broadinstitute.github.io/picard/picard-metric-definitions.html#InsertSizeMetrics) Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: for detailed explanations of each metric. for detailed explanations of each metric. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Version: null Version: null Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Options: Options: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: --help --help Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: tools. tools. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: HISTOGRAM_FILE=File HISTOGRAM_FILE=File Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: H=File File to write insert size Histogram chart to. Default value: H=File File to write insert size Histogram chart to. Default value: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: /tmp/alignmentMetrics14525890671093742022.insert_size_histogram.pdf. This option can be /tmp/alignmentMetrics14525890671093742022.insert_size_histogram.pdf. This option can be Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: set to 'null' to clear the default value. set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: DEVIATIONS=Double Generate mean, sd and plots by trimming the data down to MEDIAN + DEVIATIONS=Double Generate mean, sd and plots by trimming the data down to MEDIAN + Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: includes enough anomalous values from chimeras and other artifacts to make the mean and sd includes enough anomalous values from chimeras and other artifacts to make the mean and sd Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: grossly misleading regarding the real distribution. Default value: 10.0. This option can grossly misleading regarding the real distribution. Default value: 10.0. This option can Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: be set to 'null' to clear the default value. be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: HISTOGRAM_WIDTH=Integer HISTOGRAM_WIDTH=Integer Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: W=Integer Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail. W=Integer Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Also, when calculating mean and standard deviation, only bins <= Histogram_WIDTH will be Also, when calculating mean and standard deviation, only bins <= Histogram_WIDTH will be Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: included. Default value: null. included. Default value: null. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: MIN_HISTOGRAM_WIDTH=Integer MIN_HISTOGRAM_WIDTH=Integer Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: MW=Integer Minimum width of histogram plots. In the case when the histogram would otherwise MW=Integer Minimum width of histogram plots. In the case when the histogram would otherwise Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: betruncated to a shorter range of sizes, the MIN_HISTOGRAM_WIDTH will enforce a minimum betruncated to a shorter range of sizes, the MIN_HISTOGRAM_WIDTH will enforce a minimum Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: range. Default value: null. range. Default value: null. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: MINIMUM_PCT=Float MINIMUM_PCT=Float Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: M=Float When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that M=Float When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: have fewer than this percentage of overall reads. (Range: 0 to 1). Default value: 0.05. have fewer than this percentage of overall reads. (Range: 0 to 1). Default value: 0.05. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Default value: [ALL_READS]. This option LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Default value: [ALL_READS]. This option Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: can be set to 'null' to clear the default value. Possible values: {ALL_READS, SAMPLE, can be set to 'null' to clear the default value. Possible values: {ALL_READS, SAMPLE, Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: LIBRARY, READ_GROUP} This option may be specified 0 or more times. This option can be set LIBRARY, READ_GROUP} This option may be specified 0 or more times. This option can be set Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: to 'null' to clear the default list. to 'null' to clear the default list. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INCLUDE_DUPLICATES=Boolean If true, also include reads marked as duplicates in the insert size histogram. Default INCLUDE_DUPLICATES=Boolean If true, also include reads marked as duplicates in the insert size histogram. Default Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: value: false. This option can be set to 'null' to clear the default value. Possible value: false. This option can be set to 'null' to clear the default value. Possible Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: values: {true, false} values: {true, false} Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: I=File Input SAM or BAM file. Default value: I=File Input SAM or BAM file. Default value: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam. /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: O=File The file to write the output to. Default value: O=File The file to write the output to. Default value: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: /tmp/alignmentMetrics14525890671093742022.insert_size_metrics. This option can be set to /tmp/alignmentMetrics14525890671093742022.insert_size_metrics. This option can be set to Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 'null' to clear the default value. 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ASSUME_SORTED=Boolean ASSUME_SORTED=Boolean Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: AS=Boolean If true (default), then the sort order in the header file will be ignored. Default value: AS=Boolean If true (default), then the sort order in the header file will be ignored. Default value: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: true. This option can be set to 'null' to clear the default value. Possible values: {true, true. This option can be set to 'null' to clear the default value. Possible values: {true, Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: false} false} Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: 0. This option can be STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: 0. This option can be Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: set to 'null' to clear the default value. set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: TMP_DIR=File One or more directories with space available to be used by this program for temporary TMP_DIR=File One or more directories with space available to be used by this program for temporary Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: storage of working files Default value: null. This option may be specified 0 or more storage of working files Default value: null. This option may be specified 0 or more Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: times. times. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: VERBOSITY=LogLevel Control verbosity of logging. Default value: INFO. This option can be set to 'null' to VERBOSITY=LogLevel Control verbosity of logging. Default value: INFO. This option can be set to 'null' to Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: clear the default value. Possible values: {ERROR, WARNING, INFO, DEBUG} clear the default value. Possible values: {ERROR, WARNING, INFO, DEBUG} Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: QUIET=Boolean Whether to suppress job-summary info on System.err. Default value: false. This option can QUIET=Boolean Whether to suppress job-summary info on System.err. Default value: false. This option can Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: be set to 'null' to clear the default value. Possible values: {true, false} be set to 'null' to clear the default value. Possible values: {true, false} Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: VALIDATION_STRINGENCY=ValidationStringency VALIDATION_STRINGENCY=ValidationStringency Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Validation stringency for all SAM files read by this program. Setting stringency to Validation stringency for all SAM files read by this program. Setting stringency to Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: SILENT can improve performance when processing a BAM file in which variable-length data SILENT can improve performance when processing a BAM file in which variable-length data Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: (read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT. This (read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT. This Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: option can be set to 'null' to clear the default value. Possible values: {STRICT, LENIENT, option can be set to 'null' to clear the default value. Possible values: {STRICT, LENIENT, Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: SILENT} SILENT} Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: COMPRESSION_LEVEL=Integer Compression level for all compressed files created (e.g. BAM and VCF). Default value: 5. COMPRESSION_LEVEL=Integer Compression level for all compressed files created (e.g. BAM and VCF). Default value: 5. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: MAX_RECORDS_IN_RAM=Integer When writing files that need to be sorted, this will specify the number of records stored MAX_RECORDS_IN_RAM=Integer When writing files that need to be sorted, this will specify the number of records stored Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: in RAM before spilling to disk. Increasing this number reduces the number of file handles in RAM before spilling to disk. Increasing this number reduces the number of file handles Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: needed to sort the file, and increases the amount of RAM needed. Default value: 1000. needed to sort the file, and increases the amount of RAM needed. Default value: 1000. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: CREATE_INDEX=Boolean Whether to create an index when writing VCF or coordinate sorted BAM output. Default CREATE_INDEX=Boolean Whether to create an index when writing VCF or coordinate sorted BAM output. Default Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: value: false. This option can be set to 'null' to clear the default value. Possible value: false. This option can be set to 'null' to clear the default value. Possible Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: values: {true, false} values: {true, false} Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: CREATE_MD5_FILE=Boolean Whether to create an MD5 digest for any BAM or FASTQ files created. Default value: CREATE_MD5_FILE=Boolean Whether to create an MD5 digest for any BAM or FASTQ files created. Default value: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: false. This option can be set to 'null' to clear the default value. Possible values: false. This option can be set to 'null' to clear the default value. Possible values: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: {true, false} {true, false} Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: REFERENCE_SEQUENCE=File REFERENCE_SEQUENCE=File Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: R=File Reference sequence file. Default value: null. R=File Reference sequence file. Default value: null. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: GA4GH_CLIENT_SECRETS=String Google Genomics API client_secrets.json file path. Default value: client_secrets.json. GA4GH_CLIENT_SECRETS=String Google Genomics API client_secrets.json file path. Default value: client_secrets.json. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: USE_JDK_DEFLATER=Boolean USE_JDK_DEFLATER=Boolean Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: USE_JDK_DEFLATER=Boolean Use the JDK Deflater instead of the Intel Deflater for writing compressed output Default USE_JDK_DEFLATER=Boolean Use the JDK Deflater instead of the Intel Deflater for writing compressed output Default Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: value: false. This option can be set to 'null' to clear the default value. Possible value: false. This option can be set to 'null' to clear the default value. Possible Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: values: {true, false} values: {true, false} Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: USE_JDK_INFLATER=Boolean USE_JDK_INFLATER=Boolean Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: USE_JDK_INFLATER=Boolean Use the JDK Inflater instead of the Intel Inflater for reading compressed input Default USE_JDK_INFLATER=Boolean Use the JDK Inflater instead of the Intel Inflater for reading compressed input Default Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: value: false. This option can be set to 'null' to clear the default value. Possible value: false. This option can be set to 'null' to clear the default value. Possible Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: values: {true, false} values: {true, false} Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: options, unrecognized options are ignored. A single-valued option set in an options file options, unrecognized options are ignored. A single-valued option set in an options file Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: may be overridden by a subsequent command-line option. A line starting with '#' is may be overridden by a subsequent command-line option. A line starting with '#' is Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: considered a comment. Required. considered a comment. Required. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:52:02 GMT+14:00 2024] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:02 GMT+14:00 2024] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes. Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testMultipleMetricsFailing[6](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:02 CollectMultipleMetrics Gradle suite > Gradle test > picard.analysis.CollectMultipleMetricsTest.testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello) STANDARD_ERROR INFO 2024-07-02 11:52:02 CollectMultipleMetrics Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** CollectMultipleMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam -OUTPUT /tmp/alignmentMetrics10572170532365304613 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta -METRIC_ACCUMULATION_LEVEL ALL_READS -PROGRAM null -PROGRAM CollectAlignmentSummaryMetrics -PROGRAM CollectInsertSizeMetrics -EXTRA_ARGUMENT CollectInsertSizeMetrics::--HISTOGRAM_WIDTH hello ********** CollectMultipleMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam -OUTPUT /tmp/alignmentMetrics10572170532365304613 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta -METRIC_ACCUMULATION_LEVEL ALL_READS -PROGRAM null -PROGRAM CollectAlignmentSummaryMetrics -PROGRAM CollectInsertSizeMetrics -EXTRA_ARGUMENT CollectInsertSizeMetrics::--HISTOGRAM_WIDTH hello Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:02 RExecutor Executing R script via command: Rscript /tmp/script16785541181827354751.R INFO 2024-07-02 11:52:02 RExecutor Executing R script via command: Rscript /tmp/script16785541181827354751.R Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:02 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:52:02 ProcessExecutor [1] "Checking if R is installed" Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:52:02.873 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:02.873 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:52:02.874 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:02.874 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:52:02.874 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:02.874 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:52:02.874 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:02.874 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:52:02 GMT+14:00 2024] CollectMultipleMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=/tmp/alignmentMetrics10572170532365304613 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] EXTRA_ARGUMENT=[CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:02 GMT+14:00 2024] CollectMultipleMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=/tmp/alignmentMetrics10572170532365304613 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] EXTRA_ARGUMENT=[CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:52:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ERROR: Problem constructing Integer from the string 'hello'. ERROR: Problem constructing Integer from the string 'hello'. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: USAGE: CollectInsertSizeMetrics [options] USAGE: CollectInsertSizeMetrics [options] Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CollectInsertSizeMetrics Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CollectInsertSizeMetrics Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Collect metrics about the insert size distribution of a paired-end library. This tool provides useful metrics for Collect metrics about the insert size distribution of a paired-end library. This tool provides useful metrics for Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: validating library construction including the insert size distribution and read orientation of paired-end libraries. validating library construction including the insert size distribution and read orientation of paired-end libraries. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: The expected proportions of these metrics vary depending on the type of library preparation used, resulting from The expected proportions of these metrics vary depending on the type of library preparation used, resulting from Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: technical differences between pair-end libraries and mate-pair libraries. For a brief primer on paired-end sequencing technical differences between pair-end libraries and mate-pair libraries. For a brief primer on paired-end sequencing Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: and mate-pair reads, see the GATK Dictionary (https://www.broadinstitute.org/gatk/guide/article?id=6327). and mate-pair reads, see the GATK Dictionary (https://www.broadinstitute.org/gatk/guide/article?id=6327). Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: The CollectInsertSizeMetrics tool outputs the percentages of read pairs in each of the three orientations (FR, RF, and The CollectInsertSizeMetrics tool outputs the percentages of read pairs in each of the three orientations (FR, RF, and Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: TANDEM) as a histogram. In addition, the insert size distribution is output as both a histogram TANDEM) as a histogram. In addition, the insert size distribution is output as both a histogram Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: (.insert_size_Histogram.pdf) and as a data table (.insert_size_metrics.txt). (.insert_size_Histogram.pdf) and as a data table (.insert_size_metrics.txt). Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Note: Metrics labeled as percentages are actually expressed as fractions! Note: Metrics labeled as percentages are actually expressed as fractions! Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Usage example: Usage example: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: java -jar picard.jar CollectInsertSizeMetrics \ java -jar picard.jar CollectInsertSizeMetrics \ Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: O=insert_size_metrics.txt \ O=insert_size_metrics.txt \ Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: H=insert_size_histogram.pdf \ H=insert_size_histogram.pdf \ Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: M=0.5 M=0.5 Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Note: If processing a small file, set the minimum percentage option (M) to 0.5, otherwise an error may occur. Note: If processing a small file, set the minimum percentage option (M) to 0.5, otherwise an error may occur. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Please see InsertSizeMetrics (https://broadinstitute.github.io/picard/picard-metric-definitions.html#InsertSizeMetrics) Please see InsertSizeMetrics (https://broadinstitute.github.io/picard/picard-metric-definitions.html#InsertSizeMetrics) Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: for detailed explanations of each metric. for detailed explanations of each metric. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Version: null Version: null Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Options: Options: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: --help --help Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: tools. tools. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: HISTOGRAM_FILE=File HISTOGRAM_FILE=File Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: H=File File to write insert size Histogram chart to. Default value: H=File File to write insert size Histogram chart to. Default value: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: /tmp/alignmentMetrics10572170532365304613.insert_size_histogram.pdf. This option can be /tmp/alignmentMetrics10572170532365304613.insert_size_histogram.pdf. This option can be Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: set to 'null' to clear the default value. set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: DEVIATIONS=Double Generate mean, sd and plots by trimming the data down to MEDIAN + DEVIATIONS=Double Generate mean, sd and plots by trimming the data down to MEDIAN + Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: includes enough anomalous values from chimeras and other artifacts to make the mean and sd includes enough anomalous values from chimeras and other artifacts to make the mean and sd Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: grossly misleading regarding the real distribution. Default value: 10.0. This option can grossly misleading regarding the real distribution. Default value: 10.0. This option can Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: be set to 'null' to clear the default value. be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: HISTOGRAM_WIDTH=Integer HISTOGRAM_WIDTH=Integer Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: W=Integer Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail. W=Integer Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Also, when calculating mean and standard deviation, only bins <= Histogram_WIDTH will be Also, when calculating mean and standard deviation, only bins <= Histogram_WIDTH will be Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: included. Default value: null. included. Default value: null. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: MIN_HISTOGRAM_WIDTH=Integer MIN_HISTOGRAM_WIDTH=Integer Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: MW=Integer Minimum width of histogram plots. In the case when the histogram would otherwise MW=Integer Minimum width of histogram plots. In the case when the histogram would otherwise Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: betruncated to a shorter range of sizes, the MIN_HISTOGRAM_WIDTH will enforce a minimum betruncated to a shorter range of sizes, the MIN_HISTOGRAM_WIDTH will enforce a minimum Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: range. Default value: null. range. Default value: null. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: MINIMUM_PCT=Float MINIMUM_PCT=Float Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: M=Float When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that M=Float When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: have fewer than this percentage of overall reads. (Range: 0 to 1). Default value: 0.05. have fewer than this percentage of overall reads. (Range: 0 to 1). Default value: 0.05. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Default value: [ALL_READS]. This option LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Default value: [ALL_READS]. This option Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: can be set to 'null' to clear the default value. Possible values: {ALL_READS, SAMPLE, can be set to 'null' to clear the default value. Possible values: {ALL_READS, SAMPLE, Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: LIBRARY, READ_GROUP} This option may be specified 0 or more times. This option can be set LIBRARY, READ_GROUP} This option may be specified 0 or more times. This option can be set Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: to 'null' to clear the default list. to 'null' to clear the default list. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INCLUDE_DUPLICATES=Boolean If true, also include reads marked as duplicates in the insert size histogram. Default INCLUDE_DUPLICATES=Boolean If true, also include reads marked as duplicates in the insert size histogram. Default Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: value: false. This option can be set to 'null' to clear the default value. Possible value: false. This option can be set to 'null' to clear the default value. Possible Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: values: {true, false} values: {true, false} Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: I=File Input SAM or BAM file. Default value: I=File Input SAM or BAM file. Default value: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam. /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: O=File The file to write the output to. Default value: O=File The file to write the output to. Default value: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: /tmp/alignmentMetrics10572170532365304613.insert_size_metrics. This option can be set to /tmp/alignmentMetrics10572170532365304613.insert_size_metrics. This option can be set to Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 'null' to clear the default value. 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ASSUME_SORTED=Boolean ASSUME_SORTED=Boolean Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: AS=Boolean If true (default), then the sort order in the header file will be ignored. Default value: AS=Boolean If true (default), then the sort order in the header file will be ignored. Default value: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: true. This option can be set to 'null' to clear the default value. Possible values: {true, true. This option can be set to 'null' to clear the default value. Possible values: {true, Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: false} false} Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: 0. This option can be STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: 0. This option can be Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: set to 'null' to clear the default value. set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: TMP_DIR=File One or more directories with space available to be used by this program for temporary TMP_DIR=File One or more directories with space available to be used by this program for temporary Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: storage of working files Default value: null. This option may be specified 0 or more storage of working files Default value: null. This option may be specified 0 or more Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: times. times. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: VERBOSITY=LogLevel Control verbosity of logging. Default value: INFO. This option can be set to 'null' to VERBOSITY=LogLevel Control verbosity of logging. Default value: INFO. This option can be set to 'null' to Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: clear the default value. Possible values: {ERROR, WARNING, INFO, DEBUG} clear the default value. Possible values: {ERROR, WARNING, INFO, DEBUG} Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: QUIET=Boolean Whether to suppress job-summary info on System.err. Default value: false. This option can QUIET=Boolean Whether to suppress job-summary info on System.err. Default value: false. This option can Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: be set to 'null' to clear the default value. Possible values: {true, false} be set to 'null' to clear the default value. Possible values: {true, false} Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: VALIDATION_STRINGENCY=ValidationStringency VALIDATION_STRINGENCY=ValidationStringency Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Validation stringency for all SAM files read by this program. Setting stringency to Validation stringency for all SAM files read by this program. Setting stringency to Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: SILENT can improve performance when processing a BAM file in which variable-length data SILENT can improve performance when processing a BAM file in which variable-length data Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: (read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT. This (read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT. This Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: option can be set to 'null' to clear the default value. Possible values: {STRICT, LENIENT, option can be set to 'null' to clear the default value. Possible values: {STRICT, LENIENT, Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: SILENT} SILENT} Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: COMPRESSION_LEVEL=Integer Compression level for all compressed files created (e.g. BAM and VCF). Default value: 5. COMPRESSION_LEVEL=Integer Compression level for all compressed files created (e.g. BAM and VCF). Default value: 5. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: MAX_RECORDS_IN_RAM=Integer When writing files that need to be sorted, this will specify the number of records stored MAX_RECORDS_IN_RAM=Integer When writing files that need to be sorted, this will specify the number of records stored Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: in RAM before spilling to disk. Increasing this number reduces the number of file handles in RAM before spilling to disk. Increasing this number reduces the number of file handles Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: needed to sort the file, and increases the amount of RAM needed. Default value: 1000. needed to sort the file, and increases the amount of RAM needed. Default value: 1000. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: CREATE_INDEX=Boolean Whether to create an index when writing VCF or coordinate sorted BAM output. Default CREATE_INDEX=Boolean Whether to create an index when writing VCF or coordinate sorted BAM output. Default Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: value: false. This option can be set to 'null' to clear the default value. Possible value: false. This option can be set to 'null' to clear the default value. Possible Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: values: {true, false} values: {true, false} Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: CREATE_MD5_FILE=Boolean Whether to create an MD5 digest for any BAM or FASTQ files created. Default value: CREATE_MD5_FILE=Boolean Whether to create an MD5 digest for any BAM or FASTQ files created. Default value: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: false. This option can be set to 'null' to clear the default value. Possible values: false. This option can be set to 'null' to clear the default value. Possible values: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: {true, false} {true, false} Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: REFERENCE_SEQUENCE=File REFERENCE_SEQUENCE=File Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: R=File Reference sequence file. Default value: null. R=File Reference sequence file. Default value: null. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: GA4GH_CLIENT_SECRETS=String Google Genomics API client_secrets.json file path. Default value: client_secrets.json. GA4GH_CLIENT_SECRETS=String Google Genomics API client_secrets.json file path. Default value: client_secrets.json. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: USE_JDK_DEFLATER=Boolean USE_JDK_DEFLATER=Boolean Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: USE_JDK_DEFLATER=Boolean Use the JDK Deflater instead of the Intel Deflater for writing compressed output Default USE_JDK_DEFLATER=Boolean Use the JDK Deflater instead of the Intel Deflater for writing compressed output Default Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: value: false. This option can be set to 'null' to clear the default value. Possible value: false. This option can be set to 'null' to clear the default value. Possible Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: values: {true, false} values: {true, false} Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: USE_JDK_INFLATER=Boolean USE_JDK_INFLATER=Boolean Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: USE_JDK_INFLATER=Boolean Use the JDK Inflater instead of the Intel Inflater for reading compressed input Default USE_JDK_INFLATER=Boolean Use the JDK Inflater instead of the Intel Inflater for reading compressed input Default Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: value: false. This option can be set to 'null' to clear the default value. Possible value: false. This option can be set to 'null' to clear the default value. Possible Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: values: {true, false} values: {true, false} Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: options, unrecognized options are ignored. A single-valued option set in an options file options, unrecognized options are ignored. A single-valued option set in an options file Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: may be overridden by a subsequent command-line option. A line starting with '#' is may be overridden by a subsequent command-line option. A line starting with '#' is Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: considered a comment. Required. considered a comment. Required. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:52:02 GMT+14:00 2024] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:02 GMT+14:00 2024] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes. Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testMultipleMetricsFailing[7](CollectInsertSizeMetrics::HISTOGRAM_WIDTH=hello)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:03 CollectMultipleMetrics Gradle suite > Gradle test > picard.analysis.CollectMultipleMetricsTest.testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta) STANDARD_ERROR INFO 2024-07-02 11:52:03 CollectMultipleMetrics Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** CollectMultipleMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam -OUTPUT /tmp/alignmentMetrics14449265104450165512 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta -METRIC_ACCUMULATION_LEVEL ALL_READS -PROGRAM null -PROGRAM CollectAlignmentSummaryMetrics -PROGRAM CollectInsertSizeMetrics -EXTRA_ARGUMENT CollectInsertSizeMetrics::--REFERENCE whyNot.fasta ********** CollectMultipleMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam -OUTPUT /tmp/alignmentMetrics14449265104450165512 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta -METRIC_ACCUMULATION_LEVEL ALL_READS -PROGRAM null -PROGRAM CollectAlignmentSummaryMetrics -PROGRAM CollectInsertSizeMetrics -EXTRA_ARGUMENT CollectInsertSizeMetrics::--REFERENCE whyNot.fasta Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:03 RExecutor Executing R script via command: Rscript /tmp/script14083322520086858833.R INFO 2024-07-02 11:52:03 RExecutor Executing R script via command: Rscript /tmp/script14083322520086858833.R Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:04 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:52:04 ProcessExecutor [1] "Checking if R is installed" Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:52:04.142 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:04.142 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:52:04.143 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:04.143 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:52:04.143 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:04.143 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:52:04.143 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:04.143 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:52:04 GMT+14:00 2024] CollectMultipleMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=/tmp/alignmentMetrics14449265104450165512 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] EXTRA_ARGUMENT=[CollectInsertSizeMetrics::REFERENCE=whyNot.fasta] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:04 GMT+14:00 2024] CollectMultipleMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=/tmp/alignmentMetrics14449265104450165512 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] EXTRA_ARGUMENT=[CollectInsertSizeMetrics::REFERENCE=whyNot.fasta] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:52:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ERROR: Unrecognized option: REFERENCE ERROR: Unrecognized option: REFERENCE Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: USAGE: CollectInsertSizeMetrics [options] USAGE: CollectInsertSizeMetrics [options] Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CollectInsertSizeMetrics Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CollectInsertSizeMetrics Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Collect metrics about the insert size distribution of a paired-end library. This tool provides useful metrics for Collect metrics about the insert size distribution of a paired-end library. This tool provides useful metrics for Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: validating library construction including the insert size distribution and read orientation of paired-end libraries. validating library construction including the insert size distribution and read orientation of paired-end libraries. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: The expected proportions of these metrics vary depending on the type of library preparation used, resulting from The expected proportions of these metrics vary depending on the type of library preparation used, resulting from Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: technical differences between pair-end libraries and mate-pair libraries. For a brief primer on paired-end sequencing technical differences between pair-end libraries and mate-pair libraries. For a brief primer on paired-end sequencing Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: and mate-pair reads, see the GATK Dictionary (https://www.broadinstitute.org/gatk/guide/article?id=6327). and mate-pair reads, see the GATK Dictionary (https://www.broadinstitute.org/gatk/guide/article?id=6327). Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: The CollectInsertSizeMetrics tool outputs the percentages of read pairs in each of the three orientations (FR, RF, and The CollectInsertSizeMetrics tool outputs the percentages of read pairs in each of the three orientations (FR, RF, and Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: TANDEM) as a histogram. In addition, the insert size distribution is output as both a histogram TANDEM) as a histogram. In addition, the insert size distribution is output as both a histogram Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: (.insert_size_Histogram.pdf) and as a data table (.insert_size_metrics.txt). (.insert_size_Histogram.pdf) and as a data table (.insert_size_metrics.txt). Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Note: Metrics labeled as percentages are actually expressed as fractions! Note: Metrics labeled as percentages are actually expressed as fractions! Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Usage example: Usage example: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: java -jar picard.jar CollectInsertSizeMetrics \ java -jar picard.jar CollectInsertSizeMetrics \ Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: O=insert_size_metrics.txt \ O=insert_size_metrics.txt \ Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: H=insert_size_histogram.pdf \ H=insert_size_histogram.pdf \ Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: M=0.5 M=0.5 Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Note: If processing a small file, set the minimum percentage option (M) to 0.5, otherwise an error may occur. Note: If processing a small file, set the minimum percentage option (M) to 0.5, otherwise an error may occur. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Please see InsertSizeMetrics (https://broadinstitute.github.io/picard/picard-metric-definitions.html#InsertSizeMetrics) Please see InsertSizeMetrics (https://broadinstitute.github.io/picard/picard-metric-definitions.html#InsertSizeMetrics) Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: for detailed explanations of each metric. for detailed explanations of each metric. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Version: null Version: null Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Options: Options: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: --help --help Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: tools. tools. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: HISTOGRAM_FILE=File HISTOGRAM_FILE=File Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: H=File File to write insert size Histogram chart to. Default value: H=File File to write insert size Histogram chart to. Default value: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: /tmp/alignmentMetrics14449265104450165512.insert_size_histogram.pdf. This option can be /tmp/alignmentMetrics14449265104450165512.insert_size_histogram.pdf. This option can be Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: set to 'null' to clear the default value. set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: DEVIATIONS=Double Generate mean, sd and plots by trimming the data down to MEDIAN + DEVIATIONS=Double Generate mean, sd and plots by trimming the data down to MEDIAN + Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: includes enough anomalous values from chimeras and other artifacts to make the mean and sd includes enough anomalous values from chimeras and other artifacts to make the mean and sd Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: grossly misleading regarding the real distribution. Default value: 10.0. This option can grossly misleading regarding the real distribution. Default value: 10.0. This option can Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: be set to 'null' to clear the default value. be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: HISTOGRAM_WIDTH=Integer HISTOGRAM_WIDTH=Integer Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: W=Integer Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail. W=Integer Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Also, when calculating mean and standard deviation, only bins <= Histogram_WIDTH will be Also, when calculating mean and standard deviation, only bins <= Histogram_WIDTH will be Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: included. Default value: null. included. Default value: null. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: MIN_HISTOGRAM_WIDTH=Integer MIN_HISTOGRAM_WIDTH=Integer Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: MW=Integer Minimum width of histogram plots. In the case when the histogram would otherwise MW=Integer Minimum width of histogram plots. In the case when the histogram would otherwise Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: betruncated to a shorter range of sizes, the MIN_HISTOGRAM_WIDTH will enforce a minimum betruncated to a shorter range of sizes, the MIN_HISTOGRAM_WIDTH will enforce a minimum Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: range. Default value: null. range. Default value: null. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: MINIMUM_PCT=Float MINIMUM_PCT=Float Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: M=Float When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that M=Float When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: have fewer than this percentage of overall reads. (Range: 0 to 1). Default value: 0.05. have fewer than this percentage of overall reads. (Range: 0 to 1). Default value: 0.05. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Default value: [ALL_READS]. This option LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Default value: [ALL_READS]. This option Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: can be set to 'null' to clear the default value. Possible values: {ALL_READS, SAMPLE, can be set to 'null' to clear the default value. Possible values: {ALL_READS, SAMPLE, Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: LIBRARY, READ_GROUP} This option may be specified 0 or more times. This option can be set LIBRARY, READ_GROUP} This option may be specified 0 or more times. This option can be set Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: to 'null' to clear the default list. to 'null' to clear the default list. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INCLUDE_DUPLICATES=Boolean If true, also include reads marked as duplicates in the insert size histogram. Default INCLUDE_DUPLICATES=Boolean If true, also include reads marked as duplicates in the insert size histogram. Default Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: value: false. This option can be set to 'null' to clear the default value. Possible value: false. This option can be set to 'null' to clear the default value. Possible Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: values: {true, false} values: {true, false} Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: I=File Input SAM or BAM file. Default value: I=File Input SAM or BAM file. Default value: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam. /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: O=File The file to write the output to. Default value: O=File The file to write the output to. Default value: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: /tmp/alignmentMetrics14449265104450165512.insert_size_metrics. This option can be set to /tmp/alignmentMetrics14449265104450165512.insert_size_metrics. This option can be set to Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 'null' to clear the default value. 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ASSUME_SORTED=Boolean ASSUME_SORTED=Boolean Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: AS=Boolean If true (default), then the sort order in the header file will be ignored. Default value: AS=Boolean If true (default), then the sort order in the header file will be ignored. Default value: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: true. This option can be set to 'null' to clear the default value. Possible values: {true, true. This option can be set to 'null' to clear the default value. Possible values: {true, Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: false} false} Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: 0. This option can be STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: 0. This option can be Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: set to 'null' to clear the default value. set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: TMP_DIR=File One or more directories with space available to be used by this program for temporary TMP_DIR=File One or more directories with space available to be used by this program for temporary Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: storage of working files Default value: null. This option may be specified 0 or more storage of working files Default value: null. This option may be specified 0 or more Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: times. times. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: VERBOSITY=LogLevel Control verbosity of logging. Default value: INFO. This option can be set to 'null' to VERBOSITY=LogLevel Control verbosity of logging. Default value: INFO. This option can be set to 'null' to Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: clear the default value. Possible values: {ERROR, WARNING, INFO, DEBUG} clear the default value. Possible values: {ERROR, WARNING, INFO, DEBUG} Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: QUIET=Boolean Whether to suppress job-summary info on System.err. Default value: false. This option can QUIET=Boolean Whether to suppress job-summary info on System.err. Default value: false. This option can Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: be set to 'null' to clear the default value. Possible values: {true, false} be set to 'null' to clear the default value. Possible values: {true, false} Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: VALIDATION_STRINGENCY=ValidationStringency VALIDATION_STRINGENCY=ValidationStringency Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Validation stringency for all SAM files read by this program. Setting stringency to Validation stringency for all SAM files read by this program. Setting stringency to Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: SILENT can improve performance when processing a BAM file in which variable-length data SILENT can improve performance when processing a BAM file in which variable-length data Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: (read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT. This (read, qualities, tags) do not otherwise need to be decoded. Default value: STRICT. This Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: option can be set to 'null' to clear the default value. Possible values: {STRICT, LENIENT, option can be set to 'null' to clear the default value. Possible values: {STRICT, LENIENT, Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: SILENT} SILENT} Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: COMPRESSION_LEVEL=Integer Compression level for all compressed files created (e.g. BAM and VCF). Default value: 5. COMPRESSION_LEVEL=Integer Compression level for all compressed files created (e.g. BAM and VCF). Default value: 5. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: MAX_RECORDS_IN_RAM=Integer When writing files that need to be sorted, this will specify the number of records stored MAX_RECORDS_IN_RAM=Integer When writing files that need to be sorted, this will specify the number of records stored Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: in RAM before spilling to disk. Increasing this number reduces the number of file handles in RAM before spilling to disk. Increasing this number reduces the number of file handles Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: needed to sort the file, and increases the amount of RAM needed. Default value: 1000. needed to sort the file, and increases the amount of RAM needed. Default value: 1000. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: CREATE_INDEX=Boolean Whether to create an index when writing VCF or coordinate sorted BAM output. Default CREATE_INDEX=Boolean Whether to create an index when writing VCF or coordinate sorted BAM output. Default Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: value: false. This option can be set to 'null' to clear the default value. Possible value: false. This option can be set to 'null' to clear the default value. Possible Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: values: {true, false} values: {true, false} Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: CREATE_MD5_FILE=Boolean Whether to create an MD5 digest for any BAM or FASTQ files created. Default value: CREATE_MD5_FILE=Boolean Whether to create an MD5 digest for any BAM or FASTQ files created. Default value: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: false. This option can be set to 'null' to clear the default value. Possible values: false. This option can be set to 'null' to clear the default value. Possible values: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: {true, false} {true, false} Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: REFERENCE_SEQUENCE=File REFERENCE_SEQUENCE=File Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: R=File Reference sequence file. Default value: null. R=File Reference sequence file. Default value: null. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: GA4GH_CLIENT_SECRETS=String Google Genomics API client_secrets.json file path. Default value: client_secrets.json. GA4GH_CLIENT_SECRETS=String Google Genomics API client_secrets.json file path. Default value: client_secrets.json. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: USE_JDK_DEFLATER=Boolean USE_JDK_DEFLATER=Boolean Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: USE_JDK_DEFLATER=Boolean Use the JDK Deflater instead of the Intel Deflater for writing compressed output Default USE_JDK_DEFLATER=Boolean Use the JDK Deflater instead of the Intel Deflater for writing compressed output Default Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: value: false. This option can be set to 'null' to clear the default value. Possible value: false. This option can be set to 'null' to clear the default value. Possible Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: values: {true, false} values: {true, false} Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: USE_JDK_INFLATER=Boolean USE_JDK_INFLATER=Boolean Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: USE_JDK_INFLATER=Boolean Use the JDK Inflater instead of the Intel Inflater for reading compressed input Default USE_JDK_INFLATER=Boolean Use the JDK Inflater instead of the Intel Inflater for reading compressed input Default Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: value: false. This option can be set to 'null' to clear the default value. Possible value: false. This option can be set to 'null' to clear the default value. Possible Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: values: {true, false} values: {true, false} Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line OPTIONS_FILE=File File of OPTION_NAME=value pairs. No positional parameters allowed. Unlike command-line Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: options, unrecognized options are ignored. A single-valued option set in an options file options, unrecognized options are ignored. A single-valued option set in an options file Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: may be overridden by a subsequent command-line option. A line starting with '#' is may be overridden by a subsequent command-line option. A line starting with '#' is Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: considered a comment. Required. considered a comment. Required. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:52:04 GMT+14:00 2024] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:04 GMT+14:00 2024] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes. Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testMultipleMetricsFailing[8](CollectInsertSizeMetrics::REFERENCE=whyNot.fasta)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMultipleMetricsFailing[9](CollectInsertSizeMetrics::OUTPUT=)(picard.analysis.CollectMultipleMetricsTest) Test: Test method testMultipleMetricsFailing[9](CollectInsertSizeMetrics::OUTPUT=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:04 CollectMultipleMetrics Gradle suite > Gradle test > picard.analysis.CollectMultipleMetricsTest.testMultipleMetricsFailing[9](CollectInsertSizeMetrics::OUTPUT=) STANDARD_ERROR INFO 2024-07-02 11:52:04 CollectMultipleMetrics Test: Test method testMultipleMetricsFailing[9](CollectInsertSizeMetrics::OUTPUT=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[9](CollectInsertSizeMetrics::OUTPUT=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMultipleMetricsFailing[9](CollectInsertSizeMetrics::OUTPUT=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[9](CollectInsertSizeMetrics::OUTPUT=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMultipleMetricsFailing[9](CollectInsertSizeMetrics::OUTPUT=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMultipleMetricsFailing[9](CollectInsertSizeMetrics::OUTPUT=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[9](CollectInsertSizeMetrics::OUTPUT=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMultipleMetricsFailing[9](CollectInsertSizeMetrics::OUTPUT=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[9](CollectInsertSizeMetrics::OUTPUT=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** CollectMultipleMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam -OUTPUT /tmp/alignmentMetrics3333560890876039013 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta -METRIC_ACCUMULATION_LEVEL ALL_READS -PROGRAM null -PROGRAM CollectAlignmentSummaryMetrics -PROGRAM CollectInsertSizeMetrics -EXTRA_ARGUMENT CollectInsertSizeMetrics::--OUTPUT ********** CollectMultipleMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam -OUTPUT /tmp/alignmentMetrics3333560890876039013 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta -METRIC_ACCUMULATION_LEVEL ALL_READS -PROGRAM null -PROGRAM CollectAlignmentSummaryMetrics -PROGRAM CollectInsertSizeMetrics -EXTRA_ARGUMENT CollectInsertSizeMetrics::--OUTPUT Test: Test method testMultipleMetricsFailing[9](CollectInsertSizeMetrics::OUTPUT=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultipleMetricsFailing[9](CollectInsertSizeMetrics::OUTPUT=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[9](CollectInsertSizeMetrics::OUTPUT=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testMultipleMetricsFailing[9](CollectInsertSizeMetrics::OUTPUT=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:04 RExecutor Executing R script via command: Rscript /tmp/script9040893544157404041.R INFO 2024-07-02 11:52:04 RExecutor Executing R script via command: Rscript /tmp/script9040893544157404041.R Test: Test method testMultipleMetricsFailing[9](CollectInsertSizeMetrics::OUTPUT=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:05 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:52:05 ProcessExecutor [1] "Checking if R is installed" Test: Test method testMultipleMetricsFailing[9](CollectInsertSizeMetrics::OUTPUT=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:52:05.423 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:05.423 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleMetricsFailing[9](CollectInsertSizeMetrics::OUTPUT=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:52:05.423 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:05.423 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleMetricsFailing[9](CollectInsertSizeMetrics::OUTPUT=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:52:05.424 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:05.424 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultipleMetricsFailing[9](CollectInsertSizeMetrics::OUTPUT=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:52:05.424 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:05.424 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultipleMetricsFailing[9](CollectInsertSizeMetrics::OUTPUT=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:52:05 GMT+14:00 2024] CollectMultipleMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=/tmp/alignmentMetrics3333560890876039013 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] EXTRA_ARGUMENT=[CollectInsertSizeMetrics::OUTPUT=] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:05 GMT+14:00 2024] CollectMultipleMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=/tmp/alignmentMetrics3333560890876039013 METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics] EXTRA_ARGUMENT=[CollectInsertSizeMetrics::OUTPUT=] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMultipleMetricsFailing[9](CollectInsertSizeMetrics::OUTPUT=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:52:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMultipleMetricsFailing[9](CollectInsertSizeMetrics::OUTPUT=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:52:05 GMT+14:00 2024] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:05 GMT+14:00 2024] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes. Test: Test method testMultipleMetricsFailing[9](CollectInsertSizeMetrics::OUTPUT=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testMultipleMetricsFailing[9](CollectInsertSizeMetrics::OUTPUT=)(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:05 CollectMultipleMetrics Gradle suite > Gradle test > picard.analysis.CollectMultipleMetricsTest.testRnaSeqMetricsViaMultipleMetrics STANDARD_ERROR INFO 2024-07-02 11:52:05 CollectMultipleMetrics Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** CollectMultipleMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/rna_seq_metrics.sam -OUTPUT /tmp/tmp.9228942717363585508.rna_metrics -METRIC_ACCUMULATION_LEVEL ALL_READS -INTERVALS /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/rna_seq_metrics.interval_list -REF_FLAT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/rna_seq_metrics.refflat -IGNORE_SEQUENCE chrM -PROGRAM RnaSeqMetrics ********** CollectMultipleMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/rna_seq_metrics.sam -OUTPUT /tmp/tmp.9228942717363585508.rna_metrics -METRIC_ACCUMULATION_LEVEL ALL_READS -INTERVALS /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/rna_seq_metrics.interval_list -REF_FLAT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/rna_seq_metrics.refflat -IGNORE_SEQUENCE chrM -PROGRAM RnaSeqMetrics Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: ********** ********** Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:05 RExecutor Executing R script via command: Rscript /tmp/script2076327842386720677.R INFO 2024-07-02 11:52:05 RExecutor Executing R script via command: Rscript /tmp/script2076327842386720677.R Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:06 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:52:06 ProcessExecutor [1] "Checking if R is installed" Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:52:06.370 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:06.370 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:52:06.371 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:06.371 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:52:06.371 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:06.371 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: 11:52:06.371 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:06.371 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:52:06 GMT+14:00 2024] CollectMultipleMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/rna_seq_metrics.sam OUTPUT=/tmp/tmp.9228942717363585508.rna_metrics METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectBaseDistributionByCycle, CollectInsertSizeMetrics, MeanQualityByCycle, QualityScoreDistribution, RnaSeqMetrics] INTERVALS=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/rna_seq_metrics.interval_list REF_FLAT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/rna_seq_metrics.refflat IGNORE_SEQUENCE=[chrM] ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:06 GMT+14:00 2024] CollectMultipleMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/rna_seq_metrics.sam OUTPUT=/tmp/tmp.9228942717363585508.rna_metrics METRIC_ACCUMULATION_LEVEL=[ALL_READS] PROGRAM=[CollectAlignmentSummaryMetrics, CollectBaseDistributionByCycle, CollectInsertSizeMetrics, MeanQualityByCycle, QualityScoreDistribution, RnaSeqMetrics] INTERVALS=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/rna_seq_metrics.interval_list REF_FLAT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/rna_seq_metrics.refflat IGNORE_SEQUENCE=[chrM] ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:52:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: WARNING 2024-07-02 11:52:06 CollectAlignmentSummaryMetrics Without a REFERENCE_SEQUENCE, metrics pertaining to mismatch rates will not be collected! WARNING 2024-07-02 11:52:06 CollectAlignmentSummaryMetrics Without a REFERENCE_SEQUENCE, metrics pertaining to mismatch rates will not be collected! Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:06 CollectRnaSeqMetrics Loaded 1 genes. INFO 2024-07-02 11:52:06 CollectRnaSeqMetrics Loaded 1 genes. Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:06 RExecutor Executing R script via command: Rscript /tmp/script14478649527074808212.R /tmp/tmp.9228942717363585508.rna_metrics.alignment_summary_metrics /tmp/tmp.9228942717363585508.rna_metrics.read_length_histogram.pdf rna_seq_metrics.sam INFO 2024-07-02 11:52:06 RExecutor Executing R script via command: Rscript /tmp/script14478649527074808212.R /tmp/tmp.9228942717363585508.rna_metrics.alignment_summary_metrics /tmp/tmp.9228942717363585508.rna_metrics.read_length_histogram.pdf rna_seq_metrics.sam Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:07 ProcessExecutor null device INFO 2024-07-02 11:52:07 ProcessExecutor null device Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:07 ProcessExecutor 1 INFO 2024-07-02 11:52:07 ProcessExecutor 1 Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:07 RExecutor Executing R script via command: Rscript /tmp/script17069552414707299367.R /tmp/tmp.9228942717363585508.rna_metrics.base_distribution_by_cycle_metrics /tmp/tmp.9228942717363585508.rna_metrics.base_distribution_by_cycle.pdf rna_seq_metrics.sam INFO 2024-07-02 11:52:07 RExecutor Executing R script via command: Rscript /tmp/script17069552414707299367.R /tmp/tmp.9228942717363585508.rna_metrics.base_distribution_by_cycle_metrics /tmp/tmp.9228942717363585508.rna_metrics.base_distribution_by_cycle.pdf rna_seq_metrics.sam Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:09 ProcessExecutor null device INFO 2024-07-02 11:52:09 ProcessExecutor null device Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:09 ProcessExecutor 1 INFO 2024-07-02 11:52:09 ProcessExecutor 1 Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:09 RExecutor Executing R script via command: Rscript /tmp/script1977331400192463448.R /tmp/tmp.9228942717363585508.rna_metrics.insert_size_metrics /tmp/tmp.9228942717363585508.rna_metrics.insert_size_histogram.pdf rna_seq_metrics.sam INFO 2024-07-02 11:52:09 RExecutor Executing R script via command: Rscript /tmp/script1977331400192463448.R /tmp/tmp.9228942717363585508.rna_metrics.insert_size_metrics /tmp/tmp.9228942717363585508.rna_metrics.insert_size_histogram.pdf rna_seq_metrics.sam Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:10 ProcessExecutor null device INFO 2024-07-02 11:52:10 ProcessExecutor null device Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:10 ProcessExecutor 1 INFO 2024-07-02 11:52:10 ProcessExecutor 1 Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:10 RExecutor Executing R script via command: Rscript /tmp/script12018980796495187279.R /tmp/tmp.9228942717363585508.rna_metrics.quality_by_cycle_metrics /tmp/tmp.9228942717363585508.rna_metrics.quality_by_cycle.pdf rna_seq_metrics.sam INFO 2024-07-02 11:52:10 RExecutor Executing R script via command: Rscript /tmp/script12018980796495187279.R /tmp/tmp.9228942717363585508.rna_metrics.quality_by_cycle_metrics /tmp/tmp.9228942717363585508.rna_metrics.quality_by_cycle.pdf rna_seq_metrics.sam Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:11 ProcessExecutor null device INFO 2024-07-02 11:52:11 ProcessExecutor null device Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:11 ProcessExecutor 1 INFO 2024-07-02 11:52:11 ProcessExecutor 1 Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:11 RExecutor Executing R script via command: Rscript /tmp/script93581832242102153.R /tmp/tmp.9228942717363585508.rna_metrics.quality_distribution_metrics /tmp/tmp.9228942717363585508.rna_metrics.quality_distribution.pdf rna_seq_metrics.sam INFO 2024-07-02 11:52:11 RExecutor Executing R script via command: Rscript /tmp/script93581832242102153.R /tmp/tmp.9228942717363585508.rna_metrics.quality_distribution_metrics /tmp/tmp.9228942717363585508.rna_metrics.quality_distribution.pdf rna_seq_metrics.sam Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:11 ProcessExecutor null device INFO 2024-07-02 11:52:11 ProcessExecutor null device Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:11 ProcessExecutor 1 INFO 2024-07-02 11:52:11 ProcessExecutor 1 Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: [Tue Jul 02 11:52:11 GMT+14:00 2024] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.09 minutes. [Tue Jul 02 11:52:11 GMT+14:00 2024] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.09 minutes. Test: Test method testRnaSeqMetricsViaMultipleMetrics(picard.analysis.CollectMultipleMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testCollectOxoGMetrics(picard.analysis.CollectOxoGMetricsTest) Test: Test method testCollectOxoGMetrics(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:11 CollectOxoGMetrics Gradle suite > Gradle test > picard.analysis.CollectOxoGMetricsTest.testCollectOxoGMetrics STANDARD_ERROR INFO 2024-07-02 11:52:11 CollectOxoGMetrics Test: Test method testCollectOxoGMetrics(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: Test: Test method testCollectOxoGMetrics(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCollectOxoGMetrics(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: ********** ********** Test: Test method testCollectOxoGMetrics(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCollectOxoGMetrics(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCollectOxoGMetrics(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: ********** ********** Test: Test method testCollectOxoGMetrics(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCollectOxoGMetrics(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: ********** ********** Test: Test method testCollectOxoGMetrics(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: ********** CollectOxoGMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam -OUTPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test13943265019079577329.oxo_g_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta ********** CollectOxoGMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam -OUTPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test13943265019079577329.oxo_g_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta Test: Test method testCollectOxoGMetrics(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: ********** ********** Test: Test method testCollectOxoGMetrics(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: Test: Test method testCollectOxoGMetrics(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: Test: Test method testCollectOxoGMetrics(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: 11:52:11.736 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:11.736 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCollectOxoGMetrics(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: 11:52:11.736 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:11.736 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCollectOxoGMetrics(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: 11:52:11.736 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:11.736 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCollectOxoGMetrics(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: 11:52:11.736 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:11.736 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCollectOxoGMetrics(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: [Tue Jul 02 11:52:11 GMT+14:00 2024] CollectOxoGMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test13943265019079577329.oxo_g_metrics REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 MINIMUM_INSERT_SIZE=60 MAXIMUM_INSERT_SIZE=600 INCLUDE_NON_PF_READS=true USE_OQ=true CONTEXT_SIZE=1 STOP_AFTER=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:11 GMT+14:00 2024] CollectOxoGMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test13943265019079577329.oxo_g_metrics REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 MINIMUM_INSERT_SIZE=60 MAXIMUM_INSERT_SIZE=600 INCLUDE_NON_PF_READS=true USE_OQ=true CONTEXT_SIZE=1 STOP_AFTER=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCollectOxoGMetrics(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: [Tue Jul 02 11:52:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCollectOxoGMetrics(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:11 CollectOxoGMetrics Generated 16 context strings. INFO 2024-07-02 11:52:11 CollectOxoGMetrics Generated 16 context strings. Test: Test method testCollectOxoGMetrics(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:11 CollectOxoGMetrics Loading dbSNP File: null INFO 2024-07-02 11:52:11 CollectOxoGMetrics Loading dbSNP File: null Test: Test method testCollectOxoGMetrics(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:11 CollectOxoGMetrics Starting iteration. INFO 2024-07-02 11:52:11 CollectOxoGMetrics Starting iteration. Test: Test method testCollectOxoGMetrics(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: [Tue Jul 02 11:52:11 GMT+14:00 2024] picard.analysis.CollectOxoGMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:11 GMT+14:00 2024] picard.analysis.CollectOxoGMetrics done. Elapsed time: 0.00 minutes. Test: Test method testCollectOxoGMetrics(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testCollectOxoGMetricsLongContext(picard.analysis.CollectOxoGMetricsTest) Test: Test method testCollectOxoGMetricsLongContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:11 CollectOxoGMetrics Gradle suite > Gradle test > picard.analysis.CollectOxoGMetricsTest.testCollectOxoGMetricsLongContext STANDARD_ERROR INFO 2024-07-02 11:52:11 CollectOxoGMetrics Test: Test method testCollectOxoGMetricsLongContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: Test: Test method testCollectOxoGMetricsLongContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCollectOxoGMetricsLongContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: ********** ********** Test: Test method testCollectOxoGMetricsLongContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCollectOxoGMetricsLongContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCollectOxoGMetricsLongContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: ********** ********** Test: Test method testCollectOxoGMetricsLongContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCollectOxoGMetricsLongContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: ********** ********** Test: Test method testCollectOxoGMetricsLongContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: ********** CollectOxoGMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam -OUTPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test14774737200027335422.oxo_g_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -CONTEXT_SIZE 2 ********** CollectOxoGMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam -OUTPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test14774737200027335422.oxo_g_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -CONTEXT_SIZE 2 Test: Test method testCollectOxoGMetricsLongContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: ********** ********** Test: Test method testCollectOxoGMetricsLongContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: Test: Test method testCollectOxoGMetricsLongContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: Test: Test method testCollectOxoGMetricsLongContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: 11:52:11.759 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:11.759 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCollectOxoGMetricsLongContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: 11:52:11.759 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:11.759 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCollectOxoGMetricsLongContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: 11:52:11.759 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:11.759 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCollectOxoGMetricsLongContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: 11:52:11.759 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:11.759 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCollectOxoGMetricsLongContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: [Tue Jul 02 11:52:11 GMT+14:00 2024] CollectOxoGMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test14774737200027335422.oxo_g_metrics CONTEXT_SIZE=2 REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 MINIMUM_INSERT_SIZE=60 MAXIMUM_INSERT_SIZE=600 INCLUDE_NON_PF_READS=true USE_OQ=true STOP_AFTER=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:11 GMT+14:00 2024] CollectOxoGMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test14774737200027335422.oxo_g_metrics CONTEXT_SIZE=2 REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 MINIMUM_INSERT_SIZE=60 MAXIMUM_INSERT_SIZE=600 INCLUDE_NON_PF_READS=true USE_OQ=true STOP_AFTER=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCollectOxoGMetricsLongContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: [Tue Jul 02 11:52:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCollectOxoGMetricsLongContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:11 CollectOxoGMetrics Generated 256 context strings. INFO 2024-07-02 11:52:11 CollectOxoGMetrics Generated 256 context strings. Test: Test method testCollectOxoGMetricsLongContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:11 CollectOxoGMetrics Loading dbSNP File: null INFO 2024-07-02 11:52:11 CollectOxoGMetrics Loading dbSNP File: null Test: Test method testCollectOxoGMetricsLongContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:11 CollectOxoGMetrics Starting iteration. INFO 2024-07-02 11:52:11 CollectOxoGMetrics Starting iteration. Test: Test method testCollectOxoGMetricsLongContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: [Tue Jul 02 11:52:11 GMT+14:00 2024] picard.analysis.CollectOxoGMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:11 GMT+14:00 2024] picard.analysis.CollectOxoGMetrics done. Elapsed time: 0.00 minutes. Test: Test method testCollectOxoGMetricsLongContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testCollectOxoGMetricsShortContext(picard.analysis.CollectOxoGMetricsTest) Test: Test method testCollectOxoGMetricsShortContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:11 CollectOxoGMetrics Gradle suite > Gradle test > picard.analysis.CollectOxoGMetricsTest.testCollectOxoGMetricsShortContext STANDARD_ERROR INFO 2024-07-02 11:52:11 CollectOxoGMetrics Test: Test method testCollectOxoGMetricsShortContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: Test: Test method testCollectOxoGMetricsShortContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCollectOxoGMetricsShortContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: ********** ********** Test: Test method testCollectOxoGMetricsShortContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCollectOxoGMetricsShortContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCollectOxoGMetricsShortContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: ********** ********** Test: Test method testCollectOxoGMetricsShortContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCollectOxoGMetricsShortContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: ********** ********** Test: Test method testCollectOxoGMetricsShortContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: ********** CollectOxoGMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam -OUTPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test5906732258389150842.oxo_g_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -CONTEXT_SIZE 0 ********** CollectOxoGMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam -OUTPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test5906732258389150842.oxo_g_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -CONTEXT_SIZE 0 Test: Test method testCollectOxoGMetricsShortContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: ********** ********** Test: Test method testCollectOxoGMetricsShortContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: Test: Test method testCollectOxoGMetricsShortContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: Test: Test method testCollectOxoGMetricsShortContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: 11:52:11.788 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:11.788 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCollectOxoGMetricsShortContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: 11:52:11.792 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:11.792 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCollectOxoGMetricsShortContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: 11:52:11.792 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:11.792 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCollectOxoGMetricsShortContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: 11:52:11.792 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:11.792 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCollectOxoGMetricsShortContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: [Tue Jul 02 11:52:11 GMT+14:00 2024] CollectOxoGMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test5906732258389150842.oxo_g_metrics CONTEXT_SIZE=0 REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 MINIMUM_INSERT_SIZE=60 MAXIMUM_INSERT_SIZE=600 INCLUDE_NON_PF_READS=true USE_OQ=true STOP_AFTER=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:11 GMT+14:00 2024] CollectOxoGMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test5906732258389150842.oxo_g_metrics CONTEXT_SIZE=0 REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 MINIMUM_INSERT_SIZE=60 MAXIMUM_INSERT_SIZE=600 INCLUDE_NON_PF_READS=true USE_OQ=true STOP_AFTER=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCollectOxoGMetricsShortContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: [Tue Jul 02 11:52:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCollectOxoGMetricsShortContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:11 CollectOxoGMetrics Generated 1 context strings. INFO 2024-07-02 11:52:11 CollectOxoGMetrics Generated 1 context strings. Test: Test method testCollectOxoGMetricsShortContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:11 CollectOxoGMetrics Loading dbSNP File: null INFO 2024-07-02 11:52:11 CollectOxoGMetrics Loading dbSNP File: null Test: Test method testCollectOxoGMetricsShortContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:11 CollectOxoGMetrics Starting iteration. INFO 2024-07-02 11:52:11 CollectOxoGMetrics Starting iteration. Test: Test method testCollectOxoGMetricsShortContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: [Tue Jul 02 11:52:11 GMT+14:00 2024] picard.analysis.CollectOxoGMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:11 GMT+14:00 2024] picard.analysis.CollectOxoGMetrics done. Elapsed time: 0.00 minutes. Test: Test method testCollectOxoGMetricsShortContext(picard.analysis.CollectOxoGMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testNegativeCustomCommandLineValidation[0](5, 10, 1, [AAC], Middle base of context sequence AAC must be C)(picard.analysis.CollectOxoGMetricsTest) Running Test: Test method testNegativeCustomCommandLineValidation[1](10, 10, 1, [AAGAA, ATCAT], Context AAGAA is not 3 long as implied by CONTEXT_SIZE=1)(picard.analysis.CollectOxoGMetricsTest) Running Test: Test method testNegativeCustomCommandLineValidation[2](10, 5, 1, [ACC], MAXIMUM_INSERT_SIZE cannot be less than MINIMUM_INSERT_SIZE)(picard.analysis.CollectOxoGMetricsTest) Running Test: Test method testNegativeCustomCommandLineValidation[3](-5, 10, 1, [ACC], MINIMUM_INSERT_SIZE cannot be negative)(picard.analysis.CollectOxoGMetricsTest) Running Test: Test method testPositiveCustomCommandLineValidation[0](5, 10, 1, [ACC])(picard.analysis.CollectOxoGMetricsTest) Running Test: Test method testPositiveCustomCommandLineValidation[1](10, 10, 2, [AACAA, ATCAT])(picard.analysis.CollectOxoGMetricsTest) Running Test: Test method test(picard.analysis.CollectQualityYieldMetricsTest) Test: Test method test(picard.analysis.CollectQualityYieldMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:11 CollectQualityYieldMetrics Gradle suite > Gradle test > picard.analysis.CollectQualityYieldMetricsTest.test STANDARD_ERROR INFO 2024-07-02 11:52:11 CollectQualityYieldMetrics Test: Test method test(picard.analysis.CollectQualityYieldMetricsTest) produced standard out/err: Test: Test method test(picard.analysis.CollectQualityYieldMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method test(picard.analysis.CollectQualityYieldMetricsTest) produced standard out/err: ********** ********** Test: Test method test(picard.analysis.CollectQualityYieldMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method test(picard.analysis.CollectQualityYieldMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method test(picard.analysis.CollectQualityYieldMetricsTest) produced standard out/err: ********** ********** Test: Test method test(picard.analysis.CollectQualityYieldMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method test(picard.analysis.CollectQualityYieldMetricsTest) produced standard out/err: ********** ********** Test: Test method test(picard.analysis.CollectQualityYieldMetricsTest) produced standard out/err: ********** CollectQualityYieldMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/insert_size_metrics_test.sam -OUTPUT /tmp/test551711602553671692.quality_yield_metrics ********** CollectQualityYieldMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/insert_size_metrics_test.sam -OUTPUT /tmp/test551711602553671692.quality_yield_metrics Test: Test method test(picard.analysis.CollectQualityYieldMetricsTest) produced standard out/err: ********** ********** Test: Test method test(picard.analysis.CollectQualityYieldMetricsTest) produced standard out/err: Test: Test method test(picard.analysis.CollectQualityYieldMetricsTest) produced standard out/err: Test: Test method test(picard.analysis.CollectQualityYieldMetricsTest) produced standard out/err: 11:52:11.828 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:11.828 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method test(picard.analysis.CollectQualityYieldMetricsTest) produced standard out/err: 11:52:11.828 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:11.828 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method test(picard.analysis.CollectQualityYieldMetricsTest) produced standard out/err: 11:52:11.828 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:11.828 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method test(picard.analysis.CollectQualityYieldMetricsTest) produced standard out/err: 11:52:11.828 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:11.828 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method test(picard.analysis.CollectQualityYieldMetricsTest) produced standard out/err: [Tue Jul 02 11:52:11 GMT+14:00 2024] CollectQualityYieldMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/insert_size_metrics_test.sam OUTPUT=/tmp/test551711602553671692.quality_yield_metrics USE_ORIGINAL_QUALITIES=true INCLUDE_SECONDARY_ALIGNMENTS=false INCLUDE_SUPPLEMENTAL_ALIGNMENTS=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:11 GMT+14:00 2024] CollectQualityYieldMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/insert_size_metrics_test.sam OUTPUT=/tmp/test551711602553671692.quality_yield_metrics USE_ORIGINAL_QUALITIES=true INCLUDE_SECONDARY_ALIGNMENTS=false INCLUDE_SUPPLEMENTAL_ALIGNMENTS=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method test(picard.analysis.CollectQualityYieldMetricsTest) produced standard out/err: [Tue Jul 02 11:52:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method test(picard.analysis.CollectQualityYieldMetricsTest) produced standard out/err: [Tue Jul 02 11:52:11 GMT+14:00 2024] picard.analysis.CollectQualityYieldMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:11 GMT+14:00 2024] picard.analysis.CollectQualityYieldMetrics done. Elapsed time: 0.00 minutes. Test: Test method test(picard.analysis.CollectQualityYieldMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBasic(picard.analysis.CollectRnaSeqMetricsTest) Test: Test method testBasic(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:11 CollectRnaSeqMetrics Gradle suite > Gradle test > picard.analysis.CollectRnaSeqMetricsTest.testBasic STANDARD_ERROR INFO 2024-07-02 11:52:11 CollectRnaSeqMetrics Test: Test method testBasic(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: Test: Test method testBasic(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBasic(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** ********** Test: Test method testBasic(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBasic(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBasic(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** ********** Test: Test method testBasic(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBasic(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** ********** Test: Test method testBasic(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** CollectRnaSeqMetrics -INPUT /tmp/tmp.collectRnaSeqMetrics.17128575048344869963.sam -OUTPUT /tmp/tmp.15686298593750038551.rna_metrics -REF_FLAT /tmp/tmp.13746189318763295770.refFlat -RIBOSOMAL_INTERVALS /tmp/tmp.rRna.8510014701233509649.interval_list -STRAND_SPECIFICITY SECOND_READ_TRANSCRIPTION_STRAND -IGNORE_SEQUENCE chrM ********** CollectRnaSeqMetrics -INPUT /tmp/tmp.collectRnaSeqMetrics.17128575048344869963.sam -OUTPUT /tmp/tmp.15686298593750038551.rna_metrics -REF_FLAT /tmp/tmp.13746189318763295770.refFlat -RIBOSOMAL_INTERVALS /tmp/tmp.rRna.8510014701233509649.interval_list -STRAND_SPECIFICITY SECOND_READ_TRANSCRIPTION_STRAND -IGNORE_SEQUENCE chrM Test: Test method testBasic(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** ********** Test: Test method testBasic(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: Test: Test method testBasic(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: Test: Test method testBasic(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: 11:52:11.876 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:11.876 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBasic(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: 11:52:11.879 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:11.879 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBasic(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: 11:52:11.879 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:11.879 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBasic(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: 11:52:11.879 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:11.879 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBasic(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: [Tue Jul 02 11:52:11 GMT+14:00 2024] CollectRnaSeqMetrics REF_FLAT=/tmp/tmp.13746189318763295770.refFlat RIBOSOMAL_INTERVALS=/tmp/tmp.rRna.8510014701233509649.interval_list STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND IGNORE_SEQUENCE=[chrM] INPUT=/tmp/tmp.collectRnaSeqMetrics.17128575048344869963.sam OUTPUT=/tmp/tmp.15686298593750038551.rna_metrics MINIMUM_LENGTH=500 RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:11 GMT+14:00 2024] CollectRnaSeqMetrics REF_FLAT=/tmp/tmp.13746189318763295770.refFlat RIBOSOMAL_INTERVALS=/tmp/tmp.rRna.8510014701233509649.interval_list STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND IGNORE_SEQUENCE=[chrM] INPUT=/tmp/tmp.collectRnaSeqMetrics.17128575048344869963.sam OUTPUT=/tmp/tmp.15686298593750038551.rna_metrics MINIMUM_LENGTH=500 RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBasic(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: [Tue Jul 02 11:52:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBasic(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:11 CollectRnaSeqMetrics Loaded 1 genes. INFO 2024-07-02 11:52:11 CollectRnaSeqMetrics Loaded 1 genes. Test: Test method testBasic(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: [Tue Jul 02 11:52:11 GMT+14:00 2024] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:11 GMT+14:00 2024] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.00 minutes. Test: Test method testBasic(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMultiLevel(picard.analysis.CollectRnaSeqMetricsTest) Test: Test method testMultiLevel(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:11 CollectRnaSeqMetrics Gradle suite > Gradle test > picard.analysis.CollectRnaSeqMetricsTest.testMultiLevel STANDARD_ERROR INFO 2024-07-02 11:52:11 CollectRnaSeqMetrics Test: Test method testMultiLevel(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: Test: Test method testMultiLevel(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMultiLevel(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultiLevel(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMultiLevel(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMultiLevel(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultiLevel(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMultiLevel(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultiLevel(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** CollectRnaSeqMetrics -INPUT /tmp/tmp.collectRnaSeqMetrics.3376452588585583628.sam -OUTPUT /tmp/tmp.690047288440409125.rna_metrics -REF_FLAT /tmp/tmp.2085056308632698243.refFlat -RIBOSOMAL_INTERVALS /tmp/tmp.rRna.18427732326260593582.interval_list -STRAND_SPECIFICITY SECOND_READ_TRANSCRIPTION_STRAND -IGNORE_SEQUENCE chrM -LEVEL null -LEVEL SAMPLE -LEVEL LIBRARY ********** CollectRnaSeqMetrics -INPUT /tmp/tmp.collectRnaSeqMetrics.3376452588585583628.sam -OUTPUT /tmp/tmp.690047288440409125.rna_metrics -REF_FLAT /tmp/tmp.2085056308632698243.refFlat -RIBOSOMAL_INTERVALS /tmp/tmp.rRna.18427732326260593582.interval_list -STRAND_SPECIFICITY SECOND_READ_TRANSCRIPTION_STRAND -IGNORE_SEQUENCE chrM -LEVEL null -LEVEL SAMPLE -LEVEL LIBRARY Test: Test method testMultiLevel(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** ********** Test: Test method testMultiLevel(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: Test: Test method testMultiLevel(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: Test: Test method testMultiLevel(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: 11:52:11.935 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:11.935 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultiLevel(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: 11:52:11.935 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:11.935 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultiLevel(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: 11:52:11.935 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:11.935 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultiLevel(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: 11:52:11.935 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:11.935 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultiLevel(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: [Tue Jul 02 11:52:11 GMT+14:00 2024] CollectRnaSeqMetrics REF_FLAT=/tmp/tmp.2085056308632698243.refFlat RIBOSOMAL_INTERVALS=/tmp/tmp.rRna.18427732326260593582.interval_list STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND IGNORE_SEQUENCE=[chrM] METRIC_ACCUMULATION_LEVEL=[LIBRARY, SAMPLE] INPUT=/tmp/tmp.collectRnaSeqMetrics.3376452588585583628.sam OUTPUT=/tmp/tmp.690047288440409125.rna_metrics MINIMUM_LENGTH=500 RRNA_FRAGMENT_PERCENTAGE=0.8 ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:11 GMT+14:00 2024] CollectRnaSeqMetrics REF_FLAT=/tmp/tmp.2085056308632698243.refFlat RIBOSOMAL_INTERVALS=/tmp/tmp.rRna.18427732326260593582.interval_list STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND IGNORE_SEQUENCE=[chrM] METRIC_ACCUMULATION_LEVEL=[LIBRARY, SAMPLE] INPUT=/tmp/tmp.collectRnaSeqMetrics.3376452588585583628.sam OUTPUT=/tmp/tmp.690047288440409125.rna_metrics MINIMUM_LENGTH=500 RRNA_FRAGMENT_PERCENTAGE=0.8 ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMultiLevel(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: [Tue Jul 02 11:52:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMultiLevel(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:11 CollectRnaSeqMetrics Loaded 1 genes. INFO 2024-07-02 11:52:11 CollectRnaSeqMetrics Loaded 1 genes. Test: Test method testMultiLevel(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: [Tue Jul 02 11:52:11 GMT+14:00 2024] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:11 GMT+14:00 2024] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.00 minutes. Test: Test method testMultiLevel(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testNoIntevalsNoFragPercentage[0](null)(picard.analysis.CollectRnaSeqMetricsTest) Test: Test method testNoIntevalsNoFragPercentage[0](null)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:11 CollectRnaSeqMetrics Gradle suite > Gradle test > picard.analysis.CollectRnaSeqMetricsTest.testNoIntevalsNoFragPercentage[0](null) STANDARD_ERROR INFO 2024-07-02 11:52:11 CollectRnaSeqMetrics Test: Test method testNoIntevalsNoFragPercentage[0](null)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: Test: Test method testNoIntevalsNoFragPercentage[0](null)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testNoIntevalsNoFragPercentage[0](null)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** ********** Test: Test method testNoIntevalsNoFragPercentage[0](null)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testNoIntevalsNoFragPercentage[0](null)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testNoIntevalsNoFragPercentage[0](null)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** ********** Test: Test method testNoIntevalsNoFragPercentage[0](null)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testNoIntevalsNoFragPercentage[0](null)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** ********** Test: Test method testNoIntevalsNoFragPercentage[0](null)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** CollectRnaSeqMetrics -INPUT /tmp/tmp.collectRnaSeqMetrics.4747220463020711802.sam -OUTPUT /tmp/tmp.3002662860241938783.rna_metrics -REF_FLAT /tmp/tmp.18095828976519756467.refFlat -RIBOSOMAL_INTERVALS null -RRNA_FRAGMENT_PERCENTAGE 0.0 -STRAND_SPECIFICITY SECOND_READ_TRANSCRIPTION_STRAND -IGNORE_SEQUENCE chrM ********** CollectRnaSeqMetrics -INPUT /tmp/tmp.collectRnaSeqMetrics.4747220463020711802.sam -OUTPUT /tmp/tmp.3002662860241938783.rna_metrics -REF_FLAT /tmp/tmp.18095828976519756467.refFlat -RIBOSOMAL_INTERVALS null -RRNA_FRAGMENT_PERCENTAGE 0.0 -STRAND_SPECIFICITY SECOND_READ_TRANSCRIPTION_STRAND -IGNORE_SEQUENCE chrM Test: Test method testNoIntevalsNoFragPercentage[0](null)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** ********** Test: Test method testNoIntevalsNoFragPercentage[0](null)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: Test: Test method testNoIntevalsNoFragPercentage[0](null)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: Running Test: Test method testNoIntevalsNoFragPercentage[1](/tmp/tmp.rRna.11253554102397696672.interval_list)(picard.analysis.CollectRnaSeqMetricsTest) Test: Test method testNoIntevalsNoFragPercentage[1](/tmp/tmp.rRna.11253554102397696672.interval_list)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:12 CollectRnaSeqMetrics Gradle suite > Gradle test > picard.analysis.CollectRnaSeqMetricsTest.testNoIntevalsNoFragPercentage[1](/tmp/tmp.rRna.11253554102397696672.interval_list) STANDARD_ERROR INFO 2024-07-02 11:52:12 CollectRnaSeqMetrics Test: Test method testNoIntevalsNoFragPercentage[1](/tmp/tmp.rRna.11253554102397696672.interval_list)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: Test: Test method testNoIntevalsNoFragPercentage[1](/tmp/tmp.rRna.11253554102397696672.interval_list)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testNoIntevalsNoFragPercentage[1](/tmp/tmp.rRna.11253554102397696672.interval_list)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** ********** Test: Test method testNoIntevalsNoFragPercentage[1](/tmp/tmp.rRna.11253554102397696672.interval_list)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testNoIntevalsNoFragPercentage[1](/tmp/tmp.rRna.11253554102397696672.interval_list)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testNoIntevalsNoFragPercentage[1](/tmp/tmp.rRna.11253554102397696672.interval_list)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** ********** Test: Test method testNoIntevalsNoFragPercentage[1](/tmp/tmp.rRna.11253554102397696672.interval_list)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testNoIntevalsNoFragPercentage[1](/tmp/tmp.rRna.11253554102397696672.interval_list)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** ********** Test: Test method testNoIntevalsNoFragPercentage[1](/tmp/tmp.rRna.11253554102397696672.interval_list)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** CollectRnaSeqMetrics -INPUT /tmp/tmp.collectRnaSeqMetrics.10596973719496525101.sam -OUTPUT /tmp/tmp.9786122273918495788.rna_metrics -REF_FLAT /tmp/tmp.2509428514586937157.refFlat -RIBOSOMAL_INTERVALS /tmp/tmp.rRna.11253554102397696672.interval_list -RRNA_FRAGMENT_PERCENTAGE 0.0 -STRAND_SPECIFICITY SECOND_READ_TRANSCRIPTION_STRAND -IGNORE_SEQUENCE chrM ********** CollectRnaSeqMetrics -INPUT /tmp/tmp.collectRnaSeqMetrics.10596973719496525101.sam -OUTPUT /tmp/tmp.9786122273918495788.rna_metrics -REF_FLAT /tmp/tmp.2509428514586937157.refFlat -RIBOSOMAL_INTERVALS /tmp/tmp.rRna.11253554102397696672.interval_list -RRNA_FRAGMENT_PERCENTAGE 0.0 -STRAND_SPECIFICITY SECOND_READ_TRANSCRIPTION_STRAND -IGNORE_SEQUENCE chrM Test: Test method testNoIntevalsNoFragPercentage[1](/tmp/tmp.rRna.11253554102397696672.interval_list)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** ********** Test: Test method testNoIntevalsNoFragPercentage[1](/tmp/tmp.rRna.11253554102397696672.interval_list)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: Test: Test method testNoIntevalsNoFragPercentage[1](/tmp/tmp.rRna.11253554102397696672.interval_list)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: Test: Test method testNoIntevalsNoFragPercentage[1](/tmp/tmp.rRna.11253554102397696672.interval_list)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: 11:52:12.027 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:12.027 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoIntevalsNoFragPercentage[1](/tmp/tmp.rRna.11253554102397696672.interval_list)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: 11:52:12.027 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:12.027 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoIntevalsNoFragPercentage[1](/tmp/tmp.rRna.11253554102397696672.interval_list)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: 11:52:12.027 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:12.027 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoIntevalsNoFragPercentage[1](/tmp/tmp.rRna.11253554102397696672.interval_list)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: 11:52:12.027 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:12.027 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoIntevalsNoFragPercentage[1](/tmp/tmp.rRna.11253554102397696672.interval_list)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: [Tue Jul 02 11:52:12 GMT+14:00 2024] CollectRnaSeqMetrics REF_FLAT=/tmp/tmp.2509428514586937157.refFlat RIBOSOMAL_INTERVALS=/tmp/tmp.rRna.11253554102397696672.interval_list STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND IGNORE_SEQUENCE=[chrM] RRNA_FRAGMENT_PERCENTAGE=0.0 INPUT=/tmp/tmp.collectRnaSeqMetrics.10596973719496525101.sam OUTPUT=/tmp/tmp.9786122273918495788.rna_metrics MINIMUM_LENGTH=500 METRIC_ACCUMULATION_LEVEL=[ALL_READS] ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:12 GMT+14:00 2024] CollectRnaSeqMetrics REF_FLAT=/tmp/tmp.2509428514586937157.refFlat RIBOSOMAL_INTERVALS=/tmp/tmp.rRna.11253554102397696672.interval_list STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND IGNORE_SEQUENCE=[chrM] RRNA_FRAGMENT_PERCENTAGE=0.0 INPUT=/tmp/tmp.collectRnaSeqMetrics.10596973719496525101.sam OUTPUT=/tmp/tmp.9786122273918495788.rna_metrics MINIMUM_LENGTH=500 METRIC_ACCUMULATION_LEVEL=[ALL_READS] ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testNoIntevalsNoFragPercentage[1](/tmp/tmp.rRna.11253554102397696672.interval_list)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: [Tue Jul 02 11:52:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testNoIntevalsNoFragPercentage[1](/tmp/tmp.rRna.11253554102397696672.interval_list)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:12 CollectRnaSeqMetrics Loaded 1 genes. INFO 2024-07-02 11:52:12 CollectRnaSeqMetrics Loaded 1 genes. Test: Test method testNoIntevalsNoFragPercentage[1](/tmp/tmp.rRna.11253554102397696672.interval_list)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: WARNING 2024-07-02 11:52:12 CollectRnaSeqMetrics The RIBOSOMAL_INTERVALS file, /tmp/tmp.rRna.11253554102397696672.interval_list does not contain intervals WARNING 2024-07-02 11:52:12 CollectRnaSeqMetrics The RIBOSOMAL_INTERVALS file, /tmp/tmp.rRna.11253554102397696672.interval_list does not contain intervals Test: Test method testNoIntevalsNoFragPercentage[1](/tmp/tmp.rRna.11253554102397696672.interval_list)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: [Tue Jul 02 11:52:12 GMT+14:00 2024] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:12 GMT+14:00 2024] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.00 minutes. Test: Test method testNoIntevalsNoFragPercentage[1](/tmp/tmp.rRna.11253554102397696672.interval_list)(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testPctRibosomalBases(picard.analysis.CollectRnaSeqMetricsTest) Test: Test method testPctRibosomalBases(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:12 CollectRnaSeqMetrics Gradle suite > Gradle test > picard.analysis.CollectRnaSeqMetricsTest.testPctRibosomalBases STANDARD_ERROR INFO 2024-07-02 11:52:12 CollectRnaSeqMetrics Test: Test method testPctRibosomalBases(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: Test: Test method testPctRibosomalBases(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPctRibosomalBases(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** ********** Test: Test method testPctRibosomalBases(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPctRibosomalBases(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPctRibosomalBases(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** ********** Test: Test method testPctRibosomalBases(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPctRibosomalBases(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** ********** Test: Test method testPctRibosomalBases(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** CollectRnaSeqMetrics -INPUT /tmp/tmp.collectRnaSeqMetrics.15563011032766752408.sam -OUTPUT /tmp/tmp.2090245734338553135.rna_metrics -REF_FLAT /tmp/tmp.16429377036883652559.refFlat -RIBOSOMAL_INTERVALS /tmp/tmp.rRna.6897360968510362116.interval_list -STRAND_SPECIFICITY SECOND_READ_TRANSCRIPTION_STRAND -IGNORE_SEQUENCE chrM ********** CollectRnaSeqMetrics -INPUT /tmp/tmp.collectRnaSeqMetrics.15563011032766752408.sam -OUTPUT /tmp/tmp.2090245734338553135.rna_metrics -REF_FLAT /tmp/tmp.16429377036883652559.refFlat -RIBOSOMAL_INTERVALS /tmp/tmp.rRna.6897360968510362116.interval_list -STRAND_SPECIFICITY SECOND_READ_TRANSCRIPTION_STRAND -IGNORE_SEQUENCE chrM Test: Test method testPctRibosomalBases(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** ********** Test: Test method testPctRibosomalBases(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: Test: Test method testPctRibosomalBases(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: Test: Test method testPctRibosomalBases(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: 11:52:12.096 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:12.096 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPctRibosomalBases(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: 11:52:12.096 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:12.096 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPctRibosomalBases(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: 11:52:12.097 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:12.097 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPctRibosomalBases(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: 11:52:12.097 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:12.097 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPctRibosomalBases(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: [Tue Jul 02 11:52:12 GMT+14:00 2024] CollectRnaSeqMetrics REF_FLAT=/tmp/tmp.16429377036883652559.refFlat RIBOSOMAL_INTERVALS=/tmp/tmp.rRna.6897360968510362116.interval_list STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND IGNORE_SEQUENCE=[chrM] INPUT=/tmp/tmp.collectRnaSeqMetrics.15563011032766752408.sam OUTPUT=/tmp/tmp.2090245734338553135.rna_metrics MINIMUM_LENGTH=500 RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:12 GMT+14:00 2024] CollectRnaSeqMetrics REF_FLAT=/tmp/tmp.16429377036883652559.refFlat RIBOSOMAL_INTERVALS=/tmp/tmp.rRna.6897360968510362116.interval_list STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND IGNORE_SEQUENCE=[chrM] INPUT=/tmp/tmp.collectRnaSeqMetrics.15563011032766752408.sam OUTPUT=/tmp/tmp.2090245734338553135.rna_metrics MINIMUM_LENGTH=500 RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPctRibosomalBases(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: [Tue Jul 02 11:52:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPctRibosomalBases(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:12 CollectRnaSeqMetrics Loaded 1 genes. INFO 2024-07-02 11:52:12 CollectRnaSeqMetrics Loaded 1 genes. Test: Test method testPctRibosomalBases(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: [Tue Jul 02 11:52:12 GMT+14:00 2024] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:12 GMT+14:00 2024] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.00 minutes. Test: Test method testPctRibosomalBases(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testTranscriptionStrandMetrics(picard.analysis.CollectRnaSeqMetricsTest) Test: Test method testTranscriptionStrandMetrics(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:12 CollectRnaSeqMetrics Gradle suite > Gradle test > picard.analysis.CollectRnaSeqMetricsTest.testTranscriptionStrandMetrics STANDARD_ERROR INFO 2024-07-02 11:52:12 CollectRnaSeqMetrics Test: Test method testTranscriptionStrandMetrics(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: Test: Test method testTranscriptionStrandMetrics(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTranscriptionStrandMetrics(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** ********** Test: Test method testTranscriptionStrandMetrics(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTranscriptionStrandMetrics(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTranscriptionStrandMetrics(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** ********** Test: Test method testTranscriptionStrandMetrics(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTranscriptionStrandMetrics(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** ********** Test: Test method testTranscriptionStrandMetrics(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** CollectRnaSeqMetrics -INPUT /tmp/tmp.collectRnaSeqMetrics.8437180412163123180.sam -OUTPUT /tmp/tmp.9703000328047031742.rna_metrics -REF_FLAT /tmp/tmp.15535048962376104275.refFlat -RIBOSOMAL_INTERVALS /tmp/tmp.rRna.5321454772421923599.interval_list -STRAND_SPECIFICITY SECOND_READ_TRANSCRIPTION_STRAND -IGNORE_SEQUENCE chrM ********** CollectRnaSeqMetrics -INPUT /tmp/tmp.collectRnaSeqMetrics.8437180412163123180.sam -OUTPUT /tmp/tmp.9703000328047031742.rna_metrics -REF_FLAT /tmp/tmp.15535048962376104275.refFlat -RIBOSOMAL_INTERVALS /tmp/tmp.rRna.5321454772421923599.interval_list -STRAND_SPECIFICITY SECOND_READ_TRANSCRIPTION_STRAND -IGNORE_SEQUENCE chrM Test: Test method testTranscriptionStrandMetrics(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: ********** ********** Test: Test method testTranscriptionStrandMetrics(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: Test: Test method testTranscriptionStrandMetrics(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: Test: Test method testTranscriptionStrandMetrics(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: 11:52:12.135 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:12.135 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTranscriptionStrandMetrics(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: 11:52:12.136 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:12.136 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTranscriptionStrandMetrics(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: 11:52:12.136 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:12.136 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTranscriptionStrandMetrics(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: 11:52:12.136 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:12.136 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTranscriptionStrandMetrics(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: [Tue Jul 02 11:52:12 GMT+14:00 2024] CollectRnaSeqMetrics REF_FLAT=/tmp/tmp.15535048962376104275.refFlat RIBOSOMAL_INTERVALS=/tmp/tmp.rRna.5321454772421923599.interval_list STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND IGNORE_SEQUENCE=[chrM] INPUT=/tmp/tmp.collectRnaSeqMetrics.8437180412163123180.sam OUTPUT=/tmp/tmp.9703000328047031742.rna_metrics MINIMUM_LENGTH=500 RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:12 GMT+14:00 2024] CollectRnaSeqMetrics REF_FLAT=/tmp/tmp.15535048962376104275.refFlat RIBOSOMAL_INTERVALS=/tmp/tmp.rRna.5321454772421923599.interval_list STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND IGNORE_SEQUENCE=[chrM] INPUT=/tmp/tmp.collectRnaSeqMetrics.8437180412163123180.sam OUTPUT=/tmp/tmp.9703000328047031742.rna_metrics MINIMUM_LENGTH=500 RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTranscriptionStrandMetrics(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: [Tue Jul 02 11:52:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTranscriptionStrandMetrics(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:12 CollectRnaSeqMetrics Loaded 1 genes. INFO 2024-07-02 11:52:12 CollectRnaSeqMetrics Loaded 1 genes. Test: Test method testTranscriptionStrandMetrics(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: [Tue Jul 02 11:52:12 GMT+14:00 2024] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:12 GMT+14:00 2024] picard.analysis.CollectRnaSeqMetrics done. Elapsed time: 0.00 minutes. Test: Test method testTranscriptionStrandMetrics(picard.analysis.CollectRnaSeqMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method chrMReads(picard.metrics.CollectRrbsMetricsTest) Test: Test method chrMReads(picard.metrics.CollectRrbsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:12 CollectRrbsMetrics Gradle suite > Gradle test > picard.metrics.CollectRrbsMetricsTest.chrMReads STANDARD_ERROR INFO 2024-07-02 11:52:12 CollectRrbsMetrics Test: Test method chrMReads(picard.metrics.CollectRrbsMetricsTest) produced standard out/err: Test: Test method chrMReads(picard.metrics.CollectRrbsMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method chrMReads(picard.metrics.CollectRrbsMetricsTest) produced standard out/err: ********** ********** Test: Test method chrMReads(picard.metrics.CollectRrbsMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method chrMReads(picard.metrics.CollectRrbsMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method chrMReads(picard.metrics.CollectRrbsMetricsTest) produced standard out/err: ********** ********** Test: Test method chrMReads(picard.metrics.CollectRrbsMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method chrMReads(picard.metrics.CollectRrbsMetricsTest) produced standard out/err: ********** ********** Test: Test method chrMReads(picard.metrics.CollectRrbsMetricsTest) produced standard out/err: ********** CollectRrbsMetrics -INPUT testdata/picard/metrics/chrMReads.sam -METRICS_FILE_PREFIX /tmp/crmt.9643470798104966401.tmp/READ_TEST -REFERENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta ********** CollectRrbsMetrics -INPUT testdata/picard/metrics/chrMReads.sam -METRICS_FILE_PREFIX /tmp/crmt.9643470798104966401.tmp/READ_TEST -REFERENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta Test: Test method chrMReads(picard.metrics.CollectRrbsMetricsTest) produced standard out/err: ********** ********** Test: Test method chrMReads(picard.metrics.CollectRrbsMetricsTest) produced standard out/err: Test: Test method chrMReads(picard.metrics.CollectRrbsMetricsTest) produced standard out/err: Test: Test method chrMReads(picard.metrics.CollectRrbsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:12 RExecutor Executing R script via command: Rscript /tmp/script13386135264496793539.R INFO 2024-07-02 11:52:12 RExecutor Executing R script via command: Rscript /tmp/script13386135264496793539.R Test: Test method chrMReads(picard.metrics.CollectRrbsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:12 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:52:12 ProcessExecutor [1] "Checking if R is installed" Test: Test method chrMReads(picard.metrics.CollectRrbsMetricsTest) produced standard out/err: 11:52:12.615 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:12.615 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method chrMReads(picard.metrics.CollectRrbsMetricsTest) produced standard out/err: 11:52:12.615 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:12.615 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method chrMReads(picard.metrics.CollectRrbsMetricsTest) produced standard out/err: 11:52:12.615 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:12.615 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method chrMReads(picard.metrics.CollectRrbsMetricsTest) produced standard out/err: 11:52:12.615 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:12.615 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method chrMReads(picard.metrics.CollectRrbsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:12 GMT+14:00 2024] CollectRrbsMetrics INPUT=testdata/picard/metrics/chrMReads.sam METRICS_FILE_PREFIX=/tmp/crmt.9643470798104966401.tmp/READ_TEST REFERENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_READ_LENGTH=5 C_QUALITY_THRESHOLD=20 NEXT_BASE_QUALITY_THRESHOLD=10 MAX_MISMATCH_RATE=0.1 ASSUME_SORTED=false METRIC_ACCUMULATION_LEVEL=[ALL_READS] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:12 GMT+14:00 2024] CollectRrbsMetrics INPUT=testdata/picard/metrics/chrMReads.sam METRICS_FILE_PREFIX=/tmp/crmt.9643470798104966401.tmp/READ_TEST REFERENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_READ_LENGTH=5 C_QUALITY_THRESHOLD=20 NEXT_BASE_QUALITY_THRESHOLD=10 MAX_MISMATCH_RATE=0.1 ASSUME_SORTED=false METRIC_ACCUMULATION_LEVEL=[ALL_READS] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method chrMReads(picard.metrics.CollectRrbsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method chrMReads(picard.metrics.CollectRrbsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:12 RExecutor Executing R script via command: Rscript /tmp/script2096131958572446888.R /tmp/crmt.9643470798104966401.tmp/READ_TEST.rrbs_detail_metrics /tmp/crmt.9643470798104966401.tmp/READ_TEST.rrbs_summary_metrics /tmp/crmt.9643470798104966401.tmp/READ_TEST.rrbs_qc.pdf INFO 2024-07-02 11:52:12 RExecutor Executing R script via command: Rscript /tmp/script2096131958572446888.R /tmp/crmt.9643470798104966401.tmp/READ_TEST.rrbs_detail_metrics /tmp/crmt.9643470798104966401.tmp/READ_TEST.rrbs_summary_metrics /tmp/crmt.9643470798104966401.tmp/READ_TEST.rrbs_qc.pdf Test: Test method chrMReads(picard.metrics.CollectRrbsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 ProcessExecutor null device INFO 2024-07-02 11:52:13 ProcessExecutor null device Test: Test method chrMReads(picard.metrics.CollectRrbsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 ProcessExecutor 1 INFO 2024-07-02 11:52:13 ProcessExecutor 1 Test: Test method chrMReads(picard.metrics.CollectRrbsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.analysis.CollectRrbsMetrics done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.analysis.CollectRrbsMetrics done. Elapsed time: 0.01 minutes. Test: Test method chrMReads(picard.metrics.CollectRrbsMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method parseDirectiveBad[0](ERROR:)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveBad[1](ERRORS:READ_ORDINALITY)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveBad[2](ERROR;REFERENCE_BASE)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveBad[3](ERROR:what)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[0](ERROR, error_by_all)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[1](ERROR:ALL, error_by_all)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[2](ERROR:GC_CONTENT, error_by_gc)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[3](ERROR:READ_ORDINALITY, error_by_read_ordinality)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[4](ERROR:READ_BASE, error_by_read_base)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[5](ERROR:REFERENCE_BASE, error_by_ref_base)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[6](ERROR:PRE_DINUC, error_by_pre_dinuc)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[7](ERROR:POST_DINUC, error_by_post_dinuc)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[8](ERROR:HOMOPOLYMER_LENGTH, error_by_homopolymer_length)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[9](ERROR:HOMOPOLYMER, error_by_homopolymer_and_following_ref_base)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[10](ERROR:BINNED_HOMOPOLYMER, error_by_binned_length_homopolymer_and_following_ref_base)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[11](ERROR:FLOWCELL_TILE, error_by_tile)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[12](ERROR:READ_DIRECTION, error_by_read_direction)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[13](ERROR:CYCLE, error_by_cycle)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[14](ERROR:BINNED_CYCLE, error_by_binned_cycle)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[15](ERROR:INSERT_LENGTH, error_by_insert_length)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[16](ERROR:BASE_QUALITY, error_by_base_quality)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[17](ERROR:MAPPING_QUALITY, error_by_mapping_quality)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[18](ERROR:READ_GROUP, error_by_read_group)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[19](ERROR:MISMATCHES_IN_READ, error_by_mismatches_in_read)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[20](ERROR:ONE_BASE_PADDED_CONTEXT, error_by_one_base_padded_context)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[21](ERROR:TWO_BASE_PADDED_CONTEXT, error_by_two_base_padded_context)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[22](ERROR:CONSENSUS, error_by_consensus)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[23](ERROR:NS_IN_READ, error_by_ns_in_read)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[24](ERROR:POST_DINUC:BASE_QUALITY, error_by_post_dinuc_and_base_quality)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[25](ERROR:POST_DINUC:BASE_QUALITY:GC_CONTENT, error_by_post_dinuc_and_base_quality_and_gc)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[26]( ERROR : POST_DINUC : BASE_QUALITY : GC_CONTENT , error_by_post_dinuc_and_base_quality_and_gc)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[27](OVERLAPPING_ERROR, overlapping_error_by_all)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[28](OVERLAPPING_ERROR:ALL, overlapping_error_by_all)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[29](OVERLAPPING_ERROR:GC_CONTENT, overlapping_error_by_gc)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[30](OVERLAPPING_ERROR:READ_ORDINALITY, overlapping_error_by_read_ordinality)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[31](OVERLAPPING_ERROR:READ_BASE, overlapping_error_by_read_base)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[32](OVERLAPPING_ERROR:REFERENCE_BASE, overlapping_error_by_ref_base)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[33](OVERLAPPING_ERROR:PRE_DINUC, overlapping_error_by_pre_dinuc)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[34](OVERLAPPING_ERROR:POST_DINUC, overlapping_error_by_post_dinuc)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[35](OVERLAPPING_ERROR:HOMOPOLYMER_LENGTH, overlapping_error_by_homopolymer_length)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[36](OVERLAPPING_ERROR:HOMOPOLYMER, overlapping_error_by_homopolymer_and_following_ref_base)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[37](OVERLAPPING_ERROR:FLOWCELL_TILE, overlapping_error_by_tile)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[38](OVERLAPPING_ERROR:READ_DIRECTION, overlapping_error_by_read_direction)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[39](OVERLAPPING_ERROR:CYCLE, overlapping_error_by_cycle)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[40](OVERLAPPING_ERROR:INSERT_LENGTH, overlapping_error_by_insert_length)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method parseDirectiveGood[41](OVERLAPPING_ERROR:BASE_QUALITY, overlapping_error_by_base_quality)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testAggregatorsHaveDistinctSuffixes(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testHasDeletionBeenProcessed[0](1D, [false])(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testHasDeletionBeenProcessed[1](2D, [false, true])(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testHasDeletionBeenProcessed[2](1D1D, [false, true])(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testHasDeletionBeenProcessed[3](1D1M1D, [false, false])(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testHasDeletionBeenProcessed[4](2D1M1D, [false, true, false])(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testHasDeletionBeenProcessed[5](3M2D8M1D, [false, true, false])(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels13074618958103177283.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels13074618958103177283.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.394 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.394 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.394 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.394 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.394 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.394 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.394 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.394 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels13074618958103177283.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels13074618958103177283.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 100 loci, Processed 100 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 100 loci, Processed 100 loci, Skipped 0 loci. Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[0]([Ljava.lang.String;@6f01ea69, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels5956097517224483206.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels5956097517224483206.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.444 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.444 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.444 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.444 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.449 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.449 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.449 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.449 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels5956097517224483206.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels5956097517224483206.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 100 loci, Processed 100 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 100 loci, Processed 100 loci, Skipped 0 loci. Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[1]([Ljava.lang.String;@545ba9da, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels16314107248269076678.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels16314107248269076678.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.475 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.475 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.475 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.475 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.475 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.475 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.475 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.475 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels16314107248269076678.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels16314107248269076678.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 101 loci, Processed 101 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 101 loci, Processed 101 loci, Skipped 0 loci. Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[2]([Ljava.lang.String;@6580b426, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels10481245369671895070.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels10481245369671895070.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.505 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.505 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.505 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.505 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.505 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.505 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.505 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.505 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels10481245369671895070.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels10481245369671895070.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 100 loci, Processed 100 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 100 loci, Processed 100 loci, Skipped 0 loci. Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[3]([Ljava.lang.String;@16b13a88, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels3464519752872992682.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels3464519752872992682.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.531 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.531 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.531 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.531 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.531 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.531 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.531 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.531 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels3464519752872992682.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels3464519752872992682.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 102 loci, Processed 102 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 102 loci, Processed 102 loci, Skipped 0 loci. Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[4]([Ljava.lang.String;@529035b2, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels8833910749656495816.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels8833910749656495816.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.564 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.564 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.564 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.564 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.564 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.564 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.564 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.564 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels8833910749656495816.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels8833910749656495816.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 102 loci, Processed 102 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 102 loci, Processed 102 loci, Skipped 0 loci. Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[5]([Ljava.lang.String;@1ce386a3, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels39482913398466547.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels39482913398466547.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.580 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.580 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.580 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.580 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.581 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.581 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.581 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.581 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels39482913398466547.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels39482913398466547.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 101 loci, Processed 101 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 101 loci, Processed 101 loci, Skipped 0 loci. Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[6]([Ljava.lang.String;@5c3f93a3, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels13520410613999200742.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels13520410613999200742.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.597 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.597 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.598 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.598 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.598 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.598 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.598 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.598 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels13520410613999200742.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels13520410613999200742.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 101 loci, Processed 101 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 101 loci, Processed 101 loci, Skipped 0 loci. Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[7]([Ljava.lang.String;@38ab30a8, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels12509858218536338821.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels12509858218536338821.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.614 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.614 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.614 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.614 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.614 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.614 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.614 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.614 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels12509858218536338821.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels12509858218536338821.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 101 loci, Processed 101 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 101 loci, Processed 101 loci, Skipped 0 loci. Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[8]([Ljava.lang.String;@5ad1ebcd, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels11999399298096351976.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels11999399298096351976.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.628 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.628 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.628 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.628 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.628 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.628 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.628 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.628 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels11999399298096351976.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels11999399298096351976.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 106 loci, Processed 106 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 106 loci, Processed 106 loci, Skipped 0 loci. Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[9]([Ljava.lang.String;@3e73afdf, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels289920038534303957.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels289920038534303957.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.644 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.644 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.644 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.644 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.644 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.644 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.644 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.644 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels289920038534303957.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels289920038534303957.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 106 loci, Processed 106 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 106 loci, Processed 106 loci, Skipped 0 loci. Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[10]([Ljava.lang.String;@3faf8bec, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels5438496122654830841.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels5438496122654830841.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.663 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.663 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.663 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.663 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.663 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.663 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.663 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.663 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels5438496122654830841.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels5438496122654830841.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 61 loci, Processed 61 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 61 loci, Processed 61 loci, Skipped 0 loci. Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[11]([Ljava.lang.String;@3624ce8b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels807552892091277979.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels807552892091277979.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.679 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.679 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.679 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.679 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.679 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.679 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.679 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.679 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels807552892091277979.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels807552892091277979.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 42 loci, Processed 42 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 42 loci, Processed 42 loci, Skipped 0 loci. Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[12]([Ljava.lang.String;@50223fdc, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels8391814433501953253.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels8391814433501953253.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.697 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.697 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.698 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.698 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.698 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.698 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.698 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.698 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels8391814433501953253.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels8391814433501953253.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 42 loci, Processed 42 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 42 loci, Processed 42 loci, Skipped 0 loci. Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[13]([Ljava.lang.String;@2e11c251, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels17177315446684416161.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels17177315446684416161.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.714 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.714 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.714 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.714 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.715 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.715 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.715 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.715 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels17177315446684416161.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels17177315446684416161.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 23 loci, Processed 23 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 23 loci, Processed 23 loci, Skipped 0 loci. Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[14]([Ljava.lang.String;@7b9ab5b6, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels8132192024554900440.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels8132192024554900440.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.732 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.732 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.732 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.732 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.732 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.732 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.732 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.732 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels8132192024554900440.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels8132192024554900440.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 22 loci, Processed 22 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 22 loci, Processed 22 loci, Skipped 0 loci. Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[15]([Ljava.lang.String;@ef7065e, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels1512172804916279366.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels1512172804916279366.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.748 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.748 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.748 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.748 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.748 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.748 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.748 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.748 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels1512172804916279366.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels1512172804916279366.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 22 loci, Processed 22 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 22 loci, Processed 22 loci, Skipped 0 loci. Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[16]([Ljava.lang.String;@4c93325a, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels17206518930662871998.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels17206518930662871998.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.767 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.767 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.767 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.767 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.767 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.767 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.768 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.768 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels17206518930662871998.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels17206518930662871998.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 22 loci, Processed 22 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 22 loci, Processed 22 loci, Skipped 0 loci. Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[17]([Ljava.lang.String;@58c31e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels6279053169956741798.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels6279053169956741798.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.785 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.785 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.785 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.785 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.785 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.785 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.785 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.785 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels6279053169956741798.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels6279053169956741798.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 100 loci, Processed 100 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 100 loci, Processed 100 loci, Skipped 0 loci. Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[18]([Ljava.lang.String;@12cb14fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels4444280195808675950.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels4444280195808675950.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.801 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.801 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.801 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.801 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.802 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.802 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.802 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.802 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels4444280195808675950.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels4444280195808675950.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 100 loci, Processed 100 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 100 loci, Processed 100 loci, Skipped 0 loci. Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[19]([Ljava.lang.String;@3825b648, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels13912155350653196149.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels13912155350653196149.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.818 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.818 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.818 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.818 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.818 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.818 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.819 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.819 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels13912155350653196149.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels13912155350653196149.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 60 loci, Processed 60 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 60 loci, Processed 60 loci, Skipped 0 loci. Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[20]([Ljava.lang.String;@484aefc0, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels2696077036924671971.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels2696077036924671971.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.834 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.834 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.834 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.834 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.834 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.834 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.834 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.834 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels2696077036924671971.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels2696077036924671971.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 11 loci, Processed 11 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 11 loci, Processed 11 loci, Skipped 0 loci. Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[21]([Ljava.lang.String;@5800d928, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels3043521138206842323.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels3043521138206842323.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.848 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.848 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.849 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.849 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.849 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.849 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.849 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.849 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels3043521138206842323.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels3043521138206842323.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 10 loci, Processed 10 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 10 loci, Processed 10 loci, Skipped 0 loci. Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[22]([Ljava.lang.String;@37b28c3c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels10427903030427525417.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels10427903030427525417.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.865 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.865 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.865 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.865 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.866 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.866 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.866 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.866 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels10427903030427525417.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels10427903030427525417.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 101 loci, Processed 101 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 101 loci, Processed 101 loci, Skipped 0 loci. Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[23]([Ljava.lang.String;@57bb59c2, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels11135799270270214141.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels11135799270270214141.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.883 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.883 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.883 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.883 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.883 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.883 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.883 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.883 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels11135799270270214141.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels11135799270270214141.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 102 loci, Processed 102 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 102 loci, Processed 102 loci, Skipped 0 loci. Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[24]([Ljava.lang.String;@5a9ce616, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels13877235786308203194.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels13877235786308203194.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.902 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.902 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.902 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.902 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.903 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.903 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.903 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.903 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels13877235786308203194.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels13877235786308203194.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 64 loci, Processed 64 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 64 loci, Processed 64 loci, Skipped 0 loci. Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[25]([Ljava.lang.String;@278bca68, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels4486027396447617204.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels4486027396447617204.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.919 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.919 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.920 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.920 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.920 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.920 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.920 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.920 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels4486027396447617204.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels4486027396447617204.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 11 loci, Processed 11 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 11 loci, Processed 11 loci, Skipped 0 loci. Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[26]([Ljava.lang.String;@7b12e602, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels4448963683980973550.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels4448963683980973550.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.935 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.935 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.936 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.936 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.936 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.936 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.936 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.936 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels4448963683980973550.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels4448963683980973550.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 11 loci, Processed 11 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 11 loci, Processed 11 loci, Skipped 0 loci. Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[27]([Ljava.lang.String;@61bca28c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels7806983350941380023.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels7806983350941380023.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.950 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.950 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.950 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.950 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.951 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.951 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.951 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.951 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels7806983350941380023.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels7806983350941380023.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 63 loci, Processed 63 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 63 loci, Processed 63 loci, Skipped 0 loci. Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[28]([Ljava.lang.String;@4ec7ec7a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels2818128472408810962.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels2818128472408810962.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.966 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.966 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.966 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.966 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.966 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.966 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.966 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.966 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels2818128472408810962.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels2818128472408810962.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 63 loci, Processed 63 loci, Skipped 0 loci. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Examined 63 loci, Processed 63 loci, Skipped 0 loci. Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:13 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[29]([Ljava.lang.String;@e4083e4, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 ) STANDARD_ERROR INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels11073728837228570145.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels11073728837228570145.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.982 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.982 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.982 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.982 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.983 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:13.983 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:13.983 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:13.983 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels11073728837228570145.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:13 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels11073728837228570145.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:13 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Examined 23 loci, Processed 23 loci, Skipped 0 loci. INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Examined 23 loci, Processed 23 loci, Skipped 0 loci. Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:14 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:14 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[30]([Ljava.lang.String;@2d5c369a, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 ) STANDARD_ERROR INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels10385007793340477317.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels10385007793340477317.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:14.139 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:14.139 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:14.139 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:14.139 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:14.139 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:14.139 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:14.139 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:14.139 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:14 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels10385007793340477317.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:14 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels10385007793340477317.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Examined 22 loci, Processed 22 loci, Skipped 0 loci. INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Examined 22 loci, Processed 22 loci, Skipped 0 loci. Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:14 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:14 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[31]([Ljava.lang.String;@20e0abe1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 ) STANDARD_ERROR INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels6557113812701271578.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels6557113812701271578.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:14.156 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:14.156 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:14.156 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:14.156 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:14.157 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:14.157 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:14.157 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:14.157 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:14 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels6557113812701271578.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:14 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels6557113812701271578.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Examined 4 loci, Processed 4 loci, Skipped 0 loci. INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Examined 4 loci, Processed 4 loci, Skipped 0 loci. Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:14 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:14 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[32]([Ljava.lang.String;@1761173c, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 ) STANDARD_ERROR INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT /tmp/Indels1973904790315724520.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT /tmp/Indels1973904790315724520.bam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS INDEL_ERROR -ERROR_METRICS INDEL_ERROR:INDEL_LENGTH -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:14.279 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:14.279 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:14.279 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:14.279 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:14.279 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:14.279 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:14.279 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:14.279 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:14 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels1973904790315724520.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:14 GMT+14:00 2024] CollectSamErrorMetrics INPUT=/tmp/Indels1973904790315724520.bam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[INDEL_ERROR, INDEL_ERROR:INDEL_LENGTH] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Getting SamLocusIterator INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Getting SamLocusIterator Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Using 2 aggregators. INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Using 2 aggregators. Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Starting iteration over loci INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Starting iteration over loci Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Really starting iteration now. INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Really starting iteration now. Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Iteration complete, generating metric files INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Iteration complete, generating metric files Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Examined 22 loci, Processed 22 loci, Skipped 0 loci. INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Examined 22 loci, Processed 22 loci, Skipped 0 loci. Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Computation took 0 seconds. Computation took 0 seconds. Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:14 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:14 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIndelErrors[33]([Ljava.lang.String;@158f6210, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testOneCovariateErrorMetrics[0](.error_by_all, testdata/picard/sam/BamErrorMetrics/chrMReadsWithClips.sam, 30, ERROR_BASES 49 Q_SCORE 0 COVARIATE all TOTAL_BASES 62 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[1](.error_by_base_quality, testdata/picard/sam/BamErrorMetrics/chrMReadsWithClips.sam, 30, ERROR_BASES 41 Q_SCORE 0 COVARIATE 32 TOTAL_BASES 52 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[2](.error_by_base_quality, testdata/picard/sam/BamErrorMetrics/chrMReadsWithClips.sam, 30, ERROR_BASES 8 Q_SCORE 0 COVARIATE 33 TOTAL_BASES 10 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[3](.error_by_homopolymer_and_following_ref_base, testdata/picard/sam/BamErrorMetrics/chrMReadsWithClips.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 9,T,T TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[4](.error_by_homopolymer_and_following_ref_base, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 2,G,T TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[5](.error_by_binned_length_homopolymer_and_following_ref_base, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE SHORT_HOMOPOLYMER,G,T TOTAL_BASES 6 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[6](.error_by_read_ordinality_and_pre_dinuc, testdata/picard/sam/BamErrorMetrics/chrMReadsWithClips.sam, 30, ERROR_BASES 3 Q_SCORE 0 COVARIATE FIRST,A,A TOTAL_BASES 3 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[7](.error_by_all, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 72 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[8](.error_by_base_quality, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 32 TOTAL_BASES 51 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[9](.error_by_base_quality, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE 33 TOTAL_BASES 21 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[10](.error_by_homopolymer_and_following_ref_base, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 2,T,A TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[11](.error_by_homopolymer_and_following_ref_base, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 3,C,G TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[12](.error_by_read_ordinality_and_pre_dinuc, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE FIRST,G,T TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[13](.error_by_gc, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 0.5 TOTAL_BASES 36 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[14](.error_by_cycle, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 10 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[15](.error_by_mapping_quality, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 60 TOTAL_BASES 36 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[16](.error_by_mapping_quality, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE 50 TOTAL_BASES 36 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[17](.error_by_read_group, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 62A40.2 TOTAL_BASES 72 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[18](.error_by_mismatches_in_read, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 35 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[19](.error_by_mismatches_in_read, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 0 TOTAL_BASES 37 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[20](.error_by_one_base_padded_context, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE CAG TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[21](.error_by_one_base_padded_context, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE GTC TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[22](.error_by_one_base_padded_context, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE CCT TOTAL_BASES 3 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[23](.error_by_two_base_padded_context, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE ACGGG TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[24](.error_by_two_base_padded_context, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE GGTCT TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[25](.error_by_two_base_padded_context, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE CTTGA TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[26](.error_by_two_base_padded_context, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE CCGTG TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[27](.error_by_consensus, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE UNKNOWN TOTAL_BASES 72 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[28](.error_by_consensus, testdata/picard/sam/BamErrorMetrics/simpleSingleStrandConsensusSamWithBaseErrors.sam, 30, ERROR_BASES 2 Q_SCORE 0 COVARIATE SIMPLEX_SINGLETON TOTAL_BASES 36 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[29](.error_by_consensus, testdata/picard/sam/BamErrorMetrics/simpleSingleStrandConsensusSamWithBaseErrors.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE SIMPLEX_CONSENSUS TOTAL_BASES 36 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[30](.error_by_consensus, testdata/picard/sam/BamErrorMetrics/simpleDuplexConsensusSamWithBaseErrors.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE DUPLEX_SINGLETON TOTAL_BASES 35 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[31](.error_by_consensus, testdata/picard/sam/BamErrorMetrics/simpleDuplexConsensusSamWithBaseErrors.sam, 30, ERROR_BASES 2 Q_SCORE 0 COVARIATE DUPLEX_CONSENSUS TOTAL_BASES 36 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[32](.error_by_ns_in_read, testdata/picard/sam/BamErrorMetrics/simpleDuplexConsensusSamWithBaseErrors.sam, 30, ERROR_BASES 2 Q_SCORE 0 COVARIATE 0 TOTAL_BASES 36 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[33](.error_by_ns_in_read, testdata/picard/sam/BamErrorMetrics/simpleDuplexConsensusSamWithBaseErrors.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 35 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[34](.error_by_binned_cycle, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE QUINTILE_1 TOTAL_BASES 14 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[35](.error_by_binned_cycle, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE QUINTILE_2 TOTAL_BASES 14 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[36](.error_by_binned_cycle, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE QUINTILE_3 TOTAL_BASES 14 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[37](.error_by_binned_cycle, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE QUINTILE_4 TOTAL_BASES 14 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateErrorMetrics[38](.error_by_binned_cycle, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE QUINTILE_5 TOTAL_BASES 16 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[0](.error_by_all, testdata/picard/sam/BamErrorMetrics/chrMReadsWithClips.sam, 30, ERROR_BASES 49 Q_SCORE 0 COVARIATE all TOTAL_BASES 62 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[1](.error_by_base_quality, testdata/picard/sam/BamErrorMetrics/chrMReadsWithClips.sam, 30, ERROR_BASES 41 Q_SCORE 0 COVARIATE 32 TOTAL_BASES 52 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[2](.error_by_base_quality, testdata/picard/sam/BamErrorMetrics/chrMReadsWithClips.sam, 30, ERROR_BASES 8 Q_SCORE 0 COVARIATE 33 TOTAL_BASES 10 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[3](.error_by_homopolymer_and_following_ref_base, testdata/picard/sam/BamErrorMetrics/chrMReadsWithClips.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 9,T,T TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[4](.error_by_homopolymer_and_following_ref_base, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 2,G,T TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[5](.error_by_binned_length_homopolymer_and_following_ref_base, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE SHORT_HOMOPOLYMER,G,T TOTAL_BASES 6 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[6](.error_by_read_ordinality_and_pre_dinuc, testdata/picard/sam/BamErrorMetrics/chrMReadsWithClips.sam, 30, ERROR_BASES 3 Q_SCORE 0 COVARIATE FIRST,A,A TOTAL_BASES 3 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[7](.error_by_all, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 72 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[8](.error_by_base_quality, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 32 TOTAL_BASES 51 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[9](.error_by_base_quality, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE 33 TOTAL_BASES 21 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[10](.error_by_homopolymer_and_following_ref_base, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 2,T,A TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[11](.error_by_homopolymer_and_following_ref_base, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 3,C,G TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[12](.error_by_read_ordinality_and_pre_dinuc, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE FIRST,G,T TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[13](.error_by_gc, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 0.5 TOTAL_BASES 36 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[14](.error_by_cycle, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 10 TOTAL_BASES 2 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[15](.error_by_mapping_quality, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 60 TOTAL_BASES 36 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[16](.error_by_mapping_quality, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE 50 TOTAL_BASES 36 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[17](.error_by_read_group, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 62A40.2 TOTAL_BASES 72 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[18](.error_by_mismatches_in_read, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 35 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[19](.error_by_mismatches_in_read, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 0 TOTAL_BASES 37 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[20](.error_by_one_base_padded_context, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE CAG TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[21](.error_by_one_base_padded_context, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE GTC TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[22](.error_by_one_base_padded_context, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE CCT TOTAL_BASES 3 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[23](.error_by_two_base_padded_context, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE ACGGG TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[24](.error_by_two_base_padded_context, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE GGTCT TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[25](.error_by_two_base_padded_context, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE CTTGA TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[26](.error_by_two_base_padded_context, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE CCGTG TOTAL_BASES 1 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[27](.error_by_consensus, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE UNKNOWN TOTAL_BASES 72 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[28](.error_by_consensus, testdata/picard/sam/BamErrorMetrics/simpleSingleStrandConsensusSamWithBaseErrors.sam, 30, ERROR_BASES 2 Q_SCORE 0 COVARIATE SIMPLEX_SINGLETON TOTAL_BASES 36 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[29](.error_by_consensus, testdata/picard/sam/BamErrorMetrics/simpleSingleStrandConsensusSamWithBaseErrors.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE SIMPLEX_CONSENSUS TOTAL_BASES 36 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[30](.error_by_consensus, testdata/picard/sam/BamErrorMetrics/simpleDuplexConsensusSamWithBaseErrors.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE DUPLEX_SINGLETON TOTAL_BASES 35 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[31](.error_by_consensus, testdata/picard/sam/BamErrorMetrics/simpleDuplexConsensusSamWithBaseErrors.sam, 30, ERROR_BASES 2 Q_SCORE 0 COVARIATE DUPLEX_CONSENSUS TOTAL_BASES 36 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[32](.error_by_ns_in_read, testdata/picard/sam/BamErrorMetrics/simpleDuplexConsensusSamWithBaseErrors.sam, 30, ERROR_BASES 2 Q_SCORE 0 COVARIATE 0 TOTAL_BASES 36 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[33](.error_by_ns_in_read, testdata/picard/sam/BamErrorMetrics/simpleDuplexConsensusSamWithBaseErrors.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 35 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[34](.error_by_binned_cycle, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE QUINTILE_1 TOTAL_BASES 14 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[35](.error_by_binned_cycle, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE QUINTILE_2 TOTAL_BASES 14 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[36](.error_by_binned_cycle, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE QUINTILE_3 TOTAL_BASES 14 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[37](.error_by_binned_cycle, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE QUINTILE_4 TOTAL_BASES 14 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testOneCovariateIndelErrorMetrics[38](.error_by_binned_cycle, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE QUINTILE_5 TOTAL_BASES 16 )(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testReadCycleBin[0](0.0, QUINTILE_1)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testReadCycleBin[1](0.2, QUINTILE_1)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testReadCycleBin[2](0.20000000000000004, QUINTILE_2)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testReadCycleBin[3](0.4, QUINTILE_2)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testReadCycleBin[4](0.4000000000000001, QUINTILE_3)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testReadCycleBin[5](0.54, QUINTILE_3)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testReadCycleBin[6](0.6, QUINTILE_3)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testReadCycleBin[7](0.6000000000000001, QUINTILE_4)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testReadCycleBin[8](0.8, QUINTILE_4)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testReadCycleBin[9](0.8000000000000002, QUINTILE_5)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testReadCycleBin[10](1.0, QUINTILE_5)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testReadCycleBinError[0](1.0000000000000002)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testReadCycleBinError[1](-4.9E-324)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testReadCycleBinError[2](-1.0)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testReadCycleBinError[3](-0.1)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testReadCycleBinError[4](1.1)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testReadCycleBinError[5](100.0)(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testStratifiersHaveDistinctSuffixes(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Running Test: Test method testTooManyDirectives(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) Test: Test method testTooManyDirectives(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Gradle suite > Gradle test > picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.testTooManyDirectives STANDARD_ERROR INFO 2024-07-02 11:52:14 CollectSamErrorMetrics Test: Test method testTooManyDirectives(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testTooManyDirectives(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTooManyDirectives(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testTooManyDirectives(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTooManyDirectives(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTooManyDirectives(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testTooManyDirectives(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTooManyDirectives(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testTooManyDirectives(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** CollectSamErrorMetrics -INPUT testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS ERROR:ALL:GC_CONTENT:READ_ORDINALITY:READ_BASE:READ_DIRECTION:PAIR_ORIENTATION:PAIR_PROPERNESS:REFERENCE_BASE:PRE_DINUC:POST_DINUC:HOMOPOLYMER_LENGTH:HOMOPOLYMER:BINNED_HOMOPOLYMER:FLOWCELL_TILE:FLOWCELL_Y:FLOWCELL_X:READ_GROUP:CYCLE:BINNED_CYCLE:SOFT_CLIPS:INSERT_LENGTH:BASE_QUALITY:MAPPING_QUALITY:MISMATCHES_IN_READ:ONE_BASE_PADDED_CONTEXT:TWO_BASE_PADDED_CONTEXT:CONSENSUS:NS_IN_READ:INSERTIONS_IN_READ:DELETIONS_IN_READ:INDELS_IN_READ:INDEL_LENGTH:ALL -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf ********** CollectSamErrorMetrics -INPUT testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam -OUTPUT /tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -ERROR_METRICS ERROR:ALL:GC_CONTENT:READ_ORDINALITY:READ_BASE:READ_DIRECTION:PAIR_ORIENTATION:PAIR_PROPERNESS:REFERENCE_BASE:PRE_DINUC:POST_DINUC:HOMOPOLYMER_LENGTH:HOMOPOLYMER:BINNED_HOMOPOLYMER:FLOWCELL_TILE:FLOWCELL_Y:FLOWCELL_X:READ_GROUP:CYCLE:BINNED_CYCLE:SOFT_CLIPS:INSERT_LENGTH:BASE_QUALITY:MAPPING_QUALITY:MISMATCHES_IN_READ:ONE_BASE_PADDED_CONTEXT:TWO_BASE_PADDED_CONTEXT:CONSENSUS:NS_IN_READ:INSERTIONS_IN_READ:DELETIONS_IN_READ:INDELS_IN_READ:INDEL_LENGTH:ALL -VCF /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf Test: Test method testTooManyDirectives(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: ********** ********** Test: Test method testTooManyDirectives(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testTooManyDirectives(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Test: Test method testTooManyDirectives(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:14.548 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:14.548 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTooManyDirectives(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:14.548 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:14.548 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTooManyDirectives(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:14.548 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:14.548 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTooManyDirectives(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: 11:52:14.548 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:14.548 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTooManyDirectives(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:14 GMT+14:00 2024] CollectSamErrorMetrics INPUT=testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[ERROR, ERROR:BASE_QUALITY, ERROR:INSERT_LENGTH, ERROR:GC_CONTENT, ERROR:READ_DIRECTION, ERROR:PAIR_ORIENTATION, ERROR:HOMOPOLYMER, ERROR:BINNED_HOMOPOLYMER, ERROR:CYCLE, ERROR:READ_ORDINALITY, ERROR:READ_ORDINALITY:CYCLE, ERROR:READ_ORDINALITY:HOMOPOLYMER, ERROR:READ_ORDINALITY:GC_CONTENT, ERROR:READ_ORDINALITY:PRE_DINUC, ERROR:MAPPING_QUALITY, ERROR:READ_GROUP, ERROR:MISMATCHES_IN_READ, ERROR:ONE_BASE_PADDED_CONTEXT, OVERLAPPING_ERROR, OVERLAPPING_ERROR:BASE_QUALITY, OVERLAPPING_ERROR:INSERT_LENGTH, OVERLAPPING_ERROR:READ_ORDINALITY, OVERLAPPING_ERROR:READ_ORDINALITY:CYCLE, OVERLAPPING_ERROR:READ_ORDINALITY:HOMOPOLYMER, OVERLAPPING_ERROR:READ_ORDINALITY:GC_CONTENT, INDEL_ERROR, ERROR:ALL:GC_CONTENT:READ_ORDINALITY:READ_BASE:READ_DIRECTION:PAIR_ORIENTATION:PAIR_PROPERNESS:REFERENCE_BASE:PRE_DINUC:POST_DINUC:HOMOPOLYMER_LENGTH:HOMOPOLYMER:BINNED_HOMOPOLYMER:FLOWCELL_TILE:FLOWCELL_Y:FLOWCELL_X:READ_GROUP:CYCLE:BINNED_CYCLE:SOFT_CLIPS:INSERT_LENGTH:BASE_QUALITY:MAPPING_QUALITY:MISMATCHES_IN_READ:ONE_BASE_PADDED_CONTEXT:TWO_BASE_PADDED_CONTEXT:CONSENSUS:NS_IN_READ:INSERTIONS_IN_READ:DELETIONS_IN_READ:INDELS_IN_READ:INDEL_LENGTH:ALL] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:14 GMT+14:00 2024] CollectSamErrorMetrics INPUT=testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam OUTPUT=/tmp/CollectSamErrorMetricsTest9114420591428892487.tmp/test ERROR_METRICS=[ERROR, ERROR:BASE_QUALITY, ERROR:INSERT_LENGTH, ERROR:GC_CONTENT, ERROR:READ_DIRECTION, ERROR:PAIR_ORIENTATION, ERROR:HOMOPOLYMER, ERROR:BINNED_HOMOPOLYMER, ERROR:CYCLE, ERROR:READ_ORDINALITY, ERROR:READ_ORDINALITY:CYCLE, ERROR:READ_ORDINALITY:HOMOPOLYMER, ERROR:READ_ORDINALITY:GC_CONTENT, ERROR:READ_ORDINALITY:PRE_DINUC, ERROR:MAPPING_QUALITY, ERROR:READ_GROUP, ERROR:MISMATCHES_IN_READ, ERROR:ONE_BASE_PADDED_CONTEXT, OVERLAPPING_ERROR, OVERLAPPING_ERROR:BASE_QUALITY, OVERLAPPING_ERROR:INSERT_LENGTH, OVERLAPPING_ERROR:READ_ORDINALITY, OVERLAPPING_ERROR:READ_ORDINALITY:CYCLE, OVERLAPPING_ERROR:READ_ORDINALITY:HOMOPOLYMER, OVERLAPPING_ERROR:READ_ORDINALITY:GC_CONTENT, INDEL_ERROR, ERROR:ALL:GC_CONTENT:READ_ORDINALITY:READ_BASE:READ_DIRECTION:PAIR_ORIENTATION:PAIR_PROPERNESS:REFERENCE_BASE:PRE_DINUC:POST_DINUC:HOMOPOLYMER_LENGTH:HOMOPOLYMER:BINNED_HOMOPOLYMER:FLOWCELL_TILE:FLOWCELL_Y:FLOWCELL_X:READ_GROUP:CYCLE:BINNED_CYCLE:SOFT_CLIPS:INSERT_LENGTH:BASE_QUALITY:MAPPING_QUALITY:MISMATCHES_IN_READ:ONE_BASE_PADDED_CONTEXT:TWO_BASE_PADDED_CONTEXT:CONSENSUS:NS_IN_READ:INSERTIONS_IN_READ:DELETIONS_IN_READ:INDELS_IN_READ:INDEL_LENGTH:ALL] VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MIN_MAPPING_Q=20 MIN_BASE_Q=20 PRIOR_Q=30 MAX_LOCI=0 LONG_HOMOPOLYMER=6 LOCATION_BIN_SIZE=2500 PROBABILITY=1.0 PROGRESS_STEP_INTERVAL=100000 INTERVAL_ITERATOR=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTooManyDirectives(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTooManyDirectives(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: [Tue Jul 02 11:52:14 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:14 GMT+14:00 2024] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes. Test: Test method testTooManyDirectives(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testTooManyDirectives(picard.sam.SamErrorMetric.CollectSamErrorMetricsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method runIUPACCase(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) Test: Test method runIUPACCase(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:14 CollectSequencingArtifactMetrics Gradle suite > Gradle test > picard.analysis.artifacts.CollectSequencingArtifactMetricsTest.runIUPACCase STANDARD_ERROR INFO 2024-07-02 11:52:14 CollectSequencingArtifactMetrics Test: Test method runIUPACCase(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Test: Test method runIUPACCase(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method runIUPACCase(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method runIUPACCase(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method runIUPACCase(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method runIUPACCase(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method runIUPACCase(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method runIUPACCase(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method runIUPACCase(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** CollectSequencingArtifactMetrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/testWithIUPACBases.sam -OUTPUT /tmp/artifactMetrics.4307810906743909018.tmp/IUPAC -CONTEXT_SIZE 0 -MAXIMUM_INSERT_SIZE 30 -MINIMUM_INSERT_SIZE 30 ********** CollectSequencingArtifactMetrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/testWithIUPACBases.sam -OUTPUT /tmp/artifactMetrics.4307810906743909018.tmp/IUPAC -CONTEXT_SIZE 0 -MAXIMUM_INSERT_SIZE 30 -MINIMUM_INSERT_SIZE 30 Test: Test method runIUPACCase(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method runIUPACCase(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Test: Test method runIUPACCase(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Test: Test method runIUPACCase(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:14.583 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:14.583 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method runIUPACCase(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:14.583 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:14.583 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method runIUPACCase(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:14.584 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:14.584 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method runIUPACCase(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:14.584 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:14.584 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method runIUPACCase(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: [Tue Jul 02 11:52:14 GMT+14:00 2024] CollectSequencingArtifactMetrics MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=30 CONTEXT_SIZE=0 INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/testWithIUPACBases.sam OUTPUT=/tmp/artifactMetrics.4307810906743909018.tmp/IUPAC REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:14 GMT+14:00 2024] CollectSequencingArtifactMetrics MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=30 CONTEXT_SIZE=0 INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/testWithIUPACBases.sam OUTPUT=/tmp/artifactMetrics.4307810906743909018.tmp/IUPAC REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method runIUPACCase(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: [Tue Jul 02 11:52:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method runIUPACCase(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: [Tue Jul 02 11:52:14 GMT+14:00 2024] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:14 GMT+14:00 2024] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes. Test: Test method runIUPACCase(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) Test: Test method testContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:14 CollectSequencingArtifactMetrics Gradle suite > Gradle test > picard.analysis.artifacts.CollectSequencingArtifactMetricsTest.testContext STANDARD_ERROR INFO 2024-07-02 11:52:14 CollectSequencingArtifactMetrics Test: Test method testContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Test: Test method testContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method testContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method testContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method testContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** CollectSequencingArtifactMetrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam -OUTPUT /tmp/artifactMetrics.4307810906743909018.tmp/with_context -CONTEXT_SIZE 1 -MAXIMUM_INSERT_SIZE 30 -MINIMUM_INSERT_SIZE 30 ********** CollectSequencingArtifactMetrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam -OUTPUT /tmp/artifactMetrics.4307810906743909018.tmp/with_context -CONTEXT_SIZE 1 -MAXIMUM_INSERT_SIZE 30 -MINIMUM_INSERT_SIZE 30 Test: Test method testContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method testContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Test: Test method testContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Test: Test method testContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:14.627 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:14.627 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:14.627 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:14.627 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:14.627 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:14.627 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:14.627 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:14.627 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: [Tue Jul 02 11:52:14 GMT+14:00 2024] CollectSequencingArtifactMetrics MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=30 CONTEXT_SIZE=1 INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam OUTPUT=/tmp/artifactMetrics.4307810906743909018.tmp/with_context REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:14 GMT+14:00 2024] CollectSequencingArtifactMetrics MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=30 CONTEXT_SIZE=1 INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam OUTPUT=/tmp/artifactMetrics.4307810906743909018.tmp/with_context REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: [Tue Jul 02 11:52:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: [Tue Jul 02 11:52:14 GMT+14:00 2024] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:14 GMT+14:00 2024] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes. Test: Test method testContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testDbSnp(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) Test: Test method testDbSnp(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:14 CollectSequencingArtifactMetrics Gradle suite > Gradle test > picard.analysis.artifacts.CollectSequencingArtifactMetricsTest.testDbSnp STANDARD_ERROR INFO 2024-07-02 11:52:14 CollectSequencingArtifactMetrics Test: Test method testDbSnp(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Test: Test method testDbSnp(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDbSnp(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method testDbSnp(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDbSnp(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDbSnp(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method testDbSnp(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDbSnp(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method testDbSnp(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** CollectSequencingArtifactMetrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam -OUTPUT /tmp/artifactMetrics.4307810906743909018.tmp/with_dbsnp -CONTEXT_SIZE 0 -MAXIMUM_INSERT_SIZE 30 -DB_SNP testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.dbsnp.vcf -MINIMUM_INSERT_SIZE 30 ********** CollectSequencingArtifactMetrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam -OUTPUT /tmp/artifactMetrics.4307810906743909018.tmp/with_dbsnp -CONTEXT_SIZE 0 -MAXIMUM_INSERT_SIZE 30 -DB_SNP testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.dbsnp.vcf -MINIMUM_INSERT_SIZE 30 Test: Test method testDbSnp(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method testDbSnp(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Test: Test method testDbSnp(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Test: Test method testDbSnp(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:14.716 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:14.716 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDbSnp(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:14.716 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:14.716 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDbSnp(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:14.716 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:14.716 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDbSnp(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:14.716 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:14.716 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDbSnp(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: [Tue Jul 02 11:52:14 GMT+14:00 2024] CollectSequencingArtifactMetrics DB_SNP=testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.dbsnp.vcf MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=30 CONTEXT_SIZE=0 INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam OUTPUT=/tmp/artifactMetrics.4307810906743909018.tmp/with_dbsnp REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:14 GMT+14:00 2024] CollectSequencingArtifactMetrics DB_SNP=testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.dbsnp.vcf MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=30 CONTEXT_SIZE=0 INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam OUTPUT=/tmp/artifactMetrics.4307810906743909018.tmp/with_dbsnp REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDbSnp(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: [Tue Jul 02 11:52:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDbSnp(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: [Tue Jul 02 11:52:14 GMT+14:00 2024] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:14 GMT+14:00 2024] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes. Test: Test method testDbSnp(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIntervalList(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) Test: Test method testIntervalList(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:14 CollectSequencingArtifactMetrics Gradle suite > Gradle test > picard.analysis.artifacts.CollectSequencingArtifactMetricsTest.testIntervalList STANDARD_ERROR INFO 2024-07-02 11:52:14 CollectSequencingArtifactMetrics Test: Test method testIntervalList(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Test: Test method testIntervalList(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIntervalList(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method testIntervalList(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIntervalList(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIntervalList(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method testIntervalList(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIntervalList(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method testIntervalList(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** CollectSequencingArtifactMetrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam -OUTPUT /tmp/artifactMetrics.4307810906743909018.tmp/with_intervals -CONTEXT_SIZE 0 -MAXIMUM_INSERT_SIZE 30 -INTERVALS testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.interval_list -MINIMUM_INSERT_SIZE 30 ********** CollectSequencingArtifactMetrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam -OUTPUT /tmp/artifactMetrics.4307810906743909018.tmp/with_intervals -CONTEXT_SIZE 0 -MAXIMUM_INSERT_SIZE 30 -INTERVALS testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.interval_list -MINIMUM_INSERT_SIZE 30 Test: Test method testIntervalList(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method testIntervalList(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Test: Test method testIntervalList(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Test: Test method testIntervalList(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:14.748 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:14.748 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIntervalList(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:14.748 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:14.748 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIntervalList(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:14.748 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:14.748 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIntervalList(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:14.748 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:14.748 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIntervalList(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: [Tue Jul 02 11:52:14 GMT+14:00 2024] CollectSequencingArtifactMetrics INTERVALS=testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.interval_list MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=30 CONTEXT_SIZE=0 INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam OUTPUT=/tmp/artifactMetrics.4307810906743909018.tmp/with_intervals REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:14 GMT+14:00 2024] CollectSequencingArtifactMetrics INTERVALS=testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.interval_list MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=30 CONTEXT_SIZE=0 INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam OUTPUT=/tmp/artifactMetrics.4307810906743909018.tmp/with_intervals REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIntervalList(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: [Tue Jul 02 11:52:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIntervalList(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: [Tue Jul 02 11:52:14 GMT+14:00 2024] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:14 GMT+14:00 2024] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes. Test: Test method testIntervalList(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testLargerContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) Test: Test method testLargerContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:14 CollectSequencingArtifactMetrics Gradle suite > Gradle test > picard.analysis.artifacts.CollectSequencingArtifactMetricsTest.testLargerContext STANDARD_ERROR INFO 2024-07-02 11:52:14 CollectSequencingArtifactMetrics Test: Test method testLargerContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Test: Test method testLargerContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testLargerContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method testLargerContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testLargerContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testLargerContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method testLargerContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testLargerContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method testLargerContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** CollectSequencingArtifactMetrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam -OUTPUT /tmp/artifactMetrics.4307810906743909018.tmp/with_larger_context -CONTEXT_SIZE 2 -MAXIMUM_INSERT_SIZE 30 -MINIMUM_INSERT_SIZE 30 ********** CollectSequencingArtifactMetrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam -OUTPUT /tmp/artifactMetrics.4307810906743909018.tmp/with_larger_context -CONTEXT_SIZE 2 -MAXIMUM_INSERT_SIZE 30 -MINIMUM_INSERT_SIZE 30 Test: Test method testLargerContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method testLargerContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Test: Test method testLargerContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Test: Test method testLargerContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:14.780 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:14.780 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testLargerContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:14.780 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:14.780 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testLargerContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:14.780 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:14.780 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testLargerContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:14.780 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:14.780 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testLargerContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: [Tue Jul 02 11:52:14 GMT+14:00 2024] CollectSequencingArtifactMetrics MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=30 CONTEXT_SIZE=2 INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam OUTPUT=/tmp/artifactMetrics.4307810906743909018.tmp/with_larger_context REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:14 GMT+14:00 2024] CollectSequencingArtifactMetrics MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=30 CONTEXT_SIZE=2 INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam OUTPUT=/tmp/artifactMetrics.4307810906743909018.tmp/with_larger_context REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testLargerContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: [Tue Jul 02 11:52:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testLargerContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: [Tue Jul 02 11:52:14 GMT+14:00 2024] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:14 GMT+14:00 2024] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes. Test: Test method testLargerContext(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testNoBqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) Test: Test method testNoBqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:15 CollectSequencingArtifactMetrics Gradle suite > Gradle test > picard.analysis.artifacts.CollectSequencingArtifactMetricsTest.testNoBqCutoff STANDARD_ERROR INFO 2024-07-02 11:52:15 CollectSequencingArtifactMetrics Test: Test method testNoBqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Test: Test method testNoBqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testNoBqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method testNoBqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testNoBqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testNoBqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method testNoBqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testNoBqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method testNoBqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** CollectSequencingArtifactMetrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam -OUTPUT /tmp/artifactMetrics.4307810906743909018.tmp/no_bq_cutoff -CONTEXT_SIZE 0 -MAXIMUM_INSERT_SIZE 30 -MINIMUM_QUALITY_SCORE 0 -MINIMUM_INSERT_SIZE 30 ********** CollectSequencingArtifactMetrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam -OUTPUT /tmp/artifactMetrics.4307810906743909018.tmp/no_bq_cutoff -CONTEXT_SIZE 0 -MAXIMUM_INSERT_SIZE 30 -MINIMUM_QUALITY_SCORE 0 -MINIMUM_INSERT_SIZE 30 Test: Test method testNoBqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method testNoBqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Test: Test method testNoBqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Test: Test method testNoBqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:15.292 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:15.292 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoBqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:15.293 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:15.293 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoBqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:15.293 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:15.293 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoBqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:15.293 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:15.293 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoBqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: [Tue Jul 02 11:52:15 GMT+14:00 2024] CollectSequencingArtifactMetrics MINIMUM_QUALITY_SCORE=0 MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=30 CONTEXT_SIZE=0 INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam OUTPUT=/tmp/artifactMetrics.4307810906743909018.tmp/no_bq_cutoff REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta MINIMUM_MAPPING_QUALITY=30 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:15 GMT+14:00 2024] CollectSequencingArtifactMetrics MINIMUM_QUALITY_SCORE=0 MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=30 CONTEXT_SIZE=0 INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam OUTPUT=/tmp/artifactMetrics.4307810906743909018.tmp/no_bq_cutoff REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta MINIMUM_MAPPING_QUALITY=30 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testNoBqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: [Tue Jul 02 11:52:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testNoBqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: [Tue Jul 02 11:52:15 GMT+14:00 2024] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:15 GMT+14:00 2024] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes. Test: Test method testNoBqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testNoMqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) Test: Test method testNoMqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:15 CollectSequencingArtifactMetrics Gradle suite > Gradle test > picard.analysis.artifacts.CollectSequencingArtifactMetricsTest.testNoMqCutoff STANDARD_ERROR INFO 2024-07-02 11:52:15 CollectSequencingArtifactMetrics Test: Test method testNoMqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Test: Test method testNoMqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testNoMqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method testNoMqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testNoMqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testNoMqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method testNoMqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testNoMqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method testNoMqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** CollectSequencingArtifactMetrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam -MINIMUM_MAPPING_QUALITY 0 -OUTPUT /tmp/artifactMetrics.4307810906743909018.tmp/no_mq_cutoff -CONTEXT_SIZE 0 -MAXIMUM_INSERT_SIZE 30 -MINIMUM_INSERT_SIZE 30 ********** CollectSequencingArtifactMetrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam -MINIMUM_MAPPING_QUALITY 0 -OUTPUT /tmp/artifactMetrics.4307810906743909018.tmp/no_mq_cutoff -CONTEXT_SIZE 0 -MAXIMUM_INSERT_SIZE 30 -MINIMUM_INSERT_SIZE 30 Test: Test method testNoMqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method testNoMqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Test: Test method testNoMqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Test: Test method testNoMqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:15.326 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:15.326 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoMqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:15.326 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:15.326 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoMqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:15.327 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:15.327 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoMqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:15.327 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:15.327 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoMqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: [Tue Jul 02 11:52:15 GMT+14:00 2024] CollectSequencingArtifactMetrics MINIMUM_MAPPING_QUALITY=0 MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=30 CONTEXT_SIZE=0 INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam OUTPUT=/tmp/artifactMetrics.4307810906743909018.tmp/no_mq_cutoff REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta MINIMUM_QUALITY_SCORE=20 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:15 GMT+14:00 2024] CollectSequencingArtifactMetrics MINIMUM_MAPPING_QUALITY=0 MINIMUM_INSERT_SIZE=30 MAXIMUM_INSERT_SIZE=30 CONTEXT_SIZE=0 INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam OUTPUT=/tmp/artifactMetrics.4307810906743909018.tmp/no_mq_cutoff REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta MINIMUM_QUALITY_SCORE=20 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testNoMqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: [Tue Jul 02 11:52:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testNoMqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: [Tue Jul 02 11:52:15 GMT+14:00 2024] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:15 GMT+14:00 2024] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes. Test: Test method testNoMqCutoff(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testUnmappedMate(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) Test: Test method testUnmappedMate(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:15 CollectSequencingArtifactMetrics Gradle suite > Gradle test > picard.analysis.artifacts.CollectSequencingArtifactMetricsTest.testUnmappedMate STANDARD_ERROR INFO 2024-07-02 11:52:15 CollectSequencingArtifactMetrics Test: Test method testUnmappedMate(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Test: Test method testUnmappedMate(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testUnmappedMate(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method testUnmappedMate(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testUnmappedMate(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testUnmappedMate(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method testUnmappedMate(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testUnmappedMate(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method testUnmappedMate(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** CollectSequencingArtifactMetrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam -OUTPUT /tmp/artifactMetrics.4307810906743909018.tmp/unmapped_mate -CONTEXT_SIZE 0 -MAXIMUM_INSERT_SIZE 0 -MINIMUM_INSERT_SIZE 0 ********** CollectSequencingArtifactMetrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam -OUTPUT /tmp/artifactMetrics.4307810906743909018.tmp/unmapped_mate -CONTEXT_SIZE 0 -MAXIMUM_INSERT_SIZE 0 -MINIMUM_INSERT_SIZE 0 Test: Test method testUnmappedMate(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: ********** ********** Test: Test method testUnmappedMate(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Test: Test method testUnmappedMate(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Test: Test method testUnmappedMate(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:15.361 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:15.361 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUnmappedMate(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:15.361 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:15.361 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUnmappedMate(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:15.361 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:15.361 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUnmappedMate(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: 11:52:15.361 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:15.361 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUnmappedMate(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: [Tue Jul 02 11:52:15 GMT+14:00 2024] CollectSequencingArtifactMetrics MINIMUM_INSERT_SIZE=0 MAXIMUM_INSERT_SIZE=0 CONTEXT_SIZE=0 INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam OUTPUT=/tmp/artifactMetrics.4307810906743909018.tmp/unmapped_mate REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:15 GMT+14:00 2024] CollectSequencingArtifactMetrics MINIMUM_INSERT_SIZE=0 MAXIMUM_INSERT_SIZE=0 CONTEXT_SIZE=0 INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam OUTPUT=/tmp/artifactMetrics.4307810906743909018.tmp/unmapped_mate REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testUnmappedMate(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: [Tue Jul 02 11:52:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testUnmappedMate(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: [Tue Jul 02 11:52:15 GMT+14:00 2024] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:15 GMT+14:00 2024] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes. Test: Test method testUnmappedMate(picard.analysis.artifacts.CollectSequencingArtifactMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) Test: Test method runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:15 CollectTargetedPcrMetrics Gradle suite > Gradle test > picard.analysis.directed.CollectTargetedMetricsTest.runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000) STANDARD_ERROR INFO 2024-07-02 11:52:15 CollectTargetedPcrMetrics Test: Test method runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: Test: Test method runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** ********** Test: Test method runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** ********** Test: Test method runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** ********** Test: Test method runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** CollectTargetedPcrMetrics -TARGET_INTERVALS testdata/picard/quality/chrM.single.interval_list -INPUT /tmp/CollectTargetedMetrics11358391683139703357.bam -OUTPUT /tmp/test17021263166827635619.TargetedMetrics_Coverage -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -PER_TARGET_COVERAGE /tmp/perTarget8180380818369984825.perTargetCoverage -LEVEL ALL_READS -AMPLICON_INTERVALS testdata/picard/quality/chrM.single.interval_list -SAMPLE_SIZE 1000 ********** CollectTargetedPcrMetrics -TARGET_INTERVALS testdata/picard/quality/chrM.single.interval_list -INPUT /tmp/CollectTargetedMetrics11358391683139703357.bam -OUTPUT /tmp/test17021263166827635619.TargetedMetrics_Coverage -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -PER_TARGET_COVERAGE /tmp/perTarget8180380818369984825.perTargetCoverage -LEVEL ALL_READS -AMPLICON_INTERVALS testdata/picard/quality/chrM.single.interval_list -SAMPLE_SIZE 1000 Test: Test method runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** ********** Test: Test method runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: Test: Test method runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: Test: Test method runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: 11:52:15.399 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:15.399 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: 11:52:15.399 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:15.399 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: 11:52:15.399 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:15.399 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: 11:52:15.399 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:15.399 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: [Tue Jul 02 11:52:15 GMT+14:00 2024] CollectTargetedPcrMetrics AMPLICON_INTERVALS=testdata/picard/quality/chrM.single.interval_list TARGET_INTERVALS=[testdata/picard/quality/chrM.single.interval_list] INPUT=/tmp/CollectTargetedMetrics11358391683139703357.bam OUTPUT=/tmp/test17021263166827635619.TargetedMetrics_Coverage METRIC_ACCUMULATION_LEVEL=[ALL_READS] PER_TARGET_COVERAGE=/tmp/perTarget8180380818369984825.perTargetCoverage SAMPLE_SIZE=1000 REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta NEAR_DISTANCE=250 MINIMUM_MAPPING_QUALITY=1 MINIMUM_BASE_QUALITY=0 CLIP_OVERLAPPING_READS=false INCLUDE_INDELS=false COVERAGE_CAP=200 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:15 GMT+14:00 2024] CollectTargetedPcrMetrics AMPLICON_INTERVALS=testdata/picard/quality/chrM.single.interval_list TARGET_INTERVALS=[testdata/picard/quality/chrM.single.interval_list] INPUT=/tmp/CollectTargetedMetrics11358391683139703357.bam OUTPUT=/tmp/test17021263166827635619.TargetedMetrics_Coverage METRIC_ACCUMULATION_LEVEL=[ALL_READS] PER_TARGET_COVERAGE=/tmp/perTarget8180380818369984825.perTargetCoverage SAMPLE_SIZE=1000 REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta NEAR_DISTANCE=250 MINIMUM_MAPPING_QUALITY=1 MINIMUM_BASE_QUALITY=0 CLIP_OVERLAPPING_READS=false INCLUDE_INDELS=false COVERAGE_CAP=200 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: [Tue Jul 02 11:52:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:16 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:52:16 TheoreticalSensitivity Creating Roulette Wheel Test: Test method runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:16 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:52:16 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:16 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 11:52:16 TheoreticalSensitivity 0 sampling iterations completed Test: Test method runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:16 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:52:16 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:16 TargetMetricsCollector Calculating GC metrics INFO 2024-07-02 11:52:16 TargetMetricsCollector Calculating GC metrics Test: Test method runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: [Tue Jul 02 11:52:16 GMT+14:00 2024] picard.analysis.directed.CollectTargetedPcrMetrics done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:52:16 GMT+14:00 2024] picard.analysis.directed.CollectTargetedPcrMetrics done. Elapsed time: 0.01 minutes. Test: Test method runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) Test: Test method runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:16 CollectTargetedPcrMetrics Gradle suite > Gradle test > picard.analysis.directed.CollectTargetedMetricsTest.runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000) STANDARD_ERROR INFO 2024-07-02 11:52:16 CollectTargetedPcrMetrics Test: Test method runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: Test: Test method runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** ********** Test: Test method runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** ********** Test: Test method runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** ********** Test: Test method runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** CollectTargetedPcrMetrics -TARGET_INTERVALS testdata/picard/quality/chrM.empty.interval_list -INPUT /tmp/CollectTargetedMetrics11358391683139703357.bam -OUTPUT /tmp/test17021263166827635619.TargetedMetrics_Coverage -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -PER_TARGET_COVERAGE /tmp/perTarget8180380818369984825.perTargetCoverage -LEVEL ALL_READS -AMPLICON_INTERVALS testdata/picard/quality/chrM.empty.interval_list -SAMPLE_SIZE 1000 ********** CollectTargetedPcrMetrics -TARGET_INTERVALS testdata/picard/quality/chrM.empty.interval_list -INPUT /tmp/CollectTargetedMetrics11358391683139703357.bam -OUTPUT /tmp/test17021263166827635619.TargetedMetrics_Coverage -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -PER_TARGET_COVERAGE /tmp/perTarget8180380818369984825.perTargetCoverage -LEVEL ALL_READS -AMPLICON_INTERVALS testdata/picard/quality/chrM.empty.interval_list -SAMPLE_SIZE 1000 Test: Test method runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** ********** Test: Test method runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: Test: Test method runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: Test: Test method runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: 11:52:16.325 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:16.325 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: 11:52:16.325 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:16.325 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: 11:52:16.325 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:16.325 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: 11:52:16.325 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:16.325 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: [Tue Jul 02 11:52:16 GMT+14:00 2024] CollectTargetedPcrMetrics AMPLICON_INTERVALS=testdata/picard/quality/chrM.empty.interval_list TARGET_INTERVALS=[testdata/picard/quality/chrM.empty.interval_list] INPUT=/tmp/CollectTargetedMetrics11358391683139703357.bam OUTPUT=/tmp/test17021263166827635619.TargetedMetrics_Coverage METRIC_ACCUMULATION_LEVEL=[ALL_READS] PER_TARGET_COVERAGE=/tmp/perTarget8180380818369984825.perTargetCoverage SAMPLE_SIZE=1000 REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta NEAR_DISTANCE=250 MINIMUM_MAPPING_QUALITY=1 MINIMUM_BASE_QUALITY=0 CLIP_OVERLAPPING_READS=false INCLUDE_INDELS=false COVERAGE_CAP=200 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:16 GMT+14:00 2024] CollectTargetedPcrMetrics AMPLICON_INTERVALS=testdata/picard/quality/chrM.empty.interval_list TARGET_INTERVALS=[testdata/picard/quality/chrM.empty.interval_list] INPUT=/tmp/CollectTargetedMetrics11358391683139703357.bam OUTPUT=/tmp/test17021263166827635619.TargetedMetrics_Coverage METRIC_ACCUMULATION_LEVEL=[ALL_READS] PER_TARGET_COVERAGE=/tmp/perTarget8180380818369984825.perTargetCoverage SAMPLE_SIZE=1000 REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta NEAR_DISTANCE=250 MINIMUM_MAPPING_QUALITY=1 MINIMUM_BASE_QUALITY=0 CLIP_OVERLAPPING_READS=false INCLUDE_INDELS=false COVERAGE_CAP=200 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: [Tue Jul 02 11:52:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:16 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:52:16 TheoreticalSensitivity Creating Roulette Wheel Test: Test method runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:16 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:52:16 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:16 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 11:52:16 TheoreticalSensitivity 0 sampling iterations completed Test: Test method runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:16 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:52:16 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:16 TargetMetricsCollector Calculating GC metrics INFO 2024-07-02 11:52:16 TargetMetricsCollector Calculating GC metrics Test: Test method runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: WARNING 2024-07-02 11:52:16 TargetMetricsCollector interval of length zero found: chrM:2-1 + interval-1 skipped. WARNING 2024-07-02 11:52:16 TargetMetricsCollector interval of length zero found: chrM:2-1 + interval-1 skipped. Test: Test method runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: [Tue Jul 02 11:52:16 GMT+14:00 2024] picard.analysis.directed.CollectTargetedPcrMetrics done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:52:16 GMT+14:00 2024] picard.analysis.directed.CollectTargetedPcrMetrics done. Elapsed time: 0.01 minutes. Test: Test method runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000)(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:17 CollectTargetedPcrMetrics Gradle suite > Gradle test > picard.analysis.directed.CollectTargetedMetricsTest.runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99]) STANDARD_ERROR INFO 2024-07-02 11:52:17 CollectTargetedPcrMetrics Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** ********** Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** ********** Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** ********** Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** CollectTargetedPcrMetrics -TARGET_INTERVALS testdata/picard/quality/chrM.single.interval_list -INPUT /tmp/CollectTargetedMetrics11358391683139703357.bam -OUTPUT /tmp/test17021263166827635619.TargetedMetrics_Coverage -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -PER_TARGET_COVERAGE /tmp/perTarget8180380818369984825.perTargetCoverage -LEVEL ALL_READS -AMPLICON_INTERVALS testdata/picard/quality/chrM.single.interval_list -THEORETICAL_SENSITIVITY_OUTPUT /tmp/test3020101757453345428.TheoreticalSensitivityMetrics -SAMPLE_SIZE 2000 ********** CollectTargetedPcrMetrics -TARGET_INTERVALS testdata/picard/quality/chrM.single.interval_list -INPUT /tmp/CollectTargetedMetrics11358391683139703357.bam -OUTPUT /tmp/test17021263166827635619.TargetedMetrics_Coverage -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -PER_TARGET_COVERAGE /tmp/perTarget8180380818369984825.perTargetCoverage -LEVEL ALL_READS -AMPLICON_INTERVALS testdata/picard/quality/chrM.single.interval_list -THEORETICAL_SENSITIVITY_OUTPUT /tmp/test3020101757453345428.TheoreticalSensitivityMetrics -SAMPLE_SIZE 2000 Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** ********** Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: 11:52:17.004 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:17.004 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: 11:52:17.004 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:17.004 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: 11:52:17.004 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:17.004 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: 11:52:17.005 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:17.005 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: [Tue Jul 02 11:52:17 GMT+14:00 2024] CollectTargetedPcrMetrics AMPLICON_INTERVALS=testdata/picard/quality/chrM.single.interval_list TARGET_INTERVALS=[testdata/picard/quality/chrM.single.interval_list] INPUT=/tmp/CollectTargetedMetrics11358391683139703357.bam OUTPUT=/tmp/test17021263166827635619.TargetedMetrics_Coverage METRIC_ACCUMULATION_LEVEL=[ALL_READS] PER_TARGET_COVERAGE=/tmp/perTarget8180380818369984825.perTargetCoverage SAMPLE_SIZE=2000 THEORETICAL_SENSITIVITY_OUTPUT=/tmp/test3020101757453345428.TheoreticalSensitivityMetrics REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta NEAR_DISTANCE=250 MINIMUM_MAPPING_QUALITY=1 MINIMUM_BASE_QUALITY=0 CLIP_OVERLAPPING_READS=false INCLUDE_INDELS=false COVERAGE_CAP=200 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:17 GMT+14:00 2024] CollectTargetedPcrMetrics AMPLICON_INTERVALS=testdata/picard/quality/chrM.single.interval_list TARGET_INTERVALS=[testdata/picard/quality/chrM.single.interval_list] INPUT=/tmp/CollectTargetedMetrics11358391683139703357.bam OUTPUT=/tmp/test17021263166827635619.TargetedMetrics_Coverage METRIC_ACCUMULATION_LEVEL=[ALL_READS] PER_TARGET_COVERAGE=/tmp/perTarget8180380818369984825.perTargetCoverage SAMPLE_SIZE=2000 THEORETICAL_SENSITIVITY_OUTPUT=/tmp/test3020101757453345428.TheoreticalSensitivityMetrics REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta NEAR_DISTANCE=250 MINIMUM_MAPPING_QUALITY=1 MINIMUM_BASE_QUALITY=0 CLIP_OVERLAPPING_READS=false INCLUDE_INDELS=false COVERAGE_CAP=200 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: [Tue Jul 02 11:52:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:17 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:52:17 TheoreticalSensitivity Creating Roulette Wheel Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:17 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:52:17 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:17 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 11:52:17 TheoreticalSensitivity 0 sampling iterations completed Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:17 TheoreticalSensitivity 1000 sampling iterations completed INFO 2024-07-02 11:52:17 TheoreticalSensitivity 1000 sampling iterations completed Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:17 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:52:17 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:17 TargetMetricsCollector Calculating GC metrics INFO 2024-07-02 11:52:17 TargetMetricsCollector Calculating GC metrics Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:17 CollectTargetedPcrMetrics Calculating theoretical sentitivity at 9 allele fractions. INFO 2024-07-02 11:52:17 CollectTargetedPcrMetrics Calculating theoretical sentitivity at 9 allele fractions. Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: [Tue Jul 02 11:52:22 GMT+14:00 2024] picard.analysis.directed.CollectTargetedPcrMetrics done. Elapsed time: 0.10 minutes. [Tue Jul 02 11:52:22 GMT+14:00 2024] picard.analysis.directed.CollectTargetedPcrMetrics done. Elapsed time: 0.10 minutes. Test: Test method runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics11358391683139703357.bam, /tmp/test17021263166827635619.TargetedMetrics_Coverage, /tmp/test3020101757453345428.TheoreticalSensitivityMetrics, /tmp/perTarget8180380818369984825.perTargetCoverage, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99])(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testCoverageGetTotalOverflow(picard.analysis.directed.CollectTargetedMetricsTest) Running Test: Test method testRawBqDistributionWithSoftClips(picard.analysis.directed.CollectTargetedMetricsTest) Test: Test method testRawBqDistributionWithSoftClips(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:22 CollectTargetedPcrMetrics Gradle suite > Gradle test > picard.analysis.directed.CollectTargetedMetricsTest.testRawBqDistributionWithSoftClips STANDARD_ERROR INFO 2024-07-02 11:52:22 CollectTargetedPcrMetrics Test: Test method testRawBqDistributionWithSoftClips(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: Test: Test method testRawBqDistributionWithSoftClips(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRawBqDistributionWithSoftClips(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** ********** Test: Test method testRawBqDistributionWithSoftClips(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRawBqDistributionWithSoftClips(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRawBqDistributionWithSoftClips(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** ********** Test: Test method testRawBqDistributionWithSoftClips(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRawBqDistributionWithSoftClips(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** ********** Test: Test method testRawBqDistributionWithSoftClips(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** CollectTargetedPcrMetrics -TARGET_INTERVALS testdata/picard/quality/chrM.single.interval_list -INPUT testdata/picard/quality/chrMReadsWithClips.sam -OUTPUT /tmp/test16766983517901050277.TargetedMetrics_Coverage -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -LEVEL ALL_READS -AMPLICON_INTERVALS testdata/picard/quality/chrM.single.interval_list -SAMPLE_SIZE 0 ********** CollectTargetedPcrMetrics -TARGET_INTERVALS testdata/picard/quality/chrM.single.interval_list -INPUT testdata/picard/quality/chrMReadsWithClips.sam -OUTPUT /tmp/test16766983517901050277.TargetedMetrics_Coverage -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -LEVEL ALL_READS -AMPLICON_INTERVALS testdata/picard/quality/chrM.single.interval_list -SAMPLE_SIZE 0 Test: Test method testRawBqDistributionWithSoftClips(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: ********** ********** Test: Test method testRawBqDistributionWithSoftClips(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: Test: Test method testRawBqDistributionWithSoftClips(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: Test: Test method testRawBqDistributionWithSoftClips(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: 11:52:22.980 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:22.980 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRawBqDistributionWithSoftClips(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: 11:52:22.980 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:22.980 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRawBqDistributionWithSoftClips(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: 11:52:22.980 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:22.980 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRawBqDistributionWithSoftClips(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: 11:52:22.980 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:22.980 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRawBqDistributionWithSoftClips(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: [Tue Jul 02 11:52:22 GMT+14:00 2024] CollectTargetedPcrMetrics AMPLICON_INTERVALS=testdata/picard/quality/chrM.single.interval_list TARGET_INTERVALS=[testdata/picard/quality/chrM.single.interval_list] INPUT=testdata/picard/quality/chrMReadsWithClips.sam OUTPUT=/tmp/test16766983517901050277.TargetedMetrics_Coverage METRIC_ACCUMULATION_LEVEL=[ALL_READS] SAMPLE_SIZE=0 REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta NEAR_DISTANCE=250 MINIMUM_MAPPING_QUALITY=1 MINIMUM_BASE_QUALITY=0 CLIP_OVERLAPPING_READS=false INCLUDE_INDELS=false COVERAGE_CAP=200 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:22 GMT+14:00 2024] CollectTargetedPcrMetrics AMPLICON_INTERVALS=testdata/picard/quality/chrM.single.interval_list TARGET_INTERVALS=[testdata/picard/quality/chrM.single.interval_list] INPUT=testdata/picard/quality/chrMReadsWithClips.sam OUTPUT=/tmp/test16766983517901050277.TargetedMetrics_Coverage METRIC_ACCUMULATION_LEVEL=[ALL_READS] SAMPLE_SIZE=0 REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta NEAR_DISTANCE=250 MINIMUM_MAPPING_QUALITY=1 MINIMUM_BASE_QUALITY=0 CLIP_OVERLAPPING_READS=false INCLUDE_INDELS=false COVERAGE_CAP=200 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRawBqDistributionWithSoftClips(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: [Tue Jul 02 11:52:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRawBqDistributionWithSoftClips(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:22 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:52:22 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testRawBqDistributionWithSoftClips(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:22 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:52:22 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testRawBqDistributionWithSoftClips(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:22 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:52:22 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testRawBqDistributionWithSoftClips(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:22 TargetMetricsCollector Calculating GC metrics INFO 2024-07-02 11:52:22 TargetMetricsCollector Calculating GC metrics Test: Test method testRawBqDistributionWithSoftClips(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: [Tue Jul 02 11:52:22 GMT+14:00 2024] picard.analysis.directed.CollectTargetedPcrMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:22 GMT+14:00 2024] picard.analysis.directed.CollectTargetedPcrMetrics done. Elapsed time: 0.00 minutes. Test: Test method testRawBqDistributionWithSoftClips(picard.analysis.directed.CollectTargetedMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testAllHomRefVCF(picard.vcf.CollectVariantCallingMetricsTest) Test: Test method testAllHomRefVCF(picard.vcf.CollectVariantCallingMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:23 CollectVariantCallingMetrics Loading dbSNP file ... Gradle suite > Gradle test > picard.vcf.CollectVariantCallingMetricsTest.testAllHomRefVCF STANDARD_ERROR INFO 2024-07-02 11:52:23 CollectVariantCallingMetrics Loading dbSNP file ... Test: Test method testAllHomRefVCF(picard.vcf.CollectVariantCallingMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:23 CollectVariantCallingMetrics Starting iteration of variants. INFO 2024-07-02 11:52:23 CollectVariantCallingMetrics Starting iteration of variants. Running Test: Test method testMetricsTiny(picard.vcf.CollectVariantCallingMetricsTest) Test: Test method testMetricsTiny(picard.vcf.CollectVariantCallingMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:23 CollectVariantCallingMetrics Loading dbSNP file ... Gradle suite > Gradle test > picard.vcf.CollectVariantCallingMetricsTest.testMetricsTiny STANDARD_ERROR INFO 2024-07-02 11:52:23 CollectVariantCallingMetrics Loading dbSNP file ... Test: Test method testMetricsTiny(picard.vcf.CollectVariantCallingMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:23 CollectVariantCallingMetrics Starting iteration of variants. INFO 2024-07-02 11:52:23 CollectVariantCallingMetrics Starting iteration of variants. Running Test: Test method testMetricsTinyGVCF(picard.vcf.CollectVariantCallingMetricsTest) Test: Test method testMetricsTinyGVCF(picard.vcf.CollectVariantCallingMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:23 CollectVariantCallingMetrics Loading dbSNP file ... Gradle suite > Gradle test > picard.vcf.CollectVariantCallingMetricsTest.testMetricsTinyGVCF STANDARD_ERROR INFO 2024-07-02 11:52:23 CollectVariantCallingMetrics Loading dbSNP file ... Test: Test method testMetricsTinyGVCF(picard.vcf.CollectVariantCallingMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:23 CollectVariantCallingMetrics Starting iteration of variants. INFO 2024-07-02 11:52:23 CollectVariantCallingMetrics Starting iteration of variants. Running Test: Test method testAdapterReads[0](false)(picard.analysis.CollectWgsMetricsTest) Test: Test method testAdapterReads[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:23 CollectWgsMetrics Gradle suite > Gradle test > picard.analysis.CollectWgsMetricsTest.testAdapterReads[0](false) STANDARD_ERROR INFO 2024-07-02 11:52:23 CollectWgsMetrics Test: Test method testAdapterReads[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testAdapterReads[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testAdapterReads[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testAdapterReads[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testAdapterReads[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testAdapterReads[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testAdapterReads[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testAdapterReads[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testAdapterReads[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** CollectWgsMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/metrics/AlignedAdapterReads.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testAdapterReads1766411362970434625.wgs_metrics -SAMPLE_SIZE 10 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -USE_FAST_ALGORITHM false ********** CollectWgsMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/metrics/AlignedAdapterReads.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testAdapterReads1766411362970434625.wgs_metrics -SAMPLE_SIZE 10 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -USE_FAST_ALGORITHM false Test: Test method testAdapterReads[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testAdapterReads[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testAdapterReads[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testAdapterReads[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:23.692 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:23.692 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAdapterReads[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:23.692 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:23.692 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAdapterReads[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:23.692 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:23.692 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAdapterReads[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:23.692 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:23.692 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAdapterReads[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:23 GMT+14:00 2024] CollectWgsMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/metrics/AlignedAdapterReads.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testAdapterReads1766411362970434625.wgs_metrics SAMPLE_SIZE=10 USE_FAST_ALGORITHM=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:23 GMT+14:00 2024] CollectWgsMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/metrics/AlignedAdapterReads.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testAdapterReads1766411362970434625.wgs_metrics SAMPLE_SIZE=10 USE_FAST_ALGORITHM=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testAdapterReads[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testAdapterReads[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: WARNING 2024-07-02 11:52:23 AbstractLocusIterator SamLocusIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. WARNING 2024-07-02 11:52:23 AbstractLocusIterator SamLocusIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. Test: Test method testAdapterReads[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:23 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:52:23 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testAdapterReads[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:23 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:52:23 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testAdapterReads[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:23 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 11:52:23 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testAdapterReads[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:23 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:52:23 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testAdapterReads[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:23 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:23 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.00 minutes. Test: Test method testAdapterReads[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testAdapterReads[1](true)(picard.analysis.CollectWgsMetricsTest) Test: Test method testAdapterReads[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:23 CollectWgsMetrics Gradle suite > Gradle test > picard.analysis.CollectWgsMetricsTest.testAdapterReads[1](true) STANDARD_ERROR INFO 2024-07-02 11:52:23 CollectWgsMetrics Test: Test method testAdapterReads[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testAdapterReads[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testAdapterReads[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testAdapterReads[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testAdapterReads[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testAdapterReads[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testAdapterReads[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testAdapterReads[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testAdapterReads[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** CollectWgsMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/metrics/AlignedAdapterReads.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testAdapterReads4032553861447256206.wgs_metrics -SAMPLE_SIZE 10 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -USE_FAST_ALGORITHM true ********** CollectWgsMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/metrics/AlignedAdapterReads.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testAdapterReads4032553861447256206.wgs_metrics -SAMPLE_SIZE 10 -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -USE_FAST_ALGORITHM true Test: Test method testAdapterReads[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testAdapterReads[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testAdapterReads[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testAdapterReads[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:23.876 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:23.876 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAdapterReads[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:23.877 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:23.877 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAdapterReads[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:23.879 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:23.879 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAdapterReads[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:23.879 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:23.879 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAdapterReads[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:23 GMT+14:00 2024] CollectWgsMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/metrics/AlignedAdapterReads.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testAdapterReads4032553861447256206.wgs_metrics SAMPLE_SIZE=10 USE_FAST_ALGORITHM=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:23 GMT+14:00 2024] CollectWgsMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/metrics/AlignedAdapterReads.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testAdapterReads4032553861447256206.wgs_metrics SAMPLE_SIZE=10 USE_FAST_ALGORITHM=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testAdapterReads[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testAdapterReads[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: WARNING 2024-07-02 11:52:23 AbstractLocusIterator EdgeReadIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. WARNING 2024-07-02 11:52:23 AbstractLocusIterator EdgeReadIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. Test: Test method testAdapterReads[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:23 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:52:23 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testAdapterReads[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:23 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:52:23 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testAdapterReads[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 11:52:24 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testAdapterReads[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:52:24 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testAdapterReads[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:24 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:24 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.00 minutes. Test: Test method testAdapterReads[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 CollectWgsMetrics Gradle suite > Gradle test > picard.analysis.CollectWgsMetricsTest.testExclusions[0](false) STANDARD_ERROR INFO 2024-07-02 11:52:24 CollectWgsMetrics Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** CollectWgsMetrics -INPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testExclusions7779684061521152103.bam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testExclusions15942378923486215734.txt -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -INCLUDE_BQ_HISTOGRAM true -COVERAGE_CAP 3 -USE_FAST_ALGORITHM false ********** CollectWgsMetrics -INPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testExclusions7779684061521152103.bam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testExclusions15942378923486215734.txt -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -INCLUDE_BQ_HISTOGRAM true -COVERAGE_CAP 3 -USE_FAST_ALGORITHM false Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:24.147 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:24.147 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:24.147 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:24.147 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:24.147 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:24.147 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:24.147 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:24.147 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:24 GMT+14:00 2024] CollectWgsMetrics INPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testExclusions7779684061521152103.bam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testExclusions15942378923486215734.txt COVERAGE_CAP=3 INCLUDE_BQ_HISTOGRAM=true USE_FAST_ALGORITHM=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:24 GMT+14:00 2024] CollectWgsMetrics INPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testExclusions7779684061521152103.bam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testExclusions15942378923486215734.txt COVERAGE_CAP=3 INCLUDE_BQ_HISTOGRAM=true USE_FAST_ALGORITHM=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: WARNING 2024-07-02 11:52:24 AbstractLocusIterator SamLocusIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. WARNING 2024-07-02 11:52:24 AbstractLocusIterator SamLocusIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:52:24 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:52:24 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 11:52:24 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 TheoreticalSensitivity 1000 sampling iterations completed INFO 2024-07-02 11:52:24 TheoreticalSensitivity 1000 sampling iterations completed Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 TheoreticalSensitivity 2000 sampling iterations completed INFO 2024-07-02 11:52:24 TheoreticalSensitivity 2000 sampling iterations completed Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 TheoreticalSensitivity 3000 sampling iterations completed INFO 2024-07-02 11:52:24 TheoreticalSensitivity 3000 sampling iterations completed Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 TheoreticalSensitivity 4000 sampling iterations completed INFO 2024-07-02 11:52:24 TheoreticalSensitivity 4000 sampling iterations completed Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 TheoreticalSensitivity 5000 sampling iterations completed INFO 2024-07-02 11:52:24 TheoreticalSensitivity 5000 sampling iterations completed Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 TheoreticalSensitivity 6000 sampling iterations completed INFO 2024-07-02 11:52:24 TheoreticalSensitivity 6000 sampling iterations completed Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 TheoreticalSensitivity 7000 sampling iterations completed INFO 2024-07-02 11:52:24 TheoreticalSensitivity 7000 sampling iterations completed Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 TheoreticalSensitivity 8000 sampling iterations completed INFO 2024-07-02 11:52:24 TheoreticalSensitivity 8000 sampling iterations completed Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 TheoreticalSensitivity 9000 sampling iterations completed INFO 2024-07-02 11:52:24 TheoreticalSensitivity 9000 sampling iterations completed Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:52:24 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:24 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:52:24 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.01 minutes. Test: Test method testExclusions[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 CollectWgsMetrics Gradle suite > Gradle test > picard.analysis.CollectWgsMetricsTest.testExclusions[1](true) STANDARD_ERROR INFO 2024-07-02 11:52:24 CollectWgsMetrics Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** CollectWgsMetrics -INPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testExclusions10654490796526000470.bam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testExclusions3316188072799514838.txt -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -INCLUDE_BQ_HISTOGRAM true -COVERAGE_CAP 3 -USE_FAST_ALGORITHM true ********** CollectWgsMetrics -INPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testExclusions10654490796526000470.bam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testExclusions3316188072799514838.txt -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -INCLUDE_BQ_HISTOGRAM true -COVERAGE_CAP 3 -USE_FAST_ALGORITHM true Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:24.545 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:24.545 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:24.545 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:24.545 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:24.545 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:24.545 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:24.545 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:24.545 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:24 GMT+14:00 2024] CollectWgsMetrics INPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testExclusions10654490796526000470.bam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testExclusions3316188072799514838.txt COVERAGE_CAP=3 INCLUDE_BQ_HISTOGRAM=true USE_FAST_ALGORITHM=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:24 GMT+14:00 2024] CollectWgsMetrics INPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testExclusions10654490796526000470.bam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testExclusions3316188072799514838.txt COVERAGE_CAP=3 INCLUDE_BQ_HISTOGRAM=true USE_FAST_ALGORITHM=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: WARNING 2024-07-02 11:52:24 AbstractLocusIterator EdgeReadIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. WARNING 2024-07-02 11:52:24 AbstractLocusIterator EdgeReadIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:52:24 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:52:24 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 11:52:24 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 TheoreticalSensitivity 1000 sampling iterations completed INFO 2024-07-02 11:52:24 TheoreticalSensitivity 1000 sampling iterations completed Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 TheoreticalSensitivity 2000 sampling iterations completed INFO 2024-07-02 11:52:24 TheoreticalSensitivity 2000 sampling iterations completed Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 TheoreticalSensitivity 3000 sampling iterations completed INFO 2024-07-02 11:52:24 TheoreticalSensitivity 3000 sampling iterations completed Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 TheoreticalSensitivity 4000 sampling iterations completed INFO 2024-07-02 11:52:24 TheoreticalSensitivity 4000 sampling iterations completed Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 TheoreticalSensitivity 5000 sampling iterations completed INFO 2024-07-02 11:52:24 TheoreticalSensitivity 5000 sampling iterations completed Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 TheoreticalSensitivity 6000 sampling iterations completed INFO 2024-07-02 11:52:24 TheoreticalSensitivity 6000 sampling iterations completed Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 TheoreticalSensitivity 7000 sampling iterations completed INFO 2024-07-02 11:52:24 TheoreticalSensitivity 7000 sampling iterations completed Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 TheoreticalSensitivity 8000 sampling iterations completed INFO 2024-07-02 11:52:24 TheoreticalSensitivity 8000 sampling iterations completed Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 TheoreticalSensitivity 9000 sampling iterations completed INFO 2024-07-02 11:52:24 TheoreticalSensitivity 9000 sampling iterations completed Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:24 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:52:24 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:25 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:52:25 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.01 minutes. Test: Test method testExclusions[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testFailDifferentSequenceDictionaries(picard.analysis.CollectWgsMetricsTest) Test: Test method testFailDifferentSequenceDictionaries(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:25 CollectWgsMetrics Gradle suite > Gradle test > picard.analysis.CollectWgsMetricsTest.testFailDifferentSequenceDictionaries STANDARD_ERROR INFO 2024-07-02 11:52:25 CollectWgsMetrics Test: Test method testFailDifferentSequenceDictionaries(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testFailDifferentSequenceDictionaries(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFailDifferentSequenceDictionaries(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testFailDifferentSequenceDictionaries(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFailDifferentSequenceDictionaries(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFailDifferentSequenceDictionaries(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testFailDifferentSequenceDictionaries(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFailDifferentSequenceDictionaries(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testFailDifferentSequenceDictionaries(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** CollectWgsMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/forMetrics.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/test13304793109500913181.wgs_metrics -REFERENCE_SEQUENCE testdata/picard/reference/test.fasta ********** CollectWgsMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/forMetrics.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/test13304793109500913181.wgs_metrics -REFERENCE_SEQUENCE testdata/picard/reference/test.fasta Test: Test method testFailDifferentSequenceDictionaries(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testFailDifferentSequenceDictionaries(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testFailDifferentSequenceDictionaries(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testFailDifferentSequenceDictionaries(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:25.172 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:25.172 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFailDifferentSequenceDictionaries(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:25.172 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:25.172 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFailDifferentSequenceDictionaries(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:25.173 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:25.173 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFailDifferentSequenceDictionaries(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:25.173 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:25.173 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFailDifferentSequenceDictionaries(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:25 GMT+14:00 2024] CollectWgsMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/forMetrics.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/test13304793109500913181.wgs_metrics REFERENCE_SEQUENCE=testdata/picard/reference/test.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:25 GMT+14:00 2024] CollectWgsMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/forMetrics.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/test13304793109500913181.wgs_metrics REFERENCE_SEQUENCE=testdata/picard/reference/test.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFailDifferentSequenceDictionaries(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFailDifferentSequenceDictionaries(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:25 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:52:25 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.00 minutes. Test: Test method testFailDifferentSequenceDictionaries(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testFailDifferentSequenceDictionaries(picard.analysis.CollectWgsMetricsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:25 CollectWgsMetrics Gradle suite > Gradle test > picard.analysis.CollectWgsMetricsTest.testGiantDeletion[0](false) STANDARD_ERROR INFO 2024-07-02 11:52:25 CollectWgsMetrics Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** CollectWgsMetrics -INPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testGiantDeletion9452689621455284632.bam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testGiantDeletion9857088421466479878.txt -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -INCLUDE_BQ_HISTOGRAM true -COVERAGE_CAP 3 -USE_FAST_ALGORITHM false ********** CollectWgsMetrics -INPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testGiantDeletion9452689621455284632.bam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testGiantDeletion9857088421466479878.txt -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -INCLUDE_BQ_HISTOGRAM true -COVERAGE_CAP 3 -USE_FAST_ALGORITHM false Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:25.210 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:25.210 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:25.210 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:25.210 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:25.210 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:25.210 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:25.210 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:25.210 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:25 GMT+14:00 2024] CollectWgsMetrics INPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testGiantDeletion9452689621455284632.bam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testGiantDeletion9857088421466479878.txt COVERAGE_CAP=3 INCLUDE_BQ_HISTOGRAM=true USE_FAST_ALGORITHM=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:25 GMT+14:00 2024] CollectWgsMetrics INPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testGiantDeletion9452689621455284632.bam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testGiantDeletion9857088421466479878.txt COVERAGE_CAP=3 INCLUDE_BQ_HISTOGRAM=true USE_FAST_ALGORITHM=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: WARNING 2024-07-02 11:52:25 AbstractLocusIterator SamLocusIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. WARNING 2024-07-02 11:52:25 AbstractLocusIterator SamLocusIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:25 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:52:25 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:25 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:52:25 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:25 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 11:52:25 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:25 TheoreticalSensitivity 1000 sampling iterations completed INFO 2024-07-02 11:52:25 TheoreticalSensitivity 1000 sampling iterations completed Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:25 TheoreticalSensitivity 2000 sampling iterations completed INFO 2024-07-02 11:52:25 TheoreticalSensitivity 2000 sampling iterations completed Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:25 TheoreticalSensitivity 3000 sampling iterations completed INFO 2024-07-02 11:52:25 TheoreticalSensitivity 3000 sampling iterations completed Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:25 TheoreticalSensitivity 4000 sampling iterations completed INFO 2024-07-02 11:52:25 TheoreticalSensitivity 4000 sampling iterations completed Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:25 TheoreticalSensitivity 5000 sampling iterations completed INFO 2024-07-02 11:52:25 TheoreticalSensitivity 5000 sampling iterations completed Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:25 TheoreticalSensitivity 6000 sampling iterations completed INFO 2024-07-02 11:52:25 TheoreticalSensitivity 6000 sampling iterations completed Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:25 TheoreticalSensitivity 7000 sampling iterations completed INFO 2024-07-02 11:52:25 TheoreticalSensitivity 7000 sampling iterations completed Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:25 TheoreticalSensitivity 8000 sampling iterations completed INFO 2024-07-02 11:52:25 TheoreticalSensitivity 8000 sampling iterations completed Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:25 TheoreticalSensitivity 9000 sampling iterations completed INFO 2024-07-02 11:52:25 TheoreticalSensitivity 9000 sampling iterations completed Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:25 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:52:25 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:25 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:52:25 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.01 minutes. Test: Test method testGiantDeletion[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:25 CollectWgsMetrics Gradle suite > Gradle test > picard.analysis.CollectWgsMetricsTest.testGiantDeletion[1](true) STANDARD_ERROR INFO 2024-07-02 11:52:25 CollectWgsMetrics Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** CollectWgsMetrics -INPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testGiantDeletion17438815158017866079.bam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testGiantDeletion10118845330539496451.txt -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -INCLUDE_BQ_HISTOGRAM true -COVERAGE_CAP 3 -USE_FAST_ALGORITHM true ********** CollectWgsMetrics -INPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testGiantDeletion17438815158017866079.bam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testGiantDeletion10118845330539496451.txt -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -INCLUDE_BQ_HISTOGRAM true -COVERAGE_CAP 3 -USE_FAST_ALGORITHM true Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:25.859 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:25.859 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:25.859 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:25.859 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:25.859 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:25.859 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:25.859 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:25.859 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:25 GMT+14:00 2024] CollectWgsMetrics INPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testGiantDeletion17438815158017866079.bam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testGiantDeletion10118845330539496451.txt COVERAGE_CAP=3 INCLUDE_BQ_HISTOGRAM=true USE_FAST_ALGORITHM=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:25 GMT+14:00 2024] CollectWgsMetrics INPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testGiantDeletion17438815158017866079.bam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testGiantDeletion10118845330539496451.txt COVERAGE_CAP=3 INCLUDE_BQ_HISTOGRAM=true USE_FAST_ALGORITHM=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: WARNING 2024-07-02 11:52:25 AbstractLocusIterator EdgeReadIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. WARNING 2024-07-02 11:52:25 AbstractLocusIterator EdgeReadIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:25 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:52:25 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:25 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:52:25 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:25 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 11:52:25 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:25 TheoreticalSensitivity 1000 sampling iterations completed INFO 2024-07-02 11:52:25 TheoreticalSensitivity 1000 sampling iterations completed Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:26 TheoreticalSensitivity 2000 sampling iterations completed INFO 2024-07-02 11:52:26 TheoreticalSensitivity 2000 sampling iterations completed Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:26 TheoreticalSensitivity 3000 sampling iterations completed INFO 2024-07-02 11:52:26 TheoreticalSensitivity 3000 sampling iterations completed Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:26 TheoreticalSensitivity 4000 sampling iterations completed INFO 2024-07-02 11:52:26 TheoreticalSensitivity 4000 sampling iterations completed Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:26 TheoreticalSensitivity 5000 sampling iterations completed INFO 2024-07-02 11:52:26 TheoreticalSensitivity 5000 sampling iterations completed Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:26 TheoreticalSensitivity 6000 sampling iterations completed INFO 2024-07-02 11:52:26 TheoreticalSensitivity 6000 sampling iterations completed Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:26 TheoreticalSensitivity 7000 sampling iterations completed INFO 2024-07-02 11:52:26 TheoreticalSensitivity 7000 sampling iterations completed Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:26 TheoreticalSensitivity 8000 sampling iterations completed INFO 2024-07-02 11:52:26 TheoreticalSensitivity 8000 sampling iterations completed Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:26 TheoreticalSensitivity 9000 sampling iterations completed INFO 2024-07-02 11:52:26 TheoreticalSensitivity 9000 sampling iterations completed Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:26 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:52:26 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:26 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:52:26 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.01 minutes. Test: Test method testGiantDeletion[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIntervalOneRead[0](false)(picard.analysis.CollectWgsMetricsTest) Test: Test method testIntervalOneRead[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:26 CollectWgsMetrics Gradle suite > Gradle test > picard.analysis.CollectWgsMetricsTest.testIntervalOneRead[0](false) STANDARD_ERROR INFO 2024-07-02 11:52:26 CollectWgsMetrics Test: Test method testIntervalOneRead[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testIntervalOneRead[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIntervalOneRead[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testIntervalOneRead[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIntervalOneRead[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIntervalOneRead[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testIntervalOneRead[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIntervalOneRead[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testIntervalOneRead[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** CollectWgsMetrics -INPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testIntervalOneRead5793628336006940891.bam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testIntervalOneRead10921041526219319719.wgs_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -INTERVALS /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/smallIntervals.interval_list -SAMPLE_SIZE 1000 -USE_FAST_ALGORITHM false ********** CollectWgsMetrics -INPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testIntervalOneRead5793628336006940891.bam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testIntervalOneRead10921041526219319719.wgs_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -INTERVALS /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/smallIntervals.interval_list -SAMPLE_SIZE 1000 -USE_FAST_ALGORITHM false Test: Test method testIntervalOneRead[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testIntervalOneRead[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testIntervalOneRead[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testIntervalOneRead[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:26.407 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:26.407 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIntervalOneRead[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:26.407 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:26.407 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIntervalOneRead[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:26.407 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:26.407 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIntervalOneRead[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:26.407 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:26.407 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIntervalOneRead[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:26 GMT+14:00 2024] CollectWgsMetrics INPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testIntervalOneRead5793628336006940891.bam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testIntervalOneRead10921041526219319719.wgs_metrics SAMPLE_SIZE=1000 INTERVALS=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/smallIntervals.interval_list USE_FAST_ALGORITHM=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:26 GMT+14:00 2024] CollectWgsMetrics INPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testIntervalOneRead5793628336006940891.bam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testIntervalOneRead10921041526219319719.wgs_metrics SAMPLE_SIZE=1000 INTERVALS=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/smallIntervals.interval_list USE_FAST_ALGORITHM=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIntervalOneRead[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIntervalOneRead[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: WARNING 2024-07-02 11:52:26 AbstractLocusIterator SamLocusIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. WARNING 2024-07-02 11:52:26 AbstractLocusIterator SamLocusIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. Test: Test method testIntervalOneRead[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:26 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:52:26 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testIntervalOneRead[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:26 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:52:26 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testIntervalOneRead[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:26 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 11:52:26 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testIntervalOneRead[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:28 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:52:28 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testIntervalOneRead[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:28 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:52:28 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.04 minutes. Test: Test method testIntervalOneRead[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testIntervalOneRead[1](true)(picard.analysis.CollectWgsMetricsTest) Test: Test method testIntervalOneRead[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:28 CollectWgsMetrics Gradle suite > Gradle test > picard.analysis.CollectWgsMetricsTest.testIntervalOneRead[1](true) STANDARD_ERROR INFO 2024-07-02 11:52:28 CollectWgsMetrics Test: Test method testIntervalOneRead[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testIntervalOneRead[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIntervalOneRead[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testIntervalOneRead[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIntervalOneRead[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIntervalOneRead[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testIntervalOneRead[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIntervalOneRead[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testIntervalOneRead[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** CollectWgsMetrics -INPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testIntervalOneRead57849137672028890.bam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testIntervalOneRead5029268034423521621.wgs_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -INTERVALS /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/smallIntervals.interval_list -SAMPLE_SIZE 1000 -USE_FAST_ALGORITHM true ********** CollectWgsMetrics -INPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testIntervalOneRead57849137672028890.bam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testIntervalOneRead5029268034423521621.wgs_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -INTERVALS /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/smallIntervals.interval_list -SAMPLE_SIZE 1000 -USE_FAST_ALGORITHM true Test: Test method testIntervalOneRead[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testIntervalOneRead[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testIntervalOneRead[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testIntervalOneRead[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:28.936 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:28.936 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIntervalOneRead[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:28.937 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:28.937 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIntervalOneRead[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:28.938 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:28.938 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIntervalOneRead[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:28.938 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:28.938 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIntervalOneRead[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:28 GMT+14:00 2024] CollectWgsMetrics INPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testIntervalOneRead57849137672028890.bam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testIntervalOneRead5029268034423521621.wgs_metrics SAMPLE_SIZE=1000 INTERVALS=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/smallIntervals.interval_list USE_FAST_ALGORITHM=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:28 GMT+14:00 2024] CollectWgsMetrics INPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testIntervalOneRead57849137672028890.bam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testIntervalOneRead5029268034423521621.wgs_metrics SAMPLE_SIZE=1000 INTERVALS=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/smallIntervals.interval_list USE_FAST_ALGORITHM=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIntervalOneRead[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIntervalOneRead[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: WARNING 2024-07-02 11:52:29 AbstractLocusIterator EdgeReadIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. WARNING 2024-07-02 11:52:29 AbstractLocusIterator EdgeReadIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. Test: Test method testIntervalOneRead[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:29 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:52:29 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testIntervalOneRead[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:29 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:52:29 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testIntervalOneRead[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:29 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 11:52:29 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testIntervalOneRead[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:31 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:52:31 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testIntervalOneRead[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:31 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:52:31 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.04 minutes. Test: Test method testIntervalOneRead[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testLargeIntervals[0](false)(picard.analysis.CollectWgsMetricsTest) Test: Test method testLargeIntervals[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:31 CollectWgsMetrics Gradle suite > Gradle test > picard.analysis.CollectWgsMetricsTest.testLargeIntervals[0](false) STANDARD_ERROR INFO 2024-07-02 11:52:31 CollectWgsMetrics Test: Test method testLargeIntervals[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testLargeIntervals[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testLargeIntervals[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testLargeIntervals[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testLargeIntervals[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testLargeIntervals[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testLargeIntervals[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testLargeIntervals[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testLargeIntervals[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** CollectWgsMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/forMetrics.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/test12505222438386842556.wgs_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -INTERVALS /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/largeIntervals.interval_list -SAMPLE_SIZE 1000 -USE_FAST_ALGORITHM false ********** CollectWgsMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/forMetrics.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/test12505222438386842556.wgs_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -INTERVALS /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/largeIntervals.interval_list -SAMPLE_SIZE 1000 -USE_FAST_ALGORITHM false Test: Test method testLargeIntervals[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testLargeIntervals[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testLargeIntervals[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testLargeIntervals[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:31.185 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:31.185 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testLargeIntervals[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:31.186 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:31.186 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testLargeIntervals[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:31.186 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:31.186 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testLargeIntervals[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:31.186 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:31.186 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testLargeIntervals[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:31 GMT+14:00 2024] CollectWgsMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/forMetrics.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/test12505222438386842556.wgs_metrics SAMPLE_SIZE=1000 INTERVALS=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/largeIntervals.interval_list USE_FAST_ALGORITHM=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:31 GMT+14:00 2024] CollectWgsMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/forMetrics.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/test12505222438386842556.wgs_metrics SAMPLE_SIZE=1000 INTERVALS=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/largeIntervals.interval_list USE_FAST_ALGORITHM=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testLargeIntervals[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testLargeIntervals[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:31 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:52:31 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testLargeIntervals[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:31 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:52:31 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testLargeIntervals[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:31 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 11:52:31 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testLargeIntervals[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:33 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:52:33 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testLargeIntervals[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:33 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.03 minutes. [Tue Jul 02 11:52:33 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.03 minutes. Test: Test method testLargeIntervals[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testLargeIntervals[1](true)(picard.analysis.CollectWgsMetricsTest) Test: Test method testLargeIntervals[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:33 CollectWgsMetrics Gradle suite > Gradle test > picard.analysis.CollectWgsMetricsTest.testLargeIntervals[1](true) STANDARD_ERROR INFO 2024-07-02 11:52:33 CollectWgsMetrics Test: Test method testLargeIntervals[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testLargeIntervals[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testLargeIntervals[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testLargeIntervals[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testLargeIntervals[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testLargeIntervals[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testLargeIntervals[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testLargeIntervals[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testLargeIntervals[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** CollectWgsMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/forMetrics.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/test3587837990815261980.wgs_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -INTERVALS /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/largeIntervals.interval_list -SAMPLE_SIZE 1000 -USE_FAST_ALGORITHM true ********** CollectWgsMetrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/forMetrics.sam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/test3587837990815261980.wgs_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -INTERVALS /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/largeIntervals.interval_list -SAMPLE_SIZE 1000 -USE_FAST_ALGORITHM true Test: Test method testLargeIntervals[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testLargeIntervals[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testLargeIntervals[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testLargeIntervals[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:33.284 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:33.284 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testLargeIntervals[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:33.284 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:33.284 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testLargeIntervals[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:33.284 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:33.284 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testLargeIntervals[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:33.284 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:33.284 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testLargeIntervals[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:33 GMT+14:00 2024] CollectWgsMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/forMetrics.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/test3587837990815261980.wgs_metrics SAMPLE_SIZE=1000 INTERVALS=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/largeIntervals.interval_list USE_FAST_ALGORITHM=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:33 GMT+14:00 2024] CollectWgsMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/forMetrics.sam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/test3587837990815261980.wgs_metrics SAMPLE_SIZE=1000 INTERVALS=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/largeIntervals.interval_list USE_FAST_ALGORITHM=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testLargeIntervals[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testLargeIntervals[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:33 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:52:33 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testLargeIntervals[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:33 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:52:33 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testLargeIntervals[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:33 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 11:52:33 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testLargeIntervals[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:35 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:52:35 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testLargeIntervals[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:35 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:52:35 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.04 minutes. Test: Test method testLargeIntervals[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMetricsFromWGS[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) Test: Test method testMetricsFromWGS[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:35 CollectWgsMetrics Gradle suite > Gradle test > picard.analysis.CollectWgsMetricsTest.testMetricsFromWGS[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false) STANDARD_ERROR INFO 2024-07-02 11:52:35 CollectWgsMetrics Test: Test method testMetricsFromWGS[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testMetricsFromWGS[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMetricsFromWGS[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testMetricsFromWGS[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMetricsFromWGS[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMetricsFromWGS[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testMetricsFromWGS[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMetricsFromWGS[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testMetricsFromWGS[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** CollectWgsMetrics -INPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testMetricsFromWGS2844452905640109234.wgs_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -SAMPLE_SIZE 1000 -USE_FAST_ALGORITHM false ********** CollectWgsMetrics -INPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testMetricsFromWGS2844452905640109234.wgs_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -SAMPLE_SIZE 1000 -USE_FAST_ALGORITHM false Test: Test method testMetricsFromWGS[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testMetricsFromWGS[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testMetricsFromWGS[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testMetricsFromWGS[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:35.467 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:35.467 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMetricsFromWGS[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:35.467 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:35.467 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMetricsFromWGS[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:35.467 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:35.467 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMetricsFromWGS[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:35.467 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:35.467 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMetricsFromWGS[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:35 GMT+14:00 2024] CollectWgsMetrics INPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testMetricsFromWGS2844452905640109234.wgs_metrics SAMPLE_SIZE=1000 USE_FAST_ALGORITHM=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:35 GMT+14:00 2024] CollectWgsMetrics INPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testMetricsFromWGS2844452905640109234.wgs_metrics SAMPLE_SIZE=1000 USE_FAST_ALGORITHM=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMetricsFromWGS[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMetricsFromWGS[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:37 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:52:37 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testMetricsFromWGS[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:37 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:52:37 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testMetricsFromWGS[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:37 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 11:52:37 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testMetricsFromWGS[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:37 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:52:37 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testMetricsFromWGS[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:37 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:52:37 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.04 minutes. Test: Test method testMetricsFromWGS[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMetricsFromWGS[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) Test: Test method testMetricsFromWGS[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:37 CollectWgsMetrics Gradle suite > Gradle test > picard.analysis.CollectWgsMetricsTest.testMetricsFromWGS[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true) STANDARD_ERROR INFO 2024-07-02 11:52:37 CollectWgsMetrics Test: Test method testMetricsFromWGS[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testMetricsFromWGS[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMetricsFromWGS[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testMetricsFromWGS[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMetricsFromWGS[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMetricsFromWGS[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testMetricsFromWGS[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMetricsFromWGS[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testMetricsFromWGS[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** CollectWgsMetrics -INPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testMetricsFromWGS2691100741092874252.wgs_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -SAMPLE_SIZE 1000 -USE_FAST_ALGORITHM true ********** CollectWgsMetrics -INPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testMetricsFromWGS2691100741092874252.wgs_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -SAMPLE_SIZE 1000 -USE_FAST_ALGORITHM true Test: Test method testMetricsFromWGS[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testMetricsFromWGS[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testMetricsFromWGS[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testMetricsFromWGS[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:37.810 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:37.810 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMetricsFromWGS[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:37.810 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:37.810 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMetricsFromWGS[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:37.810 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:37.810 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMetricsFromWGS[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:37.810 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:37.810 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMetricsFromWGS[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:37 GMT+14:00 2024] CollectWgsMetrics INPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testMetricsFromWGS2691100741092874252.wgs_metrics SAMPLE_SIZE=1000 USE_FAST_ALGORITHM=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:37 GMT+14:00 2024] CollectWgsMetrics INPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testMetricsFromWGS2691100741092874252.wgs_metrics SAMPLE_SIZE=1000 USE_FAST_ALGORITHM=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMetricsFromWGS[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMetricsFromWGS[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:38 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:52:38 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testMetricsFromWGS[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:38 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:52:38 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testMetricsFromWGS[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:38 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 11:52:38 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testMetricsFromWGS[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:38 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:52:38 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testMetricsFromWGS[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:39 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:52:39 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.02 minutes. Test: Test method testMetricsFromWGS[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:39 CollectWgsMetrics Gradle suite > Gradle test > picard.analysis.CollectWgsMetricsTest.testPoorQualityBases[0](false) STANDARD_ERROR INFO 2024-07-02 11:52:39 CollectWgsMetrics Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** CollectWgsMetrics -INPUT /tmp/CollectWgsMetrics1796091176568130644.bam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testPoorQualityBases8462440927647611859.txt -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -INCLUDE_BQ_HISTOGRAM true -COVERAGE_CAP 3 -USE_FAST_ALGORITHM false ********** CollectWgsMetrics -INPUT /tmp/CollectWgsMetrics1796091176568130644.bam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testPoorQualityBases8462440927647611859.txt -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -INCLUDE_BQ_HISTOGRAM true -COVERAGE_CAP 3 -USE_FAST_ALGORITHM false Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:39.162 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:39.162 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:39.162 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:39.162 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:39.163 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:39.163 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:39.163 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:39.163 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:39 GMT+14:00 2024] CollectWgsMetrics INPUT=/tmp/CollectWgsMetrics1796091176568130644.bam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testPoorQualityBases8462440927647611859.txt COVERAGE_CAP=3 INCLUDE_BQ_HISTOGRAM=true USE_FAST_ALGORITHM=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:39 GMT+14:00 2024] CollectWgsMetrics INPUT=/tmp/CollectWgsMetrics1796091176568130644.bam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testPoorQualityBases8462440927647611859.txt COVERAGE_CAP=3 INCLUDE_BQ_HISTOGRAM=true USE_FAST_ALGORITHM=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: WARNING 2024-07-02 11:52:39 AbstractLocusIterator SamLocusIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. WARNING 2024-07-02 11:52:39 AbstractLocusIterator SamLocusIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:39 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:52:39 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:39 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:52:39 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:39 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 11:52:39 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:39 TheoreticalSensitivity 1000 sampling iterations completed INFO 2024-07-02 11:52:39 TheoreticalSensitivity 1000 sampling iterations completed Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:39 TheoreticalSensitivity 2000 sampling iterations completed INFO 2024-07-02 11:52:39 TheoreticalSensitivity 2000 sampling iterations completed Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:39 TheoreticalSensitivity 3000 sampling iterations completed INFO 2024-07-02 11:52:39 TheoreticalSensitivity 3000 sampling iterations completed Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:39 TheoreticalSensitivity 4000 sampling iterations completed INFO 2024-07-02 11:52:39 TheoreticalSensitivity 4000 sampling iterations completed Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:39 TheoreticalSensitivity 5000 sampling iterations completed INFO 2024-07-02 11:52:39 TheoreticalSensitivity 5000 sampling iterations completed Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:39 TheoreticalSensitivity 6000 sampling iterations completed INFO 2024-07-02 11:52:39 TheoreticalSensitivity 6000 sampling iterations completed Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:39 TheoreticalSensitivity 7000 sampling iterations completed INFO 2024-07-02 11:52:39 TheoreticalSensitivity 7000 sampling iterations completed Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:39 TheoreticalSensitivity 8000 sampling iterations completed INFO 2024-07-02 11:52:39 TheoreticalSensitivity 8000 sampling iterations completed Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:39 TheoreticalSensitivity 9000 sampling iterations completed INFO 2024-07-02 11:52:39 TheoreticalSensitivity 9000 sampling iterations completed Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:40 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:52:40 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:40 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:52:40 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.01 minutes. Test: Test method testPoorQualityBases[0](false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:40 CollectWgsMetrics Gradle suite > Gradle test > picard.analysis.CollectWgsMetricsTest.testPoorQualityBases[1](true) STANDARD_ERROR INFO 2024-07-02 11:52:40 CollectWgsMetrics Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** CollectWgsMetrics -INPUT /tmp/CollectWgsMetrics7129470817513505157.bam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testPoorQualityBases17863954065318507331.txt -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -INCLUDE_BQ_HISTOGRAM true -COVERAGE_CAP 3 -USE_FAST_ALGORITHM true ********** CollectWgsMetrics -INPUT /tmp/CollectWgsMetrics7129470817513505157.bam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testPoorQualityBases17863954065318507331.txt -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -INCLUDE_BQ_HISTOGRAM true -COVERAGE_CAP 3 -USE_FAST_ALGORITHM true Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:40.080 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:40.080 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:40.080 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:40.080 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:40.080 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:40.080 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:40.080 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:40.080 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:40 GMT+14:00 2024] CollectWgsMetrics INPUT=/tmp/CollectWgsMetrics7129470817513505157.bam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testPoorQualityBases17863954065318507331.txt COVERAGE_CAP=3 INCLUDE_BQ_HISTOGRAM=true USE_FAST_ALGORITHM=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:40 GMT+14:00 2024] CollectWgsMetrics INPUT=/tmp/CollectWgsMetrics7129470817513505157.bam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testPoorQualityBases17863954065318507331.txt COVERAGE_CAP=3 INCLUDE_BQ_HISTOGRAM=true USE_FAST_ALGORITHM=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: WARNING 2024-07-02 11:52:40 AbstractLocusIterator EdgeReadIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. WARNING 2024-07-02 11:52:40 AbstractLocusIterator EdgeReadIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:40 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:52:40 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:40 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:52:40 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:40 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 11:52:40 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:40 TheoreticalSensitivity 1000 sampling iterations completed INFO 2024-07-02 11:52:40 TheoreticalSensitivity 1000 sampling iterations completed Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:40 TheoreticalSensitivity 2000 sampling iterations completed INFO 2024-07-02 11:52:40 TheoreticalSensitivity 2000 sampling iterations completed Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:40 TheoreticalSensitivity 3000 sampling iterations completed INFO 2024-07-02 11:52:40 TheoreticalSensitivity 3000 sampling iterations completed Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:40 TheoreticalSensitivity 4000 sampling iterations completed INFO 2024-07-02 11:52:40 TheoreticalSensitivity 4000 sampling iterations completed Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:40 TheoreticalSensitivity 5000 sampling iterations completed INFO 2024-07-02 11:52:40 TheoreticalSensitivity 5000 sampling iterations completed Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:40 TheoreticalSensitivity 6000 sampling iterations completed INFO 2024-07-02 11:52:40 TheoreticalSensitivity 6000 sampling iterations completed Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:40 TheoreticalSensitivity 7000 sampling iterations completed INFO 2024-07-02 11:52:40 TheoreticalSensitivity 7000 sampling iterations completed Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:40 TheoreticalSensitivity 8000 sampling iterations completed INFO 2024-07-02 11:52:40 TheoreticalSensitivity 8000 sampling iterations completed Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:40 TheoreticalSensitivity 9000 sampling iterations completed INFO 2024-07-02 11:52:40 TheoreticalSensitivity 9000 sampling iterations completed Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:40 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:52:40 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:40 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:52:40 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.01 minutes. Test: Test method testPoorQualityBases[1](true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSmallIntervals[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) Test: Test method testSmallIntervals[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:40 CollectWgsMetrics Gradle suite > Gradle test > picard.analysis.CollectWgsMetricsTest.testSmallIntervals[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false) STANDARD_ERROR INFO 2024-07-02 11:52:40 CollectWgsMetrics Test: Test method testSmallIntervals[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testSmallIntervals[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSmallIntervals[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testSmallIntervals[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSmallIntervals[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSmallIntervals[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testSmallIntervals[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSmallIntervals[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testSmallIntervals[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** CollectWgsMetrics -INPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testSmallIntervals17337539949403901151.wgs_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -INTERVALS /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/smallIntervals.interval_list -SAMPLE_SIZE 1000 -COVERAGE_CAP 40000 -USE_FAST_ALGORITHM false ********** CollectWgsMetrics -INPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testSmallIntervals17337539949403901151.wgs_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -INTERVALS /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/smallIntervals.interval_list -SAMPLE_SIZE 1000 -COVERAGE_CAP 40000 -USE_FAST_ALGORITHM false Test: Test method testSmallIntervals[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testSmallIntervals[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testSmallIntervals[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testSmallIntervals[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:40.918 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:40.918 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSmallIntervals[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:40.918 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:40.918 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSmallIntervals[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:40.918 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:40.918 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSmallIntervals[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:40.918 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:40.918 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSmallIntervals[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:40 GMT+14:00 2024] CollectWgsMetrics INPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testSmallIntervals17337539949403901151.wgs_metrics COVERAGE_CAP=40000 SAMPLE_SIZE=1000 INTERVALS=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/smallIntervals.interval_list USE_FAST_ALGORITHM=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:40 GMT+14:00 2024] CollectWgsMetrics INPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testSmallIntervals17337539949403901151.wgs_metrics COVERAGE_CAP=40000 SAMPLE_SIZE=1000 INTERVALS=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/smallIntervals.interval_list USE_FAST_ALGORITHM=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSmallIntervals[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSmallIntervals[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:43 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:52:43 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testSmallIntervals[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:43 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:52:43 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testSmallIntervals[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:43 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 11:52:43 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testSmallIntervals[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:44 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:52:44 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testSmallIntervals[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:44 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:52:44 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.06 minutes. Test: Test method testSmallIntervals[0](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, false)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testSmallIntervals[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) Test: Test method testSmallIntervals[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:44 CollectWgsMetrics Gradle suite > Gradle test > picard.analysis.CollectWgsMetricsTest.testSmallIntervals[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true) STANDARD_ERROR INFO 2024-07-02 11:52:44 CollectWgsMetrics Test: Test method testSmallIntervals[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testSmallIntervals[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSmallIntervals[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testSmallIntervals[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSmallIntervals[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSmallIntervals[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testSmallIntervals[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSmallIntervals[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testSmallIntervals[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** CollectWgsMetrics -INPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testSmallIntervals5679062083888323199.wgs_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -INTERVALS /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/smallIntervals.interval_list -SAMPLE_SIZE 1000 -COVERAGE_CAP 40000 -USE_FAST_ALGORITHM true ********** CollectWgsMetrics -INPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam -OUTPUT /tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testSmallIntervals5679062083888323199.wgs_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -INTERVALS /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/smallIntervals.interval_list -SAMPLE_SIZE 1000 -COVERAGE_CAP 40000 -USE_FAST_ALGORITHM true Test: Test method testSmallIntervals[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: ********** ********** Test: Test method testSmallIntervals[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testSmallIntervals[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Test: Test method testSmallIntervals[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:44.867 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:44.867 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSmallIntervals[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:44.867 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:44.867 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSmallIntervals[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:44.868 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:44.868 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSmallIntervals[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: 11:52:44.868 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:44.868 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSmallIntervals[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:44 GMT+14:00 2024] CollectWgsMetrics INPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testSmallIntervals5679062083888323199.wgs_metrics COVERAGE_CAP=40000 SAMPLE_SIZE=1000 INTERVALS=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/smallIntervals.interval_list USE_FAST_ALGORITHM=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:44 GMT+14:00 2024] CollectWgsMetrics INPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam OUTPUT=/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/testSmallIntervals5679062083888323199.wgs_metrics COVERAGE_CAP=40000 SAMPLE_SIZE=1000 INTERVALS=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/smallIntervals.interval_list USE_FAST_ALGORITHM=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSmallIntervals[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSmallIntervals[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:46 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:52:46 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testSmallIntervals[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:46 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:52:46 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testSmallIntervals[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:46 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 11:52:46 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testSmallIntervals[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: INFO 2024-07-02 11:52:46 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:52:46 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testSmallIntervals[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: [Tue Jul 02 11:52:47 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:52:47 GMT+14:00 2024] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.04 minutes. Test: Test method testSmallIntervals[1](/tmp/pbuilder2/picard.analysis.CollectWgsMetricsTest12216109492110502125/setupBuilder4219224653925545224.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta, true)(picard.analysis.CollectWgsMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:47 CollectWgsMetricsWithNonZeroCoverage Gradle suite > Gradle test > picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest.testNoCoverage STANDARD_ERROR INFO 2024-07-02 11:52:47 CollectWgsMetricsWithNonZeroCoverage Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** ********** Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** ********** Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** ********** Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** CollectWgsMetricsWithNonZeroCoverage -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CollectWgsMetrics13650824157997350964.bam -OUTPUT /tmp/testPoorQualityBases-metrics12504107682107511135.txt -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -INCLUDE_BQ_HISTOGRAM true -COVERAGE_CAP 3 -CHART_OUTPUT /tmp/testPoorQualityBases17181395169362396182.pdf ********** CollectWgsMetricsWithNonZeroCoverage -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CollectWgsMetrics13650824157997350964.bam -OUTPUT /tmp/testPoorQualityBases-metrics12504107682107511135.txt -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -INCLUDE_BQ_HISTOGRAM true -COVERAGE_CAP 3 -CHART_OUTPUT /tmp/testPoorQualityBases17181395169362396182.pdf Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** ********** Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:47 RExecutor Executing R script via command: Rscript /tmp/script6205230022449149542.R INFO 2024-07-02 11:52:47 RExecutor Executing R script via command: Rscript /tmp/script6205230022449149542.R Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:48 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:52:48 ProcessExecutor [1] "Checking if R is installed" Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: 11:52:48.997 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:48.997 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: 11:52:48.997 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:48.997 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: 11:52:48.998 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:52:48.998 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: 11:52:48.998 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:52:48.998 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: [Tue Jul 02 11:52:48 GMT+14:00 2024] CollectWgsMetricsWithNonZeroCoverage CHART_OUTPUT=/tmp/testPoorQualityBases17181395169362396182.pdf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CollectWgsMetrics13650824157997350964.bam OUTPUT=/tmp/testPoorQualityBases-metrics12504107682107511135.txt COVERAGE_CAP=3 INCLUDE_BQ_HISTOGRAM=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:52:48 GMT+14:00 2024] CollectWgsMetricsWithNonZeroCoverage CHART_OUTPUT=/tmp/testPoorQualityBases17181395169362396182.pdf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CollectWgsMetrics13650824157997350964.bam OUTPUT=/tmp/testPoorQualityBases-metrics12504107682107511135.txt COVERAGE_CAP=3 INCLUDE_BQ_HISTOGRAM=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: [Tue Jul 02 11:52:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:52:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: WARNING 2024-07-02 11:52:49 AbstractLocusIterator SamLocusIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. WARNING 2024-07-02 11:52:49 AbstractLocusIterator SamLocusIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:49 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:52:49 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:49 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:52:49 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:49 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 11:52:49 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:49 TheoreticalSensitivity 1000 sampling iterations completed INFO 2024-07-02 11:52:49 TheoreticalSensitivity 1000 sampling iterations completed Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:49 TheoreticalSensitivity 2000 sampling iterations completed INFO 2024-07-02 11:52:49 TheoreticalSensitivity 2000 sampling iterations completed Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:50 TheoreticalSensitivity 3000 sampling iterations completed INFO 2024-07-02 11:52:50 TheoreticalSensitivity 3000 sampling iterations completed Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:50 TheoreticalSensitivity 4000 sampling iterations completed INFO 2024-07-02 11:52:50 TheoreticalSensitivity 4000 sampling iterations completed Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:51 TheoreticalSensitivity 5000 sampling iterations completed INFO 2024-07-02 11:52:51 TheoreticalSensitivity 5000 sampling iterations completed Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:51 TheoreticalSensitivity 6000 sampling iterations completed INFO 2024-07-02 11:52:51 TheoreticalSensitivity 6000 sampling iterations completed Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:52 TheoreticalSensitivity 7000 sampling iterations completed INFO 2024-07-02 11:52:52 TheoreticalSensitivity 7000 sampling iterations completed Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:52 TheoreticalSensitivity 8000 sampling iterations completed INFO 2024-07-02 11:52:52 TheoreticalSensitivity 8000 sampling iterations completed Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:53 TheoreticalSensitivity 9000 sampling iterations completed INFO 2024-07-02 11:52:53 TheoreticalSensitivity 9000 sampling iterations completed Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:53 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:52:53 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:53 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:52:53 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:53 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:52:53 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:53 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 11:52:53 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:54 TheoreticalSensitivity 1000 sampling iterations completed INFO 2024-07-02 11:52:54 TheoreticalSensitivity 1000 sampling iterations completed Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:55 TheoreticalSensitivity 2000 sampling iterations completed INFO 2024-07-02 11:52:55 TheoreticalSensitivity 2000 sampling iterations completed Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:55 TheoreticalSensitivity 3000 sampling iterations completed INFO 2024-07-02 11:52:55 TheoreticalSensitivity 3000 sampling iterations completed Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:56 TheoreticalSensitivity 4000 sampling iterations completed INFO 2024-07-02 11:52:56 TheoreticalSensitivity 4000 sampling iterations completed Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:56 TheoreticalSensitivity 5000 sampling iterations completed INFO 2024-07-02 11:52:56 TheoreticalSensitivity 5000 sampling iterations completed Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:56 TheoreticalSensitivity 6000 sampling iterations completed INFO 2024-07-02 11:52:56 TheoreticalSensitivity 6000 sampling iterations completed Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:57 TheoreticalSensitivity 7000 sampling iterations completed INFO 2024-07-02 11:52:57 TheoreticalSensitivity 7000 sampling iterations completed Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:57 TheoreticalSensitivity 8000 sampling iterations completed INFO 2024-07-02 11:52:57 TheoreticalSensitivity 8000 sampling iterations completed Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:58 TheoreticalSensitivity 9000 sampling iterations completed INFO 2024-07-02 11:52:58 TheoreticalSensitivity 9000 sampling iterations completed Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:58 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:52:58 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:52:58 RExecutor Executing R script via command: Rscript /tmp/script2282837661729282707.R /tmp/testPoorQualityBases-metrics12504107682107511135.txt /tmp/testPoorQualityBases17181395169362396182.pdf CollectWgsMetrics13650824157997350964.bam TestLibrary1 INFO 2024-07-02 11:52:58 RExecutor Executing R script via command: Rscript /tmp/script2282837661729282707.R /tmp/testPoorQualityBases-metrics12504107682107511135.txt /tmp/testPoorQualityBases17181395169362396182.pdf CollectWgsMetrics13650824157997350964.bam TestLibrary1 Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ERROR 2024-07-02 11:53:00 ProcessExecutor Warning message: ERROR 2024-07-02 11:53:00 ProcessExecutor Warning message: Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ERROR 2024-07-02 11:53:00 ProcessExecutor In as.numeric(metrics$MEAN_COVERAGE[i]) : NAs introduced by coercion ERROR 2024-07-02 11:53:00 ProcessExecutor In as.numeric(metrics$MEAN_COVERAGE[i]) : NAs introduced by coercion Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:00 ProcessExecutor null device INFO 2024-07-02 11:53:00 ProcessExecutor null device Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:00 ProcessExecutor 1 INFO 2024-07-02 11:53:00 ProcessExecutor 1 Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: [Tue Jul 02 11:53:00 GMT+14:00 2024] picard.analysis.CollectWgsMetricsWithNonZeroCoverage done. Elapsed time: 0.20 minutes. [Tue Jul 02 11:53:00 GMT+14:00 2024] picard.analysis.CollectWgsMetricsWithNonZeroCoverage done. Elapsed time: 0.20 minutes. Test: Test method testNoCoverage(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:00 CollectWgsMetricsWithNonZeroCoverage Gradle suite > Gradle test > picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest.testPoorQualityBases STANDARD_ERROR INFO 2024-07-02 11:53:00 CollectWgsMetricsWithNonZeroCoverage Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** ********** Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** ********** Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** ********** Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** CollectWgsMetricsWithNonZeroCoverage -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CollectWgsMetrics9289199660779202002.bam -OUTPUT /tmp/testExcludedBases-metrics13988767488777391581.txt -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -INCLUDE_BQ_HISTOGRAM true -COVERAGE_CAP 3 -CHART_OUTPUT /tmp/testExcludedBases15742474804252626035.pdf ********** CollectWgsMetricsWithNonZeroCoverage -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CollectWgsMetrics9289199660779202002.bam -OUTPUT /tmp/testExcludedBases-metrics13988767488777391581.txt -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta -INCLUDE_BQ_HISTOGRAM true -COVERAGE_CAP 3 -CHART_OUTPUT /tmp/testExcludedBases15742474804252626035.pdf Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** ********** Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:00 RExecutor Executing R script via command: Rscript /tmp/script18258120474261173155.R INFO 2024-07-02 11:53:00 RExecutor Executing R script via command: Rscript /tmp/script18258120474261173155.R Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:02 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:53:02 ProcessExecutor [1] "Checking if R is installed" Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: 11:53:02.081 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:02.081 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: 11:53:02.082 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:02.082 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: 11:53:02.082 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:02.082 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: 11:53:02.082 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:02.082 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: [Tue Jul 02 11:53:02 GMT+14:00 2024] CollectWgsMetricsWithNonZeroCoverage CHART_OUTPUT=/tmp/testExcludedBases15742474804252626035.pdf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CollectWgsMetrics9289199660779202002.bam OUTPUT=/tmp/testExcludedBases-metrics13988767488777391581.txt COVERAGE_CAP=3 INCLUDE_BQ_HISTOGRAM=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:02 GMT+14:00 2024] CollectWgsMetricsWithNonZeroCoverage CHART_OUTPUT=/tmp/testExcludedBases15742474804252626035.pdf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CollectWgsMetrics9289199660779202002.bam OUTPUT=/tmp/testExcludedBases-metrics13988767488777391581.txt COVERAGE_CAP=3 INCLUDE_BQ_HISTOGRAM=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/chrM.reference.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 COUNT_UNPAIRED=false SAMPLE_SIZE=10000 ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: [Tue Jul 02 11:53:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: WARNING 2024-07-02 11:53:02 AbstractLocusIterator SamLocusIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. WARNING 2024-07-02 11:53:02 AbstractLocusIterator SamLocusIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:02 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:53:02 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:02 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:53:02 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:02 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 11:53:02 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:02 TheoreticalSensitivity 1000 sampling iterations completed INFO 2024-07-02 11:53:02 TheoreticalSensitivity 1000 sampling iterations completed Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:02 TheoreticalSensitivity 2000 sampling iterations completed INFO 2024-07-02 11:53:02 TheoreticalSensitivity 2000 sampling iterations completed Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:02 TheoreticalSensitivity 3000 sampling iterations completed INFO 2024-07-02 11:53:02 TheoreticalSensitivity 3000 sampling iterations completed Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:02 TheoreticalSensitivity 4000 sampling iterations completed INFO 2024-07-02 11:53:02 TheoreticalSensitivity 4000 sampling iterations completed Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:02 TheoreticalSensitivity 5000 sampling iterations completed INFO 2024-07-02 11:53:02 TheoreticalSensitivity 5000 sampling iterations completed Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:02 TheoreticalSensitivity 6000 sampling iterations completed INFO 2024-07-02 11:53:02 TheoreticalSensitivity 6000 sampling iterations completed Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:03 TheoreticalSensitivity 7000 sampling iterations completed INFO 2024-07-02 11:53:03 TheoreticalSensitivity 7000 sampling iterations completed Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:03 TheoreticalSensitivity 8000 sampling iterations completed INFO 2024-07-02 11:53:03 TheoreticalSensitivity 8000 sampling iterations completed Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:03 TheoreticalSensitivity 9000 sampling iterations completed INFO 2024-07-02 11:53:03 TheoreticalSensitivity 9000 sampling iterations completed Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:03 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:53:03 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:03 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:53:03 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:03 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:53:03 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:03 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 11:53:03 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:03 TheoreticalSensitivity 1000 sampling iterations completed INFO 2024-07-02 11:53:03 TheoreticalSensitivity 1000 sampling iterations completed Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:03 TheoreticalSensitivity 2000 sampling iterations completed INFO 2024-07-02 11:53:03 TheoreticalSensitivity 2000 sampling iterations completed Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:03 TheoreticalSensitivity 3000 sampling iterations completed INFO 2024-07-02 11:53:03 TheoreticalSensitivity 3000 sampling iterations completed Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:03 TheoreticalSensitivity 4000 sampling iterations completed INFO 2024-07-02 11:53:03 TheoreticalSensitivity 4000 sampling iterations completed Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:03 TheoreticalSensitivity 5000 sampling iterations completed INFO 2024-07-02 11:53:03 TheoreticalSensitivity 5000 sampling iterations completed Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:03 TheoreticalSensitivity 6000 sampling iterations completed INFO 2024-07-02 11:53:03 TheoreticalSensitivity 6000 sampling iterations completed Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:04 TheoreticalSensitivity 7000 sampling iterations completed INFO 2024-07-02 11:53:04 TheoreticalSensitivity 7000 sampling iterations completed Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:04 TheoreticalSensitivity 8000 sampling iterations completed INFO 2024-07-02 11:53:04 TheoreticalSensitivity 8000 sampling iterations completed Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:04 TheoreticalSensitivity 9000 sampling iterations completed INFO 2024-07-02 11:53:04 TheoreticalSensitivity 9000 sampling iterations completed Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:04 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:53:04 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:04 RExecutor Executing R script via command: Rscript /tmp/script12881496787262603862.R /tmp/testExcludedBases-metrics13988767488777391581.txt /tmp/testExcludedBases15742474804252626035.pdf CollectWgsMetrics9289199660779202002.bam TestLibrary1 INFO 2024-07-02 11:53:04 RExecutor Executing R script via command: Rscript /tmp/script12881496787262603862.R /tmp/testExcludedBases-metrics13988767488777391581.txt /tmp/testExcludedBases15742474804252626035.pdf CollectWgsMetrics9289199660779202002.bam TestLibrary1 Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:05 ProcessExecutor null device INFO 2024-07-02 11:53:05 ProcessExecutor null device Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:05 ProcessExecutor 1 INFO 2024-07-02 11:53:05 ProcessExecutor 1 Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: [Tue Jul 02 11:53:05 GMT+14:00 2024] picard.analysis.CollectWgsMetricsWithNonZeroCoverage done. Elapsed time: 0.06 minutes. [Tue Jul 02 11:53:05 GMT+14:00 2024] picard.analysis.CollectWgsMetricsWithNonZeroCoverage done. Elapsed time: 0.06 minutes. Test: Test method testPoorQualityBases(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:05 CollectWgsMetricsWithNonZeroCoverage Gradle suite > Gradle test > picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest.testWithIntervals STANDARD_ERROR INFO 2024-07-02 11:53:05 CollectWgsMetricsWithNonZeroCoverage Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** ********** Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** ********** Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** ********** Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** CollectWgsMetricsWithNonZeroCoverage -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/forMetrics.sam -OUTPUT /tmp/test8773853313468368937.wgs_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -INTERVALS /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/largeIntervals.interval_list -SAMPLE_SIZE 1000 -CHART /tmp/test15339933263099934327.wgs_metrics.pdf ********** CollectWgsMetricsWithNonZeroCoverage -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/forMetrics.sam -OUTPUT /tmp/test8773853313468368937.wgs_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -INTERVALS /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/largeIntervals.interval_list -SAMPLE_SIZE 1000 -CHART /tmp/test15339933263099934327.wgs_metrics.pdf Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** ********** Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:06 RExecutor Executing R script via command: Rscript /tmp/script8560479781717467547.R INFO 2024-07-02 11:53:06 RExecutor Executing R script via command: Rscript /tmp/script8560479781717467547.R Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:06 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:53:06 ProcessExecutor [1] "Checking if R is installed" Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: 11:53:06.889 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:06.889 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: 11:53:06.889 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:06.889 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: 11:53:06.890 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:06.890 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: 11:53:06.890 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:06.890 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: [Tue Jul 02 11:53:06 GMT+14:00 2024] CollectWgsMetricsWithNonZeroCoverage CHART_OUTPUT=/tmp/test15339933263099934327.wgs_metrics.pdf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/forMetrics.sam OUTPUT=/tmp/test8773853313468368937.wgs_metrics SAMPLE_SIZE=1000 INTERVALS=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/largeIntervals.interval_list REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:06 GMT+14:00 2024] CollectWgsMetricsWithNonZeroCoverage CHART_OUTPUT=/tmp/test15339933263099934327.wgs_metrics.pdf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/forMetrics.sam OUTPUT=/tmp/test8773853313468368937.wgs_metrics SAMPLE_SIZE=1000 INTERVALS=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/largeIntervals.interval_list REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: [Tue Jul 02 11:53:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:06 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:53:06 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:06 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:53:06 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:06 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 11:53:06 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:13 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:53:13 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:13 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:53:13 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:13 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:53:13 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:13 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 11:53:13 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:19 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:53:19 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:19 RExecutor Executing R script via command: Rscript /tmp/script3668090882795642618.R /tmp/test8773853313468368937.wgs_metrics /tmp/test15339933263099934327.wgs_metrics.pdf forMetrics.sam INFO 2024-07-02 11:53:19 RExecutor Executing R script via command: Rscript /tmp/script3668090882795642618.R /tmp/test8773853313468368937.wgs_metrics /tmp/test15339933263099934327.wgs_metrics.pdf forMetrics.sam Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:21 ProcessExecutor null device INFO 2024-07-02 11:53:21 ProcessExecutor null device Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:21 ProcessExecutor 1 INFO 2024-07-02 11:53:21 ProcessExecutor 1 Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: [Tue Jul 02 11:53:21 GMT+14:00 2024] picard.analysis.CollectWgsMetricsWithNonZeroCoverage done. Elapsed time: 0.24 minutes. [Tue Jul 02 11:53:21 GMT+14:00 2024] picard.analysis.CollectWgsMetricsWithNonZeroCoverage done. Elapsed time: 0.24 minutes. Test: Test method testWithIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:21 CollectWgsMetricsWithNonZeroCoverage Gradle suite > Gradle test > picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest.testWithoutIntervals STANDARD_ERROR INFO 2024-07-02 11:53:21 CollectWgsMetricsWithNonZeroCoverage Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** ********** Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** ********** Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** ********** Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** CollectWgsMetricsWithNonZeroCoverage -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/forMetrics.sam -OUTPUT /tmp/test2949211239902109327.wgs_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -SAMPLE_SIZE 1000 -CHART /tmp/test1983344264605755591.wgs_metrics.pdf ********** CollectWgsMetricsWithNonZeroCoverage -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/forMetrics.sam -OUTPUT /tmp/test2949211239902109327.wgs_metrics -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -SAMPLE_SIZE 1000 -CHART /tmp/test1983344264605755591.wgs_metrics.pdf Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: ********** ********** Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:21 RExecutor Executing R script via command: Rscript /tmp/script11452618836099261530.R INFO 2024-07-02 11:53:21 RExecutor Executing R script via command: Rscript /tmp/script11452618836099261530.R Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:22 ProcessExecutor [1] "Checking if R is installed" INFO 2024-07-02 11:53:22 ProcessExecutor [1] "Checking if R is installed" Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: 11:53:22.319 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:22.319 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: 11:53:22.319 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:22.319 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: 11:53:22.319 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:22.319 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: 11:53:22.319 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:22.319 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: [Tue Jul 02 11:53:22 GMT+14:00 2024] CollectWgsMetricsWithNonZeroCoverage CHART_OUTPUT=/tmp/test1983344264605755591.wgs_metrics.pdf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/forMetrics.sam OUTPUT=/tmp/test2949211239902109327.wgs_metrics SAMPLE_SIZE=1000 REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:22 GMT+14:00 2024] CollectWgsMetricsWithNonZeroCoverage CHART_OUTPUT=/tmp/test1983344264605755591.wgs_metrics.pdf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/forMetrics.sam OUTPUT=/tmp/test2949211239902109327.wgs_metrics SAMPLE_SIZE=1000 REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 INCLUDE_BQ_HISTOGRAM=false COUNT_UNPAIRED=false ALLELE_FRACTION=[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5] USE_FAST_ALGORITHM=false READ_LENGTH=150 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: [Tue Jul 02 11:53:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:22 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:53:22 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:22 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:53:22 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:22 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 11:53:22 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:31 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:53:31 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:31 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 11:53:31 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:31 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 11:53:31 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:31 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 11:53:31 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:38 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 11:53:38 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:39 RExecutor Executing R script via command: Rscript /tmp/script1069648726148444631.R /tmp/test2949211239902109327.wgs_metrics /tmp/test1983344264605755591.wgs_metrics.pdf forMetrics.sam INFO 2024-07-02 11:53:39 RExecutor Executing R script via command: Rscript /tmp/script1069648726148444631.R /tmp/test2949211239902109327.wgs_metrics /tmp/test1983344264605755591.wgs_metrics.pdf forMetrics.sam Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:41 ProcessExecutor null device INFO 2024-07-02 11:53:41 ProcessExecutor null device Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: INFO 2024-07-02 11:53:41 ProcessExecutor 1 INFO 2024-07-02 11:53:41 ProcessExecutor 1 Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: [Tue Jul 02 11:53:41 GMT+14:00 2024] picard.analysis.CollectWgsMetricsWithNonZeroCoverage done. Elapsed time: 0.32 minutes. [Tue Jul 02 11:53:41 GMT+14:00 2024] picard.analysis.CollectWgsMetricsWithNonZeroCoverage done. Elapsed time: 0.32 minutes. Test: Test method testWithoutIntervals(picard.analysis.CollectWgsMetricsWithNonZeroCoverageTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testCombineGenotypingArrayVcfs(picard.arrays.illumina.CombineGenotypingArrayVcfsTest) Test: Test method testCombineGenotypingArrayVcfs(picard.arrays.illumina.CombineGenotypingArrayVcfsTest) produced standard out/err: INFO 2024-07-02 11:53:41 CombineGenotypingArrayVcfs Checking inputs. Gradle suite > Gradle test > picard.arrays.illumina.CombineGenotypingArrayVcfsTest.testCombineGenotypingArrayVcfs STANDARD_ERROR INFO 2024-07-02 11:53:41 CombineGenotypingArrayVcfs Checking inputs. Running Test: Test method testCombineGenotypingArrayVcfsFail(picard.arrays.illumina.CombineGenotypingArrayVcfsTest) Test: Test method testCombineGenotypingArrayVcfsFail(picard.arrays.illumina.CombineGenotypingArrayVcfsTest) produced standard out/err: INFO 2024-07-02 11:53:41 CombineGenotypingArrayVcfs Checking inputs. Gradle suite > Gradle test > picard.arrays.illumina.CombineGenotypingArrayVcfsTest.testCombineGenotypingArrayVcfsFail STANDARD_ERROR INFO 2024-07-02 11:53:41 CombineGenotypingArrayVcfs Checking inputs. Running Test: Test method testNoStartupErrorLog(picard.cmdline.CommandLineProgramStartupErrorLogTest) Test: Test method testNoStartupErrorLog(picard.cmdline.CommandLineProgramStartupErrorLogTest) produced standard out/err: 11:53:41.827 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.cmdline.CommandLineProgramStartupErrorLogTest.testNoStartupErrorLog STANDARD_ERROR 11:53:41.827 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoStartupErrorLog(picard.cmdline.CommandLineProgramStartupErrorLogTest) produced standard out/err: 11:53:41.827 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:41.827 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoStartupErrorLog(picard.cmdline.CommandLineProgramStartupErrorLogTest) produced standard out/err: 11:53:41.828 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:41.828 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoStartupErrorLog(picard.cmdline.CommandLineProgramStartupErrorLogTest) produced standard out/err: 11:53:41.828 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:41.828 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Running Test: Test method testNoStartupOutputLog(picard.cmdline.CommandLineProgramStartupErrorLogTest) Test: Test method testNoStartupOutputLog(picard.cmdline.CommandLineProgramStartupErrorLogTest) produced standard out/err: 11:53:41.855 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.cmdline.CommandLineProgramStartupErrorLogTest.testNoStartupOutputLog STANDARD_ERROR 11:53:41.855 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoStartupOutputLog(picard.cmdline.CommandLineProgramStartupErrorLogTest) produced standard out/err: 11:53:41.855 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:41.855 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoStartupOutputLog(picard.cmdline.CommandLineProgramStartupErrorLogTest) produced standard out/err: 11:53:41.856 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:41.856 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoStartupOutputLog(picard.cmdline.CommandLineProgramStartupErrorLogTest) produced standard out/err: 11:53:41.856 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:41.856 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoStartupOutputLog(picard.cmdline.CommandLineProgramStartupErrorLogTest) produced standard out/err: [Tue Jul 02 11:53:41 GMT+14:00 2024] MockCLP VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:41 GMT+14:00 2024] MockCLP VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testNoStartupOutputLog(picard.cmdline.CommandLineProgramStartupErrorLogTest) produced standard out/err: [Tue Jul 02 11:53:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testNoStartupOutputLog(picard.cmdline.CommandLineProgramStartupErrorLogTest) produced standard out/err: [Tue Jul 02 11:53:41 GMT+14:00 2024] picard.cmdline.CommandLineProgramStartupErrorLogTest$MockCLP done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:41 GMT+14:00 2024] picard.cmdline.CommandLineProgramStartupErrorLogTest$MockCLP done. Elapsed time: 0.00 minutes. Test: Test method testNoStartupOutputLog(picard.cmdline.CommandLineProgramStartupErrorLogTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testCompareMetrics[0](1.0, 1.0, true, , null)(picard.analysis.CompareMetricsTest) Running Test: Test method testCompareMetrics[1](1.0, 1.1, false, Changed by 0.10000000000000009 (relative change of 0.10000000000000009) which is outside of the allowable relative change tolerance of 0.05, 0.05)(picard.analysis.CompareMetricsTest) Running Test: Test method testCompareMetrics[2](1.0, 1.1, false, Changed by 0.10000000000000009 (relative change of 0.10000000000000009) which is outside of the allowable relative change tolerance of 0.1, 0.1)(picard.analysis.CompareMetricsTest) Running Test: Test method testCompareMetrics[3](1.0, 1.1, true, Changed by 0.10000000000000009 (relative change of 0.10000000000000009) which is within the allowable relative change tolerance of 0.1001, 0.1001)(picard.analysis.CompareMetricsTest) Running Test: Test method testCompareMetrics[4](1.0, 1.1, true, Changed by 0.10000000000000009 (relative change of 0.10000000000000009) which is within the allowable relative change tolerance of 0.2, 0.2)(picard.analysis.CompareMetricsTest) Running Test: Test method testCompareMetrics[5](1.0, 1.0, true, , null)(picard.analysis.CompareMetricsTest) Running Test: Test method testCompareMetrics[6](1.0, 1.1, false, Changed by 0.10000002384185791 (relative change of 0.10000002384185791) which is outside of the allowable relative change tolerance of 0.05, 0.05)(picard.analysis.CompareMetricsTest) Running Test: Test method testCompareMetrics[7](1.0, 1.1, false, Changed by 0.10000002384185791 (relative change of 0.10000002384185791) which is outside of the allowable relative change tolerance of 0.1, 0.1)(picard.analysis.CompareMetricsTest) Running Test: Test method testCompareMetrics[8](1.0, 1.1, true, Changed by 0.10000002384185791 (relative change of 0.10000002384185791) which is within the allowable relative change tolerance of 0.1001, 0.1001)(picard.analysis.CompareMetricsTest) Running Test: Test method testCompareMetrics[9](1.0, 1.1, true, Changed by 0.10000002384185791 (relative change of 0.10000002384185791) which is within the allowable relative change tolerance of 0.2, 0.2)(picard.analysis.CompareMetricsTest) Running Test: Test method testCompareMetrics[10](1, 1, true, , null)(picard.analysis.CompareMetricsTest) Running Test: Test method testCompareMetrics[11](1, 2, false, Changed by 1.0 (relative change of 1.0), null)(picard.analysis.CompareMetricsTest) Running Test: Test method testCompareMetrics[12](1, 0, false, Changed by -1.0 (relative change of -1.0), null)(picard.analysis.CompareMetricsTest) Running Test: Test method testCompareMetrics[13](1.0, 1.0, true, , null)(picard.analysis.CompareMetricsTest) Running Test: Test method testCompareMetrics[14](NaN, NaN, true, , null)(picard.analysis.CompareMetricsTest) Running Test: Test method testCompareMetrics[15](NaN, NaN, true, , null)(picard.analysis.CompareMetricsTest) Running Test: Test method testCompareMetrics[0](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) Test: Test method testCompareMetrics[0](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:41.884 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.analysis.CompareMetricsTest.testCompareMetrics[0](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, null, null, 1) STANDARD_ERROR 11:53:41.884 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[0](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:41.884 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:41.884 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[0](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:41.884 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:41.884 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[0](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:41.884 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:41.884 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[0](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:41 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.wgs_metrics, testdata/picard/analysis/metrics/wgs_test2.wgs_metrics] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:41 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.wgs_metrics, testdata/picard/analysis/metrics/wgs_test2.wgs_metrics] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCompareMetrics[0](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCompareMetrics[0](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: INFO 2024-07-02 11:53:41 CompareMetrics picard.analysis.WgsMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.wgs_metrics and testdata/picard/analysis/metrics/wgs_test2.wgs_metrics are NOT equal INFO 2024-07-02 11:53:41 CompareMetrics picard.analysis.WgsMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.wgs_metrics and testdata/picard/analysis/metrics/wgs_test2.wgs_metrics are NOT equal Test: Test method testCompareMetrics[0](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: ERROR 2024-07-02 11:53:41 CompareMetrics Row: 0 Metric: GENOME_TERRITORY values differ. Value1: 2745186692 Value2: 2745186691 Changed by -1.0 (relative change of -3.6427395007931214E-10) ERROR 2024-07-02 11:53:41 CompareMetrics Row: 0 Metric: GENOME_TERRITORY values differ. Value1: 2745186692 Value2: 2745186691 Changed by -1.0 (relative change of -3.6427395007931214E-10) Test: Test method testCompareMetrics[0](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: ERROR 2024-07-02 11:53:41 CompareMetrics Row: 0 Metric: SD_COVERAGE values differ. Value1: 0.059988 Value2: 0.059989 Changed by 1.000000000001E-6 (relative change of 1.6670000666816697E-5) ERROR 2024-07-02 11:53:41 CompareMetrics Row: 0 Metric: SD_COVERAGE values differ. Value1: 0.059988 Value2: 0.059989 Changed by 1.000000000001E-6 (relative change of 1.6670000666816697E-5) Test: Test method testCompareMetrics[0](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: ERROR 2024-07-02 11:53:41 CompareMetrics Metric Histograms differ ERROR 2024-07-02 11:53:41 CompareMetrics Metric Histograms differ Test: Test method testCompareMetrics[0](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:41 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:41 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. Test: Test method testCompareMetrics[0](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testCompareMetrics[0](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCompareMetrics[1](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], true, 0)(picard.analysis.CompareMetricsTest) Test: Test method testCompareMetrics[1](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], true, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:41.919 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.analysis.CompareMetricsTest.testCompareMetrics[1](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], true, 0) STANDARD_ERROR 11:53:41.919 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[1](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], true, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:41.919 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:41.919 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[1](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], true, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:41.919 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:41.919 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[1](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], true, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:41.919 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:41.919 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[1](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], true, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:41 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.wgs_metrics, testdata/picard/analysis/metrics/wgs_test2.wgs_metrics] METRICS_TO_IGNORE=[GENOME_TERRITORY] METRIC_ALLOWABLE_RELATIVE_CHANGE=[SD_COVERAGE:0.00002] IGNORE_HISTOGRAM_DIFFERENCES=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:41 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.wgs_metrics, testdata/picard/analysis/metrics/wgs_test2.wgs_metrics] METRICS_TO_IGNORE=[GENOME_TERRITORY] METRIC_ALLOWABLE_RELATIVE_CHANGE=[SD_COVERAGE:0.00002] IGNORE_HISTOGRAM_DIFFERENCES=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCompareMetrics[1](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], true, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCompareMetrics[1](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], true, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: INFO 2024-07-02 11:53:41 CompareMetrics picard.analysis.WgsMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.wgs_metrics and testdata/picard/analysis/metrics/wgs_test2.wgs_metrics are equal INFO 2024-07-02 11:53:41 CompareMetrics picard.analysis.WgsMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.wgs_metrics and testdata/picard/analysis/metrics/wgs_test2.wgs_metrics are equal Test: Test method testCompareMetrics[1](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], true, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:41 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:41 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. Test: Test method testCompareMetrics[1](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], true, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testCompareMetrics[2](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], false, 1)(picard.analysis.CompareMetricsTest) Test: Test method testCompareMetrics[2](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], false, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:41.950 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.analysis.CompareMetricsTest.testCompareMetrics[2](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], false, 1) STANDARD_ERROR 11:53:41.950 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[2](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], false, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:41.950 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:41.950 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[2](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], false, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:41.950 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:41.950 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[2](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], false, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:41.950 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:41.950 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[2](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], false, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:41 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.wgs_metrics, testdata/picard/analysis/metrics/wgs_test2.wgs_metrics] METRICS_TO_IGNORE=[GENOME_TERRITORY] METRIC_ALLOWABLE_RELATIVE_CHANGE=[SD_COVERAGE:0.00002] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:41 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.wgs_metrics, testdata/picard/analysis/metrics/wgs_test2.wgs_metrics] METRICS_TO_IGNORE=[GENOME_TERRITORY] METRIC_ALLOWABLE_RELATIVE_CHANGE=[SD_COVERAGE:0.00002] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCompareMetrics[2](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], false, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCompareMetrics[2](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], false, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: INFO 2024-07-02 11:53:41 CompareMetrics picard.analysis.WgsMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.wgs_metrics and testdata/picard/analysis/metrics/wgs_test2.wgs_metrics are NOT equal INFO 2024-07-02 11:53:41 CompareMetrics picard.analysis.WgsMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.wgs_metrics and testdata/picard/analysis/metrics/wgs_test2.wgs_metrics are NOT equal Test: Test method testCompareMetrics[2](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], false, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: ERROR 2024-07-02 11:53:41 CompareMetrics Metric Histograms differ ERROR 2024-07-02 11:53:41 CompareMetrics Metric Histograms differ Test: Test method testCompareMetrics[2](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], false, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:41 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:41 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. Test: Test method testCompareMetrics[2](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], false, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testCompareMetrics[2](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], false, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCompareMetrics[3](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], null, 1)(picard.analysis.CompareMetricsTest) Test: Test method testCompareMetrics[3](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:41.968 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.analysis.CompareMetricsTest.testCompareMetrics[3](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], null, 1) STANDARD_ERROR 11:53:41.968 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[3](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:41.968 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:41.968 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[3](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:41.977 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:41.977 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[3](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:41.977 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:41.977 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[3](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:41 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.wgs_metrics, testdata/picard/analysis/metrics/wgs_test2.wgs_metrics] METRICS_TO_IGNORE=[GENOME_TERRITORY] METRIC_ALLOWABLE_RELATIVE_CHANGE=[SD_COVERAGE:0.00002] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:41 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.wgs_metrics, testdata/picard/analysis/metrics/wgs_test2.wgs_metrics] METRICS_TO_IGNORE=[GENOME_TERRITORY] METRIC_ALLOWABLE_RELATIVE_CHANGE=[SD_COVERAGE:0.00002] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCompareMetrics[3](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCompareMetrics[3](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: INFO 2024-07-02 11:53:41 CompareMetrics picard.analysis.WgsMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.wgs_metrics and testdata/picard/analysis/metrics/wgs_test2.wgs_metrics are NOT equal INFO 2024-07-02 11:53:41 CompareMetrics picard.analysis.WgsMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.wgs_metrics and testdata/picard/analysis/metrics/wgs_test2.wgs_metrics are NOT equal Test: Test method testCompareMetrics[3](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: ERROR 2024-07-02 11:53:41 CompareMetrics Metric Histograms differ ERROR 2024-07-02 11:53:41 CompareMetrics Metric Histograms differ Test: Test method testCompareMetrics[3](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:41 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:41 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. Test: Test method testCompareMetrics[3](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testCompareMetrics[3](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00002], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCompareMetrics[4](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00001], null, 1)(picard.analysis.CompareMetricsTest) Test: Test method testCompareMetrics[4](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00001], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:41.994 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.analysis.CompareMetricsTest.testCompareMetrics[4](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00001], null, 1) STANDARD_ERROR 11:53:41.994 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[4](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00001], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:41.994 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:41.994 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[4](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00001], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:41.994 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:41.994 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[4](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00001], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:41.994 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:41.994 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[4](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00001], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:41 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.wgs_metrics, testdata/picard/analysis/metrics/wgs_test2.wgs_metrics] METRICS_TO_IGNORE=[GENOME_TERRITORY] METRIC_ALLOWABLE_RELATIVE_CHANGE=[SD_COVERAGE:0.00001] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:41 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.wgs_metrics, testdata/picard/analysis/metrics/wgs_test2.wgs_metrics] METRICS_TO_IGNORE=[GENOME_TERRITORY] METRIC_ALLOWABLE_RELATIVE_CHANGE=[SD_COVERAGE:0.00001] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCompareMetrics[4](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00001], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCompareMetrics[4](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00001], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: INFO 2024-07-02 11:53:42 CompareMetrics picard.analysis.WgsMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.wgs_metrics and testdata/picard/analysis/metrics/wgs_test2.wgs_metrics are NOT equal INFO 2024-07-02 11:53:42 CompareMetrics picard.analysis.WgsMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.wgs_metrics and testdata/picard/analysis/metrics/wgs_test2.wgs_metrics are NOT equal Test: Test method testCompareMetrics[4](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00001], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: ERROR 2024-07-02 11:53:42 CompareMetrics Row: 0 Metric: SD_COVERAGE values differ. Value1: 0.059988 Value2: 0.059989 Changed by 1.000000000001E-6 (relative change of 1.6670000666816697E-5) which is outside of the allowable relative change tolerance of 1.0E-5 ERROR 2024-07-02 11:53:42 CompareMetrics Row: 0 Metric: SD_COVERAGE values differ. Value1: 0.059988 Value2: 0.059989 Changed by 1.000000000001E-6 (relative change of 1.6670000666816697E-5) which is outside of the allowable relative change tolerance of 1.0E-5 Test: Test method testCompareMetrics[4](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00001], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: ERROR 2024-07-02 11:53:42 CompareMetrics Metric Histograms differ ERROR 2024-07-02 11:53:42 CompareMetrics Metric Histograms differ Test: Test method testCompareMetrics[4](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00001], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:42 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:42 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. Test: Test method testCompareMetrics[4](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00001], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testCompareMetrics[4](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, GENOME_TERRITORY, [SD_COVERAGE:0.00001], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCompareMetrics[5](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], true, 0)(picard.analysis.CompareMetricsTest) Test: Test method testCompareMetrics[5](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], true, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:42.007 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.analysis.CompareMetricsTest.testCompareMetrics[5](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], true, 0) STANDARD_ERROR 11:53:42.007 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[5](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], true, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:42.008 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:42.008 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[5](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], true, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:42.008 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:42.008 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[5](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], true, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:42.008 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:42.008 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[5](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], true, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:42 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.wgs_metrics, testdata/picard/analysis/metrics/wgs_test2.wgs_metrics] METRIC_ALLOWABLE_RELATIVE_CHANGE=[GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002] IGNORE_HISTOGRAM_DIFFERENCES=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:42 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.wgs_metrics, testdata/picard/analysis/metrics/wgs_test2.wgs_metrics] METRIC_ALLOWABLE_RELATIVE_CHANGE=[GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002] IGNORE_HISTOGRAM_DIFFERENCES=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCompareMetrics[5](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], true, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCompareMetrics[5](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], true, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: INFO 2024-07-02 11:53:42 CompareMetrics picard.analysis.WgsMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.wgs_metrics and testdata/picard/analysis/metrics/wgs_test2.wgs_metrics are equal INFO 2024-07-02 11:53:42 CompareMetrics picard.analysis.WgsMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.wgs_metrics and testdata/picard/analysis/metrics/wgs_test2.wgs_metrics are equal Test: Test method testCompareMetrics[5](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], true, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:42 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:42 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. Test: Test method testCompareMetrics[5](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], true, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testCompareMetrics[6](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], false, 1)(picard.analysis.CompareMetricsTest) Test: Test method testCompareMetrics[6](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], false, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:42.041 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.analysis.CompareMetricsTest.testCompareMetrics[6](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], false, 1) STANDARD_ERROR 11:53:42.041 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[6](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], false, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:42.041 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:42.041 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[6](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], false, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:42.041 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:42.041 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[6](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], false, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:42.041 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:42.041 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[6](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], false, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:42 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.wgs_metrics, testdata/picard/analysis/metrics/wgs_test2.wgs_metrics] METRIC_ALLOWABLE_RELATIVE_CHANGE=[GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:42 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.wgs_metrics, testdata/picard/analysis/metrics/wgs_test2.wgs_metrics] METRIC_ALLOWABLE_RELATIVE_CHANGE=[GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCompareMetrics[6](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], false, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCompareMetrics[6](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], false, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: INFO 2024-07-02 11:53:42 CompareMetrics picard.analysis.WgsMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.wgs_metrics and testdata/picard/analysis/metrics/wgs_test2.wgs_metrics are NOT equal INFO 2024-07-02 11:53:42 CompareMetrics picard.analysis.WgsMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.wgs_metrics and testdata/picard/analysis/metrics/wgs_test2.wgs_metrics are NOT equal Test: Test method testCompareMetrics[6](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], false, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: ERROR 2024-07-02 11:53:42 CompareMetrics Metric Histograms differ ERROR 2024-07-02 11:53:42 CompareMetrics Metric Histograms differ Test: Test method testCompareMetrics[6](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], false, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:42 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:42 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. Test: Test method testCompareMetrics[6](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], false, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testCompareMetrics[6](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], false, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCompareMetrics[7](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], null, 1)(picard.analysis.CompareMetricsTest) Test: Test method testCompareMetrics[7](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:42.054 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.analysis.CompareMetricsTest.testCompareMetrics[7](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], null, 1) STANDARD_ERROR 11:53:42.054 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[7](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:42.054 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:42.054 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[7](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:42.054 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:42.054 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[7](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:42.054 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:42.054 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[7](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:42 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.wgs_metrics, testdata/picard/analysis/metrics/wgs_test2.wgs_metrics] METRIC_ALLOWABLE_RELATIVE_CHANGE=[GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:42 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.wgs_metrics, testdata/picard/analysis/metrics/wgs_test2.wgs_metrics] METRIC_ALLOWABLE_RELATIVE_CHANGE=[GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCompareMetrics[7](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCompareMetrics[7](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: INFO 2024-07-02 11:53:42 CompareMetrics picard.analysis.WgsMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.wgs_metrics and testdata/picard/analysis/metrics/wgs_test2.wgs_metrics are NOT equal INFO 2024-07-02 11:53:42 CompareMetrics picard.analysis.WgsMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.wgs_metrics and testdata/picard/analysis/metrics/wgs_test2.wgs_metrics are NOT equal Test: Test method testCompareMetrics[7](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: ERROR 2024-07-02 11:53:42 CompareMetrics Metric Histograms differ ERROR 2024-07-02 11:53:42 CompareMetrics Metric Histograms differ Test: Test method testCompareMetrics[7](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:42 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:42 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. Test: Test method testCompareMetrics[7](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testCompareMetrics[7](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00002], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCompareMetrics[8](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00001], null, 1)(picard.analysis.CompareMetricsTest) Test: Test method testCompareMetrics[8](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00001], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:42.071 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.analysis.CompareMetricsTest.testCompareMetrics[8](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00001], null, 1) STANDARD_ERROR 11:53:42.071 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[8](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00001], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:42.071 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:42.071 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[8](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00001], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:42.071 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:42.071 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[8](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00001], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:42.071 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:42.071 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[8](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00001], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:42 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.wgs_metrics, testdata/picard/analysis/metrics/wgs_test2.wgs_metrics] METRIC_ALLOWABLE_RELATIVE_CHANGE=[GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00001] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:42 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.wgs_metrics, testdata/picard/analysis/metrics/wgs_test2.wgs_metrics] METRIC_ALLOWABLE_RELATIVE_CHANGE=[GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00001] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCompareMetrics[8](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00001], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCompareMetrics[8](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00001], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: INFO 2024-07-02 11:53:42 CompareMetrics picard.analysis.WgsMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.wgs_metrics and testdata/picard/analysis/metrics/wgs_test2.wgs_metrics are NOT equal INFO 2024-07-02 11:53:42 CompareMetrics picard.analysis.WgsMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.wgs_metrics and testdata/picard/analysis/metrics/wgs_test2.wgs_metrics are NOT equal Test: Test method testCompareMetrics[8](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00001], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: ERROR 2024-07-02 11:53:42 CompareMetrics Row: 0 Metric: SD_COVERAGE values differ. Value1: 0.059988 Value2: 0.059989 Changed by 1.000000000001E-6 (relative change of 1.6670000666816697E-5) which is outside of the allowable relative change tolerance of 1.0E-5 ERROR 2024-07-02 11:53:42 CompareMetrics Row: 0 Metric: SD_COVERAGE values differ. Value1: 0.059988 Value2: 0.059989 Changed by 1.000000000001E-6 (relative change of 1.6670000666816697E-5) which is outside of the allowable relative change tolerance of 1.0E-5 Test: Test method testCompareMetrics[8](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00001], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: ERROR 2024-07-02 11:53:42 CompareMetrics Metric Histograms differ ERROR 2024-07-02 11:53:42 CompareMetrics Metric Histograms differ Test: Test method testCompareMetrics[8](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00001], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:42 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:42 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. Test: Test method testCompareMetrics[8](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00001], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testCompareMetrics[8](wgs_test1.wgs_metrics, wgs_test2.wgs_metrics, null, [GENOME_TERRITORY:0.0001, SD_COVERAGE:0.00001], null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCompareMetrics[9](wgs_test1.wgs_metrics, wgs_test1.wgs_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) Test: Test method testCompareMetrics[9](wgs_test1.wgs_metrics, wgs_test1.wgs_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:42.088 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.analysis.CompareMetricsTest.testCompareMetrics[9](wgs_test1.wgs_metrics, wgs_test1.wgs_metrics, null, null, null, 0) STANDARD_ERROR 11:53:42.088 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[9](wgs_test1.wgs_metrics, wgs_test1.wgs_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:42.088 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:42.088 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[9](wgs_test1.wgs_metrics, wgs_test1.wgs_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:42.088 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:42.088 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[9](wgs_test1.wgs_metrics, wgs_test1.wgs_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:42.088 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:42.088 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[9](wgs_test1.wgs_metrics, wgs_test1.wgs_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:42 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.wgs_metrics, testdata/picard/analysis/metrics/wgs_test1.wgs_metrics] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:42 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.wgs_metrics, testdata/picard/analysis/metrics/wgs_test1.wgs_metrics] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCompareMetrics[9](wgs_test1.wgs_metrics, wgs_test1.wgs_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCompareMetrics[9](wgs_test1.wgs_metrics, wgs_test1.wgs_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: INFO 2024-07-02 11:53:42 CompareMetrics picard.analysis.WgsMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.wgs_metrics and testdata/picard/analysis/metrics/wgs_test1.wgs_metrics are equal INFO 2024-07-02 11:53:42 CompareMetrics picard.analysis.WgsMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.wgs_metrics and testdata/picard/analysis/metrics/wgs_test1.wgs_metrics are equal Test: Test method testCompareMetrics[9](wgs_test1.wgs_metrics, wgs_test1.wgs_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:42 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:42 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. Test: Test method testCompareMetrics[9](wgs_test1.wgs_metrics, wgs_test1.wgs_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testCompareMetrics[10](wgs_test1.raw_wgs_metrics, wgs_test2.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) Test: Test method testCompareMetrics[10](wgs_test1.raw_wgs_metrics, wgs_test2.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:42.102 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.analysis.CompareMetricsTest.testCompareMetrics[10](wgs_test1.raw_wgs_metrics, wgs_test2.raw_wgs_metrics, null, null, null, 1) STANDARD_ERROR 11:53:42.102 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[10](wgs_test1.raw_wgs_metrics, wgs_test2.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:42.102 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:42.102 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[10](wgs_test1.raw_wgs_metrics, wgs_test2.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:42.102 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:42.102 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[10](wgs_test1.raw_wgs_metrics, wgs_test2.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:42.102 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:42.102 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[10](wgs_test1.raw_wgs_metrics, wgs_test2.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:42 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.raw_wgs_metrics, testdata/picard/analysis/metrics/wgs_test2.raw_wgs_metrics] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:42 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.raw_wgs_metrics, testdata/picard/analysis/metrics/wgs_test2.raw_wgs_metrics] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCompareMetrics[10](wgs_test1.raw_wgs_metrics, wgs_test2.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCompareMetrics[10](wgs_test1.raw_wgs_metrics, wgs_test2.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: INFO 2024-07-02 11:53:43 CompareMetrics picard.analysis.CollectRawWgsMetrics$RawWgsMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.raw_wgs_metrics and testdata/picard/analysis/metrics/wgs_test2.raw_wgs_metrics are NOT equal INFO 2024-07-02 11:53:43 CompareMetrics picard.analysis.CollectRawWgsMetrics$RawWgsMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.raw_wgs_metrics and testdata/picard/analysis/metrics/wgs_test2.raw_wgs_metrics are NOT equal Test: Test method testCompareMetrics[10](wgs_test1.raw_wgs_metrics, wgs_test2.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: ERROR 2024-07-02 11:53:43 CompareMetrics Row: 0 Metric: GENOME_TERRITORY values differ. Value1: 2745186694 Value2: 2745186691 Changed by -3.0 (relative change of -1.0928218494417632E-9) ERROR 2024-07-02 11:53:43 CompareMetrics Row: 0 Metric: GENOME_TERRITORY values differ. Value1: 2745186694 Value2: 2745186691 Changed by -3.0 (relative change of -1.0928218494417632E-9) Test: Test method testCompareMetrics[10](wgs_test1.raw_wgs_metrics, wgs_test2.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: ERROR 2024-07-02 11:53:43 CompareMetrics Row: 0 Metric: PCT_EXC_BASEQ values differ. Value1: 0.122134 Value2: 0.122133 Changed by -1.000000000001E-6 (relative change of -8.187728232932681E-6) ERROR 2024-07-02 11:53:43 CompareMetrics Row: 0 Metric: PCT_EXC_BASEQ values differ. Value1: 0.122134 Value2: 0.122133 Changed by -1.000000000001E-6 (relative change of -8.187728232932681E-6) Test: Test method testCompareMetrics[10](wgs_test1.raw_wgs_metrics, wgs_test2.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: ERROR 2024-07-02 11:53:43 CompareMetrics Metric Histograms differ ERROR 2024-07-02 11:53:43 CompareMetrics Metric Histograms differ Test: Test method testCompareMetrics[10](wgs_test1.raw_wgs_metrics, wgs_test2.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:43 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:53:43 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.02 minutes. Test: Test method testCompareMetrics[10](wgs_test1.raw_wgs_metrics, wgs_test2.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testCompareMetrics[10](wgs_test1.raw_wgs_metrics, wgs_test2.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCompareMetrics[11](wgs_test1.2rows.raw_wgs_metrics, wgs_test1.2rows.raw_wgs_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) Test: Test method testCompareMetrics[11](wgs_test1.2rows.raw_wgs_metrics, wgs_test1.2rows.raw_wgs_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:43.216 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.analysis.CompareMetricsTest.testCompareMetrics[11](wgs_test1.2rows.raw_wgs_metrics, wgs_test1.2rows.raw_wgs_metrics, null, null, null, 0) STANDARD_ERROR 11:53:43.216 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[11](wgs_test1.2rows.raw_wgs_metrics, wgs_test1.2rows.raw_wgs_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:43.216 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:43.216 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[11](wgs_test1.2rows.raw_wgs_metrics, wgs_test1.2rows.raw_wgs_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:43.217 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:43.217 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[11](wgs_test1.2rows.raw_wgs_metrics, wgs_test1.2rows.raw_wgs_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:43.217 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:43.217 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[11](wgs_test1.2rows.raw_wgs_metrics, wgs_test1.2rows.raw_wgs_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:43 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.2rows.raw_wgs_metrics, testdata/picard/analysis/metrics/wgs_test1.2rows.raw_wgs_metrics] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:43 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.2rows.raw_wgs_metrics, testdata/picard/analysis/metrics/wgs_test1.2rows.raw_wgs_metrics] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCompareMetrics[11](wgs_test1.2rows.raw_wgs_metrics, wgs_test1.2rows.raw_wgs_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCompareMetrics[11](wgs_test1.2rows.raw_wgs_metrics, wgs_test1.2rows.raw_wgs_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: INFO 2024-07-02 11:53:44 CompareMetrics picard.analysis.CollectRawWgsMetrics$RawWgsMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.2rows.raw_wgs_metrics and testdata/picard/analysis/metrics/wgs_test1.2rows.raw_wgs_metrics are equal INFO 2024-07-02 11:53:44 CompareMetrics picard.analysis.CollectRawWgsMetrics$RawWgsMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.2rows.raw_wgs_metrics and testdata/picard/analysis/metrics/wgs_test1.2rows.raw_wgs_metrics are equal Test: Test method testCompareMetrics[11](wgs_test1.2rows.raw_wgs_metrics, wgs_test1.2rows.raw_wgs_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:44 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:53:44 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.02 minutes. Test: Test method testCompareMetrics[11](wgs_test1.2rows.raw_wgs_metrics, wgs_test1.2rows.raw_wgs_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testCompareMetrics[12](wgs_test1.2rows.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) Test: Test method testCompareMetrics[12](wgs_test1.2rows.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:44.553 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.analysis.CompareMetricsTest.testCompareMetrics[12](wgs_test1.2rows.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1) STANDARD_ERROR 11:53:44.553 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[12](wgs_test1.2rows.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:44.553 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:44.553 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[12](wgs_test1.2rows.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:44.554 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:44.554 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[12](wgs_test1.2rows.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:44.554 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:44.554 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[12](wgs_test1.2rows.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:44 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.2rows.raw_wgs_metrics, testdata/picard/analysis/metrics/wgs_test2.2rows.raw_wgs_metrics] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:44 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.2rows.raw_wgs_metrics, testdata/picard/analysis/metrics/wgs_test2.2rows.raw_wgs_metrics] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCompareMetrics[12](wgs_test1.2rows.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCompareMetrics[12](wgs_test1.2rows.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: INFO 2024-07-02 11:53:45 CompareMetrics picard.analysis.CollectRawWgsMetrics$RawWgsMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.2rows.raw_wgs_metrics and testdata/picard/analysis/metrics/wgs_test2.2rows.raw_wgs_metrics are NOT equal INFO 2024-07-02 11:53:45 CompareMetrics picard.analysis.CollectRawWgsMetrics$RawWgsMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.2rows.raw_wgs_metrics and testdata/picard/analysis/metrics/wgs_test2.2rows.raw_wgs_metrics are NOT equal Test: Test method testCompareMetrics[12](wgs_test1.2rows.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: ERROR 2024-07-02 11:53:45 CompareMetrics Row: 0 Metric: GENOME_TERRITORY values differ. Value1: 2745186694 Value2: 2745186691 Changed by -3.0 (relative change of -1.0928218494417632E-9) ERROR 2024-07-02 11:53:45 CompareMetrics Row: 0 Metric: GENOME_TERRITORY values differ. Value1: 2745186694 Value2: 2745186691 Changed by -3.0 (relative change of -1.0928218494417632E-9) Test: Test method testCompareMetrics[12](wgs_test1.2rows.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: ERROR 2024-07-02 11:53:45 CompareMetrics Row: 0 Metric: PCT_EXC_BASEQ values differ. Value1: 0.122134 Value2: 0.122133 Changed by -1.000000000001E-6 (relative change of -8.187728232932681E-6) ERROR 2024-07-02 11:53:45 CompareMetrics Row: 0 Metric: PCT_EXC_BASEQ values differ. Value1: 0.122134 Value2: 0.122133 Changed by -1.000000000001E-6 (relative change of -8.187728232932681E-6) Test: Test method testCompareMetrics[12](wgs_test1.2rows.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: ERROR 2024-07-02 11:53:45 CompareMetrics Row: 1 Metric: GENOME_TERRITORY values differ. Value1: 2745186694 Value2: 2745186691 Changed by -3.0 (relative change of -1.0928218494417632E-9) ERROR 2024-07-02 11:53:45 CompareMetrics Row: 1 Metric: GENOME_TERRITORY values differ. Value1: 2745186694 Value2: 2745186691 Changed by -3.0 (relative change of -1.0928218494417632E-9) Test: Test method testCompareMetrics[12](wgs_test1.2rows.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: ERROR 2024-07-02 11:53:45 CompareMetrics Row: 1 Metric: PCT_EXC_BASEQ values differ. Value1: 0.122134 Value2: 0.122133 Changed by -1.000000000001E-6 (relative change of -8.187728232932681E-6) ERROR 2024-07-02 11:53:45 CompareMetrics Row: 1 Metric: PCT_EXC_BASEQ values differ. Value1: 0.122134 Value2: 0.122133 Changed by -1.000000000001E-6 (relative change of -8.187728232932681E-6) Test: Test method testCompareMetrics[12](wgs_test1.2rows.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: ERROR 2024-07-02 11:53:45 CompareMetrics Metric Histograms differ ERROR 2024-07-02 11:53:45 CompareMetrics Metric Histograms differ Test: Test method testCompareMetrics[12](wgs_test1.2rows.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:45 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:53:45 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.02 minutes. Test: Test method testCompareMetrics[12](wgs_test1.2rows.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testCompareMetrics[12](wgs_test1.2rows.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCompareMetrics[13](wgs_test1.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) Test: Test method testCompareMetrics[13](wgs_test1.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:45.818 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.analysis.CompareMetricsTest.testCompareMetrics[13](wgs_test1.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1) STANDARD_ERROR 11:53:45.818 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[13](wgs_test1.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:45.818 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:45.818 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[13](wgs_test1.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:45.818 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:45.818 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[13](wgs_test1.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:45.818 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:45.818 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[13](wgs_test1.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:45 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.raw_wgs_metrics, testdata/picard/analysis/metrics/wgs_test2.2rows.raw_wgs_metrics] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:45 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.raw_wgs_metrics, testdata/picard/analysis/metrics/wgs_test2.2rows.raw_wgs_metrics] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCompareMetrics[13](wgs_test1.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCompareMetrics[13](wgs_test1.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: INFO 2024-07-02 11:53:46 CompareMetrics picard.analysis.CollectRawWgsMetrics$RawWgsMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.raw_wgs_metrics and testdata/picard/analysis/metrics/wgs_test2.2rows.raw_wgs_metrics are NOT equal INFO 2024-07-02 11:53:46 CompareMetrics picard.analysis.CollectRawWgsMetrics$RawWgsMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.raw_wgs_metrics and testdata/picard/analysis/metrics/wgs_test2.2rows.raw_wgs_metrics are NOT equal Test: Test method testCompareMetrics[13](wgs_test1.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: ERROR 2024-07-02 11:53:46 CompareMetrics Number of metric rows differ between /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/metrics/wgs_test1.raw_wgs_metrics and /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/metrics/wgs_test2.2rows.raw_wgs_metrics ERROR 2024-07-02 11:53:46 CompareMetrics Number of metric rows differ between /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/metrics/wgs_test1.raw_wgs_metrics and /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/analysis/metrics/wgs_test2.2rows.raw_wgs_metrics Test: Test method testCompareMetrics[13](wgs_test1.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:46 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:53:46 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.01 minutes. Test: Test method testCompareMetrics[13](wgs_test1.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testCompareMetrics[13](wgs_test1.raw_wgs_metrics, wgs_test2.2rows.raw_wgs_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCompareMetrics[14](wgs_test1.fingerprinting_summary_metrics, wgs_test2.fingerprinting_summary_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) Test: Test method testCompareMetrics[14](wgs_test1.fingerprinting_summary_metrics, wgs_test2.fingerprinting_summary_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:46.702 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.analysis.CompareMetricsTest.testCompareMetrics[14](wgs_test1.fingerprinting_summary_metrics, wgs_test2.fingerprinting_summary_metrics, null, null, null, 1) STANDARD_ERROR 11:53:46.702 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[14](wgs_test1.fingerprinting_summary_metrics, wgs_test2.fingerprinting_summary_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:46.703 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:46.703 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[14](wgs_test1.fingerprinting_summary_metrics, wgs_test2.fingerprinting_summary_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:46.703 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:46.703 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[14](wgs_test1.fingerprinting_summary_metrics, wgs_test2.fingerprinting_summary_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:46.703 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:46.703 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[14](wgs_test1.fingerprinting_summary_metrics, wgs_test2.fingerprinting_summary_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:46 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.fingerprinting_summary_metrics, testdata/picard/analysis/metrics/wgs_test2.fingerprinting_summary_metrics] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:46 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.fingerprinting_summary_metrics, testdata/picard/analysis/metrics/wgs_test2.fingerprinting_summary_metrics] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCompareMetrics[14](wgs_test1.fingerprinting_summary_metrics, wgs_test2.fingerprinting_summary_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCompareMetrics[14](wgs_test1.fingerprinting_summary_metrics, wgs_test2.fingerprinting_summary_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: INFO 2024-07-02 11:53:46 CompareMetrics picard.analysis.FingerprintingSummaryMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.fingerprinting_summary_metrics and testdata/picard/analysis/metrics/wgs_test2.fingerprinting_summary_metrics are NOT equal INFO 2024-07-02 11:53:46 CompareMetrics picard.analysis.FingerprintingSummaryMetrics Metric files testdata/picard/analysis/metrics/wgs_test1.fingerprinting_summary_metrics and testdata/picard/analysis/metrics/wgs_test2.fingerprinting_summary_metrics are NOT equal Test: Test method testCompareMetrics[14](wgs_test1.fingerprinting_summary_metrics, wgs_test2.fingerprinting_summary_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: ERROR 2024-07-02 11:53:46 CompareMetrics Row: 0 Metric: LL_EXPECTED_SAMPLE values differ. Value1: -151.58161 Value2: -1.015707 Changed by 150.56590300000002 (relative change of -0.9932992729131193) ERROR 2024-07-02 11:53:46 CompareMetrics Row: 0 Metric: LL_EXPECTED_SAMPLE values differ. Value1: -151.58161 Value2: -1.015707 Changed by 150.56590300000002 (relative change of -0.9932992729131193) Test: Test method testCompareMetrics[14](wgs_test1.fingerprinting_summary_metrics, wgs_test2.fingerprinting_summary_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: ERROR 2024-07-02 11:53:46 CompareMetrics Row: 0 Metric: LL_RANDOM_SAMPLE values differ. Value1: -152.354205 Value2: -1.788301 Changed by 150.56590400000002 (relative change of -0.9882622143576544) ERROR 2024-07-02 11:53:46 CompareMetrics Row: 0 Metric: LL_RANDOM_SAMPLE values differ. Value1: -152.354205 Value2: -1.788301 Changed by 150.56590400000002 (relative change of -0.9882622143576544) Test: Test method testCompareMetrics[14](wgs_test1.fingerprinting_summary_metrics, wgs_test2.fingerprinting_summary_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:46 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:46 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. Test: Test method testCompareMetrics[14](wgs_test1.fingerprinting_summary_metrics, wgs_test2.fingerprinting_summary_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testCompareMetrics[14](wgs_test1.fingerprinting_summary_metrics, wgs_test2.fingerprinting_summary_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCompareMetrics[15](test1.arrays_variant_calling_detail_metrics, test2.arrays_variant_calling_detail_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) Test: Test method testCompareMetrics[15](test1.arrays_variant_calling_detail_metrics, test2.arrays_variant_calling_detail_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:46.718 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.analysis.CompareMetricsTest.testCompareMetrics[15](test1.arrays_variant_calling_detail_metrics, test2.arrays_variant_calling_detail_metrics, null, null, null, 1) STANDARD_ERROR 11:53:46.718 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[15](test1.arrays_variant_calling_detail_metrics, test2.arrays_variant_calling_detail_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:46.719 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:46.719 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[15](test1.arrays_variant_calling_detail_metrics, test2.arrays_variant_calling_detail_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:46.719 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:46.719 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[15](test1.arrays_variant_calling_detail_metrics, test2.arrays_variant_calling_detail_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:46.719 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:46.719 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[15](test1.arrays_variant_calling_detail_metrics, test2.arrays_variant_calling_detail_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:46 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/test1.arrays_variant_calling_detail_metrics, testdata/picard/analysis/metrics/test2.arrays_variant_calling_detail_metrics] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:46 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/test1.arrays_variant_calling_detail_metrics, testdata/picard/analysis/metrics/test2.arrays_variant_calling_detail_metrics] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCompareMetrics[15](test1.arrays_variant_calling_detail_metrics, test2.arrays_variant_calling_detail_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCompareMetrics[15](test1.arrays_variant_calling_detail_metrics, test2.arrays_variant_calling_detail_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: INFO 2024-07-02 11:53:46 CompareMetrics picard.arrays.CollectArraysVariantCallingMetrics$ArraysVariantCallingDetailMetrics Metric files testdata/picard/analysis/metrics/test1.arrays_variant_calling_detail_metrics and testdata/picard/analysis/metrics/test2.arrays_variant_calling_detail_metrics are NOT equal INFO 2024-07-02 11:53:46 CompareMetrics picard.arrays.CollectArraysVariantCallingMetrics$ArraysVariantCallingDetailMetrics Metric files testdata/picard/analysis/metrics/test1.arrays_variant_calling_detail_metrics and testdata/picard/analysis/metrics/test2.arrays_variant_calling_detail_metrics are NOT equal Test: Test method testCompareMetrics[15](test1.arrays_variant_calling_detail_metrics, test2.arrays_variant_calling_detail_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: ERROR 2024-07-02 11:53:46 CompareMetrics Row: 0 Metric: AUTOCALL_DATE values differ. Value1: 2020-03-28T02:21:00+1400 Value2: 2019-12-14T17:05:00+1400 ERROR 2024-07-02 11:53:46 CompareMetrics Row: 0 Metric: AUTOCALL_DATE values differ. Value1: 2020-03-28T02:21:00+1400 Value2: 2019-12-14T17:05:00+1400 Test: Test method testCompareMetrics[15](test1.arrays_variant_calling_detail_metrics, test2.arrays_variant_calling_detail_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:46 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:46 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. Test: Test method testCompareMetrics[15](test1.arrays_variant_calling_detail_metrics, test2.arrays_variant_calling_detail_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testCompareMetrics[15](test1.arrays_variant_calling_detail_metrics, test2.arrays_variant_calling_detail_metrics, null, null, null, 1)(picard.analysis.CompareMetricsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCompareMetrics[16](test1.arrays_variant_calling_detail_metrics, test2.arrays_variant_calling_detail_metrics, AUTOCALL_DATE, null, null, 0)(picard.analysis.CompareMetricsTest) Test: Test method testCompareMetrics[16](test1.arrays_variant_calling_detail_metrics, test2.arrays_variant_calling_detail_metrics, AUTOCALL_DATE, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:46.730 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.analysis.CompareMetricsTest.testCompareMetrics[16](test1.arrays_variant_calling_detail_metrics, test2.arrays_variant_calling_detail_metrics, AUTOCALL_DATE, null, null, 0) STANDARD_ERROR 11:53:46.730 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[16](test1.arrays_variant_calling_detail_metrics, test2.arrays_variant_calling_detail_metrics, AUTOCALL_DATE, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:46.730 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:46.730 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[16](test1.arrays_variant_calling_detail_metrics, test2.arrays_variant_calling_detail_metrics, AUTOCALL_DATE, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:46.730 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:46.730 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[16](test1.arrays_variant_calling_detail_metrics, test2.arrays_variant_calling_detail_metrics, AUTOCALL_DATE, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:46.730 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:46.730 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[16](test1.arrays_variant_calling_detail_metrics, test2.arrays_variant_calling_detail_metrics, AUTOCALL_DATE, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:46 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/test1.arrays_variant_calling_detail_metrics, testdata/picard/analysis/metrics/test2.arrays_variant_calling_detail_metrics] METRICS_TO_IGNORE=[AUTOCALL_DATE] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:46 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/test1.arrays_variant_calling_detail_metrics, testdata/picard/analysis/metrics/test2.arrays_variant_calling_detail_metrics] METRICS_TO_IGNORE=[AUTOCALL_DATE] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCompareMetrics[16](test1.arrays_variant_calling_detail_metrics, test2.arrays_variant_calling_detail_metrics, AUTOCALL_DATE, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCompareMetrics[16](test1.arrays_variant_calling_detail_metrics, test2.arrays_variant_calling_detail_metrics, AUTOCALL_DATE, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: INFO 2024-07-02 11:53:46 CompareMetrics picard.arrays.CollectArraysVariantCallingMetrics$ArraysVariantCallingDetailMetrics Metric files testdata/picard/analysis/metrics/test1.arrays_variant_calling_detail_metrics and testdata/picard/analysis/metrics/test2.arrays_variant_calling_detail_metrics are equal INFO 2024-07-02 11:53:46 CompareMetrics picard.arrays.CollectArraysVariantCallingMetrics$ArraysVariantCallingDetailMetrics Metric files testdata/picard/analysis/metrics/test1.arrays_variant_calling_detail_metrics and testdata/picard/analysis/metrics/test2.arrays_variant_calling_detail_metrics are equal Test: Test method testCompareMetrics[16](test1.arrays_variant_calling_detail_metrics, test2.arrays_variant_calling_detail_metrics, AUTOCALL_DATE, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:46 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:46 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. Test: Test method testCompareMetrics[16](test1.arrays_variant_calling_detail_metrics, test2.arrays_variant_calling_detail_metrics, AUTOCALL_DATE, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testCompareMetrics[17](test1.arrays_variant_calling_summary_metrics, test2.arrays_variant_calling_summary_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) Test: Test method testCompareMetrics[17](test1.arrays_variant_calling_summary_metrics, test2.arrays_variant_calling_summary_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:46.732 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.analysis.CompareMetricsTest.testCompareMetrics[17](test1.arrays_variant_calling_summary_metrics, test2.arrays_variant_calling_summary_metrics, null, null, null, 0) STANDARD_ERROR 11:53:46.732 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[17](test1.arrays_variant_calling_summary_metrics, test2.arrays_variant_calling_summary_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:46.732 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:46.732 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[17](test1.arrays_variant_calling_summary_metrics, test2.arrays_variant_calling_summary_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:46.741 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:46.741 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCompareMetrics[17](test1.arrays_variant_calling_summary_metrics, test2.arrays_variant_calling_summary_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:46.741 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:46.741 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCompareMetrics[17](test1.arrays_variant_calling_summary_metrics, test2.arrays_variant_calling_summary_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:46 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/test1.arrays_variant_calling_summary_metrics, testdata/picard/analysis/metrics/test2.arrays_variant_calling_summary_metrics] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:46 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/test1.arrays_variant_calling_summary_metrics, testdata/picard/analysis/metrics/test2.arrays_variant_calling_summary_metrics] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCompareMetrics[17](test1.arrays_variant_calling_summary_metrics, test2.arrays_variant_calling_summary_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCompareMetrics[17](test1.arrays_variant_calling_summary_metrics, test2.arrays_variant_calling_summary_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: INFO 2024-07-02 11:53:46 CompareMetrics picard.arrays.CollectArraysVariantCallingMetrics$ArraysVariantCallingSummaryMetrics Metric files testdata/picard/analysis/metrics/test1.arrays_variant_calling_summary_metrics and testdata/picard/analysis/metrics/test2.arrays_variant_calling_summary_metrics are equal INFO 2024-07-02 11:53:46 CompareMetrics picard.arrays.CollectArraysVariantCallingMetrics$ArraysVariantCallingSummaryMetrics Metric files testdata/picard/analysis/metrics/test1.arrays_variant_calling_summary_metrics and testdata/picard/analysis/metrics/test2.arrays_variant_calling_summary_metrics are equal Test: Test method testCompareMetrics[17](test1.arrays_variant_calling_summary_metrics, test2.arrays_variant_calling_summary_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:46 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:46 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. Test: Test method testCompareMetrics[17](test1.arrays_variant_calling_summary_metrics, test2.arrays_variant_calling_summary_metrics, null, null, null, 0)(picard.analysis.CompareMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testFailCompareMetricsInvalidMetricToAllowableRelativeChange(picard.analysis.CompareMetricsTest) Test: Test method testFailCompareMetricsInvalidMetricToAllowableRelativeChange(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:46.744 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.analysis.CompareMetricsTest.testFailCompareMetricsInvalidMetricToAllowableRelativeChange STANDARD_ERROR 11:53:46.744 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFailCompareMetricsInvalidMetricToAllowableRelativeChange(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:46.744 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:46.744 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFailCompareMetricsInvalidMetricToAllowableRelativeChange(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:46.744 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:46.744 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFailCompareMetricsInvalidMetricToAllowableRelativeChange(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:46.744 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:46.744 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFailCompareMetricsInvalidMetricToAllowableRelativeChange(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:46 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/test1.arrays_variant_calling_detail_metrics, testdata/picard/analysis/metrics/test2.arrays_variant_calling_detail_metrics] METRIC_ALLOWABLE_RELATIVE_CHANGE=[NONEXISTENT_METRIC:0.3] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:46 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/test1.arrays_variant_calling_detail_metrics, testdata/picard/analysis/metrics/test2.arrays_variant_calling_detail_metrics] METRIC_ALLOWABLE_RELATIVE_CHANGE=[NONEXISTENT_METRIC:0.3] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFailCompareMetricsInvalidMetricToAllowableRelativeChange(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFailCompareMetricsInvalidMetricToAllowableRelativeChange(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:46 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:46 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. Test: Test method testFailCompareMetricsInvalidMetricToAllowableRelativeChange(picard.analysis.CompareMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testFailCompareMetricsInvalidMetricToAllowableRelativeChange(picard.analysis.CompareMetricsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testFailCompareMetricsInvalidMetricToIgnore(picard.analysis.CompareMetricsTest) Test: Test method testFailCompareMetricsInvalidMetricToIgnore(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:46.749 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.analysis.CompareMetricsTest.testFailCompareMetricsInvalidMetricToIgnore STANDARD_ERROR 11:53:46.749 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFailCompareMetricsInvalidMetricToIgnore(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:46.749 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:46.749 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFailCompareMetricsInvalidMetricToIgnore(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:46.749 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:46.749 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFailCompareMetricsInvalidMetricToIgnore(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:46.749 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:46.749 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFailCompareMetricsInvalidMetricToIgnore(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:46 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/test1.arrays_variant_calling_detail_metrics, testdata/picard/analysis/metrics/test2.arrays_variant_calling_detail_metrics] METRICS_TO_IGNORE=[NONEXISTENT_METRIC] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:46 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/test1.arrays_variant_calling_detail_metrics, testdata/picard/analysis/metrics/test2.arrays_variant_calling_detail_metrics] METRICS_TO_IGNORE=[NONEXISTENT_METRIC] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFailCompareMetricsInvalidMetricToIgnore(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFailCompareMetricsInvalidMetricToIgnore(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:46 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:46 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.00 minutes. Test: Test method testFailCompareMetricsInvalidMetricToIgnore(picard.analysis.CompareMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testFailCompareMetricsInvalidMetricToIgnore(picard.analysis.CompareMetricsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testFailCompareMetricsOnDifferentClasses(picard.analysis.CompareMetricsTest) Test: Test method testFailCompareMetricsOnDifferentClasses(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:46.752 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.analysis.CompareMetricsTest.testFailCompareMetricsOnDifferentClasses STANDARD_ERROR 11:53:46.752 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFailCompareMetricsOnDifferentClasses(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:46.752 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:46.752 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFailCompareMetricsOnDifferentClasses(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:46.752 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:46.752 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFailCompareMetricsOnDifferentClasses(picard.analysis.CompareMetricsTest) produced standard out/err: 11:53:46.752 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:46.752 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFailCompareMetricsOnDifferentClasses(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:46 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.wgs_metrics, testdata/picard/analysis/metrics/wgs_test1.raw_wgs_metrics] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:46 GMT+14:00 2024] CompareMetrics INPUT=[testdata/picard/analysis/metrics/wgs_test1.wgs_metrics, testdata/picard/analysis/metrics/wgs_test1.raw_wgs_metrics] IGNORE_HISTOGRAM_DIFFERENCES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFailCompareMetricsOnDifferentClasses(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFailCompareMetricsOnDifferentClasses(picard.analysis.CompareMetricsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.analysis.CompareMetrics done. Elapsed time: 0.01 minutes. Test: Test method testFailCompareMetricsOnDifferentClasses(picard.analysis.CompareMetricsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testFailCompareMetricsOnDifferentClasses(picard.analysis.CompareMetricsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:47 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false) STANDARD_ERROR INFO 2024-07-02 11:53:47 CompareSAMs Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam -O /tmp/pbuilder2/compareSam15581292507083051736.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam -O /tmp/pbuilder2/compareSam15581292507083051736.tsv Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.399 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.399 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.399 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.399 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.399 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.399 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.399 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.399 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam OUTPUT=/tmp/pbuilder2/compareSam15581292507083051736.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam OUTPUT=/tmp/pbuilder2/compareSam15581292507083051736.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Sort order differs. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false) STANDARD_OUT Sort order differs. Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: File 1: coordinate File 1: coordinate Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: File 2: null File 2: null Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Sort Order differs. Sort Order differs. Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: File 1: coordinate File 1: coordinate Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: File 2: unsorted File 2: unsorted Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Cannot compare alignments if sort orders differ. Cannot compare alignments if sort orders differ. Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. SAM files differ. Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false) STANDARD_ERROR [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:47 CompareSAMs INFO 2024-07-02 11:53:47 CompareSAMs Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam -O /tmp/pbuilder2/compareSam15581292507083051736.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam -O /tmp/pbuilder2/compareSam15581292507083051736.tsv Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.428 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.428 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.428 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.428 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.431 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.431 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.431 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.431 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam OUTPUT=/tmp/pbuilder2/compareSam15581292507083051736.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam OUTPUT=/tmp/pbuilder2/compareSam15581292507083051736.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Sort order differs. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false) STANDARD_OUT Sort order differs. Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: File 1: null File 1: null Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: File 2: coordinate File 2: coordinate Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Sort Order differs. Sort Order differs. Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: File 1: unsorted File 1: unsorted Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: File 2: coordinate File 2: coordinate Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Cannot compare alignments if sort orders differ. Cannot compare alignments if sort orders differ. Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. SAM files differ. Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false) STANDARD_ERROR [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[0](genomic_sorted.sam, unsorted.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:47 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[1](genomic_sorted.sam, chr21.sam, null, false) STANDARD_ERROR INFO 2024-07-02 11:53:47 CompareSAMs Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/chr21.sam -O /tmp/pbuilder2/compareSam15236172354479972305.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/chr21.sam -O /tmp/pbuilder2/compareSam15236172354479972305.tsv Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.460 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.460 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.460 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.460 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.460 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.460 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.460 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.460 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/chr21.sam OUTPUT=/tmp/pbuilder2/compareSam15236172354479972305.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/chr21.sam OUTPUT=/tmp/pbuilder2/compareSam15236172354479972305.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Name of sequence record 1 differs. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[1](genomic_sorted.sam, chr21.sam, null, false) STANDARD_OUT Name of sequence record 1 differs. Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: File 1: chr20 File 1: chr20 Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: File 2: chr21 File 2: chr21 Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Cannot compare coordinate-sorted SAM files because sequence dictionaries differ. Cannot compare coordinate-sorted SAM files because sequence dictionaries differ. Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. SAM files differ. Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[1](genomic_sorted.sam, chr21.sam, null, false) STANDARD_ERROR [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:47 CompareSAMs INFO 2024-07-02 11:53:47 CompareSAMs Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/chr21.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam -O /tmp/pbuilder2/compareSam15236172354479972305.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/chr21.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam -O /tmp/pbuilder2/compareSam15236172354479972305.tsv Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.488 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.488 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.490 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.490 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.490 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.490 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.490 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.490 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/chr21.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam OUTPUT=/tmp/pbuilder2/compareSam15236172354479972305.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/chr21.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam OUTPUT=/tmp/pbuilder2/compareSam15236172354479972305.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Name of sequence record 1 differs. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[1](genomic_sorted.sam, chr21.sam, null, false) STANDARD_OUT Name of sequence record 1 differs. Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: File 1: chr21 File 1: chr21 Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: File 2: chr20 File 2: chr20 Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Cannot compare coordinate-sorted SAM files because sequence dictionaries differ. Cannot compare coordinate-sorted SAM files because sequence dictionaries differ. Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. SAM files differ. Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[1](genomic_sorted.sam, chr21.sam, null, false) STANDARD_ERROR [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[1](genomic_sorted.sam, chr21.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:47 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false) STANDARD_ERROR INFO 2024-07-02 11:53:47 CompareSAMs Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam -O /tmp/pbuilder2/compareSam13481471756533574026.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam -O /tmp/pbuilder2/compareSam13481471756533574026.tsv Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.523 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.523 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.523 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.523 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.524 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.524 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.524 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.524 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam OUTPUT=/tmp/pbuilder2/compareSam13481471756533574026.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam OUTPUT=/tmp/pbuilder2/compareSam13481471756533574026.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Length of sequence dictionaries differs. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false) STANDARD_OUT Length of sequence dictionaries differs. Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: File 1: 1 File 1: 1 Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: File 2: 2 File 2: 2 Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Cannot compare coordinate-sorted SAM files because sequence dictionaries differ. Cannot compare coordinate-sorted SAM files because sequence dictionaries differ. Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. SAM files differ. Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false) STANDARD_ERROR [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:47 CompareSAMs INFO 2024-07-02 11:53:47 CompareSAMs Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam -O /tmp/pbuilder2/compareSam13481471756533574026.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam -O /tmp/pbuilder2/compareSam13481471756533574026.tsv Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.563 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.563 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.563 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.563 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.564 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.564 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.564 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.564 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam OUTPUT=/tmp/pbuilder2/compareSam13481471756533574026.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam OUTPUT=/tmp/pbuilder2/compareSam13481471756533574026.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Length of sequence dictionaries differs. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false) STANDARD_OUT Length of sequence dictionaries differs. Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: File 1: 2 File 1: 2 Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: File 2: 1 File 2: 1 Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Cannot compare coordinate-sorted SAM files because sequence dictionaries differ. Cannot compare coordinate-sorted SAM files because sequence dictionaries differ. Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. SAM files differ. Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false) STANDARD_ERROR [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[2](genomic_sorted.sam, bigger_seq_dict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:47 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true) STANDARD_ERROR INFO 2024-07-02 11:53:47 CompareSAMs Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam -O /tmp/pbuilder2/compareSam10942238692227361331.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam -O /tmp/pbuilder2/compareSam10942238692227361331.tsv Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.598 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.598 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.598 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.598 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.599 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.599 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.599 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.599 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam OUTPUT=/tmp/pbuilder2/compareSam10942238692227361331.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam OUTPUT=/tmp/pbuilder2/compareSam10942238692227361331.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files match. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true) STANDARD_OUT SAM files match. Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true) STANDARD_ERROR [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:47 CompareSAMs INFO 2024-07-02 11:53:47 CompareSAMs Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam -O /tmp/pbuilder2/compareSam10942238692227361331.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam -O /tmp/pbuilder2/compareSam10942238692227361331.tsv Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.635 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.635 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.635 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.635 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.635 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.635 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.635 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.635 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam OUTPUT=/tmp/pbuilder2/compareSam10942238692227361331.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam OUTPUT=/tmp/pbuilder2/compareSam10942238692227361331.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files match. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true) STANDARD_OUT SAM files match. Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true) STANDARD_ERROR [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[3](bigger_seq_dict.sam, bigger_seq_dict.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:47 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true) STANDARD_ERROR INFO 2024-07-02 11:53:47 CompareSAMs Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam -O /tmp/pbuilder2/compareSam8779744191357545603.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam -O /tmp/pbuilder2/compareSam8779744191357545603.tsv Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.675 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.675 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.675 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.675 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.675 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.675 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.675 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.675 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam OUTPUT=/tmp/pbuilder2/compareSam8779744191357545603.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam OUTPUT=/tmp/pbuilder2/compareSam8779744191357545603.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files match. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true) STANDARD_OUT SAM files match. Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true) STANDARD_ERROR [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:47 CompareSAMs INFO 2024-07-02 11:53:47 CompareSAMs Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam -O /tmp/pbuilder2/compareSam8779744191357545603.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam -O /tmp/pbuilder2/compareSam8779744191357545603.tsv Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.707 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.707 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.707 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.707 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.707 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.707 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.708 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.708 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam OUTPUT=/tmp/pbuilder2/compareSam8779744191357545603.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam OUTPUT=/tmp/pbuilder2/compareSam8779744191357545603.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files match. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true) STANDARD_OUT SAM files match. Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true) STANDARD_ERROR [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[4](genomic_sorted.sam, genomic_sorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:47 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true) STANDARD_ERROR INFO 2024-07-02 11:53:47 CompareSAMs Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/has_non_primary.sam -O /tmp/pbuilder2/compareSam13722559484077214601.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/has_non_primary.sam -O /tmp/pbuilder2/compareSam13722559484077214601.tsv Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.744 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.744 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.744 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.744 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.745 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.745 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.745 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.745 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/has_non_primary.sam OUTPUT=/tmp/pbuilder2/compareSam13722559484077214601.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/has_non_primary.sam OUTPUT=/tmp/pbuilder2/compareSam13722559484077214601.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files match. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true) STANDARD_OUT SAM files match. Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true) STANDARD_ERROR [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:47 CompareSAMs INFO 2024-07-02 11:53:47 CompareSAMs Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/has_non_primary.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam -O /tmp/pbuilder2/compareSam13722559484077214601.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/has_non_primary.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam -O /tmp/pbuilder2/compareSam13722559484077214601.tsv Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.779 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.779 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.779 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.779 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.779 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.779 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.779 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.779 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/has_non_primary.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam OUTPUT=/tmp/pbuilder2/compareSam13722559484077214601.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/has_non_primary.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam OUTPUT=/tmp/pbuilder2/compareSam13722559484077214601.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files match. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true) STANDARD_OUT SAM files match. Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true) STANDARD_ERROR [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[5](genomic_sorted.sam, has_non_primary.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:47 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false) STANDARD_ERROR INFO 2024-07-02 11:53:47 CompareSAMs Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_5.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_5_plus.sam -O /tmp/pbuilder2/compareSam13230278463560343659.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_5.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_5_plus.sam -O /tmp/pbuilder2/compareSam13230278463560343659.tsv Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.827 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.827 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.828 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.828 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.828 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.828 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.828 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.828 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_5.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_5_plus.sam OUTPUT=/tmp/pbuilder2/compareSam13230278463560343659.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_5.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_5_plus.sam OUTPUT=/tmp/pbuilder2/compareSam13230278463560343659.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false) STANDARD_ERROR [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:47 CompareSAMs INFO 2024-07-02 11:53:47 CompareSAMs Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_5_plus.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_5.sam -O /tmp/pbuilder2/compareSam13230278463560343659.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_5_plus.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_5.sam -O /tmp/pbuilder2/compareSam13230278463560343659.tsv Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.884 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.884 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.884 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.884 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.884 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.884 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.884 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.884 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_5_plus.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_5.sam OUTPUT=/tmp/pbuilder2/compareSam13230278463560343659.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_5_plus.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_5.sam OUTPUT=/tmp/pbuilder2/compareSam13230278463560343659.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false) STANDARD_ERROR [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:47 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false) STANDARD_ERROR INFO 2024-07-02 11:53:47 CompareSAMs Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord_diff_order.sam -O /tmp/pbuilder2/compareSam9959846974511624848.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord_diff_order.sam -O /tmp/pbuilder2/compareSam9959846974511624848.tsv Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.923 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.923 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.923 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.923 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.924 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.924 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.924 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.924 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord_diff_order.sam OUTPUT=/tmp/pbuilder2/compareSam9959846974511624848.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord_diff_order.sam OUTPUT=/tmp/pbuilder2/compareSam9959846974511624848.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false) STANDARD_ERROR [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:47 CompareSAMs INFO 2024-07-02 11:53:47 CompareSAMs Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord_diff_order.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord.sam -O /tmp/pbuilder2/compareSam9959846974511624848.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord_diff_order.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord.sam -O /tmp/pbuilder2/compareSam9959846974511624848.tsv Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.962 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.962 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.962 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.962 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.963 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:47.963 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:47.963 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:47.963 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord_diff_order.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord.sam OUTPUT=/tmp/pbuilder2/compareSam9959846974511624848.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:47 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord_diff_order.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord.sam OUTPUT=/tmp/pbuilder2/compareSam9959846974511624848.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false) STANDARD_ERROR [Tue Jul 02 11:53:47 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[7](group_same_coord.sam, group_same_coord_diff_order.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:48 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true) STANDARD_ERROR INFO 2024-07-02 11:53:48 CompareSAMs Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_same_position.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_same_position.sam -O /tmp/pbuilder2/compareSam8292239278676247075.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_same_position.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_same_position.sam -O /tmp/pbuilder2/compareSam8292239278676247075.tsv Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.030 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.030 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.031 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.031 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.031 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.031 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.031 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.031 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_same_position.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_same_position.sam OUTPUT=/tmp/pbuilder2/compareSam8292239278676247075.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_same_position.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_same_position.sam OUTPUT=/tmp/pbuilder2/compareSam8292239278676247075.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files match. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true) STANDARD_OUT SAM files match. Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true) STANDARD_ERROR [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:48 CompareSAMs INFO 2024-07-02 11:53:48 CompareSAMs Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_same_position.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_same_position.sam -O /tmp/pbuilder2/compareSam8292239278676247075.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_same_position.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_same_position.sam -O /tmp/pbuilder2/compareSam8292239278676247075.tsv Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.094 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.094 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.094 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.094 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.095 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.095 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.095 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.095 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_same_position.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_same_position.sam OUTPUT=/tmp/pbuilder2/compareSam8292239278676247075.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_same_position.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_same_position.sam OUTPUT=/tmp/pbuilder2/compareSam8292239278676247075.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files match. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true) STANDARD_OUT SAM files match. Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true) STANDARD_ERROR [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[8](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:48 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false) STANDARD_ERROR INFO 2024-07-02 11:53:48 CompareSAMs Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/diff_coords.sam -O /tmp/pbuilder2/compareSam8908468946983908930.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/diff_coords.sam -O /tmp/pbuilder2/compareSam8908468946983908930.tsv Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.156 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.156 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.156 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.156 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.156 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.156 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.156 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.156 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/diff_coords.sam OUTPUT=/tmp/pbuilder2/compareSam8908468946983908930.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/diff_coords.sam OUTPUT=/tmp/pbuilder2/compareSam8908468946983908930.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false) STANDARD_ERROR [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:48 CompareSAMs INFO 2024-07-02 11:53:48 CompareSAMs Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/diff_coords.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord.sam -O /tmp/pbuilder2/compareSam8908468946983908930.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/diff_coords.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord.sam -O /tmp/pbuilder2/compareSam8908468946983908930.tsv Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.221 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.221 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.221 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.221 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.221 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.221 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.221 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.221 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/diff_coords.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord.sam OUTPUT=/tmp/pbuilder2/compareSam8908468946983908930.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/diff_coords.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/group_same_coord.sam OUTPUT=/tmp/pbuilder2/compareSam8908468946983908930.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false) STANDARD_ERROR [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[9](group_same_coord.sam, diff_coords.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:48 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false) STANDARD_ERROR INFO 2024-07-02 11:53:48 CompareSAMs Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam -O /tmp/pbuilder2/compareSam59529494168981805.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam -O /tmp/pbuilder2/compareSam59529494168981805.tsv Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.282 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.282 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.282 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.282 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.282 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.282 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.282 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.282 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam OUTPUT=/tmp/pbuilder2/compareSam59529494168981805.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam OUTPUT=/tmp/pbuilder2/compareSam59529494168981805.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false) STANDARD_ERROR [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:48 CompareSAMs INFO 2024-07-02 11:53:48 CompareSAMs Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam -O /tmp/pbuilder2/compareSam59529494168981805.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam -O /tmp/pbuilder2/compareSam59529494168981805.tsv Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.338 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.338 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.338 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.338 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.338 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.338 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.338 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.338 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam OUTPUT=/tmp/pbuilder2/compareSam59529494168981805.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam OUTPUT=/tmp/pbuilder2/compareSam59529494168981805.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false) STANDARD_ERROR [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[10](genomic_sorted.sam, unmapped_first.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:48 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false) STANDARD_ERROR INFO 2024-07-02 11:53:48 CompareSAMs Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_second.sam -O /tmp/pbuilder2/compareSam11231623256771439784.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_second.sam -O /tmp/pbuilder2/compareSam11231623256771439784.tsv Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.395 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.395 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.395 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.395 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.395 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.395 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.395 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.395 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_second.sam OUTPUT=/tmp/pbuilder2/compareSam11231623256771439784.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_second.sam OUTPUT=/tmp/pbuilder2/compareSam11231623256771439784.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false) STANDARD_ERROR [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:48 CompareSAMs INFO 2024-07-02 11:53:48 CompareSAMs Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_second.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam -O /tmp/pbuilder2/compareSam11231623256771439784.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_second.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam -O /tmp/pbuilder2/compareSam11231623256771439784.tsv Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.456 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.456 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.456 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.456 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.456 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.456 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.456 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.456 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_second.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam OUTPUT=/tmp/pbuilder2/compareSam11231623256771439784.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_second.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam OUTPUT=/tmp/pbuilder2/compareSam11231623256771439784.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false) STANDARD_ERROR [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[11](genomic_sorted.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:48 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false) STANDARD_ERROR INFO 2024-07-02 11:53:48 CompareSAMs Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_second.sam -O /tmp/pbuilder2/compareSam2858521382611614389.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_second.sam -O /tmp/pbuilder2/compareSam2858521382611614389.tsv Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.531 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.531 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.531 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.531 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.531 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.531 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.531 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.531 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_second.sam OUTPUT=/tmp/pbuilder2/compareSam2858521382611614389.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_second.sam OUTPUT=/tmp/pbuilder2/compareSam2858521382611614389.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false) STANDARD_ERROR [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:48 CompareSAMs INFO 2024-07-02 11:53:48 CompareSAMs Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_second.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam -O /tmp/pbuilder2/compareSam2858521382611614389.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_second.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam -O /tmp/pbuilder2/compareSam2858521382611614389.tsv Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.614 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.614 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.614 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.614 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.615 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.615 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.615 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.615 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_second.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam OUTPUT=/tmp/pbuilder2/compareSam2858521382611614389.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_second.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam OUTPUT=/tmp/pbuilder2/compareSam2858521382611614389.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false) STANDARD_ERROR [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[12](unmapped_first.sam, unmapped_second.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:48 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true) STANDARD_ERROR INFO 2024-07-02 11:53:48 CompareSAMs Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam -O /tmp/pbuilder2/compareSam18324988237268930957.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam -O /tmp/pbuilder2/compareSam18324988237268930957.tsv Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.697 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.697 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.697 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.697 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.698 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.698 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.698 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.698 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam OUTPUT=/tmp/pbuilder2/compareSam18324988237268930957.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam OUTPUT=/tmp/pbuilder2/compareSam18324988237268930957.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files match. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true) STANDARD_OUT SAM files match. Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true) STANDARD_ERROR [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:48 CompareSAMs INFO 2024-07-02 11:53:48 CompareSAMs Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam -O /tmp/pbuilder2/compareSam18324988237268930957.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam -O /tmp/pbuilder2/compareSam18324988237268930957.tsv Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.747 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.747 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.747 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.747 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.747 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.747 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.747 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.747 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam OUTPUT=/tmp/pbuilder2/compareSam18324988237268930957.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unmapped_first.sam OUTPUT=/tmp/pbuilder2/compareSam18324988237268930957.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files match. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true) STANDARD_OUT SAM files match. Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true) STANDARD_ERROR [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[13](unmapped_first.sam, unmapped_first.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:48 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false) STANDARD_ERROR INFO 2024-07-02 11:53:48 CompareSAMs Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_sam_v1.6.sam -O /tmp/pbuilder2/compareSam10247829287274732723.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_sam_v1.6.sam -O /tmp/pbuilder2/compareSam10247829287274732723.tsv Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.806 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.806 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.806 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.806 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.806 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.806 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.806 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.806 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_sam_v1.6.sam OUTPUT=/tmp/pbuilder2/compareSam10247829287274732723.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_sam_v1.6.sam OUTPUT=/tmp/pbuilder2/compareSam10247829287274732723.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: File format version differs. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false) STANDARD_OUT File format version differs. Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: File 1: 1.0 File 1: 1.0 Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: File 2: 1.6 File 2: 1.6 Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. SAM files differ. Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false) STANDARD_ERROR [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:48 CompareSAMs INFO 2024-07-02 11:53:48 CompareSAMs Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_sam_v1.6.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam -O /tmp/pbuilder2/compareSam10247829287274732723.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_sam_v1.6.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam -O /tmp/pbuilder2/compareSam10247829287274732723.tsv Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.853 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.853 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.853 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.853 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.854 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.854 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.854 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.854 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_sam_v1.6.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam OUTPUT=/tmp/pbuilder2/compareSam10247829287274732723.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted_sam_v1.6.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam OUTPUT=/tmp/pbuilder2/compareSam10247829287274732723.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: File format version differs. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false) STANDARD_OUT File format version differs. Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: File 1: 1.6 File 1: 1.6 Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: File 2: 1.0 File 2: 1.0 Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. SAM files differ. Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false) STANDARD_ERROR [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[14](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:48 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[15](unsorted.sam, unsorted.sam, null, true) STANDARD_ERROR INFO 2024-07-02 11:53:48 CompareSAMs Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam -O /tmp/pbuilder2/compareSam6722884359034742612.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam -O /tmp/pbuilder2/compareSam6722884359034742612.tsv Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.904 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.904 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.904 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.904 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.904 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.904 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.904 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.904 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam OUTPUT=/tmp/pbuilder2/compareSam6722884359034742612.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam OUTPUT=/tmp/pbuilder2/compareSam6722884359034742612.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files match. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[15](unsorted.sam, unsorted.sam, null, true) STANDARD_OUT SAM files match. Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[15](unsorted.sam, unsorted.sam, null, true) STANDARD_ERROR [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:48 CompareSAMs INFO 2024-07-02 11:53:48 CompareSAMs Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam -O /tmp/pbuilder2/compareSam6722884359034742612.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam -O /tmp/pbuilder2/compareSam6722884359034742612.tsv Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.954 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.954 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.955 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.955 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.955 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:48.955 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:48.955 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:48.955 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam OUTPUT=/tmp/pbuilder2/compareSam6722884359034742612.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:48 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam OUTPUT=/tmp/pbuilder2/compareSam6722884359034742612.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files match. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[15](unsorted.sam, unsorted.sam, null, true) STANDARD_OUT SAM files match. Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[15](unsorted.sam, unsorted.sam, null, true) STANDARD_ERROR [Tue Jul 02 11:53:48 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[15](unsorted.sam, unsorted.sam, null, true)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:49 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[16](unsorted.sam, unsorted2.sam, null, false) STANDARD_ERROR INFO 2024-07-02 11:53:49 CompareSAMs Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted2.sam -O /tmp/pbuilder2/compareSam3879688072569474594.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted2.sam -O /tmp/pbuilder2/compareSam3879688072569474594.tsv Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.004 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.004 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.004 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.004 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.004 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.004 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.004 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.004 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted2.sam OUTPUT=/tmp/pbuilder2/compareSam3879688072569474594.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted2.sam OUTPUT=/tmp/pbuilder2/compareSam3879688072569474594.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[16](unsorted.sam, unsorted2.sam, null, false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[16](unsorted.sam, unsorted2.sam, null, false) STANDARD_ERROR [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:49 CompareSAMs INFO 2024-07-02 11:53:49 CompareSAMs Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted2.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam -O /tmp/pbuilder2/compareSam3879688072569474594.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted2.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam -O /tmp/pbuilder2/compareSam3879688072569474594.tsv Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.055 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.055 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.055 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.055 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.056 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.056 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.056 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.056 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted2.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam OUTPUT=/tmp/pbuilder2/compareSam3879688072569474594.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted2.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/unsorted.sam OUTPUT=/tmp/pbuilder2/compareSam3879688072569474594.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[16](unsorted.sam, unsorted2.sam, null, false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[16](unsorted.sam, unsorted2.sam, null, false) STANDARD_ERROR [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[16](unsorted.sam, unsorted2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:49 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true) STANDARD_ERROR INFO 2024-07-02 11:53:49 CompareSAMs Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict.sam -O /tmp/pbuilder2/compareSam1747050225662992109.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict.sam -O /tmp/pbuilder2/compareSam1747050225662992109.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.107 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.107 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.107 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.107 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.107 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.107 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.107 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.107 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict.sam OUTPUT=/tmp/pbuilder2/compareSam1747050225662992109.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict.sam OUTPUT=/tmp/pbuilder2/compareSam1747050225662992109.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files match. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true) STANDARD_OUT SAM files match. Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true) STANDARD_ERROR [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:49 CompareSAMs INFO 2024-07-02 11:53:49 CompareSAMs Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam -O /tmp/pbuilder2/compareSam1747050225662992109.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam -O /tmp/pbuilder2/compareSam1747050225662992109.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.170 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.170 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.170 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.170 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.170 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.170 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.170 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.170 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam OUTPUT=/tmp/pbuilder2/compareSam1747050225662992109.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam OUTPUT=/tmp/pbuilder2/compareSam1747050225662992109.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files match. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true) STANDARD_OUT SAM files match. Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true) STANDARD_ERROR [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:49 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_ERROR INFO 2024-07-02 11:53:49 CompareSAMs Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_one_align_differ.sam -O /tmp/pbuilder2/compareSam9508398867879155024.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_one_align_differ.sam -O /tmp/pbuilder2/compareSam9508398867879155024.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.221 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.221 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.221 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.221 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.221 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.221 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.221 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.221 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_one_align_differ.sam OUTPUT=/tmp/pbuilder2/compareSam9508398867879155024.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_one_align_differ.sam OUTPUT=/tmp/pbuilder2/compareSam9508398867879155024.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_ERROR [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:49 CompareSAMs INFO 2024-07-02 11:53:49 CompareSAMs Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_one_align_differ.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam -O /tmp/pbuilder2/compareSam9508398867879155024.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_one_align_differ.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam -O /tmp/pbuilder2/compareSam9508398867879155024.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.270 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.270 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.271 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.271 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.271 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.271 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.271 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.271 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_one_align_differ.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam OUTPUT=/tmp/pbuilder2/compareSam9508398867879155024.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_one_align_differ.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam OUTPUT=/tmp/pbuilder2/compareSam9508398867879155024.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_ERROR [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:49 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_ERROR INFO 2024-07-02 11:53:49 CompareSAMs Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_two_mismatch_lenient.sam -O /tmp/pbuilder2/compareSam11381623325401007091.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_two_mismatch_lenient.sam -O /tmp/pbuilder2/compareSam11381623325401007091.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.327 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.327 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.327 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.327 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.327 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.327 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.327 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.327 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_two_mismatch_lenient.sam OUTPUT=/tmp/pbuilder2/compareSam11381623325401007091.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_two_mismatch_lenient.sam OUTPUT=/tmp/pbuilder2/compareSam11381623325401007091.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_ERROR [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:49 CompareSAMs INFO 2024-07-02 11:53:49 CompareSAMs Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_two_mismatch_lenient.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam -O /tmp/pbuilder2/compareSam11381623325401007091.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_two_mismatch_lenient.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam -O /tmp/pbuilder2/compareSam11381623325401007091.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.372 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.372 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.372 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.372 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.377 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.377 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.377 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.377 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_two_mismatch_lenient.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam OUTPUT=/tmp/pbuilder2/compareSam11381623325401007091.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_two_mismatch_lenient.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam OUTPUT=/tmp/pbuilder2/compareSam11381623325401007091.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_ERROR [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:49 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_ERROR INFO 2024-07-02 11:53:49 CompareSAMs Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient.sam -O /tmp/pbuilder2/compareSam16637353988426241907.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient.sam -O /tmp/pbuilder2/compareSam16637353988426241907.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.424 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.424 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.424 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.424 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.424 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.424 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.424 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.424 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient.sam OUTPUT=/tmp/pbuilder2/compareSam16637353988426241907.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient.sam OUTPUT=/tmp/pbuilder2/compareSam16637353988426241907.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_ERROR [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:49 CompareSAMs INFO 2024-07-02 11:53:49 CompareSAMs Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam -O /tmp/pbuilder2/compareSam16637353988426241907.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam -O /tmp/pbuilder2/compareSam16637353988426241907.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam OUTPUT=/tmp/pbuilder2/compareSam16637353988426241907.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam OUTPUT=/tmp/pbuilder2/compareSam16637353988426241907.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_ERROR [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:49 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false) STANDARD_ERROR INFO 2024-07-02 11:53:49 CompareSAMs Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict.sam -O /tmp/pbuilder2/compareSam1970641976108424591.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict.sam -O /tmp/pbuilder2/compareSam1970641976108424591.tsv Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.535 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.535 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.535 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.535 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.535 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.535 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.535 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.535 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict.sam OUTPUT=/tmp/pbuilder2/compareSam1970641976108424591.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict.sam OUTPUT=/tmp/pbuilder2/compareSam1970641976108424591.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false) STANDARD_ERROR [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:49 CompareSAMs INFO 2024-07-02 11:53:49 CompareSAMs Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam -O /tmp/pbuilder2/compareSam1970641976108424591.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam -O /tmp/pbuilder2/compareSam1970641976108424591.tsv Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.604 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.604 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.604 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.604 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.604 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.604 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.604 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.604 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam OUTPUT=/tmp/pbuilder2/compareSam1970641976108424591.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base.sam OUTPUT=/tmp/pbuilder2/compareSam1970641976108424591.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false) STANDARD_ERROR [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:49 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true) STANDARD_ERROR INFO 2024-07-02 11:53:49 CompareSAMs Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict_queryname.sam -O /tmp/pbuilder2/compareSam8702424524876113710.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict_queryname.sam -O /tmp/pbuilder2/compareSam8702424524876113710.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.673 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.673 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.674 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.674 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.674 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.674 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.674 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.674 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict_queryname.sam OUTPUT=/tmp/pbuilder2/compareSam8702424524876113710.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict_queryname.sam OUTPUT=/tmp/pbuilder2/compareSam8702424524876113710.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files match. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true) STANDARD_OUT SAM files match. Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true) STANDARD_ERROR [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:49 CompareSAMs INFO 2024-07-02 11:53:49 CompareSAMs Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam -O /tmp/pbuilder2/compareSam8702424524876113710.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam -O /tmp/pbuilder2/compareSam8702424524876113710.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.737 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.737 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.737 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.737 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.737 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.737 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.737 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.737 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam OUTPUT=/tmp/pbuilder2/compareSam8702424524876113710.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam OUTPUT=/tmp/pbuilder2/compareSam8702424524876113710.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files match. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true) STANDARD_OUT SAM files match. Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true) STANDARD_ERROR [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:49 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_ERROR INFO 2024-07-02 11:53:49 CompareSAMs Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_one_align_differ_queryname.sam -O /tmp/pbuilder2/compareSam5935657940679192373.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_one_align_differ_queryname.sam -O /tmp/pbuilder2/compareSam5935657940679192373.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.784 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.784 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.784 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.784 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.784 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.784 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.784 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.784 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_one_align_differ_queryname.sam OUTPUT=/tmp/pbuilder2/compareSam5935657940679192373.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_one_align_differ_queryname.sam OUTPUT=/tmp/pbuilder2/compareSam5935657940679192373.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_ERROR [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:49 CompareSAMs INFO 2024-07-02 11:53:49 CompareSAMs Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_one_align_differ_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam -O /tmp/pbuilder2/compareSam5935657940679192373.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_one_align_differ_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam -O /tmp/pbuilder2/compareSam5935657940679192373.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.838 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.838 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.838 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.838 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.838 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.838 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.838 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.838 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_one_align_differ_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam OUTPUT=/tmp/pbuilder2/compareSam5935657940679192373.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_one_align_differ_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam OUTPUT=/tmp/pbuilder2/compareSam5935657940679192373.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_ERROR [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:49 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_ERROR INFO 2024-07-02 11:53:49 CompareSAMs Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_two_mismatch_lenient_queryname.sam -O /tmp/pbuilder2/compareSam14367766865957611827.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_two_mismatch_lenient_queryname.sam -O /tmp/pbuilder2/compareSam14367766865957611827.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.891 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.891 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.891 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.891 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.891 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.891 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.891 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.891 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_two_mismatch_lenient_queryname.sam OUTPUT=/tmp/pbuilder2/compareSam14367766865957611827.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_two_mismatch_lenient_queryname.sam OUTPUT=/tmp/pbuilder2/compareSam14367766865957611827.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_ERROR [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:49 CompareSAMs INFO 2024-07-02 11:53:49 CompareSAMs Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_two_mismatch_lenient_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam -O /tmp/pbuilder2/compareSam14367766865957611827.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_two_mismatch_lenient_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam -O /tmp/pbuilder2/compareSam14367766865957611827.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.946 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.946 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.946 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.946 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.947 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.947 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.947 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.947 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_two_mismatch_lenient_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam OUTPUT=/tmp/pbuilder2/compareSam14367766865957611827.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:49 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_two_mismatch_lenient_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam OUTPUT=/tmp/pbuilder2/compareSam14367766865957611827.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_ERROR [Tue Jul 02 11:53:49 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:49 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_ERROR INFO 2024-07-02 11:53:49 CompareSAMs Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_queryname.sam -O /tmp/pbuilder2/compareSam7538568382398811822.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_queryname.sam -O /tmp/pbuilder2/compareSam7538568382398811822.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.992 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:49.992 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:49.992 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:49.992 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.001 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.001 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.001 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.001 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_queryname.sam OUTPUT=/tmp/pbuilder2/compareSam7538568382398811822.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:50 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_queryname.sam OUTPUT=/tmp/pbuilder2/compareSam7538568382398811822.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_ERROR [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:50 CompareSAMs INFO 2024-07-02 11:53:50 CompareSAMs Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam -O /tmp/pbuilder2/compareSam7538568382398811822.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam -O /tmp/pbuilder2/compareSam7538568382398811822.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.046 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.046 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.046 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.046 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.046 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.046 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.046 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.046 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam OUTPUT=/tmp/pbuilder2/compareSam7538568382398811822.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:50 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_lenient_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam OUTPUT=/tmp/pbuilder2/compareSam7538568382398811822.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_ERROR [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:50 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false) STANDARD_ERROR INFO 2024-07-02 11:53:50 CompareSAMs Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict_queryname.sam -O /tmp/pbuilder2/compareSam1288487946242739003.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict_queryname.sam -O /tmp/pbuilder2/compareSam1288487946242739003.tsv Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.096 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.096 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.096 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.096 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.096 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.096 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.096 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.096 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict_queryname.sam OUTPUT=/tmp/pbuilder2/compareSam1288487946242739003.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:50 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict_queryname.sam OUTPUT=/tmp/pbuilder2/compareSam1288487946242739003.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false) STANDARD_ERROR [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:50 CompareSAMs INFO 2024-07-02 11:53:50 CompareSAMs Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam -O /tmp/pbuilder2/compareSam1288487946242739003.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam -O /tmp/pbuilder2/compareSam1288487946242739003.tsv Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.136 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.136 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.137 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.137 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.145 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.145 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.145 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.145 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam OUTPUT=/tmp/pbuilder2/compareSam1288487946242739003.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:50 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_four_mismatch_strict_queryname.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/duplicate_base_queryname.sam OUTPUT=/tmp/pbuilder2/compareSam1288487946242739003.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false) STANDARD_ERROR [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:50 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_ERROR INFO 2024-07-02 11:53:50 CompareSAMs Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_2.sam -O /tmp/pbuilder2/compareSam17029394820592089860.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_2.sam -O /tmp/pbuilder2/compareSam17029394820592089860.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.191 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.191 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.191 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.191 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.191 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.191 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.191 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.191 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_2.sam OUTPUT=/tmp/pbuilder2/compareSam17029394820592089860.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:50 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_2.sam OUTPUT=/tmp/pbuilder2/compareSam17029394820592089860.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_ERROR [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:50 CompareSAMs INFO 2024-07-02 11:53:50 CompareSAMs Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_2.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam -O /tmp/pbuilder2/compareSam17029394820592089860.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_2.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam -O /tmp/pbuilder2/compareSam17029394820592089860.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.241 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.241 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.241 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.241 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.241 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.241 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.242 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.242 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_2.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam OUTPUT=/tmp/pbuilder2/compareSam17029394820592089860.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:50 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_2.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/genomic_sorted.sam OUTPUT=/tmp/pbuilder2/compareSam17029394820592089860.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false) STANDARD_ERROR [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[27](genomic_sorted.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:50 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true) STANDARD_ERROR INFO 2024-07-02 11:53:50 CompareSAMs Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_1.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_2.sam -O /tmp/pbuilder2/compareSam841710811992455074.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_1.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_2.sam -O /tmp/pbuilder2/compareSam841710811992455074.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.292 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.292 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.292 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.292 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.292 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.292 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.292 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.292 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_1.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_2.sam OUTPUT=/tmp/pbuilder2/compareSam841710811992455074.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:50 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_1.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_2.sam OUTPUT=/tmp/pbuilder2/compareSam841710811992455074.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files match. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true) STANDARD_OUT SAM files match. Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true) STANDARD_ERROR [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:50 CompareSAMs INFO 2024-07-02 11:53:50 CompareSAMs Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_2.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_1.sam -O /tmp/pbuilder2/compareSam841710811992455074.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_2.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_1.sam -O /tmp/pbuilder2/compareSam841710811992455074.tsv -LENIENT_DUP true -LENIENT_LOW_MQ_ALIGNMENT true Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.342 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.342 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.342 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.342 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.342 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.342 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.342 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.342 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_2.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_1.sam OUTPUT=/tmp/pbuilder2/compareSam841710811992455074.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:50 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_2.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_1.sam OUTPUT=/tmp/pbuilder2/compareSam841710811992455074.tsv LENIENT_DUP=true LENIENT_LOW_MQ_ALIGNMENT=true LENIENT_HEADER=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files match. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true) STANDARD_OUT SAM files match. Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true) STANDARD_ERROR [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[28](mq0_1.sam, mq0_2.sam, [LENIENT_DUP=true, LENIENT_LOW_MQ_ALIGNMENT=true], true)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:50 CompareSAMs Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[29](mq0_1.sam, mq0_2.sam, null, false) STANDARD_ERROR INFO 2024-07-02 11:53:50 CompareSAMs Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_1.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_2.sam -O /tmp/pbuilder2/compareSam8361421102618549960.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_1.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_2.sam -O /tmp/pbuilder2/compareSam8361421102618549960.tsv Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.388 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.388 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.388 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.388 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.388 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.388 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.388 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.388 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_1.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_2.sam OUTPUT=/tmp/pbuilder2/compareSam8361421102618549960.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:50 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_1.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_2.sam OUTPUT=/tmp/pbuilder2/compareSam8361421102618549960.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[29](mq0_1.sam, mq0_2.sam, null, false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[29](mq0_1.sam, mq0_2.sam, null, false) STANDARD_ERROR [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: INFO 2024-07-02 11:53:50 CompareSAMs INFO 2024-07-02 11:53:50 CompareSAMs Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_2.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_1.sam -O /tmp/pbuilder2/compareSam8361421102618549960.tsv ********** CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_2.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_1.sam -O /tmp/pbuilder2/compareSam8361421102618549960.tsv Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: ********** ********** Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.445 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.445 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.445 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.445 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.445 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.445 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: 11:53:50.445 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.445 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_2.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_1.sam OUTPUT=/tmp/pbuilder2/compareSam8361421102618549960.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:50 GMT+14:00 2024] CompareSAMs /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_2.sam /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/CompareSAMs/mq0_1.sam OUTPUT=/tmp/pbuilder2/compareSam8361421102618549960.tsv LENIENT_HEADER=false LENIENT_DUP=false LENIENT_LOW_MQ_ALIGNMENT=false LENIENT_UNKNOWN_MQ_ALIGNMENT=false LOW_MQ_THRESHOLD=3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: SAM files differ. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[29](mq0_1.sam, mq0_2.sam, null, false) STANDARD_OUT SAM files differ. Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.CompareSAMsTest.testComparisons[29](mq0_1.sam, mq0_2.sam, null, false) STANDARD_ERROR [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes. Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testComparisons[29](mq0_1.sam, mq0_2.sam, null, false)(picard.sam.CompareSAMsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: INFO 2024-07-02 11:53:50 CollectOxoGMetrics Gradle suite > Gradle test > picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest.testEquivalence[0](false) STANDARD_ERROR INFO 2024-07-02 11:53:50 CollectOxoGMetrics Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** ********** Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** ********** Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** ********** Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** CollectOxoGMetrics -OUTPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test17450905096244356038.oxo_g_metrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta ********** CollectOxoGMetrics -OUTPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test17450905096244356038.oxo_g_metrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** ********** Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: 11:53:50.455 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.455 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: 11:53:50.455 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.455 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: 11:53:50.455 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.455 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: 11:53:50.455 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.455 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] CollectOxoGMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test17450905096244356038.oxo_g_metrics REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 MINIMUM_INSERT_SIZE=60 MAXIMUM_INSERT_SIZE=600 INCLUDE_NON_PF_READS=true USE_OQ=true CONTEXT_SIZE=1 STOP_AFTER=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:50 GMT+14:00 2024] CollectOxoGMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test17450905096244356038.oxo_g_metrics REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 MINIMUM_INSERT_SIZE=60 MAXIMUM_INSERT_SIZE=600 INCLUDE_NON_PF_READS=true USE_OQ=true CONTEXT_SIZE=1 STOP_AFTER=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: INFO 2024-07-02 11:53:50 CollectOxoGMetrics Generated 16 context strings. INFO 2024-07-02 11:53:50 CollectOxoGMetrics Generated 16 context strings. Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: INFO 2024-07-02 11:53:50 CollectOxoGMetrics Loading dbSNP File: null INFO 2024-07-02 11:53:50 CollectOxoGMetrics Loading dbSNP File: null Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: INFO 2024-07-02 11:53:50 CollectOxoGMetrics Starting iteration. INFO 2024-07-02 11:53:50 CollectOxoGMetrics Starting iteration. Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.analysis.CollectOxoGMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.analysis.CollectOxoGMetrics done. Elapsed time: 0.00 minutes. Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: INFO 2024-07-02 11:53:50 CollectSequencingArtifactMetrics INFO 2024-07-02 11:53:50 CollectSequencingArtifactMetrics Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** ********** Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** ********** Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** ********** Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** CollectSequencingArtifactMetrics -OUTPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test9972351553099325425 -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta ********** CollectSequencingArtifactMetrics -OUTPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test9972351553099325425 -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** ********** Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: 11:53:50.464 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.464 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: 11:53:50.465 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.465 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: 11:53:50.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: 11:53:50.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] CollectSequencingArtifactMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test9972351553099325425 REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 MINIMUM_INSERT_SIZE=60 MAXIMUM_INSERT_SIZE=600 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true CONTEXT_SIZE=1 ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:50 GMT+14:00 2024] CollectSequencingArtifactMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test9972351553099325425 REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 MINIMUM_INSERT_SIZE=60 MAXIMUM_INSERT_SIZE=600 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true CONTEXT_SIZE=1 ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes. Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: INFO 2024-07-02 11:53:50 ConvertSequencingArtifactToOxoG INFO 2024-07-02 11:53:50 ConvertSequencingArtifactToOxoG Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** ********** Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** ********** Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** ********** Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** ConvertSequencingArtifactToOxoG -OUTPUT_BASE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test4968694951635729681 -INPUT_BASE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test9972351553099325425 ********** ConvertSequencingArtifactToOxoG -OUTPUT_BASE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test4968694951635729681 -INPUT_BASE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test9972351553099325425 Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** ********** Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: 11:53:50.502 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.502 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: 11:53:50.502 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.502 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: 11:53:50.502 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.502 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: 11:53:50.502 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.502 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] ConvertSequencingArtifactToOxoG INPUT_BASE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test9972351553099325425 OUTPUT_BASE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test4968694951635729681 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:50 GMT+14:00 2024] ConvertSequencingArtifactToOxoG INPUT_BASE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test9972351553099325425 OUTPUT_BASE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test4968694951635729681 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.analysis.artifacts.ConvertSequencingArtifactToOxoG done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.analysis.artifacts.ConvertSequencingArtifactToOxoG done. Elapsed time: 0.00 minutes. Test: Test method testEquivalence[0](false)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: INFO 2024-07-02 11:53:50 CollectOxoGMetrics Gradle suite > Gradle test > picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest.testEquivalence[1](true) STANDARD_ERROR INFO 2024-07-02 11:53:50 CollectOxoGMetrics Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** ********** Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** ********** Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** ********** Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** CollectOxoGMetrics -OUTPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test1781001417522155206.oxo_g_metrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta ********** CollectOxoGMetrics -OUTPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test1781001417522155206.oxo_g_metrics -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** ********** Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: 11:53:50.523 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.523 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: 11:53:50.523 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.523 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: 11:53:50.523 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.523 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: 11:53:50.523 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.523 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] CollectOxoGMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test1781001417522155206.oxo_g_metrics REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 MINIMUM_INSERT_SIZE=60 MAXIMUM_INSERT_SIZE=600 INCLUDE_NON_PF_READS=true USE_OQ=true CONTEXT_SIZE=1 STOP_AFTER=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:50 GMT+14:00 2024] CollectOxoGMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test1781001417522155206.oxo_g_metrics REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 MINIMUM_INSERT_SIZE=60 MAXIMUM_INSERT_SIZE=600 INCLUDE_NON_PF_READS=true USE_OQ=true CONTEXT_SIZE=1 STOP_AFTER=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: INFO 2024-07-02 11:53:50 CollectOxoGMetrics Generated 16 context strings. INFO 2024-07-02 11:53:50 CollectOxoGMetrics Generated 16 context strings. Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: INFO 2024-07-02 11:53:50 CollectOxoGMetrics Loading dbSNP File: null INFO 2024-07-02 11:53:50 CollectOxoGMetrics Loading dbSNP File: null Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: INFO 2024-07-02 11:53:50 CollectOxoGMetrics Starting iteration. INFO 2024-07-02 11:53:50 CollectOxoGMetrics Starting iteration. Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.analysis.CollectOxoGMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.analysis.CollectOxoGMetrics done. Elapsed time: 0.00 minutes. Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: INFO 2024-07-02 11:53:50 CollectSequencingArtifactMetrics INFO 2024-07-02 11:53:50 CollectSequencingArtifactMetrics Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** ********** Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** ********** Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** ********** Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** CollectSequencingArtifactMetrics -OUTPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test10703860608274236750 -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta ********** CollectSequencingArtifactMetrics -OUTPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test10703860608274236750 -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** ********** Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: 11:53:50.546 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.546 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: 11:53:50.546 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.546 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: 11:53:50.546 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.546 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: 11:53:50.546 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.546 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] CollectSequencingArtifactMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test10703860608274236750 REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 MINIMUM_INSERT_SIZE=60 MAXIMUM_INSERT_SIZE=600 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true CONTEXT_SIZE=1 ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:50 GMT+14:00 2024] CollectSequencingArtifactMetrics INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/test10703860608274236750 REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 MINIMUM_INSERT_SIZE=60 MAXIMUM_INSERT_SIZE=600 INCLUDE_UNPAIRED=false INCLUDE_DUPLICATES=false INCLUDE_NON_PF_READS=false TANDEM_READS=false USE_OQ=true CONTEXT_SIZE=1 ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.00 minutes. Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: INFO 2024-07-02 11:53:50 ConvertSequencingArtifactToOxoG INFO 2024-07-02 11:53:50 ConvertSequencingArtifactToOxoG Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** ********** Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** ********** Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** ********** Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** ConvertSequencingArtifactToOxoG -OXOG_OUT testdata/picard/sam/test13640993836013752103.oxog_metrics -BAIT_BIAS_IN testdata/picard/sam/test10703860608274236750.bait_bias_detail_metrics -PRE_ADAPTER_IN testdata/picard/sam/test10703860608274236750.pre_adapter_detail_metrics ********** ConvertSequencingArtifactToOxoG -OXOG_OUT testdata/picard/sam/test13640993836013752103.oxog_metrics -BAIT_BIAS_IN testdata/picard/sam/test10703860608274236750.bait_bias_detail_metrics -PRE_ADAPTER_IN testdata/picard/sam/test10703860608274236750.pre_adapter_detail_metrics Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: ********** ********** Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: 11:53:50.574 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.574 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: 11:53:50.574 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.574 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: 11:53:50.574 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.574 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: 11:53:50.574 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.574 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] ConvertSequencingArtifactToOxoG PRE_ADAPTER_IN=testdata/picard/sam/test10703860608274236750.pre_adapter_detail_metrics BAIT_BIAS_IN=testdata/picard/sam/test10703860608274236750.bait_bias_detail_metrics OXOG_OUT=testdata/picard/sam/test13640993836013752103.oxog_metrics VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:50 GMT+14:00 2024] ConvertSequencingArtifactToOxoG PRE_ADAPTER_IN=testdata/picard/sam/test10703860608274236750.pre_adapter_detail_metrics BAIT_BIAS_IN=testdata/picard/sam/test10703860608274236750.bait_bias_detail_metrics OXOG_OUT=testdata/picard/sam/test13640993836013752103.oxog_metrics VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.analysis.artifacts.ConvertSequencingArtifactToOxoG done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.analysis.artifacts.ConvertSequencingArtifactToOxoG done. Elapsed time: 0.00 minutes. Test: Test method testEquivalence[1](true)(picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testCounterInc(picard.analysis.CounterManagerTest) Running Test: Test method testForCheckIncrement(picard.analysis.CounterManagerTest) Running Test: Test method testForCleanCounterAfter(picard.analysis.CounterManagerTest) Running Test: Test method testForClearCounter(picard.analysis.CounterManagerTest) Running Test: Test method testForCorrectCounterAfterRebase(picard.analysis.CounterManagerTest) Running Test: Test method testForCorrectOffsetAfterRebase(picard.analysis.CounterManagerTest) Running Test: Test method testForOutOfBoundCounter(picard.analysis.CounterManagerTest) Running Test: Test method testForWrongIndexInGet(picard.analysis.CounterManagerTest) Running Test: Test method testForWrongIndexInInc(picard.analysis.CounterManagerTest) Running Test: Test method testAltNames(picard.sam.CreateSequenceDictionaryTest) Test: Test method testAltNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: INFO 2024-07-02 11:53:50 CreateSequenceDictionary Gradle suite > Gradle test > picard.sam.CreateSequenceDictionaryTest.testAltNames STANDARD_ERROR INFO 2024-07-02 11:53:50 CreateSequenceDictionary Test: Test method testAltNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: Test: Test method testAltNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testAltNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** ********** Test: Test method testAltNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testAltNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testAltNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** ********** Test: Test method testAltNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testAltNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** ********** Test: Test method testAltNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** CreateSequenceDictionary -REFERENCE testdata/picard/sam/basic.fasta -AN /tmp/CreateSequenceDictionaryTest11896877113032940098.alt -OUTPUT /tmp/CreateSequenceDictionaryTest.4429408921028810336.dict -TRUNCATE_NAMES_AT_WHITESPACE true ********** CreateSequenceDictionary -REFERENCE testdata/picard/sam/basic.fasta -AN /tmp/CreateSequenceDictionaryTest11896877113032940098.alt -OUTPUT /tmp/CreateSequenceDictionaryTest.4429408921028810336.dict -TRUNCATE_NAMES_AT_WHITESPACE true Test: Test method testAltNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** ********** Test: Test method testAltNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: Test: Test method testAltNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: Test: Test method testAltNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: 11:53:50.632 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.632 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAltNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: 11:53:50.632 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.632 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAltNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: 11:53:50.632 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.632 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAltNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: 11:53:50.632 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.632 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAltNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] CreateSequenceDictionary OUTPUT=/tmp/CreateSequenceDictionaryTest.4429408921028810336.dict TRUNCATE_NAMES_AT_WHITESPACE=true ALT_NAMES=/tmp/CreateSequenceDictionaryTest11896877113032940098.alt REFERENCE=testdata/picard/sam/basic.fasta NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:50 GMT+14:00 2024] CreateSequenceDictionary OUTPUT=/tmp/CreateSequenceDictionaryTest.4429408921028810336.dict TRUNCATE_NAMES_AT_WHITESPACE=true ALT_NAMES=/tmp/CreateSequenceDictionaryTest11896877113032940098.alt REFERENCE=testdata/picard/sam/basic.fasta NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testAltNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testAltNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes. Test: Test method testAltNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBasic(picard.sam.CreateSequenceDictionaryTest) Test: Test method testBasic(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: INFO 2024-07-02 11:53:50 CreateSequenceDictionary Gradle suite > Gradle test > picard.sam.CreateSequenceDictionaryTest.testBasic STANDARD_ERROR INFO 2024-07-02 11:53:50 CreateSequenceDictionary Test: Test method testBasic(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: Test: Test method testBasic(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBasic(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** ********** Test: Test method testBasic(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBasic(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBasic(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** ********** Test: Test method testBasic(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBasic(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** ********** Test: Test method testBasic(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** CreateSequenceDictionary -REFERENCE testdata/picard/sam/basic.fasta -OUTPUT /tmp/CreateSequenceDictionaryTest.2859175805187013670.dict -TRUNCATE_NAMES_AT_WHITESPACE false ********** CreateSequenceDictionary -REFERENCE testdata/picard/sam/basic.fasta -OUTPUT /tmp/CreateSequenceDictionaryTest.2859175805187013670.dict -TRUNCATE_NAMES_AT_WHITESPACE false Test: Test method testBasic(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** ********** Test: Test method testBasic(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: Test: Test method testBasic(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: Test: Test method testBasic(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: 11:53:50.698 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.698 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBasic(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: 11:53:50.698 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.698 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBasic(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: 11:53:50.698 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.698 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBasic(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: 11:53:50.698 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.698 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBasic(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] CreateSequenceDictionary OUTPUT=/tmp/CreateSequenceDictionaryTest.2859175805187013670.dict TRUNCATE_NAMES_AT_WHITESPACE=false REFERENCE=testdata/picard/sam/basic.fasta NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:50 GMT+14:00 2024] CreateSequenceDictionary OUTPUT=/tmp/CreateSequenceDictionaryTest.2859175805187013670.dict TRUNCATE_NAMES_AT_WHITESPACE=false REFERENCE=testdata/picard/sam/basic.fasta NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBasic(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBasic(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes. Test: Test method testBasic(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testDefaultOutputFile(picard.sam.CreateSequenceDictionaryTest) Test: Test method testDefaultOutputFile(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: INFO 2024-07-02 11:53:50 CreateSequenceDictionary Gradle suite > Gradle test > picard.sam.CreateSequenceDictionaryTest.testDefaultOutputFile STANDARD_ERROR INFO 2024-07-02 11:53:50 CreateSequenceDictionary Test: Test method testDefaultOutputFile(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: Test: Test method testDefaultOutputFile(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDefaultOutputFile(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** ********** Test: Test method testDefaultOutputFile(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDefaultOutputFile(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDefaultOutputFile(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** ********** Test: Test method testDefaultOutputFile(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDefaultOutputFile(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** ********** Test: Test method testDefaultOutputFile(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** CreateSequenceDictionary -REFERENCE testdata/picard/sam/basic.fasta -TRUNCATE_NAMES_AT_WHITESPACE false ********** CreateSequenceDictionary -REFERENCE testdata/picard/sam/basic.fasta -TRUNCATE_NAMES_AT_WHITESPACE false Test: Test method testDefaultOutputFile(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** ********** Test: Test method testDefaultOutputFile(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: Test: Test method testDefaultOutputFile(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: Test: Test method testDefaultOutputFile(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: INFO 2024-07-02 11:53:50 CreateSequenceDictionary Output dictionary will be written in testdata/picard/sam/basic.dict INFO 2024-07-02 11:53:50 CreateSequenceDictionary Output dictionary will be written in testdata/picard/sam/basic.dict Test: Test method testDefaultOutputFile(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: 11:53:50.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDefaultOutputFile(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: 11:53:50.743 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.743 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDefaultOutputFile(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: 11:53:50.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDefaultOutputFile(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: 11:53:50.743 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.743 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDefaultOutputFile(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] CreateSequenceDictionary TRUNCATE_NAMES_AT_WHITESPACE=false REFERENCE=testdata/picard/sam/basic.fasta NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:50 GMT+14:00 2024] CreateSequenceDictionary TRUNCATE_NAMES_AT_WHITESPACE=false REFERENCE=testdata/picard/sam/basic.fasta NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDefaultOutputFile(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDefaultOutputFile(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes. Test: Test method testDefaultOutputFile(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testForEquivalence(picard.sam.CreateSequenceDictionaryTest) Test: Test method testForEquivalence(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: INFO 2024-07-02 11:53:50 CreateSequenceDictionary Gradle suite > Gradle test > picard.sam.CreateSequenceDictionaryTest.testForEquivalence STANDARD_ERROR INFO 2024-07-02 11:53:50 CreateSequenceDictionary Test: Test method testForEquivalence(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: Test: Test method testForEquivalence(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testForEquivalence(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** ********** Test: Test method testForEquivalence(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testForEquivalence(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testForEquivalence(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** ********** Test: Test method testForEquivalence(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testForEquivalence(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** ********** Test: Test method testForEquivalence(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** CreateSequenceDictionary -REFERENCE testdata/picard/reference/test.fasta -OUTPUT /tmp/CreateSequenceDictionaryTest.10079648754509892152.dict -TRUNCATE_NAMES_AT_WHITESPACE false ********** CreateSequenceDictionary -REFERENCE testdata/picard/reference/test.fasta -OUTPUT /tmp/CreateSequenceDictionaryTest.10079648754509892152.dict -TRUNCATE_NAMES_AT_WHITESPACE false Test: Test method testForEquivalence(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** ********** Test: Test method testForEquivalence(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: Test: Test method testForEquivalence(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: Test: Test method testForEquivalence(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: 11:53:50.792 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.792 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testForEquivalence(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: 11:53:50.792 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.792 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testForEquivalence(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: 11:53:50.792 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.792 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testForEquivalence(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: 11:53:50.792 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.792 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testForEquivalence(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] CreateSequenceDictionary OUTPUT=/tmp/CreateSequenceDictionaryTest.10079648754509892152.dict TRUNCATE_NAMES_AT_WHITESPACE=false REFERENCE=testdata/picard/reference/test.fasta NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:50 GMT+14:00 2024] CreateSequenceDictionary OUTPUT=/tmp/CreateSequenceDictionaryTest.10079648754509892152.dict TRUNCATE_NAMES_AT_WHITESPACE=false REFERENCE=testdata/picard/reference/test.fasta NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testForEquivalence(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testForEquivalence(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes. Test: Test method testForEquivalence(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testNonUniqueSequenceName(picard.sam.CreateSequenceDictionaryTest) Test: Test method testNonUniqueSequenceName(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: INFO 2024-07-02 11:53:50 CreateSequenceDictionary Gradle suite > Gradle test > picard.sam.CreateSequenceDictionaryTest.testNonUniqueSequenceName STANDARD_ERROR INFO 2024-07-02 11:53:50 CreateSequenceDictionary Test: Test method testNonUniqueSequenceName(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: Test: Test method testNonUniqueSequenceName(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testNonUniqueSequenceName(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** ********** Test: Test method testNonUniqueSequenceName(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testNonUniqueSequenceName(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testNonUniqueSequenceName(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** ********** Test: Test method testNonUniqueSequenceName(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testNonUniqueSequenceName(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** ********** Test: Test method testNonUniqueSequenceName(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** CreateSequenceDictionary -REFERENCE testdata/picard/sam/duplicate_sequence_names.fasta -OUTPUT /tmp/CreateSequenceDictionaryTest.7568830361057617106.dict -TRUNCATE_NAMES_AT_WHITESPACE true ********** CreateSequenceDictionary -REFERENCE testdata/picard/sam/duplicate_sequence_names.fasta -OUTPUT /tmp/CreateSequenceDictionaryTest.7568830361057617106.dict -TRUNCATE_NAMES_AT_WHITESPACE true Test: Test method testNonUniqueSequenceName(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** ********** Test: Test method testNonUniqueSequenceName(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: Test: Test method testNonUniqueSequenceName(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: Test: Test method testNonUniqueSequenceName(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: 11:53:50.853 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.853 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNonUniqueSequenceName(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: 11:53:50.853 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.853 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNonUniqueSequenceName(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: 11:53:50.853 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.853 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNonUniqueSequenceName(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: 11:53:50.853 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.853 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNonUniqueSequenceName(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] CreateSequenceDictionary OUTPUT=/tmp/CreateSequenceDictionaryTest.7568830361057617106.dict TRUNCATE_NAMES_AT_WHITESPACE=true REFERENCE=testdata/picard/sam/duplicate_sequence_names.fasta NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:50 GMT+14:00 2024] CreateSequenceDictionary OUTPUT=/tmp/CreateSequenceDictionaryTest.7568830361057617106.dict TRUNCATE_NAMES_AT_WHITESPACE=true REFERENCE=testdata/picard/sam/duplicate_sequence_names.fasta NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testNonUniqueSequenceName(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testNonUniqueSequenceName(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes. Test: Test method testNonUniqueSequenceName(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testNonUniqueSequenceName(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testPunctuationInReferenceNames(picard.sam.CreateSequenceDictionaryTest) Test: Test method testPunctuationInReferenceNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: INFO 2024-07-02 11:53:50 CreateSequenceDictionary Gradle suite > Gradle test > picard.sam.CreateSequenceDictionaryTest.testPunctuationInReferenceNames STANDARD_ERROR INFO 2024-07-02 11:53:50 CreateSequenceDictionary Test: Test method testPunctuationInReferenceNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: Test: Test method testPunctuationInReferenceNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPunctuationInReferenceNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** ********** Test: Test method testPunctuationInReferenceNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPunctuationInReferenceNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPunctuationInReferenceNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** ********** Test: Test method testPunctuationInReferenceNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPunctuationInReferenceNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** ********** Test: Test method testPunctuationInReferenceNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** CreateSequenceDictionary -REFERENCE testdata/picard/sam/special.fasta -AN testdata/picard/sam/special.alt -TRUNCATE_NAMES_AT_WHITESPACE false ********** CreateSequenceDictionary -REFERENCE testdata/picard/sam/special.fasta -AN testdata/picard/sam/special.alt -TRUNCATE_NAMES_AT_WHITESPACE false Test: Test method testPunctuationInReferenceNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: ********** ********** Test: Test method testPunctuationInReferenceNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: Test: Test method testPunctuationInReferenceNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: Test: Test method testPunctuationInReferenceNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: INFO 2024-07-02 11:53:50 CreateSequenceDictionary Output dictionary will be written in testdata/picard/sam/special.dict INFO 2024-07-02 11:53:50 CreateSequenceDictionary Output dictionary will be written in testdata/picard/sam/special.dict Test: Test method testPunctuationInReferenceNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: 11:53:50.901 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.901 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPunctuationInReferenceNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: 11:53:50.901 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.901 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPunctuationInReferenceNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: 11:53:50.901 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.901 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPunctuationInReferenceNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: 11:53:50.901 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.901 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPunctuationInReferenceNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] CreateSequenceDictionary TRUNCATE_NAMES_AT_WHITESPACE=false ALT_NAMES=testdata/picard/sam/special.alt REFERENCE=testdata/picard/sam/special.fasta NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:50 GMT+14:00 2024] CreateSequenceDictionary TRUNCATE_NAMES_AT_WHITESPACE=false ALT_NAMES=testdata/picard/sam/special.alt REFERENCE=testdata/picard/sam/special.fasta NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPunctuationInReferenceNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPunctuationInReferenceNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes. Test: Test method testPunctuationInReferenceNames(picard.sam.CreateSequenceDictionaryTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testCreateVerifyIDIntensityContaminationMetricsFile(picard.arrays.CreateVerifyIDIntensityContaminationMetricsFileTest) Test: Test method testCreateVerifyIDIntensityContaminationMetricsFile(picard.arrays.CreateVerifyIDIntensityContaminationMetricsFileTest) produced standard out/err: /tmp/testCreateVerifyIDIntensityContaminationMetricsFile4524308367208237632 Gradle suite > Gradle test > picard.arrays.CreateVerifyIDIntensityContaminationMetricsFileTest.testCreateVerifyIDIntensityContaminationMetricsFile STANDARD_OUT /tmp/testCreateVerifyIDIntensityContaminationMetricsFile4524308367208237632 Test: Test method testCreateVerifyIDIntensityContaminationMetricsFile(picard.arrays.CreateVerifyIDIntensityContaminationMetricsFileTest) produced standard out/err: /tmp/testCreateVerifyIDIntensityContaminationMetricsFile4524308367208237632.verifyidintensity_metrics /tmp/testCreateVerifyIDIntensityContaminationMetricsFile4524308367208237632.verifyidintensity_metrics Test: Test method testCreateVerifyIDIntensityContaminationMetricsFile(picard.arrays.CreateVerifyIDIntensityContaminationMetricsFileTest) produced standard out/err: 11:53:50.915 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.arrays.CreateVerifyIDIntensityContaminationMetricsFileTest.testCreateVerifyIDIntensityContaminationMetricsFile STANDARD_ERROR 11:53:50.915 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCreateVerifyIDIntensityContaminationMetricsFile(picard.arrays.CreateVerifyIDIntensityContaminationMetricsFileTest) produced standard out/err: 11:53:50.915 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.915 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCreateVerifyIDIntensityContaminationMetricsFile(picard.arrays.CreateVerifyIDIntensityContaminationMetricsFileTest) produced standard out/err: 11:53:50.915 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.915 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCreateVerifyIDIntensityContaminationMetricsFile(picard.arrays.CreateVerifyIDIntensityContaminationMetricsFileTest) produced standard out/err: 11:53:50.915 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.915 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCreateVerifyIDIntensityContaminationMetricsFile(picard.arrays.CreateVerifyIDIntensityContaminationMetricsFileTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] CreateVerifyIDIntensityContaminationMetricsFile INPUT=testdata/picard/arrays/VerifyIDIntensity.txt OUTPUT=/tmp/testCreateVerifyIDIntensityContaminationMetricsFile4524308367208237632 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:50 GMT+14:00 2024] CreateVerifyIDIntensityContaminationMetricsFile INPUT=testdata/picard/arrays/VerifyIDIntensity.txt OUTPUT=/tmp/testCreateVerifyIDIntensityContaminationMetricsFile4524308367208237632 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCreateVerifyIDIntensityContaminationMetricsFile(picard.arrays.CreateVerifyIDIntensityContaminationMetricsFileTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCreateVerifyIDIntensityContaminationMetricsFile(picard.arrays.CreateVerifyIDIntensityContaminationMetricsFileTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile done. Elapsed time: 0.00 minutes. Test: Test method testCreateVerifyIDIntensityContaminationMetricsFile(picard.arrays.CreateVerifyIDIntensityContaminationMetricsFileTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testFailCreateVerifyIDIntensityContaminationMetricsFile(picard.arrays.CreateVerifyIDIntensityContaminationMetricsFileTest) Test: Test method testFailCreateVerifyIDIntensityContaminationMetricsFile(picard.arrays.CreateVerifyIDIntensityContaminationMetricsFileTest) produced standard out/err: /tmp/testFailCreateVerifyIDIntensityContaminationMetricsFile756834971263114494 Gradle suite > Gradle test > picard.arrays.CreateVerifyIDIntensityContaminationMetricsFileTest.testFailCreateVerifyIDIntensityContaminationMetricsFile STANDARD_OUT /tmp/testFailCreateVerifyIDIntensityContaminationMetricsFile756834971263114494 Test: Test method testFailCreateVerifyIDIntensityContaminationMetricsFile(picard.arrays.CreateVerifyIDIntensityContaminationMetricsFileTest) produced standard out/err: /tmp/testFailCreateVerifyIDIntensityContaminationMetricsFile756834971263114494.verifyidintensity_metrics /tmp/testFailCreateVerifyIDIntensityContaminationMetricsFile756834971263114494.verifyidintensity_metrics Test: Test method testFailCreateVerifyIDIntensityContaminationMetricsFile(picard.arrays.CreateVerifyIDIntensityContaminationMetricsFileTest) produced standard out/err: 11:53:50.928 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.arrays.CreateVerifyIDIntensityContaminationMetricsFileTest.testFailCreateVerifyIDIntensityContaminationMetricsFile STANDARD_ERROR 11:53:50.928 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFailCreateVerifyIDIntensityContaminationMetricsFile(picard.arrays.CreateVerifyIDIntensityContaminationMetricsFileTest) produced standard out/err: 11:53:50.928 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.928 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFailCreateVerifyIDIntensityContaminationMetricsFile(picard.arrays.CreateVerifyIDIntensityContaminationMetricsFileTest) produced standard out/err: 11:53:50.928 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:50.928 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFailCreateVerifyIDIntensityContaminationMetricsFile(picard.arrays.CreateVerifyIDIntensityContaminationMetricsFileTest) produced standard out/err: 11:53:50.928 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:50.928 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFailCreateVerifyIDIntensityContaminationMetricsFile(picard.arrays.CreateVerifyIDIntensityContaminationMetricsFileTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] CreateVerifyIDIntensityContaminationMetricsFile INPUT=testdata/picard/arrays/input.vcf OUTPUT=/tmp/testFailCreateVerifyIDIntensityContaminationMetricsFile756834971263114494 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:50 GMT+14:00 2024] CreateVerifyIDIntensityContaminationMetricsFile INPUT=testdata/picard/arrays/input.vcf OUTPUT=/tmp/testFailCreateVerifyIDIntensityContaminationMetricsFile756834971263114494 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFailCreateVerifyIDIntensityContaminationMetricsFile(picard.arrays.CreateVerifyIDIntensityContaminationMetricsFileTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFailCreateVerifyIDIntensityContaminationMetricsFile(picard.arrays.CreateVerifyIDIntensityContaminationMetricsFileTest) produced standard out/err: [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:50 GMT+14:00 2024] picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile done. Elapsed time: 0.00 minutes. Test: Test method testFailCreateVerifyIDIntensityContaminationMetricsFile(picard.arrays.CreateVerifyIDIntensityContaminationMetricsFileTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testFailCreateVerifyIDIntensityContaminationMetricsFile(picard.arrays.CreateVerifyIDIntensityContaminationMetricsFileTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:53 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null) STANDARD_ERROR INFO 2024-07-02 11:53:53 CrosscheckFingerprints Test: Test method checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting1674543678880802827test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_to_NA12892.txt ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting1674543678880802827test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_to_NA12892.txt Test: Test method checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.735 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:53.735 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.736 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:53.736 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.745 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:53.745 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.745 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:53.745 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.745 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:53.745 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.745 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:53.745 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:53 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_to_NA12892.txt SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting1674543678880802827test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:53 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_to_NA12892.txt SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting1674543678880802827test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:53 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:53:53 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:53 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:53:53 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:53 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:53:53 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:53 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:53 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method checkSampleMapFailuresData[0](testdata/picard/fingerprint/NA12891_to_NA12892.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:53 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null) STANDARD_ERROR INFO 2024-07-02 11:53:53 CrosscheckFingerprints Test: Test method checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting5722852875055665364test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892_to_NA12891.txt ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting5722852875055665364test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892_to_NA12891.txt Test: Test method checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.786 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:53.786 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.787 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:53.787 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.788 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:53.788 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.788 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:53.788 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.788 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:53.788 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.788 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:53.788 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:53 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892_to_NA12891.txt SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting5722852875055665364test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:53 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892_to_NA12891.txt SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting5722852875055665364test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:53 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:53:53 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:53 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:53:53 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:53 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:53:53 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:53 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:53 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method checkSampleMapFailuresData[1](testdata/picard/fingerprint/NA12892_to_NA12891.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:53 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null) STANDARD_ERROR INFO 2024-07-02 11:53:53 CrosscheckFingerprints Test: Test method checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting14562172863967631165test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/too_many_fields.txt ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting14562172863967631165test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/too_many_fields.txt Test: Test method checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.820 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:53.820 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.820 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:53.820 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.823 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:53.823 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.823 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:53.823 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.824 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:53.824 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.824 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:53.824 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:53 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/too_many_fields.txt SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting14562172863967631165test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:53 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/too_many_fields.txt SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting14562172863967631165test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:53 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:53:53 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:53 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:53:53 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:53 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:53:53 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:53 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:53 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method checkSampleMapFailuresData[2](testdata/picard/fingerprint/too_many_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:53 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null) STANDARD_ERROR INFO 2024-07-02 11:53:53 CrosscheckFingerprints Test: Test method checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting4112291115491289639test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/too_few_fields.txt ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting4112291115491289639test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/too_few_fields.txt Test: Test method checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.852 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:53.852 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.852 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:53.852 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.859 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:53.859 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.859 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:53.859 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.859 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:53.859 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.859 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:53.859 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:53 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/too_few_fields.txt SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting4112291115491289639test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:53 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/too_few_fields.txt SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting4112291115491289639test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:53 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:53:53 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:53 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:53:53 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:53 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:53:53 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:53 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:53 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method checkSampleMapFailuresData[3](testdata/picard/fingerprint/too_few_fields.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:53 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null) STANDARD_ERROR INFO 2024-07-02 11:53:53 CrosscheckFingerprints Test: Test method checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting13370771911700696229test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/DuplicateKey.txt ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting13370771911700696229test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/DuplicateKey.txt Test: Test method checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.903 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:53.903 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.903 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:53.903 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.904 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:53.904 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.904 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:53.904 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.904 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:53.904 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.904 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:53.904 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:53 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/DuplicateKey.txt SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting13370771911700696229test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:53 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/DuplicateKey.txt SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting13370771911700696229test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:53 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:53:53 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:53 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:53:53 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:53 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:53:53 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:53 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:53 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method checkSampleMapFailuresData[4](testdata/picard/fingerprint/DuplicateKey.txt, null)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:53 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt) STANDARD_ERROR INFO 2024-07-02 11:53:53 CrosscheckFingerprints Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting13584125809389442601test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -SECOND_INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/too_many_fields.txt ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting13584125809389442601test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -SECOND_INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/too_many_fields.txt Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.943 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:53.943 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.943 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:53.943 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.947 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:53.947 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.947 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:53.947 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.947 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:53.947 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:53.947 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:53.947 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:53 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] SECOND_INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/too_many_fields.txt CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting13584125809389442601test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:53 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] SECOND_INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/too_many_fields.txt CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting13584125809389442601test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:53 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:53:53 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:53 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:53:53 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:53 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:53:53 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:53 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:53:53 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:53:54 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:54 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method checkSampleMapFailuresData[5](null, testdata/picard/fingerprint/too_many_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt) STANDARD_ERROR INFO 2024-07-02 11:53:54 CrosscheckFingerprints Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting14076225847204153884test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -SECOND_INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/too_few_fields.txt ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting14076225847204153884test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -SECOND_INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/too_few_fields.txt Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.015 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:54.015 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.016 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:54.016 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.020 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:54.020 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.020 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:54.020 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.020 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:54.020 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.020 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:54.020 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] SECOND_INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/too_few_fields.txt CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting14076225847204153884test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:54 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] SECOND_INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/too_few_fields.txt CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting14076225847204153884test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:53:54 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:53:54 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:53:54 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:53:54 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:53:54 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:54 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method checkSampleMapFailuresData[6](null, testdata/picard/fingerprint/too_few_fields.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt) STANDARD_ERROR INFO 2024-07-02 11:53:54 CrosscheckFingerprints Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting5454915110426115749test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -SECOND_INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/DuplicateKey.txt ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting5454915110426115749test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -SECOND_INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/DuplicateKey.txt Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.087 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:54.087 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.087 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:54.087 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.088 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:54.088 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.088 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:54.088 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.097 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:54.097 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.097 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:54.097 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] SECOND_INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/DuplicateKey.txt CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting5454915110426115749test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:54 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] SECOND_INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/DuplicateKey.txt CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting5454915110426115749test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:53:54 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:53:54 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:53:54 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:53:54 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:53:54 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:54 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method checkSampleMapFailuresData[7](null, testdata/picard/fingerprint/DuplicateKey.txt)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false) STANDARD_ERROR INFO 2024-07-02 11:53:54 CrosscheckFingerprints Test: Test method testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -INPUT /tmp/fingerprint3859807643852947023.vcf -INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting5621818913139177271test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -INPUT /tmp/fingerprint3859807643852947023.vcf -INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting5621818913139177271test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE Test: Test method testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.152 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:54.152 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.152 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:54.152 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.157 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:54.157 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.157 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:54.157 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.157 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:54.157 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.157 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:54.157 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] OUTPUT=/tmp/Fingerprinting5621818913139177271test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:54 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] OUTPUT=/tmp/Fingerprinting5621818913139177271test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Fingerprinting 4 INPUT files. INFO 2024-07-02 11:53:54 CrosscheckFingerprints Fingerprinting 4 INPUT files. Test: Test method testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 FingerprintChecker Processed files. 4 fingerprints found in map. INFO 2024-07-02 11:53:54 FingerprintChecker Processed files. 4 fingerprints found in map. Test: Test method testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:53:54 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints All FILEs are related as expected. INFO 2024-07-02 11:53:54 CrosscheckFingerprints All FILEs are related as expected. Test: Test method testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:54 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCheckFiles[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false) STANDARD_ERROR INFO 2024-07-02 11:53:54 CrosscheckFingerprints Test: Test method testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -INPUT /tmp/fingerprint3859807643852947023.vcf -INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting11888551233982484019test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -INPUT /tmp/fingerprint3859807643852947023.vcf -INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting11888551233982484019test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE Test: Test method testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.238 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:54.238 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.238 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:54.238 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.239 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:54.239 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.239 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:54.239 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.239 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:54.239 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.239 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:54.239 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] OUTPUT=/tmp/Fingerprinting11888551233982484019test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:54 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] OUTPUT=/tmp/Fingerprinting11888551233982484019test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Fingerprinting 3 INPUT files. INFO 2024-07-02 11:53:54 CrosscheckFingerprints Fingerprinting 3 INPUT files. Test: Test method testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 FingerprintChecker Processed files. 4 fingerprints found in map. INFO 2024-07-02 11:53:54 FingerprintChecker Processed files. 4 fingerprints found in map. Test: Test method testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:53:54 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints All FILEs are related as expected. INFO 2024-07-02 11:53:54 CrosscheckFingerprints All FILEs are related as expected. Test: Test method testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:54 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCheckFiles[1]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false) STANDARD_ERROR INFO 2024-07-02 11:53:54 CrosscheckFingerprints Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3612930247560801544.vcf -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint3859807643852947023.vcf -INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting11622874941537222563test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3612930247560801544.vcf -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint3859807643852947023.vcf -INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting11622874941537222563test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.290 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:54.290 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.290 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:54.290 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.291 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:54.291 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.291 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:54.291 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.291 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:54.291 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.291 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:54.291 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] OUTPUT=/tmp/Fingerprinting11622874941537222563test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:54 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] OUTPUT=/tmp/Fingerprinting11622874941537222563test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Fingerprinting 4 INPUT files. INFO 2024-07-02 11:53:54 CrosscheckFingerprints Fingerprinting 4 INPUT files. Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 FingerprintChecker Processed files. 4 fingerprints found in map. INFO 2024-07-02 11:53:54 FingerprintChecker Processed files. 4 fingerprints found in map. Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:53:54 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:53:54 CrosscheckFingerprints 6 FILEs did not relate as expected. WARNING 2024-07-02 11:53:54 CrosscheckFingerprints 6 FILEs did not relate as expected. Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:54 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testCheckFiles[2]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false) STANDARD_ERROR INFO 2024-07-02 11:53:54 CrosscheckFingerprints Test: Test method testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -INPUT /tmp/fingerprint6359724907451755992.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -OUTPUT /tmp/Fingerprinting16476898692120799324test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -INPUT /tmp/fingerprint6359724907451755992.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -OUTPUT /tmp/Fingerprinting16476898692120799324test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE Test: Test method testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.352 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:54.352 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.352 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:54.352 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.354 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:54.354 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.354 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:54.354 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.354 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:54.354 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.354 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:54.354 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf] OUTPUT=/tmp/Fingerprinting16476898692120799324test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:54 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf] OUTPUT=/tmp/Fingerprinting16476898692120799324test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Fingerprinting 4 INPUT files. INFO 2024-07-02 11:53:54 CrosscheckFingerprints Fingerprinting 4 INPUT files. Test: Test method testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 FingerprintChecker Processed files. 3 fingerprints found in map. INFO 2024-07-02 11:53:54 FingerprintChecker Processed files. 3 fingerprints found in map. Test: Test method testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:53:54 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints All FILEs are related as expected. INFO 2024-07-02 11:53:54 CrosscheckFingerprints All FILEs are related as expected. Test: Test method testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:54 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCheckFiles[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false) STANDARD_ERROR INFO 2024-07-02 11:53:54 CrosscheckFingerprints Test: Test method testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -INPUT /tmp/fingerprint6359724907451755992.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -OUTPUT /tmp/Fingerprinting2606222268469628164test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -INPUT /tmp/fingerprint6359724907451755992.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -OUTPUT /tmp/Fingerprinting2606222268469628164test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE Test: Test method testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.408 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:54.408 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.408 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:54.408 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.409 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:54.409 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.409 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:54.409 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.409 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:54.409 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.410 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:54.410 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf] OUTPUT=/tmp/Fingerprinting2606222268469628164test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:54 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf] OUTPUT=/tmp/Fingerprinting2606222268469628164test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Fingerprinting 3 INPUT files. INFO 2024-07-02 11:53:54 CrosscheckFingerprints Fingerprinting 3 INPUT files. Test: Test method testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 FingerprintChecker Processed files. 4 fingerprints found in map. INFO 2024-07-02 11:53:54 FingerprintChecker Processed files. 4 fingerprints found in map. Test: Test method testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:53:54 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints All FILEs are related as expected. INFO 2024-07-02 11:53:54 CrosscheckFingerprints All FILEs are related as expected. Test: Test method testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:54 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCheckFiles[4]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false) STANDARD_ERROR INFO 2024-07-02 11:53:54 CrosscheckFingerprints Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -INPUT /tmp/fingerprint3859807643852947023.vcf -INPUT /tmp/fingerprint3612930247560801544.vcf -OUTPUT /tmp/Fingerprinting10962302551474495608test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -INPUT /tmp/fingerprint3859807643852947023.vcf -INPUT /tmp/fingerprint3612930247560801544.vcf -OUTPUT /tmp/Fingerprinting10962302551474495608test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.466 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:54.466 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.466 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:54.466 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.467 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:54.467 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.467 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:54.467 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.468 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:54.468 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.468 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:54.468 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf] OUTPUT=/tmp/Fingerprinting10962302551474495608test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:54 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf] OUTPUT=/tmp/Fingerprinting10962302551474495608test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Fingerprinting 3 INPUT files. INFO 2024-07-02 11:53:54 CrosscheckFingerprints Fingerprinting 3 INPUT files. Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 FingerprintChecker Processed files. 4 fingerprints found in map. INFO 2024-07-02 11:53:54 FingerprintChecker Processed files. 4 fingerprints found in map. Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:53:54 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:53:54 CrosscheckFingerprints 6 FILEs did not relate as expected. WARNING 2024-07-02 11:53:54 CrosscheckFingerprints 6 FILEs did not relate as expected. Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:54 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testCheckFiles[5]([/tmp/fingerprint1275962480367888787.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false) STANDARD_ERROR INFO 2024-07-02 11:53:54 CrosscheckFingerprints Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -INPUT /tmp/fingerprint3859807643852947023.vcf -INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting14159829911310195674test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -INPUT /tmp/fingerprint3859807643852947023.vcf -INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting14159829911310195674test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.510 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:54.510 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.510 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:54.510 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.511 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:54.511 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.511 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:54.511 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.511 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:54.511 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.511 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:54.511 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] OUTPUT=/tmp/Fingerprinting14159829911310195674test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:54 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] OUTPUT=/tmp/Fingerprinting14159829911310195674test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Fingerprinting 6 INPUT files. INFO 2024-07-02 11:53:54 CrosscheckFingerprints Fingerprinting 6 INPUT files. Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:53:54 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:53:54 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:53:54 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:53:54 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 FingerprintChecker Processed files. 106 fingerprints found in map. INFO 2024-07-02 11:53:54 FingerprintChecker Processed files. 106 fingerprints found in map. Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:53:54 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints All FILEs are related as expected. INFO 2024-07-02 11:53:54 CrosscheckFingerprints All FILEs are related as expected. Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:53:54 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCheckFiles[6]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 36, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false) STANDARD_ERROR INFO 2024-07-02 11:53:54 CrosscheckFingerprints Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/fingerprint3859807643852947023.vcf -INPUT /tmp/fingerprint3086553580626660194.vcf -OUTPUT /tmp/Fingerprinting13324589790889735967test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE ********** CrosscheckFingerprints -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/fingerprint3859807643852947023.vcf -INPUT /tmp/fingerprint3086553580626660194.vcf -OUTPUT /tmp/Fingerprinting13324589790889735967test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.992 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:54.992 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.992 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:54.992 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.994 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:54.994 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.994 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:54.994 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.994 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:54.994 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:54.994 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:54.994 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf] OUTPUT=/tmp/Fingerprinting13324589790889735967test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:54 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf] OUTPUT=/tmp/Fingerprinting13324589790889735967test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:54 CrosscheckFingerprints Fingerprinting 4 INPUT files. INFO 2024-07-02 11:53:54 CrosscheckFingerprints Fingerprinting 4 INPUT files. Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:55 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:53:55 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:55 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:53:55 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:55 FingerprintChecker Processed files. 56 fingerprints found in map. INFO 2024-07-02 11:53:55 FingerprintChecker Processed files. 56 fingerprints found in map. Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:55 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:53:55 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:53:55 CrosscheckFingerprints 6 FILEs did not relate as expected. WARNING 2024-07-02 11:53:55 CrosscheckFingerprints 6 FILEs did not relate as expected. Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:55 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:53:55 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testCheckFiles[7]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3086553580626660194.vcf], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:55 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true) STANDARD_ERROR INFO 2024-07-02 11:53:55 CrosscheckFingerprints Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/fingerprint17481944644093970365.vcf -OUTPUT /tmp/Fingerprinting4163503773571452821test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/fingerprint17481944644093970365.vcf -OUTPUT /tmp/Fingerprinting4163503773571452821test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:55.458 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:55.458 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:55.459 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:55.459 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:55.460 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:55.460 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:55.460 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:55.460 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:55.460 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:55.460 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:55.460 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:55.460 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:55 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf] OUTPUT=/tmp/Fingerprinting4163503773571452821test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:55 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf] OUTPUT=/tmp/Fingerprinting4163503773571452821test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:55 CrosscheckFingerprints Fingerprinting 4 INPUT files. INFO 2024-07-02 11:53:55 CrosscheckFingerprints Fingerprinting 4 INPUT files. Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:55 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:53:55 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:55 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:53:55 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:55 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:53:55 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:55 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:53:55 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:55 CrosscheckFingerprints All FILEs are related as expected. INFO 2024-07-02 11:53:55 CrosscheckFingerprints All FILEs are related as expected. Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:55 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:53:55 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCheckFiles[8]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:55 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true) STANDARD_ERROR INFO 2024-07-02 11:53:55 CrosscheckFingerprints Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting15450226664654840795test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting15450226664654840795test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:55.888 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:55.888 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:55.888 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:55.888 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:55.894 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:55.894 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:55.894 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:55.894 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:55.894 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:55.894 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:55.894 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:55.894 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:55 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] OUTPUT=/tmp/Fingerprinting15450226664654840795test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:55 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] OUTPUT=/tmp/Fingerprinting15450226664654840795test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:55 CrosscheckFingerprints Fingerprinting 4 INPUT files. INFO 2024-07-02 11:53:55 CrosscheckFingerprints Fingerprinting 4 INPUT files. Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:55 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:53:55 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:56 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:53:56 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:56 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:53:56 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:56 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:53:56 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:56 FingerprintChecker Processed files. 104 fingerprints found in map. INFO 2024-07-02 11:53:56 FingerprintChecker Processed files. 104 fingerprints found in map. Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:56 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:53:56 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:56 CrosscheckFingerprints All FILEs are related as expected. INFO 2024-07-02 11:53:56 CrosscheckFingerprints All FILEs are related as expected. Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:56 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:53:56 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.02 minutes. Test: Test method testCheckFiles[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 16, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:56 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true) STANDARD_ERROR INFO 2024-07-02 11:53:56 CrosscheckFingerprints Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting1510332918038777780test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting1510332918038777780test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:56.960 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:56.960 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:56.960 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:56.960 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:56.961 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:56.961 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:56.961 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:56.961 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:56.962 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:56.962 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:56.962 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:56.962 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:56 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] OUTPUT=/tmp/Fingerprinting1510332918038777780test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:56 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] OUTPUT=/tmp/Fingerprinting1510332918038777780test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:56 CrosscheckFingerprints Fingerprinting 3 INPUT files. INFO 2024-07-02 11:53:56 CrosscheckFingerprints Fingerprinting 3 INPUT files. Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:56 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:53:56 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:57 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:53:57 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:57 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:53:57 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:57 FingerprintChecker Processed files. 78 fingerprints found in map. INFO 2024-07-02 11:53:57 FingerprintChecker Processed files. 78 fingerprints found in map. Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:57 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:53:57 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:57 CrosscheckFingerprints All FILEs are related as expected. INFO 2024-07-02 11:53:57 CrosscheckFingerprints All FILEs are related as expected. Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:57 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:53:57 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCheckFiles[10]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 9, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:57 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false) STANDARD_ERROR INFO 2024-07-02 11:53:57 CrosscheckFingerprints Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting430773353374750851test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting430773353374750851test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:57.532 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:57.532 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:57.532 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:57.532 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:57.533 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:57.533 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:57.533 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:57.533 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:57.533 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:57.533 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:57.533 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:57.533 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:57 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] OUTPUT=/tmp/Fingerprinting430773353374750851test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:57 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] OUTPUT=/tmp/Fingerprinting430773353374750851test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:57 CrosscheckFingerprints Fingerprinting 4 INPUT files. INFO 2024-07-02 11:53:57 CrosscheckFingerprints Fingerprinting 4 INPUT files. Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:57 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:53:57 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:57 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:53:57 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:57 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:53:57 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:53:58 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 106 fingerprints found in map. INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 106 fingerprints found in map. Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:53:58 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:53:58 CrosscheckFingerprints 6 FILEs did not relate as expected. WARNING 2024-07-02 11:53:58 CrosscheckFingerprints 6 FILEs did not relate as expected. Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:53:58 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Test: Test method testCheckFiles[11]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false) STANDARD_ERROR INFO 2024-07-02 11:53:58 CrosscheckFingerprints Test: Test method testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -INPUT /tmp/fingerprint3859807643852947023.vcf -INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting5325831601371375183test.crosscheck_metrics -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -INPUT /tmp/fingerprint3859807643852947023.vcf -INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting5325831601371375183test.crosscheck_metrics -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE Test: Test method testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.365 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:58.365 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.366 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:58.366 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.367 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:58.367 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.367 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:58.367 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.367 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:58.367 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.367 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:58.367 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] OUTPUT=/tmp/Fingerprinting5325831601371375183test.crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:58 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] OUTPUT=/tmp/Fingerprinting5325831601371375183test.crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 4 INPUT files. INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 4 INPUT files. Test: Test method testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 4 fingerprints found in map. INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 4 fingerprints found in map. Test: Test method testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:53:58 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints All FILEs are related as expected. INFO 2024-07-02 11:53:58 CrosscheckFingerprints All FILEs are related as expected. Test: Test method testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:58 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCheckPaths[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 16, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false) STANDARD_ERROR INFO 2024-07-02 11:53:58 CrosscheckFingerprints Test: Test method testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint17481944644093970365.vcf -INPUT /tmp/fingerprint3859807643852947023.vcf -INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting7988457179084052898test.crosscheck_metrics -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE ********** CrosscheckFingerprints -INPUT /tmp/fingerprint17481944644093970365.vcf -INPUT /tmp/fingerprint3859807643852947023.vcf -INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting7988457179084052898test.crosscheck_metrics -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE Test: Test method testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.429 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:58.429 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.437 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:58.437 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.438 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:58.438 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.438 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:58.438 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.438 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:58.438 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.438 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:58.438 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] OUTPUT=/tmp/Fingerprinting7988457179084052898test.crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:58 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] OUTPUT=/tmp/Fingerprinting7988457179084052898test.crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 3 INPUT files. INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 3 INPUT files. Test: Test method testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 3 fingerprints found in map. INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 3 fingerprints found in map. Test: Test method testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:53:58 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints All FILEs are related as expected. INFO 2024-07-02 11:53:58 CrosscheckFingerprints All FILEs are related as expected. Test: Test method testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:58 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCheckPaths[1]([/tmp/fingerprint17481944644093970365.vcf, /tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false) STANDARD_ERROR INFO 2024-07-02 11:53:58 CrosscheckFingerprints Test: Test method testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn -OUTPUT /tmp/Fingerprinting3682681790651823306test.crosscheck_metrics -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE ********** CrosscheckFingerprints -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn -OUTPUT /tmp/Fingerprinting3682681790651823306test.crosscheck_metrics -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE Test: Test method testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.477 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:58.477 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.477 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:58.477 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.478 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:58.478 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.478 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:58.478 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.478 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:58.478 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.478 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:58.478 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn] OUTPUT=/tmp/Fingerprinting3682681790651823306test.crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:58 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn] OUTPUT=/tmp/Fingerprinting3682681790651823306test.crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 3 INPUT files. INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 3 INPUT files. Test: Test method testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 3 fingerprints found in map. INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 3 fingerprints found in map. Test: Test method testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:53:58 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints All FILEs are related as expected. INFO 2024-07-02 11:53:58 CrosscheckFingerprints All FILEs are related as expected. Test: Test method testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:58 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCheckPaths[2]([/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/crosscheck6555575141539509727.fofn], /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt, 0, 9, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true) STANDARD_ERROR INFO 2024-07-02 11:53:58 CrosscheckFingerprints Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting7715033651515073476test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting7715033651515073476test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.527 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:58.527 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.527 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:58.527 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.528 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:58.528 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.528 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:58.528 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.528 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:58.528 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.528 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:58.528 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] OUTPUT=/tmp/Fingerprinting7715033651515073476test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:58 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] OUTPUT=/tmp/Fingerprinting7715033651515073476test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:53:58 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:53:58 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:53:58 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:58 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCheckSamples[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true) STANDARD_ERROR INFO 2024-07-02 11:53:58 CrosscheckFingerprints Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting9770704129809199574test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting9770704129809199574test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.603 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:58.603 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.603 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:58.603 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.604 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:58.604 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.604 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:58.604 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.604 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:58.604 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.604 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:58.604 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] OUTPUT=/tmp/Fingerprinting9770704129809199574test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:58 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] OUTPUT=/tmp/Fingerprinting9770704129809199574test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:53:58 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:53:58 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:53:58 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:58 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCheckSamples[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true) STANDARD_ERROR INFO 2024-07-02 11:53:58 CrosscheckFingerprints Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint7004491781434766928.vcf -INPUT /tmp/fingerprint12537519721137435765.vcf -INPUT /tmp/fingerprint10061884668032474124.vcf -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting1349715523628653217test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -INPUT /tmp/fingerprint7004491781434766928.vcf -INPUT /tmp/fingerprint12537519721137435765.vcf -INPUT /tmp/fingerprint10061884668032474124.vcf -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting1349715523628653217test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.669 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:58.669 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.670 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:58.670 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.671 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:58.671 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.671 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:58.671 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.671 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:58.671 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.671 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:58.671 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] OUTPUT=/tmp/Fingerprinting1349715523628653217test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:58 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] OUTPUT=/tmp/Fingerprinting1349715523628653217test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:53:58 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 3 INPUT files. INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 3 INPUT files. Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 6 fingerprints found in map. INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 6 fingerprints found in map. Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:53:58 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:53:58 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:58 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCheckSamples[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false) STANDARD_ERROR INFO 2024-07-02 11:53:58 CrosscheckFingerprints Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3612930247560801544.vcf -INPUT /tmp/fingerprint3086553580626660194.vcf -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting8044010598794099619test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3612930247560801544.vcf -INPUT /tmp/fingerprint3086553580626660194.vcf -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting8044010598794099619test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.745 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:58.745 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.745 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:58.745 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.747 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:58.747 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.747 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:58.747 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.747 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:58.747 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.747 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:58.747 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] OUTPUT=/tmp/Fingerprinting8044010598794099619test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:58 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] OUTPUT=/tmp/Fingerprinting8044010598794099619test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:53:58 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:53:58 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:53:58 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:53:58 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:58 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Test: Test method testCheckSamples[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true) STANDARD_ERROR INFO 2024-07-02 11:53:58 CrosscheckFingerprints Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint6359724907451755992.vcf -SECOND_INPUT /tmp/fingerprint17481944644093970365.vcf -OUTPUT /tmp/Fingerprinting9160082710604387154test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint6359724907451755992.vcf -SECOND_INPUT /tmp/fingerprint17481944644093970365.vcf -OUTPUT /tmp/Fingerprinting9160082710604387154test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.820 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:58.820 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.820 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:58.820 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.830 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:58.830 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.830 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:58.830 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.830 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:58.830 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.830 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:58.830 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf] OUTPUT=/tmp/Fingerprinting9160082710604387154test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:58 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf] OUTPUT=/tmp/Fingerprinting9160082710604387154test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:53:58 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:53:58 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:53:58 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:58 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCheckSamples[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true) STANDARD_ERROR INFO 2024-07-02 11:53:58 CrosscheckFingerprints Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/fingerprint6359724907451755992.vcf -SECOND_INPUT /tmp/fingerprint17481944644093970365.vcf -OUTPUT /tmp/Fingerprinting15315547565603412903test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/fingerprint6359724907451755992.vcf -SECOND_INPUT /tmp/fingerprint17481944644093970365.vcf -OUTPUT /tmp/Fingerprinting15315547565603412903test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.892 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:58.892 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.901 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:58.901 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.902 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:58.902 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.902 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:58.902 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.902 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:58.902 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.903 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:58.903 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf] OUTPUT=/tmp/Fingerprinting15315547565603412903test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:58 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf] OUTPUT=/tmp/Fingerprinting15315547565603412903test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:53:58 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:53:58 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:53:58 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:58 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCheckSamples[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true) STANDARD_ERROR INFO 2024-07-02 11:53:58 CrosscheckFingerprints Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting3269419915051432845test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting3269419915051432845test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.928 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:58.928 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.929 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:58.929 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.930 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:58.930 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.930 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:58.930 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.930 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:58.930 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.930 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:58.930 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] OUTPUT=/tmp/Fingerprinting3269419915051432845test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:58 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] OUTPUT=/tmp/Fingerprinting3269419915051432845test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:53:58 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:53:58 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:53:58 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:53:58 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:53:58 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:58 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCheckSamples[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false) STANDARD_ERROR INFO 2024-07-02 11:53:58 CrosscheckFingerprints Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint3612930247560801544.vcf -OUTPUT /tmp/Fingerprinting6239737071656126479test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint3612930247560801544.vcf -OUTPUT /tmp/Fingerprinting6239737071656126479test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.995 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:58.995 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.995 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:58.995 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.996 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:58.996 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.996 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:58.996 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.996 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:58.996 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:58.996 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:58.996 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf] OUTPUT=/tmp/Fingerprinting6239737071656126479test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:58 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf] OUTPUT=/tmp/Fingerprinting6239737071656126479test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:58 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:53:58 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:59 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:53:59 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:59 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:53:59 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:59 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:53:59 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:59 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:53:59 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:59 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:53:59 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:53:59 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:53:59 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:59 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:59 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Test: Test method testCheckSamples[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:59 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true) STANDARD_ERROR INFO 2024-07-02 11:53:59 CrosscheckFingerprints Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint7004491781434766928.vcf -INPUT /tmp/fingerprint12537519721137435765.vcf -INPUT /tmp/fingerprint10061884668032474124.vcf -SECOND_INPUT /tmp/fingerprint6359724907451755992.vcf -SECOND_INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -OUTPUT /tmp/Fingerprinting5908448089759986080test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -INPUT /tmp/fingerprint7004491781434766928.vcf -INPUT /tmp/fingerprint12537519721137435765.vcf -INPUT /tmp/fingerprint10061884668032474124.vcf -SECOND_INPUT /tmp/fingerprint6359724907451755992.vcf -SECOND_INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -OUTPUT /tmp/Fingerprinting5908448089759986080test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:59.065 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:59.065 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:59.065 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:59.065 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:59.066 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:59.066 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:59.066 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:59.066 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:59.066 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:59.066 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:59.066 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:59.066 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:59 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf] SECOND_INPUT=[/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] OUTPUT=/tmp/Fingerprinting5908448089759986080test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:59 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf] SECOND_INPUT=[/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] OUTPUT=/tmp/Fingerprinting5908448089759986080test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:59 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:53:59 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:59 CrosscheckFingerprints Fingerprinting 3 INPUT files. INFO 2024-07-02 11:53:59 CrosscheckFingerprints Fingerprinting 3 INPUT files. Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:59 FingerprintChecker Processed files. 6 fingerprints found in map. INFO 2024-07-02 11:53:59 FingerprintChecker Processed files. 6 fingerprints found in map. Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:59 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:53:59 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:59 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:53:59 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:59 FingerprintChecker Processed files. 26 fingerprints found in map. INFO 2024-07-02 11:53:59 FingerprintChecker Processed files. 26 fingerprints found in map. Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:59 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:53:59 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:59 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:53:59 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:59 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:53:59 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCheckSamples[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:59 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true) STANDARD_ERROR INFO 2024-07-02 11:53:59 CrosscheckFingerprints Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting6195969195156962988test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting6195969195156962988test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:59.317 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:53:59.317 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:59.317 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:53:59.317 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:59.319 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:59.319 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:59.319 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:59.319 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:59.319 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:53:59.319 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:53:59.319 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:53:59.319 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:59 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] OUTPUT=/tmp/Fingerprinting6195969195156962988test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:53:59 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] OUTPUT=/tmp/Fingerprinting6195969195156962988test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:53:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:53:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:59 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:53:59 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:59 CrosscheckFingerprints Fingerprinting 4 INPUT files. INFO 2024-07-02 11:53:59 CrosscheckFingerprints Fingerprinting 4 INPUT files. Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:59 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:53:59 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:59 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:53:59 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:53:59 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:53:59 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:00 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:00 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:00 FingerprintChecker Processed files. 104 fingerprints found in map. INFO 2024-07-02 11:54:00 FingerprintChecker Processed files. 104 fingerprints found in map. Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:00 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:54:00 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:00 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:00 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:00 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:54:00 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:00 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:54:00 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:00 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:54:00 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.02 minutes. Test: Test method testCheckSamples[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:00 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false) STANDARD_ERROR INFO 2024-07-02 11:54:00 CrosscheckFingerprints Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting2740138368763486045test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting2740138368763486045test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:00.432 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:00.432 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:00.432 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:00.432 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:00.442 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:00.442 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:00.442 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:00.442 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:00.442 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:00.442 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:00.442 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:00.442 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:00 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] OUTPUT=/tmp/Fingerprinting2740138368763486045test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:00 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] OUTPUT=/tmp/Fingerprinting2740138368763486045test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:00 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:54:00 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:00 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:00 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:00 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:54:00 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:00 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:54:00 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:00 FingerprintChecker Processed files. 54 fingerprints found in map. INFO 2024-07-02 11:54:00 FingerprintChecker Processed files. 54 fingerprints found in map. Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:00 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:54:00 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:00 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:00 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:00 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:54:00 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:00 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:54:00 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:00 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:00 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Test: Test method testCheckSamples[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:00 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true) STANDARD_ERROR INFO 2024-07-02 11:54:00 CrosscheckFingerprints Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/fingerprint17481944644093970365.vcf -OUTPUT /tmp/Fingerprinting18129290634979918028test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/fingerprint17481944644093970365.vcf -OUTPUT /tmp/Fingerprinting18129290634979918028test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:00.831 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:00.831 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:00.831 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:00.831 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:00.832 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:00.832 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:00.832 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:00.832 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:00.833 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:00.833 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:00.833 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:00.833 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:00 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf] OUTPUT=/tmp/Fingerprinting18129290634979918028test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:00 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf] OUTPUT=/tmp/Fingerprinting18129290634979918028test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:00 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:54:00 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:00 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:00 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:00 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:54:00 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 FingerprintChecker Processed files. 26 fingerprints found in map. INFO 2024-07-02 11:54:01 FingerprintChecker Processed files. 26 fingerprints found in map. Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:54:01 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:01 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 FingerprintChecker Processed files. 27 fingerprints found in map. INFO 2024-07-02 11:54:01 FingerprintChecker Processed files. 27 fingerprints found in map. Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:54:01 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:54:01 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:01 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:01 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCheckSamples[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false) STANDARD_ERROR INFO 2024-07-02 11:54:01 CrosscheckFingerprints Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/fingerprint15046719082929058843.vcf -OUTPUT /tmp/Fingerprinting10966833728841844730test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/fingerprint15046719082929058843.vcf -OUTPUT /tmp/Fingerprinting10966833728841844730test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:01.258 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:01.258 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:01.258 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:01.258 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:01.259 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:01.259 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:01.259 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:01.259 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:01.259 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:01.259 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:01.259 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:01.259 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:01 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf] OUTPUT=/tmp/Fingerprinting10966833728841844730test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:01 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf] OUTPUT=/tmp/Fingerprinting10966833728841844730test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:54:01 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:01 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:54:01 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 FingerprintChecker Processed files. 28 fingerprints found in map. INFO 2024-07-02 11:54:01 FingerprintChecker Processed files. 28 fingerprints found in map. Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:54:01 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:01 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 FingerprintChecker Processed files. 27 fingerprints found in map. INFO 2024-07-02 11:54:01 FingerprintChecker Processed files. 27 fingerprints found in map. Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:54:01 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:01 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:54:01 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:01 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:01 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Test: Test method testCheckSamples[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false) STANDARD_ERROR INFO 2024-07-02 11:54:01 CrosscheckFingerprints Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint6359724907451755992.vcf -SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting4996150453099557568test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint6359724907451755992.vcf -SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting4996150453099557568test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:01.519 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:01.519 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:01.520 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:01.520 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:01.520 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:01.520 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:01.525 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:01.525 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:01.526 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:01.526 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:01.526 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:01.526 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:01 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] OUTPUT=/tmp/Fingerprinting4996150453099557568test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:01 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] OUTPUT=/tmp/Fingerprinting4996150453099557568test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:54:01 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:01 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:01 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:54:01 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:54:01 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 FingerprintChecker Processed files. 28 fingerprints found in map. INFO 2024-07-02 11:54:01 FingerprintChecker Processed files. 28 fingerprints found in map. Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:54:01 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:01 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:54:01 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:01 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:01 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Test: Test method testCheckSamples[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false) STANDARD_ERROR INFO 2024-07-02 11:54:01 CrosscheckFingerprints Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/fingerprint6359724907451755992.vcf -SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting9799446848803240889test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/fingerprint6359724907451755992.vcf -SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting9799446848803240889test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:01.684 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:01.684 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:01.684 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:01.684 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:01.685 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:01.685 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:01.685 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:01.685 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:01.685 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:01.685 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:01.685 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:01.685 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:01 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] OUTPUT=/tmp/Fingerprinting9799446848803240889test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:01 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] OUTPUT=/tmp/Fingerprinting9799446848803240889test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:54:01 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:01 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:01 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:54:01 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:54:01 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 FingerprintChecker Processed files. 28 fingerprints found in map. INFO 2024-07-02 11:54:01 FingerprintChecker Processed files. 28 fingerprints found in map. Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:54:01 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:01 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:54:01 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:01 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:01 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Test: Test method testCheckSamples[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true) STANDARD_ERROR INFO 2024-07-02 11:54:01 CrosscheckFingerprints Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting8797290393457453446test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting8797290393457453446test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:01.804 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:01.804 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:01.804 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:01.804 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:01.806 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:01.806 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:01.807 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:01.807 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:01.807 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:01.807 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:01.807 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:01.807 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:01 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] OUTPUT=/tmp/Fingerprinting8797290393457453446test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:01 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] OUTPUT=/tmp/Fingerprinting8797290393457453446test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:54:01 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:01 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:54:01 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:01 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:54:01 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:02 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:02 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:02 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:54:02 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:02 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:02 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:02 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:02 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:02 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:02 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:02 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:54:02 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:02 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:54:02 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:02 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:02 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCheckSamples[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:02 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true) STANDARD_ERROR INFO 2024-07-02 11:54:02 CrosscheckFingerprints Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting10519757120327378715test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting10519757120327378715test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:02.232 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:02.232 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:02.241 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:02.241 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:02.243 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:02.243 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:02.243 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:02.243 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:02.243 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:02.243 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:02.243 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:02.243 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:02 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] OUTPUT=/tmp/Fingerprinting10519757120327378715test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:02 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] OUTPUT=/tmp/Fingerprinting10519757120327378715test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:02 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:54:02 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:02 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:02 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:02 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:54:02 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:02 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:54:02 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:02 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:02 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:02 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:54:02 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:02 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:02 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:02 FingerprintChecker Processed files. 26 fingerprints found in map. INFO 2024-07-02 11:54:02 FingerprintChecker Processed files. 26 fingerprints found in map. Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:02 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:54:02 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:02 CrosscheckFingerprints sample NA12892 is missing from RIGHT group ERROR 2024-07-02 11:54:02 CrosscheckFingerprints sample NA12892 is missing from RIGHT group Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:02 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:54:02 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:02 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:02 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Test: Test method testCheckSamples[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:02 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true) STANDARD_ERROR INFO 2024-07-02 11:54:02 CrosscheckFingerprints Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting1781747349012176712test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting1781747349012176712test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:02.857 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:02.857 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:02.858 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:02.858 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:02.859 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:02.859 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:02.859 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:02.859 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:02.859 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:02.859 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:02.859 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:02.859 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:02 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] OUTPUT=/tmp/Fingerprinting1781747349012176712test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:02 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] OUTPUT=/tmp/Fingerprinting1781747349012176712test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:02 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:54:02 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:02 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:02 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:02 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:54:02 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:03 FingerprintChecker Processed files. 27 fingerprints found in map. INFO 2024-07-02 11:54:03 FingerprintChecker Processed files. 27 fingerprints found in map. Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:03 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:54:03 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:03 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:03 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:03 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:03 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:03 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:03 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:03 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:54:03 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:03 CrosscheckFingerprints sample NA12892 is missing from LEFT group ERROR 2024-07-02 11:54:03 CrosscheckFingerprints sample NA12892 is missing from LEFT group Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:03 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:54:03 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:03 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:03 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Test: Test method testCheckSamples[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:03 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false) STANDARD_ERROR INFO 2024-07-02 11:54:03 CrosscheckFingerprints Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting6330986142223737699test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting6330986142223737699test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:03.519 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:03.519 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:03.519 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:03.519 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:03.520 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:03.520 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:03.520 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:03.520 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:03.521 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:03.521 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:03.521 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:03.521 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:03 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] OUTPUT=/tmp/Fingerprinting6330986142223737699test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:03 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] OUTPUT=/tmp/Fingerprinting6330986142223737699test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:03 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:54:03 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:03 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:03 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:03 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:54:03 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:03 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:54:03 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:03 FingerprintChecker Processed files. 54 fingerprints found in map. INFO 2024-07-02 11:54:03 FingerprintChecker Processed files. 54 fingerprints found in map. Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:03 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:54:03 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:03 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:03 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:03 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:03 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:04 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:04 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:04 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:54:04 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:04 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:54:04 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:04 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:04 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Test: Test method testCheckSamples[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:04 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false) STANDARD_ERROR INFO 2024-07-02 11:54:04 CrosscheckFingerprints Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting14363285676236480242test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting14363285676236480242test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:04.158 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:04.158 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:04.158 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:04.158 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:04.159 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:04.159 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:04.159 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:04.159 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:04.159 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:04.159 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:04.159 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:04.159 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:04 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] OUTPUT=/tmp/Fingerprinting14363285676236480242test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:04 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] OUTPUT=/tmp/Fingerprinting14363285676236480242test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:04 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:54:04 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:04 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:04 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:04 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:54:04 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:04 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:54:04 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:04 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:04 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:04 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:54:04 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:04 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:54:04 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:04 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:54:04 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:04 FingerprintChecker Processed files. 54 fingerprints found in map. INFO 2024-07-02 11:54:04 FingerprintChecker Processed files. 54 fingerprints found in map. Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:04 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:54:04 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:04 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:54:04 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:04 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:04 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Test: Test method testCheckSamples[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:04 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false) STANDARD_ERROR INFO 2024-07-02 11:54:04 CrosscheckFingerprints Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint6454488665071355617.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting10364420362730157323test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint6454488665071355617.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting10364420362730157323test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:04.934 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:04.934 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:04.934 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:04.934 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:04.936 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:04.936 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:04.936 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:04.936 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:04.936 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:04.936 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:04.936 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:04.936 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:04 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf] OUTPUT=/tmp/Fingerprinting10364420362730157323test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:04 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf] OUTPUT=/tmp/Fingerprinting10364420362730157323test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:04 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:54:04 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:04 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:04 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:04 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:04 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:04 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:54:04 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:04 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:04 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:04 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:54:04 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:04 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:54:04 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:04 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:04 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Test: Test method testCheckSamples[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:05 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram) STANDARD_ERROR INFO 2024-07-02 11:54:05 CrosscheckFingerprints Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam -OUTPUT /tmp/Fingerprinting.bam.comparison12967593537958791773crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam -OUTPUT /tmp/Fingerprinting.bam.comparison12967593537958791773crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:05.017 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:05.017 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:05.018 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:05.018 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:05.019 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:05.019 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:05.019 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:05.019 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:05.019 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:05.019 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:05.019 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:05.019 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:05 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam] OUTPUT=/tmp/Fingerprinting.bam.comparison12967593537958791773crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:05 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam] OUTPUT=/tmp/Fingerprinting.bam.comparison12967593537958791773crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:05 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:05 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:05 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam) INFO 2024-07-02 11:54:05 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam) Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:05 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam) INFO 2024-07-02 11:54:05 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam) Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:05 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:54:05 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:05 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:05 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:05 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:05 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:05 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:05 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:05 CrosscheckFingerprints INFO 2024-07-02 11:54:05 CrosscheckFingerprints Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram -OUTPUT /tmp/Fingerprinting.cram.comparison15514817399849875548crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram -OUTPUT /tmp/Fingerprinting.cram.comparison15514817399849875548crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:05.255 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:05.255 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:05.255 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:05.255 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:05.257 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:05.257 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:05.257 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:05.257 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:05.257 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:05.257 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:05.257 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:05.257 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:05 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram] OUTPUT=/tmp/Fingerprinting.cram.comparison15514817399849875548crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:05 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram] OUTPUT=/tmp/Fingerprinting.cram.comparison15514817399849875548crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:05 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:05 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:05 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram) INFO 2024-07-02 11:54:05 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram) Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:05 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram) INFO 2024-07-02 11:54:05 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram) Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:05 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:54:05 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:05 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:05 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:05 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:05 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:05 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:05 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCramBamComparison[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:05 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram) STANDARD_ERROR INFO 2024-07-02 11:54:05 CrosscheckFingerprints Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam -OUTPUT /tmp/Fingerprinting.bam.comparison17729086907640362835crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam -OUTPUT /tmp/Fingerprinting.bam.comparison17729086907640362835crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:05.952 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:05.952 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:05.952 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:05.952 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:05.962 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:05.962 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:05.962 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:05.962 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:05.962 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:05.962 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:05.962 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:05.962 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:05 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam] OUTPUT=/tmp/Fingerprinting.bam.comparison17729086907640362835crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:05 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam] OUTPUT=/tmp/Fingerprinting.bam.comparison17729086907640362835crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:05 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:05 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:05 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam) INFO 2024-07-02 11:54:05 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam) Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:06 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam) INFO 2024-07-02 11:54:06 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam) Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:06 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:06 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:06 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:06 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:06 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:06 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:06 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:06 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:06 CrosscheckFingerprints INFO 2024-07-02 11:54:06 CrosscheckFingerprints Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram -OUTPUT /tmp/Fingerprinting.cram.comparison13575015989465503932crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram -OUTPUT /tmp/Fingerprinting.cram.comparison13575015989465503932crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:06.173 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:06.173 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:06.173 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:06.173 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:06.174 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:06.174 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:06.174 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:06.174 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:06.174 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:06.174 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:06.174 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:06.174 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:06 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram] OUTPUT=/tmp/Fingerprinting.cram.comparison13575015989465503932crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:06 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram] OUTPUT=/tmp/Fingerprinting.cram.comparison13575015989465503932crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:06 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:06 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:06 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram) INFO 2024-07-02 11:54:06 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram) Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:06 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram) INFO 2024-07-02 11:54:06 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram) Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:06 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:06 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:06 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:06 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:06 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:06 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:06 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:06 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCramBamComparison[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:06 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram) STANDARD_ERROR INFO 2024-07-02 11:54:06 CrosscheckFingerprints Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam -OUTPUT /tmp/Fingerprinting.bam.comparison9537803992606925869crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam -OUTPUT /tmp/Fingerprinting.bam.comparison9537803992606925869crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:06.745 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:06.745 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:06.745 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:06.745 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:06.746 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:06.746 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:06.746 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:06.746 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:06.747 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:06.747 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:06.747 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:06.747 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:06 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam] OUTPUT=/tmp/Fingerprinting.bam.comparison9537803992606925869crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:06 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam] OUTPUT=/tmp/Fingerprinting.bam.comparison9537803992606925869crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:06 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:06 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:06 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam) INFO 2024-07-02 11:54:06 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam) Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:06 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam) INFO 2024-07-02 11:54:06 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam) Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:06 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:54:06 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:06 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:06 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:06 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:06 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:06 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:06 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:07 CrosscheckFingerprints INFO 2024-07-02 11:54:07 CrosscheckFingerprints Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram -OUTPUT /tmp/Fingerprinting.cram.comparison1424835229004203277crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram -OUTPUT /tmp/Fingerprinting.cram.comparison1424835229004203277crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:07.018 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:07.018 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:07.018 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:07.018 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:07.018 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:07.018 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:07.018 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:07.018 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:07.019 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:07.019 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:07.019 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:07.019 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:07 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram] OUTPUT=/tmp/Fingerprinting.cram.comparison1424835229004203277crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:07 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram] OUTPUT=/tmp/Fingerprinting.cram.comparison1424835229004203277crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:07 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:07 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:07 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram) INFO 2024-07-02 11:54:07 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram) Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:07 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram) INFO 2024-07-02 11:54:07 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram) Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:07 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:54:07 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:07 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:07 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:07 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:07 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:07 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:07 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCramBamComparison[2](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:07 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram) STANDARD_ERROR INFO 2024-07-02 11:54:07 CrosscheckFingerprints Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam -OUTPUT /tmp/Fingerprinting.bam.comparison5312133180451919427crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam -OUTPUT /tmp/Fingerprinting.bam.comparison5312133180451919427crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:07.615 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:07.615 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:07.615 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:07.615 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:07.615 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:07.615 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:07.616 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:07.616 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:07.616 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:07.616 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:07.616 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:07.616 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:07 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam] OUTPUT=/tmp/Fingerprinting.bam.comparison5312133180451919427crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:07 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam] OUTPUT=/tmp/Fingerprinting.bam.comparison5312133180451919427crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:07 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:07 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:07 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam) INFO 2024-07-02 11:54:07 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam) Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:07 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam) INFO 2024-07-02 11:54:07 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam) Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:07 FingerprintChecker Processed files. 51 fingerprints found in map. INFO 2024-07-02 11:54:07 FingerprintChecker Processed files. 51 fingerprints found in map. Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:07 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:07 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:07 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:07 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:07 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:07 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:07 CrosscheckFingerprints INFO 2024-07-02 11:54:07 CrosscheckFingerprints Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram -OUTPUT /tmp/Fingerprinting.cram.comparison4403204815899819999crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram -OUTPUT /tmp/Fingerprinting.cram.comparison4403204815899819999crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:07.879 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:07.879 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:07.880 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:07.880 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:07.880 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:07.880 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:07.880 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:07.880 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:07.881 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:07.881 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:07.881 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:07.881 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:07 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram] OUTPUT=/tmp/Fingerprinting.cram.comparison4403204815899819999crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:07 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram] OUTPUT=/tmp/Fingerprinting.cram.comparison4403204815899819999crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:07 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:07 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:07 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram) INFO 2024-07-02 11:54:07 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram) Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:08 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram) INFO 2024-07-02 11:54:08 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram) Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:08 FingerprintChecker Processed files. 51 fingerprints found in map. INFO 2024-07-02 11:54:08 FingerprintChecker Processed files. 51 fingerprints found in map. Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:08 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:08 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:08 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:08 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:08 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:08 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCramBamComparison[3](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam16393669725835160362.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:08 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram) STANDARD_ERROR INFO 2024-07-02 11:54:08 CrosscheckFingerprints Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam -OUTPUT /tmp/Fingerprinting.bam.comparison15599598581699102769crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam -OUTPUT /tmp/Fingerprinting.bam.comparison15599598581699102769crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:08.380 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:08.380 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:08.380 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:08.380 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:08.389 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:08.389 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:08.389 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:08.389 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:08.389 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:08.389 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:08.389 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:08.389 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:08 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam] OUTPUT=/tmp/Fingerprinting.bam.comparison15599598581699102769crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:08 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam] OUTPUT=/tmp/Fingerprinting.bam.comparison15599598581699102769crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:08 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:08 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:08 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam) INFO 2024-07-02 11:54:08 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam) Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:08 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam) INFO 2024-07-02 11:54:08 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam) Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:08 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:08 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:08 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:08 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:08 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:08 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:08 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:08 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:08 CrosscheckFingerprints INFO 2024-07-02 11:54:08 CrosscheckFingerprints Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram -OUTPUT /tmp/Fingerprinting.cram.comparison2867678595529722084crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram -OUTPUT /tmp/Fingerprinting.cram.comparison2867678595529722084crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:08.728 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:08.728 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:08.728 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:08.728 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:08.729 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:08.729 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:08.729 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:08.729 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:08.729 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:08.729 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:08.729 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:08.729 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:08 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram] OUTPUT=/tmp/Fingerprinting.cram.comparison2867678595529722084crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:08 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram] OUTPUT=/tmp/Fingerprinting.cram.comparison2867678595529722084crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:08 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:08 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:08 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram) INFO 2024-07-02 11:54:08 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram) Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:09 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram) INFO 2024-07-02 11:54:09 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram) Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:09 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:09 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:09 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:09 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:09 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:09 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:09 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:09 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCramBamComparison[4](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam1289658725010144987.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:09 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram) STANDARD_ERROR INFO 2024-07-02 11:54:09 CrosscheckFingerprints Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam -OUTPUT /tmp/Fingerprinting.bam.comparison17725121604078452835crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam -OUTPUT /tmp/Fingerprinting.bam.comparison17725121604078452835crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:09.459 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:09.459 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:09.459 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:09.459 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:09.460 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:09.460 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:09.460 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:09.460 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:09.461 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:09.461 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:09.461 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:09.461 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:09 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam] OUTPUT=/tmp/Fingerprinting.bam.comparison17725121604078452835crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:09 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam] OUTPUT=/tmp/Fingerprinting.bam.comparison17725121604078452835crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:09 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:09 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:09 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam) INFO 2024-07-02 11:54:09 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam) Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:09 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam) INFO 2024-07-02 11:54:09 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam) Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:09 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:54:09 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:09 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:09 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:09 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:09 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:09 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:09 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:09 CrosscheckFingerprints INFO 2024-07-02 11:54:09 CrosscheckFingerprints Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram -OUTPUT /tmp/Fingerprinting.cram.comparison602464525210536438crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram -OUTPUT /tmp/Fingerprinting.cram.comparison602464525210536438crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:09.874 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:09.874 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:09.874 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:09.874 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:09.875 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:09.875 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:09.875 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:09.875 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:09.875 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:09.875 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:09.875 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:09.875 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:09 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram] OUTPUT=/tmp/Fingerprinting.cram.comparison602464525210536438crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:09 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram] OUTPUT=/tmp/Fingerprinting.cram.comparison602464525210536438crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:09 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:09 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:09 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram) INFO 2024-07-02 11:54:09 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram) Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:10 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram) INFO 2024-07-02 11:54:10 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram) Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:10 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:54:10 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:10 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:10 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:10 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:10 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:10 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:10 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCramBamComparison[5](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam16305327198327155857.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam13802833511421639170.bam, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:10 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram) STANDARD_ERROR INFO 2024-07-02 11:54:10 CrosscheckFingerprints Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram -SECOND_INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram -OUTPUT /tmp/Fingerprinting4250844499222149668NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram -SECOND_INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram -OUTPUT /tmp/Fingerprinting4250844499222149668NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:10.507 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:10.507 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:10.507 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:10.507 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:10.508 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:54:10.508 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: USAGE: CrosscheckFingerprints [options] USAGE: CrosscheckFingerprints [options] Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CrosscheckFingerprints Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CrosscheckFingerprints Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Checks that all data in the set of input files appear to come from the same individual. Can be used to cross-check Checks that all data in the set of input files appear to come from the same individual. Can be used to cross-check Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: readgroups, libraries, samples, or files. Operates on SAM/BAM/CRAM and VCF (including gVCF and gzipped-VCF). readgroups, libraries, samples, or files. Operates on SAM/BAM/CRAM and VCF (including gVCF and gzipped-VCF). Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Summary Summary Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Checks if all the genetic data within a set of files appear to come from the same individual. It quickly determines Checks if all the genetic data within a set of files appear to come from the same individual. It quickly determines Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: whether a group's genotype matches that of an input file by selective sampling, and has been designed to work well for whether a group's genotype matches that of an input file by selective sampling, and has been designed to work well for Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: low-depth SAM (as well as high depth ones and VCFs.) The tool collects fingerprints (essentially, genotype information low-depth SAM (as well as high depth ones and VCFs.) The tool collects fingerprints (essentially, genotype information Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: from different parts of the genome) at the finest level available in the data (readgroup for read-data files and sample from different parts of the genome) at the finest level available in the data (readgroup for read-data files and sample Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: for variant-data files) and then optionally aggregates it by library, sample or file, to increase power and provide for variant-data files) and then optionally aggregates it by library, sample or file, to increase power and provide Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: results at the desired resolution. Output is in a "Moltenized" format, one row per comparison. The results are emitted results at the desired resolution. Output is in a "Moltenized" format, one row per comparison. The results are emitted Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: into a CrosscheckMetric metric file. In this format the output will include the LOD score and also tumor-aware LOD score into a CrosscheckMetric metric file. In this format the output will include the LOD score and also tumor-aware LOD score Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: which can help assess identity even in the presence of a severe loss of heterozygosity with high purity (which could which can help assess identity even in the presence of a severe loss of heterozygosity with high purity (which could Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: cause it to otherwise fail to notice that samples are from the same individual.) A matrix output is also available to cause it to otherwise fail to notice that samples are from the same individual.) A matrix output is also available to Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: facilitate visual inspection of crosscheck results. facilitate visual inspection of crosscheck results. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Since there can be many rows of output in the metric file, we recommend the use of ClusterCrosscheckMetrics as a Since there can be many rows of output in the metric file, we recommend the use of ClusterCrosscheckMetrics as a Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: follow-up step to running CrosscheckFingerprints. follow-up step to running CrosscheckFingerprints. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: There are cases where one would like to identify a few groups out of a collection of many possible groups (say to link a There are cases where one would like to identify a few groups out of a collection of many possible groups (say to link a Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: SAM to its correct sample in a multi-sample VCF. In this case one would not case for the cross-checking of the various SAM to its correct sample in a multi-sample VCF. In this case one would not case for the cross-checking of the various Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: samples in the VCF against each other, but only in checking the identity of the SAM against the various samples in the samples in the VCF against each other, but only in checking the identity of the SAM against the various samples in the Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: VCF. The SECOND_INPUT is provided for this use-case. With SECOND_INPUT provided, CrosscheckFingerprints does the VCF. The SECOND_INPUT is provided for this use-case. With SECOND_INPUT provided, CrosscheckFingerprints does the Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: following: following: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: - aggregation of data happens independently for the input files in INPUT and SECOND_INPUT. - aggregation of data happens independently for the input files in INPUT and SECOND_INPUT. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: - aggregation of data happens at the SAMPLE level - aggregation of data happens at the SAMPLE level Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: - each samples from INPUT will only be compared to that same sample in SECOND_INPUT. - each samples from INPUT will only be compared to that same sample in SECOND_INPUT. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: - MATRIX_OUTPUT is disabled. - MATRIX_OUTPUT is disabled. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: In some cases, the groups collected may not have any observations (calls for a VCF, reads for a SAM) at fingerprinting In some cases, the groups collected may not have any observations (calls for a VCF, reads for a SAM) at fingerprinting Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: sites, or a sample in INPUT may be missing from the SECOND_INPUT. These cases are handled as follows: If running in sites, or a sample in INPUT may be missing from the SECOND_INPUT. These cases are handled as follows: If running in Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: CHECK_SAME_SAMPLES mode with INPUT and SECOND_INPUT, and either INPUT or SECOND_INPUT includes a sample not found in the CHECK_SAME_SAMPLES mode with INPUT and SECOND_INPUT, and either INPUT or SECOND_INPUT includes a sample not found in the Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: other, or contains a sample with no observations at any fingerprinting sites, an error will be logged and the tool will other, or contains a sample with no observations at any fingerprinting sites, an error will be logged and the tool will Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: return EXIT_CODE_WHEN_MISMATCH. In all other running modes, when any group which is being crosschecked does not have any return EXIT_CODE_WHEN_MISMATCH. In all other running modes, when any group which is being crosschecked does not have any Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: observations at fingerprinting sites, a warning is logged. As long as there is at least one comparison where both sides observations at fingerprinting sites, a warning is logged. As long as there is at least one comparison where both sides Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: have observations at fingerprinting sites, the tool will return zero. However, if all comparisons have at least one have observations at fingerprinting sites, the tool will return zero. However, if all comparisons have at least one Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: side with no observations at fingerprinting sites, an error will be logged and the tool will return side with no observations at fingerprinting sites, an error will be logged and the tool will return Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: EXIT_CODE_WHEN_NO_VALID_CHECKS. EXIT_CODE_WHEN_NO_VALID_CHECKS. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Examples Examples Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Check that all the readgroups from a sample match each other: Check that all the readgroups from a sample match each other: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: java -jar picard.jar CrosscheckFingerprints \ java -jar picard.jar CrosscheckFingerprints \ Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INPUT=sample.with.many.readgroups.bam \ INPUT=sample.with.many.readgroups.bam \ Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: HAPLOTYPE_MAP=fingerprinting_haplotype_database.txt \ HAPLOTYPE_MAP=fingerprinting_haplotype_database.txt \ Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: LOD_THRESHOLD=-5 \ LOD_THRESHOLD=-5 \ Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: OUTPUT=sample.crosscheck_metrics OUTPUT=sample.crosscheck_metrics Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Check that all the readgroups match as expected when providing reads from two samples from the same individual: Check that all the readgroups match as expected when providing reads from two samples from the same individual: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: java -jar picard.jar CrosscheckFingerprints \ java -jar picard.jar CrosscheckFingerprints \ Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INPUT=sample.one.with.many.readgroups.bam \ INPUT=sample.one.with.many.readgroups.bam \ Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INPUT=sample.two.with.many.readgroups.bam \ INPUT=sample.two.with.many.readgroups.bam \ Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: HAPLOTYPE_MAP=fingerprinting_haplotype_database.txt \ HAPLOTYPE_MAP=fingerprinting_haplotype_database.txt \ Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: LOD_THRESHOLD=-5 \ LOD_THRESHOLD=-5 \ Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: EXPECT_ALL_GROUPS_TO_MATCH=true \ EXPECT_ALL_GROUPS_TO_MATCH=true \ Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: OUTPUT=sample.crosscheck_metrics OUTPUT=sample.crosscheck_metrics Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Detailed Explanation Detailed Explanation Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: This tool calculates the LOD score for identity check between "groups" of data in the INPUT files as defined by the This tool calculates the LOD score for identity check between "groups" of data in the INPUT files as defined by the Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: CROSSCHECK_BY argument. A positive value indicates that the data seems to have come from the same individual or, in CROSSCHECK_BY argument. A positive value indicates that the data seems to have come from the same individual or, in Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: other words the identity checks out. The scale is logarithmic (base 10), so a LOD of 6 indicates that it is 1,000,000 other words the identity checks out. The scale is logarithmic (base 10), so a LOD of 6 indicates that it is 1,000,000 Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: more likely that the data matches the genotypes than not. A negative value indicates that the data do not match. A score more likely that the data matches the genotypes than not. A negative value indicates that the data do not match. A score Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: that is near zero is inconclusive and can result from low coverage or non-informative genotypes. Each group is assigned that is near zero is inconclusive and can result from low coverage or non-informative genotypes. Each group is assigned Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: a sample identifier (for SAM this is taken from the SM tag in the appropriate readgroup header line, for VCF this is a sample identifier (for SAM this is taken from the SM tag in the appropriate readgroup header line, for VCF this is Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: taken from the column label in the file-header. After combining all the data from the same group together, an taken from the column label in the file-header. After combining all the data from the same group together, an Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: all-against-all comparison is performed. Results are categorized as one of EXPECTED_MATCH, EXPECTED_MISMATCH, all-against-all comparison is performed. Results are categorized as one of EXPECTED_MATCH, EXPECTED_MISMATCH, Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: UNEXPECTED_MATCH, UNEXPECTED_MISMATCH, or AMBIGUOUS depending on the LOD score and on whether the sample identifiers of UNEXPECTED_MATCH, UNEXPECTED_MISMATCH, or AMBIGUOUS depending on the LOD score and on whether the sample identifiers of Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: the groups agree: LOD scores that are less than LOD_THRESHOLD are considered mismatches, and those greater than the groups agree: LOD scores that are less than LOD_THRESHOLD are considered mismatches, and those greater than Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: -LOD_THRESHOLD are matches (between is ambiguous). If the sample identifiers are equal, the groups are expected to -LOD_THRESHOLD are matches (between is ambiguous). If the sample identifiers are equal, the groups are expected to Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: match. They are expected to mismatch otherwise. match. They are expected to mismatch otherwise. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: The identity check makes use of haplotype blocks defined in the HAPLOTYPE_MAP file to enable it to have higher The identity check makes use of haplotype blocks defined in the HAPLOTYPE_MAP file to enable it to have higher Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: statistical power for detecting identity or swap by aggregating data from several SNPs in the haplotype block. This statistical power for detecting identity or swap by aggregating data from several SNPs in the haplotype block. This Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: enables an identity check of samples with very low coverage (e.g. ~1x mean coverage). enables an identity check of samples with very low coverage (e.g. ~1x mean coverage). Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: When provided a VCF, the identity check looks at the PL, GL and GT fields (in that order) and uses the first one that it When provided a VCF, the identity check looks at the PL, GL and GT fields (in that order) and uses the first one that it Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: finds. finds. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Version: null Version: null Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Options: Options: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: --help --help Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: tools. tools. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INPUT=String INPUT=String Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: I=String One or more input files (or lists of files) with which to compare fingerprints. Default I=String One or more input files (or lists of files) with which to compare fingerprints. Default Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: value: null. This option must be specified at least 1 times. value: null. This option must be specified at least 1 times. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the INPUT data (in column INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the INPUT data (in column Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 1) and the sample as it should be used for comparisons to SECOND_INPUT (in the second 1) and the sample as it should be used for comparisons to SECOND_INPUT (in the second Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: column). Need only include the samples that change. Values in column 1 should be unique. column). Need only include the samples that change. Values in column 1 should be unique. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Values in column 2 should be unique even in union with the remaining unmapped samples. Values in column 2 should be unique even in union with the remaining unmapped samples. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Should only be used with SECOND_INPUT. Default value: null. Cannot be used in Should only be used with SECOND_INPUT. Default value: null. Cannot be used in Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: conjuction with option(s) INPUT_SAMPLE_FILE_MAP conjuction with option(s) INPUT_SAMPLE_FILE_MAP Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INPUT_SAMPLE_FILE_MAP=File A tsv with two columns representing the sample as it should be used for comparisons to INPUT_SAMPLE_FILE_MAP=File A tsv with two columns representing the sample as it should be used for comparisons to Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: SECOND_INPUT (in the first column) and the source file (in INPUT) for the fingerprint (in SECOND_INPUT (in the first column) and the source file (in INPUT) for the fingerprint (in Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: the second column). Need only to include the samples that change. Values in column 1 the second column). Need only to include the samples that change. Values in column 1 Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: should be unique even in union with the remaining unmapped samples. Values in column 2 should be unique even in union with the remaining unmapped samples. Values in column 2 Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: should be unique in the file. Will error if more than one sample is found in a file should be unique in the file. Will error if more than one sample is found in a file Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: (multi-sample VCF) pointed to in column 2. Should only be used in the presence of (multi-sample VCF) pointed to in column 2. Should only be used in the presence of Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: SECOND_INPUT. Default value: null. Cannot be used in conjuction with option(s) SECOND_INPUT. Default value: null. Cannot be used in conjuction with option(s) Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INPUT_SAMPLE_MAP INPUT_SAMPLE_MAP Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: SECOND_INPUT=String SECOND_INPUT=String Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: SI=String A second set of input files (or lists of files) with which to compare fingerprints. If SI=String A second set of input files (or lists of files) with which to compare fingerprints. If Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: this option is provided the tool compares each sample in INPUT with the sample from this option is provided the tool compares each sample in INPUT with the sample from Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: SECOND_INPUT that has the same sample ID. In addition, data will be grouped by SAMPLE SECOND_INPUT that has the same sample ID. In addition, data will be grouped by SAMPLE Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: regardless of the value of CROSSCHECK_BY. When operating in this mode, each sample in regardless of the value of CROSSCHECK_BY. When operating in this mode, each sample in Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INPUT must also have a corresponding sample in SECOND_INPUT. If this is violated, the tool INPUT must also have a corresponding sample in SECOND_INPUT. If this is violated, the tool Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: will proceed to check the matching samples, but report the missing samples and return a will proceed to check the matching samples, but report the missing samples and return a Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: non-zero error-code. Default value: null. This option may be specified 0 or more times. non-zero error-code. Default value: null. This option may be specified 0 or more times. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Cannot be used in conjuction with option(s) MATRIX_OUTPUT (MO) Cannot be used in conjuction with option(s) MATRIX_OUTPUT (MO) Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: SECOND_INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the SECOND_INPUT data (in SECOND_INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the SECOND_INPUT data (in Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: column 1) and the sample as it should be used for comparisons to INPUT (in the second column 1) and the sample as it should be used for comparisons to INPUT (in the second Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: column). Note that in case of unrolling files (file-of-filenames) one would need to column). Note that in case of unrolling files (file-of-filenames) one would need to Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: reference the final file, i.e. the file that contains the genomic data. Need only include reference the final file, i.e. the file that contains the genomic data. Need only include Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: the samples that change. Values in column 1 should be unique. Values in column 2 should be the samples that change. Values in column 1 should be unique. Values in column 2 should be Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: unique even in union with the remaining unmapped samples. Should only be used with unique even in union with the remaining unmapped samples. Should only be used with Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: SECOND_INPUT. Default value: null. SECOND_INPUT. Default value: null. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: CROSSCHECK_MODE=CrosscheckModeAn argument that controls how crosschecking with both INPUT and SECOND_INPUT should occur. CROSSCHECK_MODE=CrosscheckModeAn argument that controls how crosschecking with both INPUT and SECOND_INPUT should occur. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Default value: CHECK_SAME_SAMPLE. This option can be set to 'null' to clear the default Default value: CHECK_SAME_SAMPLE. This option can be set to 'null' to clear the default Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: value. Possible values: { value. Possible values: { Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: CHECK_SAME_SAMPLE (In this mode, each sample in INPUT will only be checked against a CHECK_SAME_SAMPLE (In this mode, each sample in INPUT will only be checked against a Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: single corresponding sample in SECOND_INPUT. If a corresponding sample cannot be found, single corresponding sample in SECOND_INPUT. If a corresponding sample cannot be found, Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: the program will proceed, but report the missing samples and return the value specified in the program will proceed, but report the missing samples and return the value specified in Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: EXIT_CODE_WHEN_MISMATCH. The corresponding samples are those that equal each other, after EXIT_CODE_WHEN_MISMATCH. The corresponding samples are those that equal each other, after Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: possible renaming via INPUT_SAMPLE_MAP and SECOND_INPUT_SAMPLE_MAP. In this mode possible renaming via INPUT_SAMPLE_MAP and SECOND_INPUT_SAMPLE_MAP. In this mode Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: CROSSCHECK_BY must be SAMPLE.) CROSSCHECK_BY must be SAMPLE.) Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: CHECK_ALL_OTHERS (In this mode, each sample in INPUT will be checked against all the CHECK_ALL_OTHERS (In this mode, each sample in INPUT will be checked against all the Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: samples in SECOND_INPUT.) samples in SECOND_INPUT.) Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: } } Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: O=File Optional output file to write metrics to. Default is to write to stdout. Default value: O=File Optional output file to write metrics to. Default is to write to stdout. Default value: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: null. null. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: MATRIX_OUTPUT=File MATRIX_OUTPUT=File Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: MO=File Optional output file to write matrix of LOD scores to. This is less informative than the MO=File Optional output file to write matrix of LOD scores to. This is less informative than the Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: metrics output and only contains Normal-Normal LOD score (i.e. doesn't account for Loss of metrics output and only contains Normal-Normal LOD score (i.e. doesn't account for Loss of Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Heterozygosity). It is however sometimes easier to use visually. Default value: null. Heterozygosity). It is however sometimes easier to use visually. Default value: null. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Cannot be used in conjuction with option(s) SECOND_INPUT (SI) Cannot be used in conjuction with option(s) SECOND_INPUT (SI) Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: HAPLOTYPE_MAP=File HAPLOTYPE_MAP=File Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: H=File The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for H=File The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: fingerprinting. See https://software.broadinstitute.org/gatk/documentation/article?id=9526 fingerprinting. See https://software.broadinstitute.org/gatk/documentation/article?id=9526 Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: for details. Required. for details. Required. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: LOD_THRESHOLD=Double LOD_THRESHOLD=Double Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: LOD=Double If any two groups (with the same sample name) match with a LOD score lower than the LOD=Double If any two groups (with the same sample name) match with a LOD score lower than the Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: threshold the tool will exit with a non-zero code to indicate error. Program will also threshold the tool will exit with a non-zero code to indicate error. Program will also Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: exit with an error if it finds two groups with different sample name that match with a LOD exit with an error if it finds two groups with different sample name that match with a LOD Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: score greater than -LOD_THRESHOLD. score greater than -LOD_THRESHOLD. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: LOD score 0 means equal likelihood that the groups match vs. come from different LOD score 0 means equal likelihood that the groups match vs. come from different Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: individuals, negative LOD score -N, mean 10^N time more likely that the groups are from individuals, negative LOD score -N, mean 10^N time more likely that the groups are from Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: different individuals, and +N means 10^N times more likely that the groups are from the different individuals, and +N means 10^N times more likely that the groups are from the Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: same individual. Default value: 0.0. This option can be set to 'null' to clear the same individual. Default value: 0.0. This option can be set to 'null' to clear the Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: default value. default value. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: CROSSCHECK_BY=DataType Specificies which data-type should be used as the basic comparison unit. Fingerprints from CROSSCHECK_BY=DataType Specificies which data-type should be used as the basic comparison unit. Fingerprints from Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: readgroups can be "rolled-up" to the LIBRARY, SAMPLE, or FILE level before being compared. readgroups can be "rolled-up" to the LIBRARY, SAMPLE, or FILE level before being compared. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Fingerprints from VCF can be be compared by SAMPLE or FILE. Default value: READGROUP. Fingerprints from VCF can be be compared by SAMPLE or FILE. Default value: READGROUP. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: This option can be set to 'null' to clear the default value. Possible values: {FILE, This option can be set to 'null' to clear the default value. Possible values: {FILE, Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: SAMPLE, LIBRARY, READGROUP} SAMPLE, LIBRARY, READGROUP} Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: NUM_THREADS=Integer The number of threads to use to process files and generate fingerprints. Default value: NUM_THREADS=Integer The number of threads to use to process files and generate fingerprints. Default value: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 1. This option can be set to 'null' to clear the default value. 1. This option can be set to 'null' to clear the default value. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: CALCULATE_TUMOR_AWARE_RESULTS=Boolean CALCULATE_TUMOR_AWARE_RESULTS=Boolean Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: specifies whether the Tumor-aware result should be calculated. These are time consuming specifies whether the Tumor-aware result should be calculated. These are time consuming Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: and can roughly double the runtime of the tool. When crosschecking many groups not and can roughly double the runtime of the tool. When crosschecking many groups not Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: calculating the tumor-aware results can result in a significant speedup. Default value: calculating the tumor-aware results can result in a significant speedup. Default value: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: true. This option can be set to 'null' to clear the default value. Possible values: {true, true. This option can be set to 'null' to clear the default value. Possible values: {true, Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: false} false} Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ALLOW_DUPLICATE_READS=Boolean Allow the use of duplicate reads in performing the comparison. Can be useful when ALLOW_DUPLICATE_READS=Boolean Allow the use of duplicate reads in performing the comparison. Can be useful when Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: duplicate marking has been overly aggressive and coverage is low. Default value: false. duplicate marking has been overly aggressive and coverage is low. Default value: false. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: This option can be set to 'null' to clear the default value. Possible values: {true, This option can be set to 'null' to clear the default value. Possible values: {true, Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: false} false} Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: GENOTYPING_ERROR_RATE=Double Assumed genotyping error rate that provides a floor on the probability that a genotype GENOTYPING_ERROR_RATE=Double Assumed genotyping error rate that provides a floor on the probability that a genotype Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: comes from the expected sample. Must be greater than zero. Default value: 0.01. This comes from the expected sample. Must be greater than zero. Default value: 0.01. This Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: option can be set to 'null' to clear the default value. option can be set to 'null' to clear the default value. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: OUTPUT_ERRORS_ONLY=Boolean If true then only groups that do not relate to each other as expected will have their LODs OUTPUT_ERRORS_ONLY=Boolean If true then only groups that do not relate to each other as expected will have their LODs Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: reported. Default value: false. This option can be set to 'null' to clear the default reported. Default value: false. This option can be set to 'null' to clear the default Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: LOSS_OF_HET_RATE=Double The rate at which a heterozygous genotype in a normal sample turns into a homozygous (via LOSS_OF_HET_RATE=Double The rate at which a heterozygous genotype in a normal sample turns into a homozygous (via Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: loss of heterozygosity) in the tumor (model assumes independent events, so this needs to loss of heterozygosity) in the tumor (model assumes independent events, so this needs to Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: be larger than reality). Default value: 0.5. This option can be set to 'null' to clear be larger than reality). Default value: 0.5. This option can be set to 'null' to clear Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: the default value. the default value. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: EXPECT_ALL_GROUPS_TO_MATCH=Boolean EXPECT_ALL_GROUPS_TO_MATCH=Boolean Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Expect all groups' fingerprints to match, irrespective of their sample names. By default Expect all groups' fingerprints to match, irrespective of their sample names. By default Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: (with this value set to false), groups (readgroups, libraries, files, or samples) with (with this value set to false), groups (readgroups, libraries, files, or samples) with Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: different sample names are expected to mismatch, and those with the same sample name are different sample names are expected to mismatch, and those with the same sample name are Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: expected to match. Default value: false. This option can be set to 'null' to clear the expected to match. Default value: false. This option can be set to 'null' to clear the Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: default value. Possible values: {true, false} default value. Possible values: {true, false} Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: EXIT_CODE_WHEN_MISMATCH=Integer EXIT_CODE_WHEN_MISMATCH=Integer Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: When one or more mismatches between groups is detected, exit with this value instead of 0. When one or more mismatches between groups is detected, exit with this value instead of 0. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Default value: 1. This option can be set to 'null' to clear the default value. Default value: 1. This option can be set to 'null' to clear the default value. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: EXIT_CODE_WHEN_NO_VALID_CHECKS=Integer EXIT_CODE_WHEN_NO_VALID_CHECKS=Integer Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: When all LOD score are zero, exit with this value. Default value: 1. This option can be When all LOD score are zero, exit with this value. Default value: 1. This option can be Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: set to 'null' to clear the default value. set to 'null' to clear the default value. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=Double MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=Double Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Maximal effect of any single haplotype block on outcome (-log10 of maximal likelihood Maximal effect of any single haplotype block on outcome (-log10 of maximal likelihood Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: difference between the different values for the three possible genotypes). Default value: difference between the different values for the three possible genotypes). Default value: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 3.0. This option can be set to 'null' to clear the default value. 3.0. This option can be set to 'null' to clear the default value. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: TEST_INPUT_READABILITY=BooleanWhen true code will check for readability on input files (this can be slow on cloud TEST_INPUT_READABILITY=BooleanWhen true code will check for readability on input files (this can be slow on cloud Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: access) Default value: true. This option can be set to 'null' to clear the default value. access) Default value: true. This option can be set to 'null' to clear the default value. Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Possible values: {true, false} Possible values: {true, false} Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[0](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: REFERENCE must be provided when using CRAM as input. REFERENCE must be provided when using CRAM as input. Running Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:10 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) STANDARD_ERROR INFO 2024-07-02 11:54:10 CrosscheckFingerprints Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting4154993121580679643NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting4154993121580679643NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:10.731 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:10.731 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:10.731 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:10.731 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:10.732 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:54:10.732 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: USAGE: CrosscheckFingerprints [options] USAGE: CrosscheckFingerprints [options] Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CrosscheckFingerprints Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CrosscheckFingerprints Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Checks that all data in the set of input files appear to come from the same individual. Can be used to cross-check Checks that all data in the set of input files appear to come from the same individual. Can be used to cross-check Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: readgroups, libraries, samples, or files. Operates on SAM/BAM/CRAM and VCF (including gVCF and gzipped-VCF). readgroups, libraries, samples, or files. Operates on SAM/BAM/CRAM and VCF (including gVCF and gzipped-VCF). Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Summary Summary Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Checks if all the genetic data within a set of files appear to come from the same individual. It quickly determines Checks if all the genetic data within a set of files appear to come from the same individual. It quickly determines Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: whether a group's genotype matches that of an input file by selective sampling, and has been designed to work well for whether a group's genotype matches that of an input file by selective sampling, and has been designed to work well for Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: low-depth SAM (as well as high depth ones and VCFs.) The tool collects fingerprints (essentially, genotype information low-depth SAM (as well as high depth ones and VCFs.) The tool collects fingerprints (essentially, genotype information Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: from different parts of the genome) at the finest level available in the data (readgroup for read-data files and sample from different parts of the genome) at the finest level available in the data (readgroup for read-data files and sample Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: for variant-data files) and then optionally aggregates it by library, sample or file, to increase power and provide for variant-data files) and then optionally aggregates it by library, sample or file, to increase power and provide Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: results at the desired resolution. Output is in a "Moltenized" format, one row per comparison. The results are emitted results at the desired resolution. Output is in a "Moltenized" format, one row per comparison. The results are emitted Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: into a CrosscheckMetric metric file. In this format the output will include the LOD score and also tumor-aware LOD score into a CrosscheckMetric metric file. In this format the output will include the LOD score and also tumor-aware LOD score Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: which can help assess identity even in the presence of a severe loss of heterozygosity with high purity (which could which can help assess identity even in the presence of a severe loss of heterozygosity with high purity (which could Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: cause it to otherwise fail to notice that samples are from the same individual.) A matrix output is also available to cause it to otherwise fail to notice that samples are from the same individual.) A matrix output is also available to Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: facilitate visual inspection of crosscheck results. facilitate visual inspection of crosscheck results. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Since there can be many rows of output in the metric file, we recommend the use of ClusterCrosscheckMetrics as a Since there can be many rows of output in the metric file, we recommend the use of ClusterCrosscheckMetrics as a Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: follow-up step to running CrosscheckFingerprints. follow-up step to running CrosscheckFingerprints. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: There are cases where one would like to identify a few groups out of a collection of many possible groups (say to link a There are cases where one would like to identify a few groups out of a collection of many possible groups (say to link a Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: SAM to its correct sample in a multi-sample VCF. In this case one would not case for the cross-checking of the various SAM to its correct sample in a multi-sample VCF. In this case one would not case for the cross-checking of the various Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: samples in the VCF against each other, but only in checking the identity of the SAM against the various samples in the samples in the VCF against each other, but only in checking the identity of the SAM against the various samples in the Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: VCF. The SECOND_INPUT is provided for this use-case. With SECOND_INPUT provided, CrosscheckFingerprints does the VCF. The SECOND_INPUT is provided for this use-case. With SECOND_INPUT provided, CrosscheckFingerprints does the Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: following: following: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: - aggregation of data happens independently for the input files in INPUT and SECOND_INPUT. - aggregation of data happens independently for the input files in INPUT and SECOND_INPUT. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: - aggregation of data happens at the SAMPLE level - aggregation of data happens at the SAMPLE level Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: - each samples from INPUT will only be compared to that same sample in SECOND_INPUT. - each samples from INPUT will only be compared to that same sample in SECOND_INPUT. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: - MATRIX_OUTPUT is disabled. - MATRIX_OUTPUT is disabled. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: In some cases, the groups collected may not have any observations (calls for a VCF, reads for a SAM) at fingerprinting In some cases, the groups collected may not have any observations (calls for a VCF, reads for a SAM) at fingerprinting Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: sites, or a sample in INPUT may be missing from the SECOND_INPUT. These cases are handled as follows: If running in sites, or a sample in INPUT may be missing from the SECOND_INPUT. These cases are handled as follows: If running in Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: CHECK_SAME_SAMPLES mode with INPUT and SECOND_INPUT, and either INPUT or SECOND_INPUT includes a sample not found in the CHECK_SAME_SAMPLES mode with INPUT and SECOND_INPUT, and either INPUT or SECOND_INPUT includes a sample not found in the Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: other, or contains a sample with no observations at any fingerprinting sites, an error will be logged and the tool will other, or contains a sample with no observations at any fingerprinting sites, an error will be logged and the tool will Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: return EXIT_CODE_WHEN_MISMATCH. In all other running modes, when any group which is being crosschecked does not have any return EXIT_CODE_WHEN_MISMATCH. In all other running modes, when any group which is being crosschecked does not have any Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: observations at fingerprinting sites, a warning is logged. As long as there is at least one comparison where both sides observations at fingerprinting sites, a warning is logged. As long as there is at least one comparison where both sides Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: have observations at fingerprinting sites, the tool will return zero. However, if all comparisons have at least one have observations at fingerprinting sites, the tool will return zero. However, if all comparisons have at least one Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: side with no observations at fingerprinting sites, an error will be logged and the tool will return side with no observations at fingerprinting sites, an error will be logged and the tool will return Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: EXIT_CODE_WHEN_NO_VALID_CHECKS. EXIT_CODE_WHEN_NO_VALID_CHECKS. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Examples Examples Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Check that all the readgroups from a sample match each other: Check that all the readgroups from a sample match each other: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: java -jar picard.jar CrosscheckFingerprints \ java -jar picard.jar CrosscheckFingerprints \ Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INPUT=sample.with.many.readgroups.bam \ INPUT=sample.with.many.readgroups.bam \ Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: HAPLOTYPE_MAP=fingerprinting_haplotype_database.txt \ HAPLOTYPE_MAP=fingerprinting_haplotype_database.txt \ Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: LOD_THRESHOLD=-5 \ LOD_THRESHOLD=-5 \ Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: OUTPUT=sample.crosscheck_metrics OUTPUT=sample.crosscheck_metrics Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Check that all the readgroups match as expected when providing reads from two samples from the same individual: Check that all the readgroups match as expected when providing reads from two samples from the same individual: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: java -jar picard.jar CrosscheckFingerprints \ java -jar picard.jar CrosscheckFingerprints \ Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INPUT=sample.one.with.many.readgroups.bam \ INPUT=sample.one.with.many.readgroups.bam \ Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INPUT=sample.two.with.many.readgroups.bam \ INPUT=sample.two.with.many.readgroups.bam \ Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: HAPLOTYPE_MAP=fingerprinting_haplotype_database.txt \ HAPLOTYPE_MAP=fingerprinting_haplotype_database.txt \ Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: LOD_THRESHOLD=-5 \ LOD_THRESHOLD=-5 \ Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: EXPECT_ALL_GROUPS_TO_MATCH=true \ EXPECT_ALL_GROUPS_TO_MATCH=true \ Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: OUTPUT=sample.crosscheck_metrics OUTPUT=sample.crosscheck_metrics Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Detailed Explanation Detailed Explanation Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: This tool calculates the LOD score for identity check between "groups" of data in the INPUT files as defined by the This tool calculates the LOD score for identity check between "groups" of data in the INPUT files as defined by the Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: CROSSCHECK_BY argument. A positive value indicates that the data seems to have come from the same individual or, in CROSSCHECK_BY argument. A positive value indicates that the data seems to have come from the same individual or, in Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: other words the identity checks out. The scale is logarithmic (base 10), so a LOD of 6 indicates that it is 1,000,000 other words the identity checks out. The scale is logarithmic (base 10), so a LOD of 6 indicates that it is 1,000,000 Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: more likely that the data matches the genotypes than not. A negative value indicates that the data do not match. A score more likely that the data matches the genotypes than not. A negative value indicates that the data do not match. A score Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: that is near zero is inconclusive and can result from low coverage or non-informative genotypes. Each group is assigned that is near zero is inconclusive and can result from low coverage or non-informative genotypes. Each group is assigned Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: a sample identifier (for SAM this is taken from the SM tag in the appropriate readgroup header line, for VCF this is a sample identifier (for SAM this is taken from the SM tag in the appropriate readgroup header line, for VCF this is Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: taken from the column label in the file-header. After combining all the data from the same group together, an taken from the column label in the file-header. After combining all the data from the same group together, an Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: all-against-all comparison is performed. Results are categorized as one of EXPECTED_MATCH, EXPECTED_MISMATCH, all-against-all comparison is performed. Results are categorized as one of EXPECTED_MATCH, EXPECTED_MISMATCH, Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: UNEXPECTED_MATCH, UNEXPECTED_MISMATCH, or AMBIGUOUS depending on the LOD score and on whether the sample identifiers of UNEXPECTED_MATCH, UNEXPECTED_MISMATCH, or AMBIGUOUS depending on the LOD score and on whether the sample identifiers of Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: the groups agree: LOD scores that are less than LOD_THRESHOLD are considered mismatches, and those greater than the groups agree: LOD scores that are less than LOD_THRESHOLD are considered mismatches, and those greater than Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: -LOD_THRESHOLD are matches (between is ambiguous). If the sample identifiers are equal, the groups are expected to -LOD_THRESHOLD are matches (between is ambiguous). If the sample identifiers are equal, the groups are expected to Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: match. They are expected to mismatch otherwise. match. They are expected to mismatch otherwise. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: The identity check makes use of haplotype blocks defined in the HAPLOTYPE_MAP file to enable it to have higher The identity check makes use of haplotype blocks defined in the HAPLOTYPE_MAP file to enable it to have higher Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: statistical power for detecting identity or swap by aggregating data from several SNPs in the haplotype block. This statistical power for detecting identity or swap by aggregating data from several SNPs in the haplotype block. This Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: enables an identity check of samples with very low coverage (e.g. ~1x mean coverage). enables an identity check of samples with very low coverage (e.g. ~1x mean coverage). Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: When provided a VCF, the identity check looks at the PL, GL and GT fields (in that order) and uses the first one that it When provided a VCF, the identity check looks at the PL, GL and GT fields (in that order) and uses the first one that it Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: finds. finds. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Version: null Version: null Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Options: Options: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: --help --help Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: tools. tools. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INPUT=String INPUT=String Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: I=String One or more input files (or lists of files) with which to compare fingerprints. Default I=String One or more input files (or lists of files) with which to compare fingerprints. Default Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: value: null. This option must be specified at least 1 times. value: null. This option must be specified at least 1 times. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the INPUT data (in column INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the INPUT data (in column Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 1) and the sample as it should be used for comparisons to SECOND_INPUT (in the second 1) and the sample as it should be used for comparisons to SECOND_INPUT (in the second Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: column). Need only include the samples that change. Values in column 1 should be unique. column). Need only include the samples that change. Values in column 1 should be unique. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Values in column 2 should be unique even in union with the remaining unmapped samples. Values in column 2 should be unique even in union with the remaining unmapped samples. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Should only be used with SECOND_INPUT. Default value: null. Cannot be used in Should only be used with SECOND_INPUT. Default value: null. Cannot be used in Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: conjuction with option(s) INPUT_SAMPLE_FILE_MAP conjuction with option(s) INPUT_SAMPLE_FILE_MAP Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INPUT_SAMPLE_FILE_MAP=File A tsv with two columns representing the sample as it should be used for comparisons to INPUT_SAMPLE_FILE_MAP=File A tsv with two columns representing the sample as it should be used for comparisons to Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: SECOND_INPUT (in the first column) and the source file (in INPUT) for the fingerprint (in SECOND_INPUT (in the first column) and the source file (in INPUT) for the fingerprint (in Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: the second column). Need only to include the samples that change. Values in column 1 the second column). Need only to include the samples that change. Values in column 1 Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: should be unique even in union with the remaining unmapped samples. Values in column 2 should be unique even in union with the remaining unmapped samples. Values in column 2 Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: should be unique in the file. Will error if more than one sample is found in a file should be unique in the file. Will error if more than one sample is found in a file Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: (multi-sample VCF) pointed to in column 2. Should only be used in the presence of (multi-sample VCF) pointed to in column 2. Should only be used in the presence of Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: SECOND_INPUT. Default value: null. Cannot be used in conjuction with option(s) SECOND_INPUT. Default value: null. Cannot be used in conjuction with option(s) Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INPUT_SAMPLE_MAP INPUT_SAMPLE_MAP Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: SECOND_INPUT=String SECOND_INPUT=String Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: SI=String A second set of input files (or lists of files) with which to compare fingerprints. If SI=String A second set of input files (or lists of files) with which to compare fingerprints. If Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: this option is provided the tool compares each sample in INPUT with the sample from this option is provided the tool compares each sample in INPUT with the sample from Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: SECOND_INPUT that has the same sample ID. In addition, data will be grouped by SAMPLE SECOND_INPUT that has the same sample ID. In addition, data will be grouped by SAMPLE Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: regardless of the value of CROSSCHECK_BY. When operating in this mode, each sample in regardless of the value of CROSSCHECK_BY. When operating in this mode, each sample in Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INPUT must also have a corresponding sample in SECOND_INPUT. If this is violated, the tool INPUT must also have a corresponding sample in SECOND_INPUT. If this is violated, the tool Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: will proceed to check the matching samples, but report the missing samples and return a will proceed to check the matching samples, but report the missing samples and return a Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: non-zero error-code. Default value: null. This option may be specified 0 or more times. non-zero error-code. Default value: null. This option may be specified 0 or more times. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Cannot be used in conjuction with option(s) MATRIX_OUTPUT (MO) Cannot be used in conjuction with option(s) MATRIX_OUTPUT (MO) Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: SECOND_INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the SECOND_INPUT data (in SECOND_INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the SECOND_INPUT data (in Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: column 1) and the sample as it should be used for comparisons to INPUT (in the second column 1) and the sample as it should be used for comparisons to INPUT (in the second Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: column). Note that in case of unrolling files (file-of-filenames) one would need to column). Note that in case of unrolling files (file-of-filenames) one would need to Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: reference the final file, i.e. the file that contains the genomic data. Need only include reference the final file, i.e. the file that contains the genomic data. Need only include Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: the samples that change. Values in column 1 should be unique. Values in column 2 should be the samples that change. Values in column 1 should be unique. Values in column 2 should be Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: unique even in union with the remaining unmapped samples. Should only be used with unique even in union with the remaining unmapped samples. Should only be used with Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: SECOND_INPUT. Default value: null. SECOND_INPUT. Default value: null. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: CROSSCHECK_MODE=CrosscheckModeAn argument that controls how crosschecking with both INPUT and SECOND_INPUT should occur. CROSSCHECK_MODE=CrosscheckModeAn argument that controls how crosschecking with both INPUT and SECOND_INPUT should occur. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Default value: CHECK_SAME_SAMPLE. This option can be set to 'null' to clear the default Default value: CHECK_SAME_SAMPLE. This option can be set to 'null' to clear the default Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: value. Possible values: { value. Possible values: { Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: CHECK_SAME_SAMPLE (In this mode, each sample in INPUT will only be checked against a CHECK_SAME_SAMPLE (In this mode, each sample in INPUT will only be checked against a Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: single corresponding sample in SECOND_INPUT. If a corresponding sample cannot be found, single corresponding sample in SECOND_INPUT. If a corresponding sample cannot be found, Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: the program will proceed, but report the missing samples and return the value specified in the program will proceed, but report the missing samples and return the value specified in Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: EXIT_CODE_WHEN_MISMATCH. The corresponding samples are those that equal each other, after EXIT_CODE_WHEN_MISMATCH. The corresponding samples are those that equal each other, after Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: possible renaming via INPUT_SAMPLE_MAP and SECOND_INPUT_SAMPLE_MAP. In this mode possible renaming via INPUT_SAMPLE_MAP and SECOND_INPUT_SAMPLE_MAP. In this mode Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: CROSSCHECK_BY must be SAMPLE.) CROSSCHECK_BY must be SAMPLE.) Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: CHECK_ALL_OTHERS (In this mode, each sample in INPUT will be checked against all the CHECK_ALL_OTHERS (In this mode, each sample in INPUT will be checked against all the Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: samples in SECOND_INPUT.) samples in SECOND_INPUT.) Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: } } Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: O=File Optional output file to write metrics to. Default is to write to stdout. Default value: O=File Optional output file to write metrics to. Default is to write to stdout. Default value: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: null. null. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: MATRIX_OUTPUT=File MATRIX_OUTPUT=File Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: MO=File Optional output file to write matrix of LOD scores to. This is less informative than the MO=File Optional output file to write matrix of LOD scores to. This is less informative than the Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: metrics output and only contains Normal-Normal LOD score (i.e. doesn't account for Loss of metrics output and only contains Normal-Normal LOD score (i.e. doesn't account for Loss of Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Heterozygosity). It is however sometimes easier to use visually. Default value: null. Heterozygosity). It is however sometimes easier to use visually. Default value: null. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Cannot be used in conjuction with option(s) SECOND_INPUT (SI) Cannot be used in conjuction with option(s) SECOND_INPUT (SI) Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: HAPLOTYPE_MAP=File HAPLOTYPE_MAP=File Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: H=File The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for H=File The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: fingerprinting. See https://software.broadinstitute.org/gatk/documentation/article?id=9526 fingerprinting. See https://software.broadinstitute.org/gatk/documentation/article?id=9526 Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: for details. Required. for details. Required. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: LOD_THRESHOLD=Double LOD_THRESHOLD=Double Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: LOD=Double If any two groups (with the same sample name) match with a LOD score lower than the LOD=Double If any two groups (with the same sample name) match with a LOD score lower than the Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: threshold the tool will exit with a non-zero code to indicate error. Program will also threshold the tool will exit with a non-zero code to indicate error. Program will also Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: exit with an error if it finds two groups with different sample name that match with a LOD exit with an error if it finds two groups with different sample name that match with a LOD Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: score greater than -LOD_THRESHOLD. score greater than -LOD_THRESHOLD. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: LOD score 0 means equal likelihood that the groups match vs. come from different LOD score 0 means equal likelihood that the groups match vs. come from different Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: individuals, negative LOD score -N, mean 10^N time more likely that the groups are from individuals, negative LOD score -N, mean 10^N time more likely that the groups are from Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: different individuals, and +N means 10^N times more likely that the groups are from the different individuals, and +N means 10^N times more likely that the groups are from the Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: same individual. Default value: 0.0. This option can be set to 'null' to clear the same individual. Default value: 0.0. This option can be set to 'null' to clear the Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: default value. default value. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: CROSSCHECK_BY=DataType Specificies which data-type should be used as the basic comparison unit. Fingerprints from CROSSCHECK_BY=DataType Specificies which data-type should be used as the basic comparison unit. Fingerprints from Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: readgroups can be "rolled-up" to the LIBRARY, SAMPLE, or FILE level before being compared. readgroups can be "rolled-up" to the LIBRARY, SAMPLE, or FILE level before being compared. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Fingerprints from VCF can be be compared by SAMPLE or FILE. Default value: READGROUP. Fingerprints from VCF can be be compared by SAMPLE or FILE. Default value: READGROUP. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: This option can be set to 'null' to clear the default value. Possible values: {FILE, This option can be set to 'null' to clear the default value. Possible values: {FILE, Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: SAMPLE, LIBRARY, READGROUP} SAMPLE, LIBRARY, READGROUP} Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: NUM_THREADS=Integer The number of threads to use to process files and generate fingerprints. Default value: NUM_THREADS=Integer The number of threads to use to process files and generate fingerprints. Default value: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 1. This option can be set to 'null' to clear the default value. 1. This option can be set to 'null' to clear the default value. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: CALCULATE_TUMOR_AWARE_RESULTS=Boolean CALCULATE_TUMOR_AWARE_RESULTS=Boolean Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: specifies whether the Tumor-aware result should be calculated. These are time consuming specifies whether the Tumor-aware result should be calculated. These are time consuming Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: and can roughly double the runtime of the tool. When crosschecking many groups not and can roughly double the runtime of the tool. When crosschecking many groups not Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: calculating the tumor-aware results can result in a significant speedup. Default value: calculating the tumor-aware results can result in a significant speedup. Default value: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: true. This option can be set to 'null' to clear the default value. Possible values: {true, true. This option can be set to 'null' to clear the default value. Possible values: {true, Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: false} false} Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ALLOW_DUPLICATE_READS=Boolean Allow the use of duplicate reads in performing the comparison. Can be useful when ALLOW_DUPLICATE_READS=Boolean Allow the use of duplicate reads in performing the comparison. Can be useful when Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: duplicate marking has been overly aggressive and coverage is low. Default value: false. duplicate marking has been overly aggressive and coverage is low. Default value: false. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: This option can be set to 'null' to clear the default value. Possible values: {true, This option can be set to 'null' to clear the default value. Possible values: {true, Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: false} false} Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: GENOTYPING_ERROR_RATE=Double Assumed genotyping error rate that provides a floor on the probability that a genotype GENOTYPING_ERROR_RATE=Double Assumed genotyping error rate that provides a floor on the probability that a genotype Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: comes from the expected sample. Must be greater than zero. Default value: 0.01. This comes from the expected sample. Must be greater than zero. Default value: 0.01. This Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: option can be set to 'null' to clear the default value. option can be set to 'null' to clear the default value. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: OUTPUT_ERRORS_ONLY=Boolean If true then only groups that do not relate to each other as expected will have their LODs OUTPUT_ERRORS_ONLY=Boolean If true then only groups that do not relate to each other as expected will have their LODs Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: reported. Default value: false. This option can be set to 'null' to clear the default reported. Default value: false. This option can be set to 'null' to clear the default Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: LOSS_OF_HET_RATE=Double The rate at which a heterozygous genotype in a normal sample turns into a homozygous (via LOSS_OF_HET_RATE=Double The rate at which a heterozygous genotype in a normal sample turns into a homozygous (via Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: loss of heterozygosity) in the tumor (model assumes independent events, so this needs to loss of heterozygosity) in the tumor (model assumes independent events, so this needs to Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: be larger than reality). Default value: 0.5. This option can be set to 'null' to clear be larger than reality). Default value: 0.5. This option can be set to 'null' to clear Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: the default value. the default value. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: EXPECT_ALL_GROUPS_TO_MATCH=Boolean EXPECT_ALL_GROUPS_TO_MATCH=Boolean Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Expect all groups' fingerprints to match, irrespective of their sample names. By default Expect all groups' fingerprints to match, irrespective of their sample names. By default Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: (with this value set to false), groups (readgroups, libraries, files, or samples) with (with this value set to false), groups (readgroups, libraries, files, or samples) with Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: different sample names are expected to mismatch, and those with the same sample name are different sample names are expected to mismatch, and those with the same sample name are Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: expected to match. Default value: false. This option can be set to 'null' to clear the expected to match. Default value: false. This option can be set to 'null' to clear the Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: default value. Possible values: {true, false} default value. Possible values: {true, false} Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: EXIT_CODE_WHEN_MISMATCH=Integer EXIT_CODE_WHEN_MISMATCH=Integer Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: When one or more mismatches between groups is detected, exit with this value instead of 0. When one or more mismatches between groups is detected, exit with this value instead of 0. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Default value: 1. This option can be set to 'null' to clear the default value. Default value: 1. This option can be set to 'null' to clear the default value. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: EXIT_CODE_WHEN_NO_VALID_CHECKS=Integer EXIT_CODE_WHEN_NO_VALID_CHECKS=Integer Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: When all LOD score are zero, exit with this value. Default value: 1. This option can be When all LOD score are zero, exit with this value. Default value: 1. This option can be Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: set to 'null' to clear the default value. set to 'null' to clear the default value. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=Double MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=Double Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Maximal effect of any single haplotype block on outcome (-log10 of maximal likelihood Maximal effect of any single haplotype block on outcome (-log10 of maximal likelihood Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: difference between the different values for the three possible genotypes). Default value: difference between the different values for the three possible genotypes). Default value: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 3.0. This option can be set to 'null' to clear the default value. 3.0. This option can be set to 'null' to clear the default value. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: TEST_INPUT_READABILITY=BooleanWhen true code will check for readability on input files (this can be slow on cloud TEST_INPUT_READABILITY=BooleanWhen true code will check for readability on input files (this can be slow on cloud Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: access) Default value: true. This option can be set to 'null' to clear the default value. access) Default value: true. This option can be set to 'null' to clear the default value. Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Possible values: {true, false} Possible values: {true, false} Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[1](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: REFERENCE must be provided when using CRAM as input. REFERENCE must be provided when using CRAM as input. Running Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:10 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram) STANDARD_ERROR INFO 2024-07-02 11:54:10 CrosscheckFingerprints Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram -OUTPUT /tmp/Fingerprinting7518848054390408276NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram -OUTPUT /tmp/Fingerprinting7518848054390408276NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:10.996 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:10.996 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:10.996 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:10.996 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:10.997 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:54:10.997 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: USAGE: CrosscheckFingerprints [options] USAGE: CrosscheckFingerprints [options] Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CrosscheckFingerprints Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CrosscheckFingerprints Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Checks that all data in the set of input files appear to come from the same individual. Can be used to cross-check Checks that all data in the set of input files appear to come from the same individual. Can be used to cross-check Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: readgroups, libraries, samples, or files. Operates on SAM/BAM/CRAM and VCF (including gVCF and gzipped-VCF). readgroups, libraries, samples, or files. Operates on SAM/BAM/CRAM and VCF (including gVCF and gzipped-VCF). Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Summary Summary Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Checks if all the genetic data within a set of files appear to come from the same individual. It quickly determines Checks if all the genetic data within a set of files appear to come from the same individual. It quickly determines Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: whether a group's genotype matches that of an input file by selective sampling, and has been designed to work well for whether a group's genotype matches that of an input file by selective sampling, and has been designed to work well for Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: low-depth SAM (as well as high depth ones and VCFs.) The tool collects fingerprints (essentially, genotype information low-depth SAM (as well as high depth ones and VCFs.) The tool collects fingerprints (essentially, genotype information Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: from different parts of the genome) at the finest level available in the data (readgroup for read-data files and sample from different parts of the genome) at the finest level available in the data (readgroup for read-data files and sample Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: for variant-data files) and then optionally aggregates it by library, sample or file, to increase power and provide for variant-data files) and then optionally aggregates it by library, sample or file, to increase power and provide Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: results at the desired resolution. Output is in a "Moltenized" format, one row per comparison. The results are emitted results at the desired resolution. Output is in a "Moltenized" format, one row per comparison. The results are emitted Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: into a CrosscheckMetric metric file. In this format the output will include the LOD score and also tumor-aware LOD score into a CrosscheckMetric metric file. In this format the output will include the LOD score and also tumor-aware LOD score Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: which can help assess identity even in the presence of a severe loss of heterozygosity with high purity (which could which can help assess identity even in the presence of a severe loss of heterozygosity with high purity (which could Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: cause it to otherwise fail to notice that samples are from the same individual.) A matrix output is also available to cause it to otherwise fail to notice that samples are from the same individual.) A matrix output is also available to Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: facilitate visual inspection of crosscheck results. facilitate visual inspection of crosscheck results. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Since there can be many rows of output in the metric file, we recommend the use of ClusterCrosscheckMetrics as a Since there can be many rows of output in the metric file, we recommend the use of ClusterCrosscheckMetrics as a Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: follow-up step to running CrosscheckFingerprints. follow-up step to running CrosscheckFingerprints. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: There are cases where one would like to identify a few groups out of a collection of many possible groups (say to link a There are cases where one would like to identify a few groups out of a collection of many possible groups (say to link a Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: SAM to its correct sample in a multi-sample VCF. In this case one would not case for the cross-checking of the various SAM to its correct sample in a multi-sample VCF. In this case one would not case for the cross-checking of the various Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: samples in the VCF against each other, but only in checking the identity of the SAM against the various samples in the samples in the VCF against each other, but only in checking the identity of the SAM against the various samples in the Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: VCF. The SECOND_INPUT is provided for this use-case. With SECOND_INPUT provided, CrosscheckFingerprints does the VCF. The SECOND_INPUT is provided for this use-case. With SECOND_INPUT provided, CrosscheckFingerprints does the Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: following: following: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: - aggregation of data happens independently for the input files in INPUT and SECOND_INPUT. - aggregation of data happens independently for the input files in INPUT and SECOND_INPUT. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: - aggregation of data happens at the SAMPLE level - aggregation of data happens at the SAMPLE level Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: - each samples from INPUT will only be compared to that same sample in SECOND_INPUT. - each samples from INPUT will only be compared to that same sample in SECOND_INPUT. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: - MATRIX_OUTPUT is disabled. - MATRIX_OUTPUT is disabled. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: In some cases, the groups collected may not have any observations (calls for a VCF, reads for a SAM) at fingerprinting In some cases, the groups collected may not have any observations (calls for a VCF, reads for a SAM) at fingerprinting Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: sites, or a sample in INPUT may be missing from the SECOND_INPUT. These cases are handled as follows: If running in sites, or a sample in INPUT may be missing from the SECOND_INPUT. These cases are handled as follows: If running in Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: CHECK_SAME_SAMPLES mode with INPUT and SECOND_INPUT, and either INPUT or SECOND_INPUT includes a sample not found in the CHECK_SAME_SAMPLES mode with INPUT and SECOND_INPUT, and either INPUT or SECOND_INPUT includes a sample not found in the Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: other, or contains a sample with no observations at any fingerprinting sites, an error will be logged and the tool will other, or contains a sample with no observations at any fingerprinting sites, an error will be logged and the tool will Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: return EXIT_CODE_WHEN_MISMATCH. In all other running modes, when any group which is being crosschecked does not have any return EXIT_CODE_WHEN_MISMATCH. In all other running modes, when any group which is being crosschecked does not have any Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: observations at fingerprinting sites, a warning is logged. As long as there is at least one comparison where both sides observations at fingerprinting sites, a warning is logged. As long as there is at least one comparison where both sides Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: have observations at fingerprinting sites, the tool will return zero. However, if all comparisons have at least one have observations at fingerprinting sites, the tool will return zero. However, if all comparisons have at least one Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: side with no observations at fingerprinting sites, an error will be logged and the tool will return side with no observations at fingerprinting sites, an error will be logged and the tool will return Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: EXIT_CODE_WHEN_NO_VALID_CHECKS. EXIT_CODE_WHEN_NO_VALID_CHECKS. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Examples Examples Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Check that all the readgroups from a sample match each other: Check that all the readgroups from a sample match each other: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: java -jar picard.jar CrosscheckFingerprints \ java -jar picard.jar CrosscheckFingerprints \ Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INPUT=sample.with.many.readgroups.bam \ INPUT=sample.with.many.readgroups.bam \ Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: HAPLOTYPE_MAP=fingerprinting_haplotype_database.txt \ HAPLOTYPE_MAP=fingerprinting_haplotype_database.txt \ Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: LOD_THRESHOLD=-5 \ LOD_THRESHOLD=-5 \ Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: OUTPUT=sample.crosscheck_metrics OUTPUT=sample.crosscheck_metrics Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Check that all the readgroups match as expected when providing reads from two samples from the same individual: Check that all the readgroups match as expected when providing reads from two samples from the same individual: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: java -jar picard.jar CrosscheckFingerprints \ java -jar picard.jar CrosscheckFingerprints \ Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INPUT=sample.one.with.many.readgroups.bam \ INPUT=sample.one.with.many.readgroups.bam \ Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INPUT=sample.two.with.many.readgroups.bam \ INPUT=sample.two.with.many.readgroups.bam \ Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: HAPLOTYPE_MAP=fingerprinting_haplotype_database.txt \ HAPLOTYPE_MAP=fingerprinting_haplotype_database.txt \ Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: LOD_THRESHOLD=-5 \ LOD_THRESHOLD=-5 \ Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: EXPECT_ALL_GROUPS_TO_MATCH=true \ EXPECT_ALL_GROUPS_TO_MATCH=true \ Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: OUTPUT=sample.crosscheck_metrics OUTPUT=sample.crosscheck_metrics Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Detailed Explanation Detailed Explanation Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: This tool calculates the LOD score for identity check between "groups" of data in the INPUT files as defined by the This tool calculates the LOD score for identity check between "groups" of data in the INPUT files as defined by the Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: CROSSCHECK_BY argument. A positive value indicates that the data seems to have come from the same individual or, in CROSSCHECK_BY argument. A positive value indicates that the data seems to have come from the same individual or, in Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: other words the identity checks out. The scale is logarithmic (base 10), so a LOD of 6 indicates that it is 1,000,000 other words the identity checks out. The scale is logarithmic (base 10), so a LOD of 6 indicates that it is 1,000,000 Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: more likely that the data matches the genotypes than not. A negative value indicates that the data do not match. A score more likely that the data matches the genotypes than not. A negative value indicates that the data do not match. A score Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: that is near zero is inconclusive and can result from low coverage or non-informative genotypes. Each group is assigned that is near zero is inconclusive and can result from low coverage or non-informative genotypes. Each group is assigned Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: a sample identifier (for SAM this is taken from the SM tag in the appropriate readgroup header line, for VCF this is a sample identifier (for SAM this is taken from the SM tag in the appropriate readgroup header line, for VCF this is Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: taken from the column label in the file-header. After combining all the data from the same group together, an taken from the column label in the file-header. After combining all the data from the same group together, an Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: all-against-all comparison is performed. Results are categorized as one of EXPECTED_MATCH, EXPECTED_MISMATCH, all-against-all comparison is performed. Results are categorized as one of EXPECTED_MATCH, EXPECTED_MISMATCH, Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: UNEXPECTED_MATCH, UNEXPECTED_MISMATCH, or AMBIGUOUS depending on the LOD score and on whether the sample identifiers of UNEXPECTED_MATCH, UNEXPECTED_MISMATCH, or AMBIGUOUS depending on the LOD score and on whether the sample identifiers of Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: the groups agree: LOD scores that are less than LOD_THRESHOLD are considered mismatches, and those greater than the groups agree: LOD scores that are less than LOD_THRESHOLD are considered mismatches, and those greater than Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: -LOD_THRESHOLD are matches (between is ambiguous). If the sample identifiers are equal, the groups are expected to -LOD_THRESHOLD are matches (between is ambiguous). If the sample identifiers are equal, the groups are expected to Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: match. They are expected to mismatch otherwise. match. They are expected to mismatch otherwise. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: The identity check makes use of haplotype blocks defined in the HAPLOTYPE_MAP file to enable it to have higher The identity check makes use of haplotype blocks defined in the HAPLOTYPE_MAP file to enable it to have higher Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: statistical power for detecting identity or swap by aggregating data from several SNPs in the haplotype block. This statistical power for detecting identity or swap by aggregating data from several SNPs in the haplotype block. This Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: enables an identity check of samples with very low coverage (e.g. ~1x mean coverage). enables an identity check of samples with very low coverage (e.g. ~1x mean coverage). Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: When provided a VCF, the identity check looks at the PL, GL and GT fields (in that order) and uses the first one that it When provided a VCF, the identity check looks at the PL, GL and GT fields (in that order) and uses the first one that it Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: finds. finds. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Version: null Version: null Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Options: Options: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: --help --help Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: tools. tools. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INPUT=String INPUT=String Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: I=String One or more input files (or lists of files) with which to compare fingerprints. Default I=String One or more input files (or lists of files) with which to compare fingerprints. Default Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: value: null. This option must be specified at least 1 times. value: null. This option must be specified at least 1 times. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the INPUT data (in column INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the INPUT data (in column Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 1) and the sample as it should be used for comparisons to SECOND_INPUT (in the second 1) and the sample as it should be used for comparisons to SECOND_INPUT (in the second Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: column). Need only include the samples that change. Values in column 1 should be unique. column). Need only include the samples that change. Values in column 1 should be unique. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Values in column 2 should be unique even in union with the remaining unmapped samples. Values in column 2 should be unique even in union with the remaining unmapped samples. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Should only be used with SECOND_INPUT. Default value: null. Cannot be used in Should only be used with SECOND_INPUT. Default value: null. Cannot be used in Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: conjuction with option(s) INPUT_SAMPLE_FILE_MAP conjuction with option(s) INPUT_SAMPLE_FILE_MAP Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INPUT_SAMPLE_FILE_MAP=File A tsv with two columns representing the sample as it should be used for comparisons to INPUT_SAMPLE_FILE_MAP=File A tsv with two columns representing the sample as it should be used for comparisons to Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: SECOND_INPUT (in the first column) and the source file (in INPUT) for the fingerprint (in SECOND_INPUT (in the first column) and the source file (in INPUT) for the fingerprint (in Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: the second column). Need only to include the samples that change. Values in column 1 the second column). Need only to include the samples that change. Values in column 1 Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: should be unique even in union with the remaining unmapped samples. Values in column 2 should be unique even in union with the remaining unmapped samples. Values in column 2 Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: should be unique in the file. Will error if more than one sample is found in a file should be unique in the file. Will error if more than one sample is found in a file Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: (multi-sample VCF) pointed to in column 2. Should only be used in the presence of (multi-sample VCF) pointed to in column 2. Should only be used in the presence of Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: SECOND_INPUT. Default value: null. Cannot be used in conjuction with option(s) SECOND_INPUT. Default value: null. Cannot be used in conjuction with option(s) Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INPUT_SAMPLE_MAP INPUT_SAMPLE_MAP Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: SECOND_INPUT=String SECOND_INPUT=String Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: SI=String A second set of input files (or lists of files) with which to compare fingerprints. If SI=String A second set of input files (or lists of files) with which to compare fingerprints. If Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: this option is provided the tool compares each sample in INPUT with the sample from this option is provided the tool compares each sample in INPUT with the sample from Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: SECOND_INPUT that has the same sample ID. In addition, data will be grouped by SAMPLE SECOND_INPUT that has the same sample ID. In addition, data will be grouped by SAMPLE Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: regardless of the value of CROSSCHECK_BY. When operating in this mode, each sample in regardless of the value of CROSSCHECK_BY. When operating in this mode, each sample in Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INPUT must also have a corresponding sample in SECOND_INPUT. If this is violated, the tool INPUT must also have a corresponding sample in SECOND_INPUT. If this is violated, the tool Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: will proceed to check the matching samples, but report the missing samples and return a will proceed to check the matching samples, but report the missing samples and return a Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: non-zero error-code. Default value: null. This option may be specified 0 or more times. non-zero error-code. Default value: null. This option may be specified 0 or more times. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Cannot be used in conjuction with option(s) MATRIX_OUTPUT (MO) Cannot be used in conjuction with option(s) MATRIX_OUTPUT (MO) Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: SECOND_INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the SECOND_INPUT data (in SECOND_INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the SECOND_INPUT data (in Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: column 1) and the sample as it should be used for comparisons to INPUT (in the second column 1) and the sample as it should be used for comparisons to INPUT (in the second Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: column). Note that in case of unrolling files (file-of-filenames) one would need to column). Note that in case of unrolling files (file-of-filenames) one would need to Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: reference the final file, i.e. the file that contains the genomic data. Need only include reference the final file, i.e. the file that contains the genomic data. Need only include Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: the samples that change. Values in column 1 should be unique. Values in column 2 should be the samples that change. Values in column 1 should be unique. Values in column 2 should be Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: unique even in union with the remaining unmapped samples. Should only be used with unique even in union with the remaining unmapped samples. Should only be used with Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: SECOND_INPUT. Default value: null. SECOND_INPUT. Default value: null. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: CROSSCHECK_MODE=CrosscheckModeAn argument that controls how crosschecking with both INPUT and SECOND_INPUT should occur. CROSSCHECK_MODE=CrosscheckModeAn argument that controls how crosschecking with both INPUT and SECOND_INPUT should occur. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Default value: CHECK_SAME_SAMPLE. This option can be set to 'null' to clear the default Default value: CHECK_SAME_SAMPLE. This option can be set to 'null' to clear the default Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: value. Possible values: { value. Possible values: { Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: CHECK_SAME_SAMPLE (In this mode, each sample in INPUT will only be checked against a CHECK_SAME_SAMPLE (In this mode, each sample in INPUT will only be checked against a Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: single corresponding sample in SECOND_INPUT. If a corresponding sample cannot be found, single corresponding sample in SECOND_INPUT. If a corresponding sample cannot be found, Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: the program will proceed, but report the missing samples and return the value specified in the program will proceed, but report the missing samples and return the value specified in Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: EXIT_CODE_WHEN_MISMATCH. The corresponding samples are those that equal each other, after EXIT_CODE_WHEN_MISMATCH. The corresponding samples are those that equal each other, after Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: possible renaming via INPUT_SAMPLE_MAP and SECOND_INPUT_SAMPLE_MAP. In this mode possible renaming via INPUT_SAMPLE_MAP and SECOND_INPUT_SAMPLE_MAP. In this mode Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: CROSSCHECK_BY must be SAMPLE.) CROSSCHECK_BY must be SAMPLE.) Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: CHECK_ALL_OTHERS (In this mode, each sample in INPUT will be checked against all the CHECK_ALL_OTHERS (In this mode, each sample in INPUT will be checked against all the Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: samples in SECOND_INPUT.) samples in SECOND_INPUT.) Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: } } Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: O=File Optional output file to write metrics to. Default is to write to stdout. Default value: O=File Optional output file to write metrics to. Default is to write to stdout. Default value: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: null. null. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: MATRIX_OUTPUT=File MATRIX_OUTPUT=File Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: MO=File Optional output file to write matrix of LOD scores to. This is less informative than the MO=File Optional output file to write matrix of LOD scores to. This is less informative than the Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: metrics output and only contains Normal-Normal LOD score (i.e. doesn't account for Loss of metrics output and only contains Normal-Normal LOD score (i.e. doesn't account for Loss of Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Heterozygosity). It is however sometimes easier to use visually. Default value: null. Heterozygosity). It is however sometimes easier to use visually. Default value: null. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Cannot be used in conjuction with option(s) SECOND_INPUT (SI) Cannot be used in conjuction with option(s) SECOND_INPUT (SI) Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: HAPLOTYPE_MAP=File HAPLOTYPE_MAP=File Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: H=File The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for H=File The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: fingerprinting. See https://software.broadinstitute.org/gatk/documentation/article?id=9526 fingerprinting. See https://software.broadinstitute.org/gatk/documentation/article?id=9526 Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: for details. Required. for details. Required. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: LOD_THRESHOLD=Double LOD_THRESHOLD=Double Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: LOD=Double If any two groups (with the same sample name) match with a LOD score lower than the LOD=Double If any two groups (with the same sample name) match with a LOD score lower than the Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: threshold the tool will exit with a non-zero code to indicate error. Program will also threshold the tool will exit with a non-zero code to indicate error. Program will also Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: exit with an error if it finds two groups with different sample name that match with a LOD exit with an error if it finds two groups with different sample name that match with a LOD Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: score greater than -LOD_THRESHOLD. score greater than -LOD_THRESHOLD. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: LOD score 0 means equal likelihood that the groups match vs. come from different LOD score 0 means equal likelihood that the groups match vs. come from different Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: individuals, negative LOD score -N, mean 10^N time more likely that the groups are from individuals, negative LOD score -N, mean 10^N time more likely that the groups are from Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: different individuals, and +N means 10^N times more likely that the groups are from the different individuals, and +N means 10^N times more likely that the groups are from the Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: same individual. Default value: 0.0. This option can be set to 'null' to clear the same individual. Default value: 0.0. This option can be set to 'null' to clear the Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: default value. default value. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: CROSSCHECK_BY=DataType Specificies which data-type should be used as the basic comparison unit. Fingerprints from CROSSCHECK_BY=DataType Specificies which data-type should be used as the basic comparison unit. Fingerprints from Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: readgroups can be "rolled-up" to the LIBRARY, SAMPLE, or FILE level before being compared. readgroups can be "rolled-up" to the LIBRARY, SAMPLE, or FILE level before being compared. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Fingerprints from VCF can be be compared by SAMPLE or FILE. Default value: READGROUP. Fingerprints from VCF can be be compared by SAMPLE or FILE. Default value: READGROUP. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: This option can be set to 'null' to clear the default value. Possible values: {FILE, This option can be set to 'null' to clear the default value. Possible values: {FILE, Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: SAMPLE, LIBRARY, READGROUP} SAMPLE, LIBRARY, READGROUP} Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: NUM_THREADS=Integer The number of threads to use to process files and generate fingerprints. Default value: NUM_THREADS=Integer The number of threads to use to process files and generate fingerprints. Default value: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 1. This option can be set to 'null' to clear the default value. 1. This option can be set to 'null' to clear the default value. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: CALCULATE_TUMOR_AWARE_RESULTS=Boolean CALCULATE_TUMOR_AWARE_RESULTS=Boolean Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: specifies whether the Tumor-aware result should be calculated. These are time consuming specifies whether the Tumor-aware result should be calculated. These are time consuming Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: and can roughly double the runtime of the tool. When crosschecking many groups not and can roughly double the runtime of the tool. When crosschecking many groups not Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: calculating the tumor-aware results can result in a significant speedup. Default value: calculating the tumor-aware results can result in a significant speedup. Default value: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: true. This option can be set to 'null' to clear the default value. Possible values: {true, true. This option can be set to 'null' to clear the default value. Possible values: {true, Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: false} false} Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ALLOW_DUPLICATE_READS=Boolean Allow the use of duplicate reads in performing the comparison. Can be useful when ALLOW_DUPLICATE_READS=Boolean Allow the use of duplicate reads in performing the comparison. Can be useful when Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: duplicate marking has been overly aggressive and coverage is low. Default value: false. duplicate marking has been overly aggressive and coverage is low. Default value: false. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: This option can be set to 'null' to clear the default value. Possible values: {true, This option can be set to 'null' to clear the default value. Possible values: {true, Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: false} false} Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: GENOTYPING_ERROR_RATE=Double Assumed genotyping error rate that provides a floor on the probability that a genotype GENOTYPING_ERROR_RATE=Double Assumed genotyping error rate that provides a floor on the probability that a genotype Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: comes from the expected sample. Must be greater than zero. Default value: 0.01. This comes from the expected sample. Must be greater than zero. Default value: 0.01. This Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: option can be set to 'null' to clear the default value. option can be set to 'null' to clear the default value. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: OUTPUT_ERRORS_ONLY=Boolean If true then only groups that do not relate to each other as expected will have their LODs OUTPUT_ERRORS_ONLY=Boolean If true then only groups that do not relate to each other as expected will have their LODs Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: reported. Default value: false. This option can be set to 'null' to clear the default reported. Default value: false. This option can be set to 'null' to clear the default Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: LOSS_OF_HET_RATE=Double The rate at which a heterozygous genotype in a normal sample turns into a homozygous (via LOSS_OF_HET_RATE=Double The rate at which a heterozygous genotype in a normal sample turns into a homozygous (via Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: loss of heterozygosity) in the tumor (model assumes independent events, so this needs to loss of heterozygosity) in the tumor (model assumes independent events, so this needs to Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: be larger than reality). Default value: 0.5. This option can be set to 'null' to clear be larger than reality). Default value: 0.5. This option can be set to 'null' to clear Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: the default value. the default value. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: EXPECT_ALL_GROUPS_TO_MATCH=Boolean EXPECT_ALL_GROUPS_TO_MATCH=Boolean Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Expect all groups' fingerprints to match, irrespective of their sample names. By default Expect all groups' fingerprints to match, irrespective of their sample names. By default Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: (with this value set to false), groups (readgroups, libraries, files, or samples) with (with this value set to false), groups (readgroups, libraries, files, or samples) with Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: different sample names are expected to mismatch, and those with the same sample name are different sample names are expected to mismatch, and those with the same sample name are Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: expected to match. Default value: false. This option can be set to 'null' to clear the expected to match. Default value: false. This option can be set to 'null' to clear the Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: default value. Possible values: {true, false} default value. Possible values: {true, false} Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: EXIT_CODE_WHEN_MISMATCH=Integer EXIT_CODE_WHEN_MISMATCH=Integer Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: When one or more mismatches between groups is detected, exit with this value instead of 0. When one or more mismatches between groups is detected, exit with this value instead of 0. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Default value: 1. This option can be set to 'null' to clear the default value. Default value: 1. This option can be set to 'null' to clear the default value. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: EXIT_CODE_WHEN_NO_VALID_CHECKS=Integer EXIT_CODE_WHEN_NO_VALID_CHECKS=Integer Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: When all LOD score are zero, exit with this value. Default value: 1. This option can be When all LOD score are zero, exit with this value. Default value: 1. This option can be Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: set to 'null' to clear the default value. set to 'null' to clear the default value. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=Double MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=Double Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Maximal effect of any single haplotype block on outcome (-log10 of maximal likelihood Maximal effect of any single haplotype block on outcome (-log10 of maximal likelihood Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: difference between the different values for the three possible genotypes). Default value: difference between the different values for the three possible genotypes). Default value: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 3.0. This option can be set to 'null' to clear the default value. 3.0. This option can be set to 'null' to clear the default value. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: TEST_INPUT_READABILITY=BooleanWhen true code will check for readability on input files (this can be slow on cloud TEST_INPUT_READABILITY=BooleanWhen true code will check for readability on input files (this can be slow on cloud Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: access) Default value: true. This option can be set to 'null' to clear the default value. access) Default value: true. This option can be set to 'null' to clear the default value. Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Possible values: {true, false} Possible values: {true, false} Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCramsWithNoReference[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: REFERENCE must be provided when using CRAM as input. REFERENCE must be provided when using CRAM as input. Running Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:11 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0) STANDARD_ERROR INFO 2024-07-02 11:54:11 CrosscheckFingerprints Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting14346130945917200276NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY LIBRARY ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting14346130945917200276NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY LIBRARY Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:11.340 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:11.340 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:11.353 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:11.353 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:11.354 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:11.354 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:11.354 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:11.354 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:11.354 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:11.354 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:11.354 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:11.354 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:11 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] OUTPUT=/tmp/Fingerprinting14346130945917200276NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=LIBRARY CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:11 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] OUTPUT=/tmp/Fingerprinting14346130945917200276NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=LIBRARY CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:11 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:11 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:11 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:54:11 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:11 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:11 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:11 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:54:11 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:11 CrosscheckFingerprints Cross-checking all LIBRARY against each other INFO 2024-07-02 11:54:11 CrosscheckFingerprints Cross-checking all LIBRARY against each other Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:11 CrosscheckFingerprints All LIBRARYs are related as expected. INFO 2024-07-02 11:54:11 CrosscheckFingerprints All LIBRARYs are related as expected. Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:11 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:11 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:11 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0) STANDARD_ERROR INFO 2024-07-02 11:54:11 CrosscheckFingerprints Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -OUTPUT /tmp/Fingerprinting1357797695191740587NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY LIBRARY ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -OUTPUT /tmp/Fingerprinting1357797695191740587NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY LIBRARY Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:11.699 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:11.699 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:11.699 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:11.699 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:11.700 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:11.700 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:11.700 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:11.700 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:11.700 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:11.700 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:11.700 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:11.700 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:11 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] OUTPUT=/tmp/Fingerprinting1357797695191740587NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=LIBRARY CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:11 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] OUTPUT=/tmp/Fingerprinting1357797695191740587NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=LIBRARY CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:11 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:11 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:11 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:54:11 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:11 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:54:11 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:11 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:11 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:11 CrosscheckFingerprints Cross-checking all LIBRARY against each other INFO 2024-07-02 11:54:11 CrosscheckFingerprints Cross-checking all LIBRARY against each other Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:11 CrosscheckFingerprints All LIBRARYs are related as expected. INFO 2024-07-02 11:54:11 CrosscheckFingerprints All LIBRARYs are related as expected. Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:11 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:11 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:11 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0) STANDARD_ERROR INFO 2024-07-02 11:54:11 CrosscheckFingerprints Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting1806530368895715625NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY LIBRARY ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting1806530368895715625NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY LIBRARY Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:11.897 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:11.897 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:11.897 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:11.897 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:11.898 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:11.898 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:11.898 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:11.898 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:11.898 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:11.898 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:11.898 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:11.898 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:11 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] OUTPUT=/tmp/Fingerprinting1806530368895715625NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=LIBRARY CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:11 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] OUTPUT=/tmp/Fingerprinting1806530368895715625NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=LIBRARY CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:11 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:11 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:11 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:11 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:12 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:12 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:12 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:12 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:12 CrosscheckFingerprints Cross-checking all LIBRARY against each other INFO 2024-07-02 11:54:12 CrosscheckFingerprints Cross-checking all LIBRARY against each other Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:12 CrosscheckFingerprints All LIBRARYs are related as expected. INFO 2024-07-02 11:54:12 CrosscheckFingerprints All LIBRARYs are related as expected. Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:12 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:12 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:12 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0) STANDARD_ERROR INFO 2024-07-02 11:54:12 CrosscheckFingerprints Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -OUTPUT /tmp/Fingerprinting15902368598657743413NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY LIBRARY ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -OUTPUT /tmp/Fingerprinting15902368598657743413NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY LIBRARY Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:12.233 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:12.233 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:12.233 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:12.233 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:12.234 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:12.234 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:12.234 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:12.234 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:12.234 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:12.234 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:12.234 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:12.234 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:12 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam] OUTPUT=/tmp/Fingerprinting15902368598657743413NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=LIBRARY CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:12 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam] OUTPUT=/tmp/Fingerprinting15902368598657743413NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=LIBRARY CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:12 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:12 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:12 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:12 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:12 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:54:12 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:12 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:54:12 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:12 CrosscheckFingerprints Cross-checking all LIBRARY against each other INFO 2024-07-02 11:54:12 CrosscheckFingerprints Cross-checking all LIBRARY against each other Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:12 CrosscheckFingerprints All LIBRARYs are related as expected. INFO 2024-07-02 11:54:12 CrosscheckFingerprints All LIBRARYs are related as expected. Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:12 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:12 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:12 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1) STANDARD_ERROR INFO 2024-07-02 11:54:12 CrosscheckFingerprints Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam -OUTPUT /tmp/Fingerprinting15387842720564692159NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY LIBRARY ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam -OUTPUT /tmp/Fingerprinting15387842720564692159NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY LIBRARY Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:12.601 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:12.601 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:12.601 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:12.601 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:12.602 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:12.602 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:12.602 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:12.602 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:12.602 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:12.602 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:12.602 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:12.602 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:12 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam] OUTPUT=/tmp/Fingerprinting15387842720564692159NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=LIBRARY CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:12 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam] OUTPUT=/tmp/Fingerprinting15387842720564692159NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=LIBRARY CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:12 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:12 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:12 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:54:12 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:12 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam) WARNING 2024-07-02 11:54:12 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam) Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:12 FingerprintChecker Processed files. 54 fingerprints found in map. INFO 2024-07-02 11:54:12 FingerprintChecker Processed files. 54 fingerprints found in map. Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:12 CrosscheckFingerprints Cross-checking all LIBRARY against each other INFO 2024-07-02 11:54:12 CrosscheckFingerprints Cross-checking all LIBRARY against each other Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:12 CrosscheckFingerprints 2 LIBRARYs did not relate as expected. WARNING 2024-07-02 11:54:12 CrosscheckFingerprints 2 LIBRARYs did not relate as expected. Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:12 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:12 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:12 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1) STANDARD_ERROR INFO 2024-07-02 11:54:12 CrosscheckFingerprints Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam -OUTPUT /tmp/Fingerprinting4523394870730424661NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY LIBRARY ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam -OUTPUT /tmp/Fingerprinting4523394870730424661NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY LIBRARY Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:12.794 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:12.794 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:12.795 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:12.795 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:12.795 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:12.795 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:12.795 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:12.795 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:12.796 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:12.796 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:12.796 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:12.796 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:12 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam] OUTPUT=/tmp/Fingerprinting4523394870730424661NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=LIBRARY CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:12 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam] OUTPUT=/tmp/Fingerprinting4523394870730424661NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=LIBRARY CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:12 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:12 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:12 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:54:12 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:12 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam) WARNING 2024-07-02 11:54:12 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam) Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:13 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:13 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:13 CrosscheckFingerprints Cross-checking all LIBRARY against each other INFO 2024-07-02 11:54:13 CrosscheckFingerprints Cross-checking all LIBRARY against each other Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:13 CrosscheckFingerprints 2 LIBRARYs did not relate as expected. WARNING 2024-07-02 11:54:13 CrosscheckFingerprints 2 LIBRARYs did not relate as expected. Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:13 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:13 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:13 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1) STANDARD_ERROR INFO 2024-07-02 11:54:13 CrosscheckFingerprints Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam -OUTPUT /tmp/Fingerprinting7470208829591894781NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY LIBRARY ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam -OUTPUT /tmp/Fingerprinting7470208829591894781NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY LIBRARY Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:13.083 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:13.083 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:13.083 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:13.083 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:13.084 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:13.084 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:13.084 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:13.084 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:13.084 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:13.084 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:13.084 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:13.084 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:13 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam] OUTPUT=/tmp/Fingerprinting7470208829591894781NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=LIBRARY CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:13 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam] OUTPUT=/tmp/Fingerprinting7470208829591894781NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=LIBRARY CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:13 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:13 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:13 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:13 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:13 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam) WARNING 2024-07-02 11:54:13 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam) Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:13 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:54:13 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:13 CrosscheckFingerprints Cross-checking all LIBRARY against each other INFO 2024-07-02 11:54:13 CrosscheckFingerprints Cross-checking all LIBRARY against each other Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:13 CrosscheckFingerprints 2 LIBRARYs did not relate as expected. WARNING 2024-07-02 11:54:13 CrosscheckFingerprints 2 LIBRARYs did not relate as expected. Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:13 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:13 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:13 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1) STANDARD_ERROR INFO 2024-07-02 11:54:13 CrosscheckFingerprints Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam -OUTPUT /tmp/Fingerprinting5441755446553675230NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY LIBRARY ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam -OUTPUT /tmp/Fingerprinting5441755446553675230NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY LIBRARY Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:13.545 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:13.545 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:13.545 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:13.545 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:13.546 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:13.546 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:13.546 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:13.546 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:13.546 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:13.546 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:13.546 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:13.546 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:13 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam] OUTPUT=/tmp/Fingerprinting5441755446553675230NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=LIBRARY CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:13 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam] OUTPUT=/tmp/Fingerprinting5441755446553675230NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=LIBRARY CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:13 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:13 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:13 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:13 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:13 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam) WARNING 2024-07-02 11:54:13 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam) Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:13 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:54:13 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:13 CrosscheckFingerprints Cross-checking all LIBRARY against each other INFO 2024-07-02 11:54:13 CrosscheckFingerprints Cross-checking all LIBRARY against each other Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:13 CrosscheckFingerprints 2 LIBRARYs did not relate as expected. WARNING 2024-07-02 11:54:13 CrosscheckFingerprints 2 LIBRARYs did not relate as expected. Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:13 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:13 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:13 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckLBsWithClustering STANDARD_ERROR INFO 2024-07-02 11:54:13 CrosscheckFingerprints Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam -OUTPUT /tmp/Fingerprinting1041117802709868608NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY LIBRARY ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam -OUTPUT /tmp/Fingerprinting1041117802709868608NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY LIBRARY Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:13.920 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:13.920 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:13.920 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:13.920 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:13.920 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:13.920 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:13.920 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:13.920 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:13.921 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:13.921 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:13.921 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:13.921 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:13 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam] OUTPUT=/tmp/Fingerprinting1041117802709868608NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=LIBRARY CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:13 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam] OUTPUT=/tmp/Fingerprinting1041117802709868608NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=LIBRARY CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:13 CrosscheckFingerprints Fingerprinting 5 INPUT files. INFO 2024-07-02 11:54:13 CrosscheckFingerprints Fingerprinting 5 INPUT files. Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:13 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:54:13 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:14 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:14 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:14 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:54:14 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:14 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:14 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:14 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam) WARNING 2024-07-02 11:54:14 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam) Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:14 FingerprintChecker Processed files. 131 fingerprints found in map. INFO 2024-07-02 11:54:14 FingerprintChecker Processed files. 131 fingerprints found in map. Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:14 CrosscheckFingerprints Cross-checking all LIBRARY against each other INFO 2024-07-02 11:54:14 CrosscheckFingerprints Cross-checking all LIBRARY against each other Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:14 CrosscheckFingerprints 8 LIBRARYs did not relate as expected. WARNING 2024-07-02 11:54:14 CrosscheckFingerprints 8 LIBRARYs did not relate as expected. Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:14 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:54:14 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.02 minutes. Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:14 ClusterCrosscheckMetrics INFO 2024-07-02 11:54:14 ClusterCrosscheckMetrics Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ClusterCrosscheckMetrics -INPUT /tmp/Fingerprinting1041117802709868608NA1291.LB.crosscheck_metrics -OUTPUT /tmp/Fingerprinting10677358490634596430NA1291.LB.crosscheck_cluster_metrics -LOD_THRESHOLD 1.0 ********** ClusterCrosscheckMetrics -INPUT /tmp/Fingerprinting1041117802709868608NA1291.LB.crosscheck_metrics -OUTPUT /tmp/Fingerprinting10677358490634596430NA1291.LB.crosscheck_cluster_metrics -LOD_THRESHOLD 1.0 Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:14.997 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:14.997 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:14.997 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:14.997 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:14.998 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:14.998 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:14.998 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:14.998 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:14 GMT+14:00 2024] ClusterCrosscheckMetrics INPUT=/tmp/Fingerprinting1041117802709868608NA1291.LB.crosscheck_metrics OUTPUT=/tmp/Fingerprinting10677358490634596430NA1291.LB.crosscheck_cluster_metrics LOD_THRESHOLD=1.0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:14 GMT+14:00 2024] ClusterCrosscheckMetrics INPUT=/tmp/Fingerprinting1041117802709868608NA1291.LB.crosscheck_metrics OUTPUT=/tmp/Fingerprinting10677358490634596430NA1291.LB.crosscheck_cluster_metrics LOD_THRESHOLD=1.0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:15 GMT+14:00 2024] picard.fingerprint.ClusterCrosscheckMetrics done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:15 GMT+14:00 2024] picard.fingerprint.ClusterCrosscheckMetrics done. Elapsed time: 0.00 minutes. Test: Test method testCrossCheckLBsWithClustering(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:15 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809) STANDARD_ERROR INFO 2024-07-02 11:54:15 CrosscheckFingerprints Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting4135752779271139811NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting4135752779271139811NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:15.037 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:15.037 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:15.038 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:15.038 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:15.039 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:15.039 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:15.039 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:15.039 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:15.039 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:15.039 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:15.039 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:15.039 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:15 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] OUTPUT=/tmp/Fingerprinting4135752779271139811NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:15 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] OUTPUT=/tmp/Fingerprinting4135752779271139811NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:15 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:15 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:15 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:54:15 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:15 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:15 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:15 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:54:15 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:15 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:15 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:15 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:15 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:15 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:15 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:15 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704) STANDARD_ERROR INFO 2024-07-02 11:54:15 CrosscheckFingerprints Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -OUTPUT /tmp/Fingerprinting2745320298605516055NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -OUTPUT /tmp/Fingerprinting2745320298605516055NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:15.898 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:15.898 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:15.898 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:15.898 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:15.899 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:15.899 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:15.899 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:15.899 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:15.899 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:15.899 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:15.899 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:15.899 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:15 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] OUTPUT=/tmp/Fingerprinting2745320298605516055NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:15 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] OUTPUT=/tmp/Fingerprinting2745320298605516055NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:15 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:15 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:15 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:54:15 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:16 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:54:16 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:16 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:16 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:16 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:16 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:16 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:16 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:16 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:16 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:16 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809) STANDARD_ERROR INFO 2024-07-02 11:54:16 CrosscheckFingerprints Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting1119210160292842143NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting1119210160292842143NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:16.857 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:16.857 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:16.858 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:16.858 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:16.859 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:16.859 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:16.859 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:16.859 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:16.859 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:16.859 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:16.859 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:16.859 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:16 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] OUTPUT=/tmp/Fingerprinting1119210160292842143NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:16 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] OUTPUT=/tmp/Fingerprinting1119210160292842143NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:16 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:16 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:16 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:54:16 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:17 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:17 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:17 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:54:17 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:17 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:17 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:17 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:17 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:17 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:17 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:17 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601) STANDARD_ERROR INFO 2024-07-02 11:54:17 CrosscheckFingerprints Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting15107206285597111742NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting15107206285597111742NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:17.605 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:17.605 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:17.605 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:17.605 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:17.606 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:17.606 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:17.606 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:17.606 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:17.606 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:17.606 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:17.607 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:17.607 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:17 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] OUTPUT=/tmp/Fingerprinting15107206285597111742NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:17 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] OUTPUT=/tmp/Fingerprinting15107206285597111742NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:17 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:17 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:17 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:54:17 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:17 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:17 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:18 FingerprintChecker Processed files. 51 fingerprints found in map. INFO 2024-07-02 11:54:18 FingerprintChecker Processed files. 51 fingerprints found in map. Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:18 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:18 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:18 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:18 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:18 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:18 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:18 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704) STANDARD_ERROR INFO 2024-07-02 11:54:18 CrosscheckFingerprints Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting18430587534424630604NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting18430587534424630604NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:18.473 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:18.473 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:18.474 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:18.474 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:18.475 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:18.475 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:18.475 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:18.475 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:18.475 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:18.475 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:18.475 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:18.475 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:18 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] OUTPUT=/tmp/Fingerprinting18430587534424630604NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:18 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] OUTPUT=/tmp/Fingerprinting18430587534424630604NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:18 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:18 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:18 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:18 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:18 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:18 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:18 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:18 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:18 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:18 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:19 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:19 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:19 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:19 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:19 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809) STANDARD_ERROR INFO 2024-07-02 11:54:19 CrosscheckFingerprints Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -OUTPUT /tmp/Fingerprinting10572567531387891046NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -OUTPUT /tmp/Fingerprinting10572567531387891046NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:19.276 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:19.276 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:19.289 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:19.289 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:19.291 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:19.291 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:19.291 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:19.291 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:19.291 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:19.291 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:19.291 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:19.291 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:19 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam] OUTPUT=/tmp/Fingerprinting10572567531387891046NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:19 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam] OUTPUT=/tmp/Fingerprinting10572567531387891046NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:19 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:19 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:19 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:19 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:19 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:54:19 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:19 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:54:19 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:19 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:19 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:20 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:20 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:20 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:20 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:20 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809) STANDARD_ERROR INFO 2024-07-02 11:54:20 CrosscheckFingerprints Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting3626642124451938789NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting3626642124451938789NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:20.104 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:20.104 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:20.104 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:20.104 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:20.117 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:20.117 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:20.117 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:20.117 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:20.117 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:20.117 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:20.117 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:20.117 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:20 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] OUTPUT=/tmp/Fingerprinting3626642124451938789NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:20 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] OUTPUT=/tmp/Fingerprinting3626642124451938789NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:20 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:20 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:20 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:54:20 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:20 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:20 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:20 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:54:20 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:20 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:20 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:21 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:21 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:21 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:54:21 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.02 minutes. Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:21 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704) STANDARD_ERROR INFO 2024-07-02 11:54:21 CrosscheckFingerprints Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -OUTPUT /tmp/Fingerprinting4205610478522179028NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -OUTPUT /tmp/Fingerprinting4205610478522179028NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:21.143 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:21.143 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:21.143 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:21.143 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:21.144 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:21.144 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:21.144 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:21.144 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:21.161 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:21.161 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:21.161 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:21.161 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:21 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] OUTPUT=/tmp/Fingerprinting4205610478522179028NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:21 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] OUTPUT=/tmp/Fingerprinting4205610478522179028NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:21 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:21 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:21 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:54:21 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:21 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:54:21 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:21 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:21 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:21 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:21 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:21 CrosscheckFingerprints 84 READGROUPs did not relate as expected. WARNING 2024-07-02 11:54:21 CrosscheckFingerprints 84 READGROUPs did not relate as expected. Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:21 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:21 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:21 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809) STANDARD_ERROR INFO 2024-07-02 11:54:21 CrosscheckFingerprints Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting3291511737587820926NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting3291511737587820926NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:21.878 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:21.878 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:21.878 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:21.878 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:21.879 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:21.879 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:21.879 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:21.879 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:21.880 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:21.880 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:21.880 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:21.880 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:21 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] OUTPUT=/tmp/Fingerprinting3291511737587820926NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:21 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] OUTPUT=/tmp/Fingerprinting3291511737587820926NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:21 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:21 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:21 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:54:21 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:22 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:22 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:22 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:54:22 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:22 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:22 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:22 CrosscheckFingerprints 138 READGROUPs did not relate as expected. WARNING 2024-07-02 11:54:22 CrosscheckFingerprints 138 READGROUPs did not relate as expected. Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:22 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:54:22 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.02 minutes. Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:22 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601) STANDARD_ERROR INFO 2024-07-02 11:54:22 CrosscheckFingerprints Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting12419958132644849885NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting12419958132644849885NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:22.898 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:22.898 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:22.899 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:22.899 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:22.899 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:22.899 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:22.899 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:22.899 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:22.900 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:22.900 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:22.900 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:22.900 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:22 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] OUTPUT=/tmp/Fingerprinting12419958132644849885NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:22 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] OUTPUT=/tmp/Fingerprinting12419958132644849885NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:22 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:22 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:22 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:54:22 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:23 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:23 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:23 FingerprintChecker Processed files. 51 fingerprints found in map. INFO 2024-07-02 11:54:23 FingerprintChecker Processed files. 51 fingerprints found in map. Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:23 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:23 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:23 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:23 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:23 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:23 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:23 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704) STANDARD_ERROR INFO 2024-07-02 11:54:23 CrosscheckFingerprints Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting8689316607659387399NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting8689316607659387399NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:23.735 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:23.735 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:23.735 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:23.735 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:23.736 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:23.736 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:23.736 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:23.736 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:23.745 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:23.745 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:23.745 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:23.745 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:23 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] OUTPUT=/tmp/Fingerprinting8689316607659387399NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:23 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] OUTPUT=/tmp/Fingerprinting8689316607659387399NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:23 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:23 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:23 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:23 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:23 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:23 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:24 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:24 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:24 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:24 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:24 CrosscheckFingerprints 188 READGROUPs did not relate as expected. WARNING 2024-07-02 11:54:24 CrosscheckFingerprints 188 READGROUPs did not relate as expected. Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:24 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:24 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:24 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809) STANDARD_ERROR INFO 2024-07-02 11:54:24 CrosscheckFingerprints Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -OUTPUT /tmp/Fingerprinting16149476611218268262NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -OUTPUT /tmp/Fingerprinting16149476611218268262NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:24.511 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:24.511 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:24.511 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:24.511 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:24.512 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:24.512 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:24.512 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:24.512 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:24.512 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:24.512 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:24.512 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:24.512 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:24 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam] OUTPUT=/tmp/Fingerprinting16149476611218268262NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:24 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam] OUTPUT=/tmp/Fingerprinting16149476611218268262NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:24 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:24 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:24 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:24 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:24 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:54:24 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:24 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:54:24 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:24 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:24 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:25 CrosscheckFingerprints 138 READGROUPs did not relate as expected. WARNING 2024-07-02 11:54:25 CrosscheckFingerprints 138 READGROUPs did not relate as expected. Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:25 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:25 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:25 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809) STANDARD_ERROR INFO 2024-07-02 11:54:25 CrosscheckFingerprints Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram -OUTPUT /tmp/Fingerprinting6777070022881335978NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram -OUTPUT /tmp/Fingerprinting6777070022881335978NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:25.206 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:25.206 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:25.206 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:25.206 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:25.207 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:25.207 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:25.207 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:25.207 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:25.207 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:25.207 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:25.207 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:25.207 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:25 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram] OUTPUT=/tmp/Fingerprinting6777070022881335978NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:25 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram] OUTPUT=/tmp/Fingerprinting6777070022881335978NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:25 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:25 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:25 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram) INFO 2024-07-02 11:54:25 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram) Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:25 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram) INFO 2024-07-02 11:54:25 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram) Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:25 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:54:25 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:25 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:25 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:25 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:25 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:25 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:25 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[12](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:26 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704) STANDARD_ERROR INFO 2024-07-02 11:54:26 CrosscheckFingerprints Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram -OUTPUT /tmp/Fingerprinting10069496394508356524NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram -OUTPUT /tmp/Fingerprinting10069496394508356524NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:26.012 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:26.012 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:26.012 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:26.012 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:26.025 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:26.025 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:26.025 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:26.025 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:26.026 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:26.026 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:26.026 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:26.026 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:26 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram] OUTPUT=/tmp/Fingerprinting10069496394508356524NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:26 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram] OUTPUT=/tmp/Fingerprinting10069496394508356524NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:26 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:26 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:26 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram) INFO 2024-07-02 11:54:26 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram) Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:26 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram) INFO 2024-07-02 11:54:26 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram) Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:26 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:26 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:26 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:26 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:26 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:26 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:26 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:26 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[13](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:26 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809) STANDARD_ERROR INFO 2024-07-02 11:54:26 CrosscheckFingerprints Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram -OUTPUT /tmp/Fingerprinting7855487513243041377NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram -OUTPUT /tmp/Fingerprinting7855487513243041377NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:26.741 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:26.741 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:26.742 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:26.742 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:26.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:26.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:26.743 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:26.743 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:26.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:26.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:26.743 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:26.743 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:26 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram] OUTPUT=/tmp/Fingerprinting7855487513243041377NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:26 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram] OUTPUT=/tmp/Fingerprinting7855487513243041377NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:26 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:26 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:26 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram) INFO 2024-07-02 11:54:26 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram) Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:26 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram) INFO 2024-07-02 11:54:26 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram) Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:27 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:54:27 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:27 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:27 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:27 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:27 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:27 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:27 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[14](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1156579328 Runtime.totalMemory()=1156579328 Running Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:27 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601) STANDARD_ERROR INFO 2024-07-02 11:54:27 CrosscheckFingerprints Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram -OUTPUT /tmp/Fingerprinting7574743987400942831NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram -OUTPUT /tmp/Fingerprinting7574743987400942831NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:27.381 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:27.381 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:27.381 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:27.381 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:27.390 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:27.390 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:27.390 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:27.390 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:27.390 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:27.390 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:27.390 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:27.390 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:27 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram] OUTPUT=/tmp/Fingerprinting7574743987400942831NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:27 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram] OUTPUT=/tmp/Fingerprinting7574743987400942831NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:27 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:27 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:27 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram) INFO 2024-07-02 11:54:27 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram) Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:27 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram) INFO 2024-07-02 11:54:27 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram) Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:27 FingerprintChecker Processed files. 51 fingerprints found in map. INFO 2024-07-02 11:54:27 FingerprintChecker Processed files. 51 fingerprints found in map. Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:27 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:27 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:28 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:28 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:28 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:28 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[15](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, false, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:28 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704) STANDARD_ERROR INFO 2024-07-02 11:54:28 CrosscheckFingerprints Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram -OUTPUT /tmp/Fingerprinting11008585181657253947NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram -OUTPUT /tmp/Fingerprinting11008585181657253947NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:28.165 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:28.165 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:28.165 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:28.165 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:28.166 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:28.166 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:28.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:28.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:28.166 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:28.166 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:28.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:28.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:28 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram] OUTPUT=/tmp/Fingerprinting11008585181657253947NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:28 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram] OUTPUT=/tmp/Fingerprinting11008585181657253947NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:28 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:28 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:28 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram) INFO 2024-07-02 11:54:28 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram) Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:28 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram) INFO 2024-07-02 11:54:28 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram) Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:28 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:28 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:28 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:28 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:28 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:28 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:28 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:28 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[16](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, false, 0, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:28 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809) STANDARD_ERROR INFO 2024-07-02 11:54:28 CrosscheckFingerprints Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram -OUTPUT /tmp/Fingerprinting11720756851553771524NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram -OUTPUT /tmp/Fingerprinting11720756851553771524NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:28.812 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:28.812 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:28.812 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:28.812 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:28.829 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:28.829 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:28.829 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:28.829 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:28.829 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:28.829 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:28.829 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:28.829 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:28 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram] OUTPUT=/tmp/Fingerprinting11720756851553771524NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:28 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram] OUTPUT=/tmp/Fingerprinting11720756851553771524NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:28 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:28 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:28 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram) INFO 2024-07-02 11:54:28 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram) Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:29 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram) INFO 2024-07-02 11:54:29 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram) Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:29 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:54:29 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:29 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:29 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:29 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:29 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:29 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:29 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[17](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, false, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:29 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809) STANDARD_ERROR INFO 2024-07-02 11:54:29 CrosscheckFingerprints Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram -OUTPUT /tmp/Fingerprinting3218927207780872000NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram -OUTPUT /tmp/Fingerprinting3218927207780872000NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:29.671 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:29.671 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:29.671 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:29.671 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:29.672 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:29.672 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:29.672 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:29.672 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:29.672 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:29.672 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:29.672 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:29.672 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:29 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram] OUTPUT=/tmp/Fingerprinting3218927207780872000NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:29 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram] OUTPUT=/tmp/Fingerprinting3218927207780872000NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:29 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:29 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:29 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram) INFO 2024-07-02 11:54:29 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram) Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:29 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram) INFO 2024-07-02 11:54:29 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram) Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:30 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:54:30 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:30 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:30 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:30 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:30 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:30 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:30 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[18](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 0, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:30 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704) STANDARD_ERROR INFO 2024-07-02 11:54:30 CrosscheckFingerprints Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram -OUTPUT /tmp/Fingerprinting5040033134904301573NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram -OUTPUT /tmp/Fingerprinting5040033134904301573NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:30.364 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:30.364 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:30.364 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:30.364 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:30.377 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:30.377 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:30.377 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:30.377 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:30.378 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:30.378 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:30.378 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:30.378 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:30 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram] OUTPUT=/tmp/Fingerprinting5040033134904301573NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:30 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram] OUTPUT=/tmp/Fingerprinting5040033134904301573NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:30 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:30 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:30 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram) INFO 2024-07-02 11:54:30 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram) Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:30 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram) INFO 2024-07-02 11:54:30 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram) Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:30 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:30 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:30 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:30 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:31 CrosscheckFingerprints 58 READGROUPs did not relate as expected. WARNING 2024-07-02 11:54:31 CrosscheckFingerprints 58 READGROUPs did not relate as expected. Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:31 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:31 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testCrossCheckRGs[19](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:31 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809) STANDARD_ERROR INFO 2024-07-02 11:54:31 CrosscheckFingerprints Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram -OUTPUT /tmp/Fingerprinting13454752286220179829NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram -OUTPUT /tmp/Fingerprinting13454752286220179829NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:31.119 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:31.119 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:31.119 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:31.119 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:31.120 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:31.120 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:31.120 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:31.120 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:31.120 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:31.120 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:31.120 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:31.120 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:31 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram] OUTPUT=/tmp/Fingerprinting13454752286220179829NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:31 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram] OUTPUT=/tmp/Fingerprinting13454752286220179829NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:31 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:31 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:31 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram) INFO 2024-07-02 11:54:31 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram) Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:31 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram) INFO 2024-07-02 11:54:31 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram) Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:31 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:54:31 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:31 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:31 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:31 CrosscheckFingerprints 48 READGROUPs did not relate as expected. WARNING 2024-07-02 11:54:31 CrosscheckFingerprints 48 READGROUPs did not relate as expected. Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:31 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:31 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testCrossCheckRGs[20](/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:31 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601) STANDARD_ERROR INFO 2024-07-02 11:54:31 CrosscheckFingerprints Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram -OUTPUT /tmp/Fingerprinting106313188000924768NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram -OUTPUT /tmp/Fingerprinting106313188000924768NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:31.886 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:31.886 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:31.886 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:31.886 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:31.887 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:31.887 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:31.887 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:31.887 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:31.888 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:31.888 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:31.888 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:31.888 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:31 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram] OUTPUT=/tmp/Fingerprinting106313188000924768NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:31 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram] OUTPUT=/tmp/Fingerprinting106313188000924768NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:31 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:31 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:31 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram) INFO 2024-07-02 11:54:31 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram) Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:32 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram) INFO 2024-07-02 11:54:32 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram) Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:32 FingerprintChecker Processed files. 51 fingerprints found in map. INFO 2024-07-02 11:54:32 FingerprintChecker Processed files. 51 fingerprints found in map. Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:32 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:32 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:32 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:32 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:32 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:32 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[21](/tmp/NA12892.over.fingerprints.shifted.for.crams.r1.sam3074662964578609585.cram, /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, true, 0, 2601)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:32 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704) STANDARD_ERROR INFO 2024-07-02 11:54:32 CrosscheckFingerprints Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram -OUTPUT /tmp/Fingerprinting13638386766310062960NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram -OUTPUT /tmp/Fingerprinting13638386766310062960NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:32.484 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:32.484 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:32.484 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:32.484 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:32.493 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:32.493 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:32.493 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:32.493 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:32.493 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:32.493 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:32.493 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:32.493 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:32 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram] OUTPUT=/tmp/Fingerprinting13638386766310062960NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:32 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram] OUTPUT=/tmp/Fingerprinting13638386766310062960NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:32 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:32 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:32 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram) INFO 2024-07-02 11:54:32 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram) Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:32 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram) INFO 2024-07-02 11:54:32 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram) Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:32 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:32 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:32 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:32 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:33 CrosscheckFingerprints 8 READGROUPs did not relate as expected. WARNING 2024-07-02 11:54:33 CrosscheckFingerprints 8 READGROUPs did not relate as expected. Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:33 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:33 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testCrossCheckRGs[22](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r2.sam5389701079788216421.cram, true, 1, 2704)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:33 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809) STANDARD_ERROR INFO 2024-07-02 11:54:33 CrosscheckFingerprints Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram -OUTPUT /tmp/Fingerprinting10450604895871429256NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram -INPUT /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram -OUTPUT /tmp/Fingerprinting10450604895871429256NA1291.RG.crosscheck_metrics -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true -R testdata/picard/fingerprint/reference.shifted.for.crams.fasta -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:33.243 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:33.243 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:33.243 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:33.243 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:33.244 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:33.244 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:33.244 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:33.244 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:33.244 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:33.244 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:33.244 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:33.244 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:33 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram] OUTPUT=/tmp/Fingerprinting10450604895871429256NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:33 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram] OUTPUT=/tmp/Fingerprinting10450604895871429256NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true REFERENCE_SEQUENCE=testdata/picard/fingerprint/reference.shifted.for.crams.fasta CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:33 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:33 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:33 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram) INFO 2024-07-02 11:54:33 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram) Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:33 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram) INFO 2024-07-02 11:54:33 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram) Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:33 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:54:33 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:33 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:33 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:34 CrosscheckFingerprints 48 READGROUPs did not relate as expected. WARNING 2024-07-02 11:54:34 CrosscheckFingerprints 48 READGROUPs did not relate as expected. Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:34 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:34 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testCrossCheckRGs[23](/tmp/NA12892.over.fingerprints.shifted.for.crams.r2.sam9879606734653187445.cram, /tmp/NA12891.over.fingerprints.shifted.for.crams.r1.sam14952068365858854983.cram, true, 1, 2809)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:34 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1) STANDARD_ERROR INFO 2024-07-02 11:54:34 CrosscheckFingerprints Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting6754353948512383656NA1291.SM.crosscheck_metrics -MATRIX_OUTPUT /tmp/Fingerprinting15868514083006415924NA1291.SM.matrix -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting6754353948512383656NA1291.SM.crosscheck_metrics -MATRIX_OUTPUT /tmp/Fingerprinting15868514083006415924NA1291.SM.matrix -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:34.142 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:34.142 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:34.143 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:34.143 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:34.144 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:34.144 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:34.144 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:34.144 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:34.144 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:34.144 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:34.144 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:34.144 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:34 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] OUTPUT=/tmp/Fingerprinting6754353948512383656NA1291.SM.crosscheck_metrics MATRIX_OUTPUT=/tmp/Fingerprinting15868514083006415924NA1291.SM.matrix HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:34 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] OUTPUT=/tmp/Fingerprinting6754353948512383656NA1291.SM.crosscheck_metrics MATRIX_OUTPUT=/tmp/Fingerprinting15868514083006415924NA1291.SM.matrix HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:34 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:34 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:34 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:54:34 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:34 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:34 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:34 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:54:34 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:34 CrosscheckFingerprints Cross-checking all SAMPLE against each other INFO 2024-07-02 11:54:34 CrosscheckFingerprints Cross-checking all SAMPLE against each other Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:34 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:54:34 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:34 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:34 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:34 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2) STANDARD_ERROR INFO 2024-07-02 11:54:34 CrosscheckFingerprints Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -OUTPUT /tmp/Fingerprinting9115048440789874558NA1291.SM.crosscheck_metrics -MATRIX_OUTPUT /tmp/Fingerprinting15575978301540494744NA1291.SM.matrix -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -OUTPUT /tmp/Fingerprinting9115048440789874558NA1291.SM.crosscheck_metrics -MATRIX_OUTPUT /tmp/Fingerprinting15575978301540494744NA1291.SM.matrix -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:34.607 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:34.607 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:34.607 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:34.607 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:34.608 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:34.608 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:34.608 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:34.608 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:34.608 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:34.608 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:34.608 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:34.608 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:34 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] OUTPUT=/tmp/Fingerprinting9115048440789874558NA1291.SM.crosscheck_metrics MATRIX_OUTPUT=/tmp/Fingerprinting15575978301540494744NA1291.SM.matrix HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:34 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] OUTPUT=/tmp/Fingerprinting9115048440789874558NA1291.SM.crosscheck_metrics MATRIX_OUTPUT=/tmp/Fingerprinting15575978301540494744NA1291.SM.matrix HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:34 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:34 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:34 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:54:34 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:34 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:54:34 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:35 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:35 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:35 CrosscheckFingerprints Cross-checking all SAMPLE against each other INFO 2024-07-02 11:54:35 CrosscheckFingerprints Cross-checking all SAMPLE against each other Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:35 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:54:35 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:35 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:35 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:35 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2) STANDARD_ERROR INFO 2024-07-02 11:54:35 CrosscheckFingerprints Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting1864743071117463600NA1291.SM.crosscheck_metrics -MATRIX_OUTPUT /tmp/Fingerprinting13571253591690245018NA1291.SM.matrix -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting1864743071117463600NA1291.SM.crosscheck_metrics -MATRIX_OUTPUT /tmp/Fingerprinting13571253591690245018NA1291.SM.matrix -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:35.043 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:35.043 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:35.043 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:35.043 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:35.044 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:35.044 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:35.044 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:35.044 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:35.044 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:35.044 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:35.044 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:35.044 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:35 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] OUTPUT=/tmp/Fingerprinting1864743071117463600NA1291.SM.crosscheck_metrics MATRIX_OUTPUT=/tmp/Fingerprinting13571253591690245018NA1291.SM.matrix HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:35 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] OUTPUT=/tmp/Fingerprinting1864743071117463600NA1291.SM.crosscheck_metrics MATRIX_OUTPUT=/tmp/Fingerprinting13571253591690245018NA1291.SM.matrix HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:35 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:35 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:35 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:35 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:35 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:35 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:35 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:35 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:35 CrosscheckFingerprints Cross-checking all SAMPLE against each other INFO 2024-07-02 11:54:35 CrosscheckFingerprints Cross-checking all SAMPLE against each other Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:35 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:54:35 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:35 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:35 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:35 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1) STANDARD_ERROR INFO 2024-07-02 11:54:35 CrosscheckFingerprints Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting14356595526502015901NA1291.SM.crosscheck_metrics -MATRIX_OUTPUT /tmp/Fingerprinting11637166813018567224NA1291.SM.matrix -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting14356595526502015901NA1291.SM.crosscheck_metrics -MATRIX_OUTPUT /tmp/Fingerprinting11637166813018567224NA1291.SM.matrix -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:35.387 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:35.387 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:35.387 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:35.387 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:35.388 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:35.388 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:35.388 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:35.388 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:35.388 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:35.388 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:35.389 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:35.389 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:35 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] OUTPUT=/tmp/Fingerprinting14356595526502015901NA1291.SM.crosscheck_metrics MATRIX_OUTPUT=/tmp/Fingerprinting11637166813018567224NA1291.SM.matrix HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:35 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] OUTPUT=/tmp/Fingerprinting14356595526502015901NA1291.SM.crosscheck_metrics MATRIX_OUTPUT=/tmp/Fingerprinting11637166813018567224NA1291.SM.matrix HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:35 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:35 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:35 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:35 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:35 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:54:35 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:35 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:54:35 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:35 CrosscheckFingerprints Cross-checking all SAMPLE against each other INFO 2024-07-02 11:54:35 CrosscheckFingerprints Cross-checking all SAMPLE against each other Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:35 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:54:35 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:35 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:35 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:35 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2) STANDARD_ERROR INFO 2024-07-02 11:54:35 CrosscheckFingerprints Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting3968243170266504788NA1291.SM.crosscheck_metrics -MATRIX_OUTPUT /tmp/Fingerprinting7320728999252183885NA1291.SM.matrix -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting3968243170266504788NA1291.SM.crosscheck_metrics -MATRIX_OUTPUT /tmp/Fingerprinting7320728999252183885NA1291.SM.matrix -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:35.956 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:35.956 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:35.956 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:35.956 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:35.969 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:35.969 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:35.969 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:35.969 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:35.970 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:35.970 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:35.970 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:35.970 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:35 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] OUTPUT=/tmp/Fingerprinting3968243170266504788NA1291.SM.crosscheck_metrics MATRIX_OUTPUT=/tmp/Fingerprinting7320728999252183885NA1291.SM.matrix HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:35 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] OUTPUT=/tmp/Fingerprinting3968243170266504788NA1291.SM.crosscheck_metrics MATRIX_OUTPUT=/tmp/Fingerprinting7320728999252183885NA1291.SM.matrix HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:35 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:35 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:35 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:35 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:36 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:54:36 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:36 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:54:36 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:36 CrosscheckFingerprints Cross-checking all SAMPLE against each other INFO 2024-07-02 11:54:36 CrosscheckFingerprints Cross-checking all SAMPLE against each other Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:36 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:54:36 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:36 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:36 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:36 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1) STANDARD_ERROR INFO 2024-07-02 11:54:36 CrosscheckFingerprints Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting15604347298782162127NA1291.SM.crosscheck_metrics -MATRIX_OUTPUT /tmp/Fingerprinting2402171088438542914NA1291.SM.matrix -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting15604347298782162127NA1291.SM.crosscheck_metrics -MATRIX_OUTPUT /tmp/Fingerprinting2402171088438542914NA1291.SM.matrix -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:36.287 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:36.287 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:36.287 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:36.287 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:36.288 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:36.288 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:36.288 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:36.288 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:36.288 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:36.288 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:36.288 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:36.288 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:36 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] OUTPUT=/tmp/Fingerprinting15604347298782162127NA1291.SM.crosscheck_metrics MATRIX_OUTPUT=/tmp/Fingerprinting2402171088438542914NA1291.SM.matrix HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:36 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] OUTPUT=/tmp/Fingerprinting15604347298782162127NA1291.SM.crosscheck_metrics MATRIX_OUTPUT=/tmp/Fingerprinting2402171088438542914NA1291.SM.matrix HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:36 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:36 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:36 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:54:36 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:36 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:54:36 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:36 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:36 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:36 CrosscheckFingerprints Cross-checking all SAMPLE against each other INFO 2024-07-02 11:54:36 CrosscheckFingerprints Cross-checking all SAMPLE against each other Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:36 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:54:36 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:36 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:36 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 0, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:36 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2) STANDARD_ERROR INFO 2024-07-02 11:54:36 CrosscheckFingerprints Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting9898840982703227381NA1291.SM.crosscheck_metrics -MATRIX_OUTPUT /tmp/Fingerprinting12520204583001672919NA1291.SM.matrix -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting9898840982703227381NA1291.SM.crosscheck_metrics -MATRIX_OUTPUT /tmp/Fingerprinting12520204583001672919NA1291.SM.matrix -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:36.864 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:36.864 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:36.864 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:36.864 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:36.873 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:36.873 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:36.873 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:36.873 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:36.873 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:36.873 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:36.874 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:36.874 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:36 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] OUTPUT=/tmp/Fingerprinting9898840982703227381NA1291.SM.crosscheck_metrics MATRIX_OUTPUT=/tmp/Fingerprinting12520204583001672919NA1291.SM.matrix HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:36 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] OUTPUT=/tmp/Fingerprinting9898840982703227381NA1291.SM.crosscheck_metrics MATRIX_OUTPUT=/tmp/Fingerprinting12520204583001672919NA1291.SM.matrix HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:36 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:36 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:36 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:54:36 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:37 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:54:37 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:37 FingerprintChecker Processed files. 54 fingerprints found in map. INFO 2024-07-02 11:54:37 FingerprintChecker Processed files. 54 fingerprints found in map. Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:37 CrosscheckFingerprints Cross-checking all SAMPLE against each other INFO 2024-07-02 11:54:37 CrosscheckFingerprints Cross-checking all SAMPLE against each other Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:37 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:54:37 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:37 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:37 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1, 2)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:37 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0) STANDARD_ERROR INFO 2024-07-02 11:54:37 CrosscheckFingerprints Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting2738374825321072111NA1291.Sources.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting2738374825321072111NA1291.Sources.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:37.563 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:37.563 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:37.564 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:37.564 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:37.564 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:37.564 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:37.564 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:37.564 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:37.577 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:37.577 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:37.577 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:37.577 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:37 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] OUTPUT=/tmp/Fingerprinting2738374825321072111NA1291.Sources.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:37 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] OUTPUT=/tmp/Fingerprinting2738374825321072111NA1291.Sources.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:37 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:37 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:37 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:54:37 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:38 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:38 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:38 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:54:38 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:38 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:54:38 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:38 CrosscheckFingerprints All FILEs are related as expected. INFO 2024-07-02 11:54:38 CrosscheckFingerprints All FILEs are related as expected. Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:38 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:38 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckSources[0](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:38 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0) STANDARD_ERROR INFO 2024-07-02 11:54:38 CrosscheckFingerprints Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting8870511045639208477NA1291.Sources.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting8870511045639208477NA1291.Sources.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:38.298 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:38.298 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:38.298 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:38.298 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:38.299 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:38.299 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:38.299 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:38.299 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:38.299 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:38.299 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:38.299 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:38.299 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:38 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] OUTPUT=/tmp/Fingerprinting8870511045639208477NA1291.Sources.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:38 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] OUTPUT=/tmp/Fingerprinting8870511045639208477NA1291.Sources.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:38 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:38 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:38 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:54:38 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:38 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:38 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:38 FingerprintChecker Processed files. 51 fingerprints found in map. INFO 2024-07-02 11:54:38 FingerprintChecker Processed files. 51 fingerprints found in map. Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:38 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:54:38 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:38 CrosscheckFingerprints All FILEs are related as expected. INFO 2024-07-02 11:54:38 CrosscheckFingerprints All FILEs are related as expected. Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:38 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:38 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckSources[1](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:38 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0) STANDARD_ERROR INFO 2024-07-02 11:54:38 CrosscheckFingerprints Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -OUTPUT /tmp/Fingerprinting16259024967517168556NA1291.Sources.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -OUTPUT /tmp/Fingerprinting16259024967517168556NA1291.Sources.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:38.726 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:38.726 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:38.726 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:38.726 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:38.727 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:38.727 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:38.727 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:38.727 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:38.727 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:38.727 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:38.727 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:38.727 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:38 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] OUTPUT=/tmp/Fingerprinting16259024967517168556NA1291.Sources.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:38 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] OUTPUT=/tmp/Fingerprinting16259024967517168556NA1291.Sources.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:38 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:38 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:38 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:54:38 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:38 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:54:38 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:39 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:39 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:39 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:54:39 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:39 CrosscheckFingerprints All FILEs are related as expected. INFO 2024-07-02 11:54:39 CrosscheckFingerprints All FILEs are related as expected. Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:39 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:39 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckSources[2](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:39 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0) STANDARD_ERROR INFO 2024-07-02 11:54:39 CrosscheckFingerprints Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting12191774729562744780NA1291.Sources.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting12191774729562744780NA1291.Sources.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:39.046 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:39.046 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:39.046 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:39.046 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:39.047 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:39.047 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:39.047 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:39.047 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:39.047 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:39.047 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:39.047 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:39.047 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:39 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] OUTPUT=/tmp/Fingerprinting12191774729562744780NA1291.Sources.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:39 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] OUTPUT=/tmp/Fingerprinting12191774729562744780NA1291.Sources.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:39 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:39 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:39 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:39 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:39 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:39 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:39 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:39 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:39 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:54:39 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:39 CrosscheckFingerprints All FILEs are related as expected. INFO 2024-07-02 11:54:39 CrosscheckFingerprints All FILEs are related as expected. Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:39 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:39 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckSources[3](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, 0)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:39 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1) STANDARD_ERROR INFO 2024-07-02 11:54:39 CrosscheckFingerprints Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting7844955275418600039NA1291.Sources.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting7844955275418600039NA1291.Sources.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:39.506 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:39.506 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:39.506 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:39.506 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:39.507 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:39.507 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:39.507 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:39.507 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:39.507 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:39.507 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:39.507 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:39.507 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:39 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] OUTPUT=/tmp/Fingerprinting7844955275418600039NA1291.Sources.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:39 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] OUTPUT=/tmp/Fingerprinting7844955275418600039NA1291.Sources.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:39 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:39 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:39 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:39 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:39 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:54:39 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:39 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:54:39 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:39 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:54:39 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:39 CrosscheckFingerprints 2 FILEs did not relate as expected. WARNING 2024-07-02 11:54:39 CrosscheckFingerprints 2 FILEs did not relate as expected. Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:39 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:39 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testCrossCheckSources[4](/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:39 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1) STANDARD_ERROR INFO 2024-07-02 11:54:39 CrosscheckFingerprints Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting2004078596290039680NA1291.Sources.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting2004078596290039680NA1291.Sources.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:39.918 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:39.918 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:39.918 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:39.918 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:39.919 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:39.919 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:39.919 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:39.919 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:39.920 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:39.920 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:39.920 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:39.920 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:39 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] OUTPUT=/tmp/Fingerprinting2004078596290039680NA1291.Sources.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:39 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] OUTPUT=/tmp/Fingerprinting2004078596290039680NA1291.Sources.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:39 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:39 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:39 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:39 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:40 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:54:40 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:40 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:54:40 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:40 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:54:40 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:40 CrosscheckFingerprints 2 FILEs did not relate as expected. WARNING 2024-07-02 11:54:40 CrosscheckFingerprints 2 FILEs did not relate as expected. Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:40 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:40 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testCrossCheckSources[5](/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:40 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1) STANDARD_ERROR INFO 2024-07-02 11:54:40 CrosscheckFingerprints Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting17126315166912969008NA1291.Sources.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting17126315166912969008NA1291.Sources.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:40.742 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:40.742 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:40.742 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:40.742 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:40.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:40.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:40.743 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:40.743 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:40.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:40.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:40.743 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:40.743 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:40 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] OUTPUT=/tmp/Fingerprinting17126315166912969008NA1291.Sources.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:40 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] OUTPUT=/tmp/Fingerprinting17126315166912969008NA1291.Sources.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:40 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:40 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:40 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:54:40 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:54:41 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:41 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:54:41 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:41 CrosscheckFingerprints 2 FILEs did not relate as expected. WARNING 2024-07-02 11:54:41 CrosscheckFingerprints 2 FILEs did not relate as expected. Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:41 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:41 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testCrossCheckSources[6](/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1) STANDARD_ERROR INFO 2024-07-02 11:54:41 CrosscheckFingerprints Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting12726412556826419427NA1291.Sources.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting12726412556826419427NA1291.Sources.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY FILE Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.255 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:41.255 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.255 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:41.255 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.256 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:41.256 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.256 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:41.256 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.256 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:41.256 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.256 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:41.256 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:41 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] OUTPUT=/tmp/Fingerprinting12726412556826419427NA1291.Sources.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:41 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] OUTPUT=/tmp/Fingerprinting12726412556826419427NA1291.Sources.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:41 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:54:41 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:54:41 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 FingerprintChecker Processed files. 54 fingerprints found in map. INFO 2024-07-02 11:54:41 FingerprintChecker Processed files. 54 fingerprints found in map. Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:54:41 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:41 CrosscheckFingerprints 2 FILEs did not relate as expected. WARNING 2024-07-02 11:54:41 CrosscheckFingerprints 2 FILEs did not relate as expected. Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:41 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:41 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testCrossCheckSources[7](/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, 1)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true) STANDARD_ERROR INFO 2024-07-02 11:54:41 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison10299730021792617433crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -INPUT /tmp/fingerprint3086553580626660194.vcf -SECOND_INPUT /tmp/fingerprint1275962480367888787.vcf ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison10299730021792617433crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -INPUT /tmp/fingerprint3086553580626660194.vcf -SECOND_INPUT /tmp/fingerprint1275962480367888787.vcf Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.700 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:41.700 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.700 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:41.700 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.713 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:41.713 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.713 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:41.713 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.713 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:41.713 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.713 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:41.713 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:41 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf] SECOND_INPUT=[/tmp/fingerprint1275962480367888787.vcf] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison10299730021792617433crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:41 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf] SECOND_INPUT=[/tmp/fingerprint1275962480367888787.vcf] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison10299730021792617433crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:54:41 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:41 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. WARNING 2024-07-02 11:54:41 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:41 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:54:41 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:54:41 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:41 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:54:41 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:41 CrosscheckFingerprints sample NA12892 is missing from LEFT group ERROR 2024-07-02 11:54:41 CrosscheckFingerprints sample NA12892 is missing from LEFT group Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:41 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:54:41 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:41 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:41 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 CrosscheckFingerprints INFO 2024-07-02 11:54:41 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison10299730021792617433crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -SECOND_INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint1275962480367888787.vcf ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison10299730021792617433crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -SECOND_INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint1275962480367888787.vcf Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.790 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:41.790 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.790 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:41.790 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.791 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:41.791 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.791 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:41.791 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.792 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:41.792 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.792 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:41.792 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:41 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint3086553580626660194.vcf] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison10299730021792617433crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:41 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint3086553580626660194.vcf] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison10299730021792617433crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:54:41 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:41 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. WARNING 2024-07-02 11:54:41 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:41 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:41 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:54:41 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:54:41 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:54:41 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:41 CrosscheckFingerprints sample NA12892 is missing from RIGHT group ERROR 2024-07-02 11:54:41 CrosscheckFingerprints sample NA12892 is missing from RIGHT group Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:41 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:54:41 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:41 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:41 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[0]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true) STANDARD_ERROR INFO 2024-07-02 11:54:41 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison2775508120727064633crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -INPUT testdata/picard/fingerprint/NA12891.vcf -SECOND_INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison2775508120727064633crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -INPUT testdata/picard/fingerprint/NA12891.vcf -SECOND_INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.864 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:41.864 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.864 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:41.864 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.870 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:41.870 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.870 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:41.870 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.870 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:41.870 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.870 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:41.870 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:41 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.vcf] SECOND_INPUT=[testdata/picard/fingerprint/NA12891andNA12892.vcf] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison2775508120727064633crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:41 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.vcf] SECOND_INPUT=[testdata/picard/fingerprint/NA12891andNA12892.vcf] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison2775508120727064633crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:54:41 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:41 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. WARNING 2024-07-02 11:54:41 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:41 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:41 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.vcf going to read through it all. WARNING 2024-07-02 11:54:41 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.vcf going to read through it all. Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:54:41 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:54:41 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:41 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all. WARNING 2024-07-02 11:54:41 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all. Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:41 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:54:41 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:41 CrosscheckFingerprints sample NA12892 is missing from LEFT group ERROR 2024-07-02 11:54:41 CrosscheckFingerprints sample NA12892 is missing from LEFT group Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:41 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:54:41 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:41 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:41 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 CrosscheckFingerprints INFO 2024-07-02 11:54:41 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison2775508120727064633crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -SECOND_INPUT testdata/picard/fingerprint/NA12891.vcf -INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison2775508120727064633crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -SECOND_INPUT testdata/picard/fingerprint/NA12891.vcf -INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.928 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:41.928 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.928 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:41.928 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.937 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:41.937 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.937 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:41.937 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.937 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:41.937 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.938 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:41.938 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:41 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891andNA12892.vcf] SECOND_INPUT=[testdata/picard/fingerprint/NA12891.vcf] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison2775508120727064633crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:41 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891andNA12892.vcf] SECOND_INPUT=[testdata/picard/fingerprint/NA12891.vcf] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison2775508120727064633crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:54:41 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:41 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. WARNING 2024-07-02 11:54:41 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:41 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:41 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all. WARNING 2024-07-02 11:54:41 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all. Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:41 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:54:41 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:41 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.vcf going to read through it all. WARNING 2024-07-02 11:54:41 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.vcf going to read through it all. Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:54:41 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:54:41 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:41 CrosscheckFingerprints sample NA12892 is missing from RIGHT group ERROR 2024-07-02 11:54:41 CrosscheckFingerprints sample NA12892 is missing from RIGHT group Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:41 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:54:41 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:41 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:41 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[1]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true) STANDARD_ERROR INFO 2024-07-02 11:54:41 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison12912806045940067369crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -INPUT /tmp/fingerprint5867520670411385388.vcf -SECOND_INPUT /tmp/fingerprint1275962480367888787.vcf ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison12912806045940067369crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -INPUT /tmp/fingerprint5867520670411385388.vcf -SECOND_INPUT /tmp/fingerprint1275962480367888787.vcf Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.981 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:41.981 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.989 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:41.989 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.990 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:41.990 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.991 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:41.991 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.991 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:41.991 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:41.991 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:41.991 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:41 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint5867520670411385388.vcf] SECOND_INPUT=[/tmp/fingerprint1275962480367888787.vcf] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison12912806045940067369crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:41 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint5867520670411385388.vcf] SECOND_INPUT=[/tmp/fingerprint1275962480367888787.vcf] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison12912806045940067369crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:41 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:54:41 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:41 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. WARNING 2024-07-02 11:54:41 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:42 CrosscheckFingerprints sample NA12891 from LEFT group was not fingerprinted. Probably there are no reads/variants at fingerprinting sites. ERROR 2024-07-02 11:54:42 CrosscheckFingerprints sample NA12891 from LEFT group was not fingerprinted. Probably there are no reads/variants at fingerprinting sites. Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:42 CrosscheckFingerprints LOD score of zero found when checking sample fingerprints. Probably there are no reads/variants at fingerprinting sites for one of the samples ERROR 2024-07-02 11:54:42 CrosscheckFingerprints LOD score of zero found when checking sample fingerprints. Probably there are no reads/variants at fingerprinting sites for one of the samples Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:42 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:54:42 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:42 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints INFO 2024-07-02 11:54:42 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison12912806045940067369crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -SECOND_INPUT /tmp/fingerprint5867520670411385388.vcf -INPUT /tmp/fingerprint1275962480367888787.vcf ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison12912806045940067369crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -SECOND_INPUT /tmp/fingerprint5867520670411385388.vcf -INPUT /tmp/fingerprint1275962480367888787.vcf Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.099 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:42.099 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.099 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:42.099 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.100 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:42.100 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.100 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:42.100 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.100 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:42.100 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.100 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:42.100 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint5867520670411385388.vcf] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison12912806045940067369crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:42 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint5867520670411385388.vcf] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison12912806045940067369crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:54:42 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:42 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. WARNING 2024-07-02 11:54:42 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:42 CrosscheckFingerprints sample NA12891 from RIGHT group was not fingerprinted. Probably there are no reads/variants at fingerprinting sites. ERROR 2024-07-02 11:54:42 CrosscheckFingerprints sample NA12891 from RIGHT group was not fingerprinted. Probably there are no reads/variants at fingerprinting sites. Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:42 CrosscheckFingerprints LOD score of zero found when checking sample fingerprints. Probably there are no reads/variants at fingerprinting sites for one of the samples ERROR 2024-07-02 11:54:42 CrosscheckFingerprints LOD score of zero found when checking sample fingerprints. Probably there are no reads/variants at fingerprinting sites for one of the samples Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:42 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:54:42 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:42 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[2]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true) STANDARD_ERROR INFO 2024-07-02 11:54:42 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison10246700768409272208crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -INPUT testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf -SECOND_INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison10246700768409272208crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -INPUT testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf -SECOND_INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.171 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:42.171 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.171 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:42.171 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.172 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:42.172 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.172 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:42.172 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.172 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:42.172 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.172 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:42.172 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf] SECOND_INPUT=[testdata/picard/fingerprint/NA12891andNA12892.vcf] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison10246700768409272208crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:42 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf] SECOND_INPUT=[testdata/picard/fingerprint/NA12891andNA12892.vcf] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison10246700768409272208crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:54:42 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:42 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. WARNING 2024-07-02 11:54:42 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:42 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf going to read through it all. WARNING 2024-07-02 11:54:42 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf going to read through it all. Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:42 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all. WARNING 2024-07-02 11:54:42 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all. Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:42 CrosscheckFingerprints sample NA12891 from LEFT group was not fingerprinted. Probably there are no reads/variants at fingerprinting sites. ERROR 2024-07-02 11:54:42 CrosscheckFingerprints sample NA12891 from LEFT group was not fingerprinted. Probably there are no reads/variants at fingerprinting sites. Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:42 CrosscheckFingerprints LOD score of zero found when checking sample fingerprints. Probably there are no reads/variants at fingerprinting sites for one of the samples ERROR 2024-07-02 11:54:42 CrosscheckFingerprints LOD score of zero found when checking sample fingerprints. Probably there are no reads/variants at fingerprinting sites for one of the samples Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:42 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:54:42 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:42 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints INFO 2024-07-02 11:54:42 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison10246700768409272208crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -SECOND_INPUT testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf -INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison10246700768409272208crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -SECOND_INPUT testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf -INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.230 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:42.230 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.230 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:42.230 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.231 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:42.231 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.231 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:42.231 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.232 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:42.232 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.232 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:42.232 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891andNA12892.vcf] SECOND_INPUT=[testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison10246700768409272208crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:42 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891andNA12892.vcf] SECOND_INPUT=[testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison10246700768409272208crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:54:42 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:42 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. WARNING 2024-07-02 11:54:42 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:42 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all. WARNING 2024-07-02 11:54:42 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all. Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:42 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf going to read through it all. WARNING 2024-07-02 11:54:42 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf going to read through it all. Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:42 CrosscheckFingerprints sample NA12891 from RIGHT group was not fingerprinted. Probably there are no reads/variants at fingerprinting sites. ERROR 2024-07-02 11:54:42 CrosscheckFingerprints sample NA12891 from RIGHT group was not fingerprinted. Probably there are no reads/variants at fingerprinting sites. Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:42 CrosscheckFingerprints LOD score of zero found when checking sample fingerprints. Probably there are no reads/variants at fingerprinting sites for one of the samples ERROR 2024-07-02 11:54:42 CrosscheckFingerprints LOD score of zero found when checking sample fingerprints. Probably there are no reads/variants at fingerprinting sites for one of the samples Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:42 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:54:42 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:42 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[3]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false) STANDARD_ERROR INFO 2024-07-02 11:54:42 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison3701235101872930011crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT /tmp/fingerprint3086553580626660194.vcf -SECOND_INPUT /tmp/fingerprint1275962480367888787.vcf -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison3701235101872930011crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT /tmp/fingerprint3086553580626660194.vcf -SECOND_INPUT /tmp/fingerprint1275962480367888787.vcf -CROSSCHECK_BY SAMPLE Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.284 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:42.284 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.285 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:42.285 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.302 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:42.302 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.302 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:42.302 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.302 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:42.302 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.302 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:42.302 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf] SECOND_INPUT=[/tmp/fingerprint1275962480367888787.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison3701235101872930011crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:42 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf] SECOND_INPUT=[/tmp/fingerprint1275962480367888787.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison3701235101872930011crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:54:42 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:54:42 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:42 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints INFO 2024-07-02 11:54:42 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison3701235101872930011crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -CROSSCHECK_BY SAMPLE -SECOND_INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint1275962480367888787.vcf ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison3701235101872930011crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -CROSSCHECK_BY SAMPLE -SECOND_INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint1275962480367888787.vcf Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.348 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:42.348 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.348 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:42.348 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.349 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:42.349 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.365 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:42.365 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.365 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:42.365 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.365 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:42.365 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint3086553580626660194.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison3701235101872930011crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:42 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint3086553580626660194.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison3701235101872930011crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:54:42 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:54:42 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:42 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testMissingOrNoFingerprintingSites[4]([/tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false) STANDARD_ERROR INFO 2024-07-02 11:54:42 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison13480161016937993072crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT testdata/picard/fingerprint/NA12891.vcf -SECOND_INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison13480161016937993072crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT testdata/picard/fingerprint/NA12891.vcf -SECOND_INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf -CROSSCHECK_BY SAMPLE Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.420 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:42.420 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.420 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:42.420 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.433 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:42.433 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.433 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:42.433 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.434 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:42.434 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.434 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:42.434 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.vcf] SECOND_INPUT=[testdata/picard/fingerprint/NA12891andNA12892.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison13480161016937993072crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:42 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.vcf] SECOND_INPUT=[testdata/picard/fingerprint/NA12891andNA12892.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison13480161016937993072crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:54:42 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:42 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.vcf going to read through it all. WARNING 2024-07-02 11:54:42 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.vcf going to read through it all. Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:42 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all. WARNING 2024-07-02 11:54:42 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all. Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:54:42 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:42 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints INFO 2024-07-02 11:54:42 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison13480161016937993072crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -CROSSCHECK_BY SAMPLE -SECOND_INPUT testdata/picard/fingerprint/NA12891.vcf -INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison13480161016937993072crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -CROSSCHECK_BY SAMPLE -SECOND_INPUT testdata/picard/fingerprint/NA12891.vcf -INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.480 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:42.480 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.480 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:42.480 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.493 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:42.493 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.493 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:42.493 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.493 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:42.493 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.493 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:42.493 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891andNA12892.vcf] SECOND_INPUT=[testdata/picard/fingerprint/NA12891.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison13480161016937993072crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:42 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891andNA12892.vcf] SECOND_INPUT=[testdata/picard/fingerprint/NA12891.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison13480161016937993072crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:54:42 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:42 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all. WARNING 2024-07-02 11:54:42 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all. Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:42 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.vcf going to read through it all. WARNING 2024-07-02 11:54:42 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.vcf going to read through it all. Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:54:42 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:42 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testMissingOrNoFingerprintingSites[5]([testdata/picard/fingerprint/NA12891.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false) STANDARD_ERROR INFO 2024-07-02 11:54:42 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison404895148108582878crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT /tmp/fingerprint5867520670411385388.vcf -SECOND_INPUT /tmp/fingerprint1275962480367888787.vcf -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison404895148108582878crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT /tmp/fingerprint5867520670411385388.vcf -SECOND_INPUT /tmp/fingerprint1275962480367888787.vcf -CROSSCHECK_BY SAMPLE Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.544 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:42.544 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.544 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:42.544 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.558 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:42.558 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.558 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:42.558 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.558 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:42.558 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.558 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:42.558 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint5867520670411385388.vcf] SECOND_INPUT=[/tmp/fingerprint1275962480367888787.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison404895148108582878crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:42 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint5867520670411385388.vcf] SECOND_INPUT=[/tmp/fingerprint1275962480367888787.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison404895148108582878crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:54:42 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:42 CrosscheckFingerprints NA12891 was not fingerprinted in LEFT group. It probably has no calls/reads overlapping fingerprinting sites. WARNING 2024-07-02 11:54:42 CrosscheckFingerprints NA12891 was not fingerprinted in LEFT group. It probably has no calls/reads overlapping fingerprinting sites. Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:54:42 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:42 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints INFO 2024-07-02 11:54:42 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison404895148108582878crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -CROSSCHECK_BY SAMPLE -SECOND_INPUT /tmp/fingerprint5867520670411385388.vcf -INPUT /tmp/fingerprint1275962480367888787.vcf ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison404895148108582878crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -CROSSCHECK_BY SAMPLE -SECOND_INPUT /tmp/fingerprint5867520670411385388.vcf -INPUT /tmp/fingerprint1275962480367888787.vcf Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.604 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:42.604 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.604 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:42.604 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.618 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:42.618 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.618 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:42.618 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.618 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:42.618 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.618 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:42.618 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint5867520670411385388.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison404895148108582878crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:42 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint5867520670411385388.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison404895148108582878crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:54:42 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:42 CrosscheckFingerprints NA12891 was not fingerprinted in RIGHT group. It probably has no calls/reads overlapping fingerprinting sites. WARNING 2024-07-02 11:54:42 CrosscheckFingerprints NA12891 was not fingerprinted in RIGHT group. It probably has no calls/reads overlapping fingerprinting sites. Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:54:42 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:42 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testMissingOrNoFingerprintingSites[6]([/tmp/fingerprint5867520670411385388.vcf], [/tmp/fingerprint1275962480367888787.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false) STANDARD_ERROR INFO 2024-07-02 11:54:42 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison16013493909022884515crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf -SECOND_INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison16013493909022884515crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf -SECOND_INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf -CROSSCHECK_BY SAMPLE Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.713 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:42.713 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.714 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:42.714 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.715 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:42.715 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.715 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:42.715 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.715 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:42.715 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.715 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:42.715 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf] SECOND_INPUT=[testdata/picard/fingerprint/NA12891andNA12892.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison16013493909022884515crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:42 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf] SECOND_INPUT=[testdata/picard/fingerprint/NA12891andNA12892.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison16013493909022884515crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:54:42 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:42 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf going to read through it all. WARNING 2024-07-02 11:54:42 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf going to read through it all. Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:42 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all. WARNING 2024-07-02 11:54:42 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all. Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:42 CrosscheckFingerprints NA12891 was not fingerprinted in LEFT group. It probably has no calls/reads overlapping fingerprinting sites. WARNING 2024-07-02 11:54:42 CrosscheckFingerprints NA12891 was not fingerprinted in LEFT group. It probably has no calls/reads overlapping fingerprinting sites. Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:54:42 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:42 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints INFO 2024-07-02 11:54:42 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison16013493909022884515crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -CROSSCHECK_BY SAMPLE -SECOND_INPUT testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf -INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison16013493909022884515crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -CROSSCHECK_BY SAMPLE -SECOND_INPUT testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf -INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.772 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:42.772 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.789 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:42.789 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.790 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:42.790 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.790 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:42.790 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.791 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:42.791 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.791 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:42.791 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891andNA12892.vcf] SECOND_INPUT=[testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison16013493909022884515crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:42 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891andNA12892.vcf] SECOND_INPUT=[testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison16013493909022884515crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:54:42 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:42 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all. WARNING 2024-07-02 11:54:42 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all. Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:42 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf going to read through it all. WARNING 2024-07-02 11:54:42 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf going to read through it all. Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:42 CrosscheckFingerprints NA12891 was not fingerprinted in RIGHT group. It probably has no calls/reads overlapping fingerprinting sites. WARNING 2024-07-02 11:54:42 CrosscheckFingerprints NA12891 was not fingerprinted in RIGHT group. It probably has no calls/reads overlapping fingerprinting sites. Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:54:42 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:42 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testMissingOrNoFingerprintingSites[7]([testdata/picard/fingerprint/NA12891.no.fp.sites.and.NA12892.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true) STANDARD_ERROR INFO 2024-07-02 11:54:42 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison18147630698430700150crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT /tmp/fingerprint10995276373434349698.vcf -SECOND_INPUT /tmp/fingerprint1275962480367888787.vcf -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison18147630698430700150crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT /tmp/fingerprint10995276373434349698.vcf -SECOND_INPUT /tmp/fingerprint1275962480367888787.vcf -CROSSCHECK_BY SAMPLE Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.848 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:42.848 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.848 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:42.848 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.862 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:42.862 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.862 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:42.862 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.862 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:42.862 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.862 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:42.862 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint10995276373434349698.vcf] SECOND_INPUT=[/tmp/fingerprint1275962480367888787.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison18147630698430700150crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:42 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint10995276373434349698.vcf] SECOND_INPUT=[/tmp/fingerprint1275962480367888787.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison18147630698430700150crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:54:42 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:42 CrosscheckFingerprints NA12891 was not fingerprinted in LEFT group. It probably has no calls/reads overlapping fingerprinting sites. WARNING 2024-07-02 11:54:42 CrosscheckFingerprints NA12891 was not fingerprinted in LEFT group. It probably has no calls/reads overlapping fingerprinting sites. Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:42 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites ERROR 2024-07-02 11:54:42 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:42 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints INFO 2024-07-02 11:54:42 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison18147630698430700150crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -CROSSCHECK_BY SAMPLE -SECOND_INPUT /tmp/fingerprint10995276373434349698.vcf -INPUT /tmp/fingerprint1275962480367888787.vcf ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison18147630698430700150crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -CROSSCHECK_BY SAMPLE -SECOND_INPUT /tmp/fingerprint10995276373434349698.vcf -INPUT /tmp/fingerprint1275962480367888787.vcf Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.919 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:42.919 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.919 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:42.919 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.920 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:42.920 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.920 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:42.920 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.921 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:42.921 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.937 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:42.937 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint10995276373434349698.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison18147630698430700150crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:42 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint10995276373434349698.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison18147630698430700150crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:54:42 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:54:42 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:42 CrosscheckFingerprints NA12891 was not fingerprinted in RIGHT group. It probably has no calls/reads overlapping fingerprinting sites. WARNING 2024-07-02 11:54:42 CrosscheckFingerprints NA12891 was not fingerprinted in RIGHT group. It probably has no calls/reads overlapping fingerprinting sites. Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:42 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites ERROR 2024-07-02 11:54:42 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:42 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[8]([/tmp/fingerprint10995276373434349698.vcf], [/tmp/fingerprint1275962480367888787.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true) STANDARD_ERROR INFO 2024-07-02 11:54:42 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison11802278950018400201crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT testdata/picard/fingerprint/NA12891.no.fp.sites.vcf -SECOND_INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison11802278950018400201crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT testdata/picard/fingerprint/NA12891.no.fp.sites.vcf -SECOND_INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf -CROSSCHECK_BY SAMPLE Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.987 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:42.987 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.987 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:42.987 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.988 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:42.988 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.988 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:42.988 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.997 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:42.997 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:42.997 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:42.997 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.no.fp.sites.vcf] SECOND_INPUT=[testdata/picard/fingerprint/NA12891andNA12892.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison11802278950018400201crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:42 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.no.fp.sites.vcf] SECOND_INPUT=[testdata/picard/fingerprint/NA12891andNA12892.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison11802278950018400201crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:54:42 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:42 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:43 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.no.fp.sites.vcf going to read through it all. WARNING 2024-07-02 11:54:43 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.no.fp.sites.vcf going to read through it all. Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:43 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:54:43 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:43 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:54:43 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:43 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all. WARNING 2024-07-02 11:54:43 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all. Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:43 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:43 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:43 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:54:43 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:43 CrosscheckFingerprints NA12891 was not fingerprinted in LEFT group. It probably has no calls/reads overlapping fingerprinting sites. WARNING 2024-07-02 11:54:43 CrosscheckFingerprints NA12891 was not fingerprinted in LEFT group. It probably has no calls/reads overlapping fingerprinting sites. Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:43 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites ERROR 2024-07-02 11:54:43 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:43 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:43 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:43 CrosscheckFingerprints INFO 2024-07-02 11:54:43 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison11802278950018400201crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -CROSSCHECK_BY SAMPLE -SECOND_INPUT testdata/picard/fingerprint/NA12891.no.fp.sites.vcf -INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison11802278950018400201crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -CROSSCHECK_BY SAMPLE -SECOND_INPUT testdata/picard/fingerprint/NA12891.no.fp.sites.vcf -INPUT testdata/picard/fingerprint/NA12891andNA12892.vcf Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:43.047 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:43.047 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:43.047 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:43.047 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:43.048 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:43.048 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:43.048 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:43.048 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:43.048 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:43.048 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:43.048 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:43.048 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:43 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891andNA12892.vcf] SECOND_INPUT=[testdata/picard/fingerprint/NA12891.no.fp.sites.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison11802278950018400201crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:43 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891andNA12892.vcf] SECOND_INPUT=[testdata/picard/fingerprint/NA12891.no.fp.sites.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison11802278950018400201crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:43 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:54:43 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:43 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:43 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:43 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all. WARNING 2024-07-02 11:54:43 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891andNA12892.vcf going to read through it all. Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:43 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:54:43 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:43 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:54:43 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:43 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.no.fp.sites.vcf going to read through it all. WARNING 2024-07-02 11:54:43 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.no.fp.sites.vcf going to read through it all. Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:43 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:54:43 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:43 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:54:43 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:43 CrosscheckFingerprints NA12891 was not fingerprinted in RIGHT group. It probably has no calls/reads overlapping fingerprinting sites. WARNING 2024-07-02 11:54:43 CrosscheckFingerprints NA12891 was not fingerprinted in RIGHT group. It probably has no calls/reads overlapping fingerprinting sites. Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:43 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites ERROR 2024-07-02 11:54:43 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:43 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:43 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[9]([testdata/picard/fingerprint/NA12891.no.fp.sites.vcf], [testdata/picard/fingerprint/NA12891andNA12892.vcf], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:43 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true) STANDARD_ERROR INFO 2024-07-02 11:54:43 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison752994350076268582crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison752994350076268582crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:43.103 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:43.103 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:43.103 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:43.103 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:43.104 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:43.104 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:43.104 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:43.104 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:43.112 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:43.112 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:43.113 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:43.113 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:43 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison752994350076268582crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:43 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison752994350076268582crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:43 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:54:43 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:43 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. WARNING 2024-07-02 11:54:43 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:43 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:43 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:43 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:54:43 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:43 FingerprintChecker Processed files. 25 fingerprints found in map. INFO 2024-07-02 11:54:43 FingerprintChecker Processed files. 25 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:43 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:54:43 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:43 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:43 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:43 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:43 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:43 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:43 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:43 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:54:43 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:43 CrosscheckFingerprints sample NA12891 is missing from LEFT group ERROR 2024-07-02 11:54:43 CrosscheckFingerprints sample NA12891 is missing from LEFT group Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:43 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:54:43 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:43 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:43 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:43 CrosscheckFingerprints INFO 2024-07-02 11:54:43 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison752994350076268582crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -SECOND_INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison752994350076268582crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -SECOND_INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:43.759 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:43.759 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:43.759 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:43.759 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:43.760 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:43.760 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:43.760 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:43.760 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:43.760 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:43.760 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:43.760 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:43.760 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:43 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] SECOND_INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison752994350076268582crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:43 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] SECOND_INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison752994350076268582crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:43 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:54:43 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:43 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. WARNING 2024-07-02 11:54:43 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:43 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:43 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:43 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:43 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:44 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:44 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:44 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:44 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:44 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:54:44 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:44 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:54:44 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:44 FingerprintChecker Processed files. 25 fingerprints found in map. INFO 2024-07-02 11:54:44 FingerprintChecker Processed files. 25 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:44 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:54:44 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:44 CrosscheckFingerprints sample NA12891 is missing from RIGHT group ERROR 2024-07-02 11:54:44 CrosscheckFingerprints sample NA12891 is missing from RIGHT group Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:44 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:54:44 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:44 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:44 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[10]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:44 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true) STANDARD_ERROR INFO 2024-07-02 11:54:44 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison6578507595466824949crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -SECOND_INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -SECOND_INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison6578507595466824949crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -SECOND_INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -SECOND_INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:44.632 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:44.632 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:44.632 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:44.632 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:44.633 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:44.633 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:44.633 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:44.633 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:44.634 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:44.634 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:44.634 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:44.634 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:44 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam] SECOND_INPUT=[testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison6578507595466824949crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:44 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam] SECOND_INPUT=[testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison6578507595466824949crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:44 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:54:44 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:44 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. WARNING 2024-07-02 11:54:44 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:44 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:44 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:44 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) WARNING 2024-07-02 11:54:44 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:44 FingerprintChecker Processed files. 25 fingerprints found in map. INFO 2024-07-02 11:54:44 FingerprintChecker Processed files. 25 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:44 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:54:44 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:44 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) WARNING 2024-07-02 11:54:44 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:45 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) WARNING 2024-07-02 11:54:45 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:45 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:45 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:45 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:54:45 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:45 CrosscheckFingerprints sample NA12891 is missing from LEFT group ERROR 2024-07-02 11:54:45 CrosscheckFingerprints sample NA12891 is missing from LEFT group Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:45 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:54:45 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:45 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:45 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:45 CrosscheckFingerprints INFO 2024-07-02 11:54:45 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison6578507595466824949crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -SECOND_INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison6578507595466824949crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -SECOND_INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:45.372 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:45.372 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:45.387 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:45.387 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:45.388 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:45.388 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:45.388 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:45.388 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:45.389 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:45.389 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:45.389 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:45.389 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:45 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam] SECOND_INPUT=[testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison6578507595466824949crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:45 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam] SECOND_INPUT=[testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison6578507595466824949crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:45 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:54:45 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:45 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. WARNING 2024-07-02 11:54:45 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:45 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:45 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:45 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) WARNING 2024-07-02 11:54:45 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:45 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) WARNING 2024-07-02 11:54:45 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:45 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:45 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:45 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:54:45 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:45 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) WARNING 2024-07-02 11:54:45 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:45 FingerprintChecker Processed files. 25 fingerprints found in map. INFO 2024-07-02 11:54:45 FingerprintChecker Processed files. 25 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:45 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:54:45 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:45 CrosscheckFingerprints sample NA12891 is missing from RIGHT group ERROR 2024-07-02 11:54:45 CrosscheckFingerprints sample NA12891 is missing from RIGHT group Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:45 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:54:45 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:45 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:45 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[11]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 1, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:45 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true) STANDARD_ERROR INFO 2024-07-02 11:54:45 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison13725439406909693513crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -INPUT /tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison13725439406909693513crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -INPUT /tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:45.974 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:45.974 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:45.974 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:45.974 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:45.975 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:45.975 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:45.975 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:45.975 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:45.975 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:45.975 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:45.975 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:45.975 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:45 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison13725439406909693513crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:45 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison13725439406909693513crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:45 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:54:45 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:45 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. WARNING 2024-07-02 11:54:45 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:45 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:45 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:46 FingerprintChecker Reading an indexed file (/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam) INFO 2024-07-02 11:54:46 FingerprintChecker Reading an indexed file (/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam) Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:46 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:54:46 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:46 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:46 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:46 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:54:46 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:46 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:46 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:46 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:46 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:46 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:46 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:46 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:54:46 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:46 CrosscheckFingerprints LOD score of zero found when checking sample fingerprints. Probably there are no reads/variants at fingerprinting sites for one of the samples ERROR 2024-07-02 11:54:46 CrosscheckFingerprints LOD score of zero found when checking sample fingerprints. Probably there are no reads/variants at fingerprinting sites for one of the samples Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:46 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:54:46 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:46 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:46 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:46 CrosscheckFingerprints INFO 2024-07-02 11:54:46 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison13725439406909693513crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -SECOND_INPUT /tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison13725439406909693513crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -SECOND_INPUT /tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:46.872 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:46.872 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:46.872 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:46.872 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:46.874 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:46.874 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:46.874 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:46.874 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:46.874 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:46.874 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:46.874 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:46.874 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:46 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] SECOND_INPUT=[/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison13725439406909693513crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:46 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] SECOND_INPUT=[/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison13725439406909693513crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:46 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:54:46 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:46 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. WARNING 2024-07-02 11:54:46 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:46 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:46 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:46 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:46 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:47 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:47 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:47 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:47 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:47 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:54:47 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:47 FingerprintChecker Reading an indexed file (/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam) INFO 2024-07-02 11:54:47 FingerprintChecker Reading an indexed file (/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam) Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:47 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:54:47 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:48 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:48 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:48 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:54:48 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:48 CrosscheckFingerprints LOD score of zero found when checking sample fingerprints. Probably there are no reads/variants at fingerprinting sites for one of the samples ERROR 2024-07-02 11:54:48 CrosscheckFingerprints LOD score of zero found when checking sample fingerprints. Probably there are no reads/variants at fingerprinting sites for one of the samples Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:48 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:54:48 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:48 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:54:48 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.02 minutes. Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[12]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:48 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true) STANDARD_ERROR INFO 2024-07-02 11:54:48 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison1553774449474553717crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -INPUT testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam -INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -SECOND_INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -SECOND_INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison1553774449474553717crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -INPUT testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam -INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -SECOND_INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -SECOND_INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:48.119 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:48.119 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:48.119 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:48.119 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:48.120 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:48.120 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:48.120 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:48.120 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:48.120 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:48.120 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:48.120 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:48.120 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:48 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam] SECOND_INPUT=[testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison1553774449474553717crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:48 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam] SECOND_INPUT=[testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison1553774449474553717crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:48 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:54:48 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:48 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. WARNING 2024-07-02 11:54:48 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:48 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:48 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:48 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam) WARNING 2024-07-02 11:54:48 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam) Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:48 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) WARNING 2024-07-02 11:54:48 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:48 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:48 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:48 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:54:48 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:48 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) WARNING 2024-07-02 11:54:48 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:48 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) WARNING 2024-07-02 11:54:48 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:48 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:48 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:48 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:54:48 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:48 CrosscheckFingerprints LOD score of zero found when checking sample fingerprints. Probably there are no reads/variants at fingerprinting sites for one of the samples ERROR 2024-07-02 11:54:48 CrosscheckFingerprints LOD score of zero found when checking sample fingerprints. Probably there are no reads/variants at fingerprinting sites for one of the samples Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:48 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:54:48 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:48 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:48 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:48 CrosscheckFingerprints INFO 2024-07-02 11:54:48 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison1553774449474553717crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -SECOND_INPUT testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam -SECOND_INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison1553774449474553717crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_SAME_SAMPLE -SECOND_INPUT testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam -SECOND_INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:49.004 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:49.004 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:49.004 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:49.004 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:49.005 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:49.005 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:49.005 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:49.005 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:49.006 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:49.006 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:49.006 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:49.006 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:49 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam] SECOND_INPUT=[testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison1553774449474553717crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:49 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam] SECOND_INPUT=[testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam] CROSSCHECK_MODE=CHECK_SAME_SAMPLE OUTPUT=/tmp/Fingerprinting.comparison1553774449474553717crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:49 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. INFO 2024-07-02 11:54:49 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_SAME_SAMPLE. NOT doing cross-check. Will only compare each SAMPLE in INPUT against that sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:49 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. WARNING 2024-07-02 11:54:49 CrosscheckFingerprints CROSSCHECK_BY is not SAMPLE, This doesn't make sense in non-crosscheck mode. Setting CROSSCHECK_BY to SAMPLE. Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:49 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:49 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:49 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) WARNING 2024-07-02 11:54:49 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:49 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) WARNING 2024-07-02 11:54:49 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:49 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:49 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:49 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:54:49 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:49 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam) WARNING 2024-07-02 11:54:49 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam) Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:49 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) WARNING 2024-07-02 11:54:49 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:49 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:49 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:49 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. INFO 2024-07-02 11:54:49 CrosscheckFingerprints Checking each sample in INPUT with the same sample in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:49 CrosscheckFingerprints LOD score of zero found when checking sample fingerprints. Probably there are no reads/variants at fingerprinting sites for one of the samples ERROR 2024-07-02 11:54:49 CrosscheckFingerprints LOD score of zero found when checking sample fingerprints. Probably there are no reads/variants at fingerprinting sites for one of the samples Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:49 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:54:49 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:49 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:49 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[13]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 2, CHECK_SAME_SAMPLE, null, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:49 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false) STANDARD_ERROR INFO 2024-07-02 11:54:49 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison3169682354608057196crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison3169682354608057196crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -CROSSCHECK_BY SAMPLE Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:49.739 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:49.739 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:49.739 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:49.739 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:49.740 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:49.740 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:49.740 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:49.740 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:49.740 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:49.740 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:49.740 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:49.740 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:49 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison3169682354608057196crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:49 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison3169682354608057196crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:49 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:54:49 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:49 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:49 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:49 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:54:49 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:49 FingerprintChecker Processed files. 25 fingerprints found in map. INFO 2024-07-02 11:54:49 FingerprintChecker Processed files. 25 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:49 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:54:49 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:50 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:50 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:50 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:50 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:50 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:50 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:50 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:54:50 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:50 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:54:50 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:50 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:54:50 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.02 minutes. Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:50 CrosscheckFingerprints INFO 2024-07-02 11:54:50 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison3169682354608057196crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -CROSSCHECK_BY SAMPLE -SECOND_INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison3169682354608057196crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -CROSSCHECK_BY SAMPLE -SECOND_INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:50.678 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:50.678 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:50.678 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:50.678 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:50.679 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:50.679 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:50.679 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:50.679 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:50.680 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:50.680 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:50.680 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:50.680 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:50 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] SECOND_INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison3169682354608057196crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:50 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] SECOND_INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison3169682354608057196crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:50 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:54:50 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:50 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:50 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:50 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:50 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:50 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:50 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:51 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:51 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:51 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:54:51 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:51 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:54:51 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:51 FingerprintChecker Processed files. 25 fingerprints found in map. INFO 2024-07-02 11:54:51 FingerprintChecker Processed files. 25 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:51 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:54:51 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:51 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:54:51 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:51 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:51 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testMissingOrNoFingerprintingSites[14]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:51 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false) STANDARD_ERROR INFO 2024-07-02 11:54:51 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison2180648641280962709crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -SECOND_INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -SECOND_INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison2180648641280962709crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -SECOND_INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -SECOND_INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam -CROSSCHECK_BY SAMPLE Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:51.287 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:51.287 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:51.287 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:51.287 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:51.288 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:51.288 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:51.288 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:51.288 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:51.288 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:51.288 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:51.288 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:51.288 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:51 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam] SECOND_INPUT=[testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison2180648641280962709crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:51 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam] SECOND_INPUT=[testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison2180648641280962709crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:51 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:54:51 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:51 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:51 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:51 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) WARNING 2024-07-02 11:54:51 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:51 FingerprintChecker Processed files. 25 fingerprints found in map. INFO 2024-07-02 11:54:51 FingerprintChecker Processed files. 25 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:51 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:54:51 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:51 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) WARNING 2024-07-02 11:54:51 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:51 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) WARNING 2024-07-02 11:54:51 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:52 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:52 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:52 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:54:52 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:52 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:54:52 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:52 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:52 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:52 CrosscheckFingerprints INFO 2024-07-02 11:54:52 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison2180648641280962709crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -CROSSCHECK_BY SAMPLE -SECOND_INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison2180648641280962709crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -CROSSCHECK_BY SAMPLE -SECOND_INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:52.082 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:52.082 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:52.082 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:52.082 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:52.083 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:52.083 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:52.083 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:52.083 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:52.083 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:52.083 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:52.083 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:52.083 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:52 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam] SECOND_INPUT=[testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison2180648641280962709crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:52 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam] SECOND_INPUT=[testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison2180648641280962709crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:52 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:54:52 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:52 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:52 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:52 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) WARNING 2024-07-02 11:54:52 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:52 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) WARNING 2024-07-02 11:54:52 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:52 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:52 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:52 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:54:52 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:52 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) WARNING 2024-07-02 11:54:52 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:52 FingerprintChecker Processed files. 25 fingerprints found in map. INFO 2024-07-02 11:54:52 FingerprintChecker Processed files. 25 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:52 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:54:52 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:52 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:54:52 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:52 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:52 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testMissingOrNoFingerprintingSites[15]([testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 2, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:52 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false) STANDARD_ERROR INFO 2024-07-02 11:54:52 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison11321843263995801536crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT /tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison11321843263995801536crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT /tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -CROSSCHECK_BY SAMPLE Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:52.734 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:52.734 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:52.734 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:52.734 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:52.735 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:52.735 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:52.735 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:52.735 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:52.735 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:52.735 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:52.735 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:52.735 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:52 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison11321843263995801536crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:52 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison11321843263995801536crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:52 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:54:52 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:52 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:52 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:52 FingerprintChecker Reading an indexed file (/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam) INFO 2024-07-02 11:54:52 FingerprintChecker Reading an indexed file (/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam) Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:52 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:54:52 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:53 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:53 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:53 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:54:53 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:53 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:53 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:53 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:53 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:53 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:53 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:53 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:54:53 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:53 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:54:53 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:53 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:54:53 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.02 minutes. Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:53 CrosscheckFingerprints INFO 2024-07-02 11:54:53 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison11321843263995801536crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -CROSSCHECK_BY SAMPLE -SECOND_INPUT /tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison11321843263995801536crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -CROSSCHECK_BY SAMPLE -SECOND_INPUT /tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:53.906 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:53.906 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:53.906 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:53.906 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:53.907 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:53.907 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:53.907 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:53.907 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:53.907 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:53.907 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:53.907 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:53.907 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:53 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] SECOND_INPUT=[/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison11321843263995801536crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:53 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] SECOND_INPUT=[/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison11321843263995801536crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:53 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:54:53 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:53 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:53 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:53 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:53 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:54 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:54 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:54 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:54 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:54 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:54:54 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:54 FingerprintChecker Reading an indexed file (/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam) INFO 2024-07-02 11:54:54 FingerprintChecker Reading an indexed file (/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam) Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:54 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:54:54 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:54 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:54 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:54 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:54:54 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:54 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:54:54 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:54 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:54 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testMissingOrNoFingerprintingSites[16]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:54 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false) STANDARD_ERROR INFO 2024-07-02 11:54:54 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison4223893895287800591crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam -INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -SECOND_INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -SECOND_INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison4223893895287800591crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam -INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -SECOND_INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -SECOND_INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam -CROSSCHECK_BY SAMPLE Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:54.513 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:54.513 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:54.513 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:54.513 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:54.514 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:54.514 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:54.514 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:54.514 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:54.515 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:54.515 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:54.515 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:54.515 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:54 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam] SECOND_INPUT=[testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison4223893895287800591crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:54 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam] SECOND_INPUT=[testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison4223893895287800591crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:54 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:54:54 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:54 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:54 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:54 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam) WARNING 2024-07-02 11:54:54 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam) Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:54 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) WARNING 2024-07-02 11:54:54 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:54 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:54 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:54 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:54:54 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:55 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) WARNING 2024-07-02 11:54:55 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:55 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) WARNING 2024-07-02 11:54:55 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:55 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:55 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:55 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:54:55 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:55 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:54:55 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:55 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:55 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:55 CrosscheckFingerprints INFO 2024-07-02 11:54:55 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison4223893895287800591crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -CROSSCHECK_BY SAMPLE -SECOND_INPUT testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam -SECOND_INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison4223893895287800591crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -CROSSCHECK_BY SAMPLE -SECOND_INPUT testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam -SECOND_INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:55.302 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:55.302 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:55.303 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:55.303 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:55.304 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:55.304 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:55.304 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:55.304 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:55.304 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:55.304 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:55.304 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:55.304 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:55 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam] SECOND_INPUT=[testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison4223893895287800591crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:55 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam] SECOND_INPUT=[testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison4223893895287800591crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:55 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:54:55 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:55 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:55 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:55 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) WARNING 2024-07-02 11:54:55 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:55 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) WARNING 2024-07-02 11:54:55 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:56 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:56 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:56 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:54:56 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:56 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam) WARNING 2024-07-02 11:54:56 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam) Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:56 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) WARNING 2024-07-02 11:54:56 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:56 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:56 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:56 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:54:56 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:56 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:54:56 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:56 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:54:56 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.02 minutes. Test: Test method testMissingOrNoFingerprintingSites[17]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 0, 4, CHECK_ALL_OTHERS, SAMPLE, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:56 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true) STANDARD_ERROR INFO 2024-07-02 11:54:56 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison11439066180659882612crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT /tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison11439066180659882612crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT /tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -CROSSCHECK_BY SAMPLE Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:56.706 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:56.706 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:56.706 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:56.706 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:56.707 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:56.707 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:56.707 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:56.707 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:56.707 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:56.707 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:56.707 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:56.707 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:56 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison11439066180659882612crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:56 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison11439066180659882612crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:56 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:54:56 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:56 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:56 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:56 FingerprintChecker Reading an indexed file (/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam) INFO 2024-07-02 11:54:56 FingerprintChecker Reading an indexed file (/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam) Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:56 FingerprintChecker Processed files. 27 fingerprints found in map. INFO 2024-07-02 11:54:56 FingerprintChecker Processed files. 27 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:56 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:54:56 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:57 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:57 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:57 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:57 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:57 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:57 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:57 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:54:57 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:57 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites ERROR 2024-07-02 11:54:57 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:57 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:57 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:57 CrosscheckFingerprints INFO 2024-07-02 11:54:57 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison11439066180659882612crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -CROSSCHECK_BY SAMPLE -SECOND_INPUT /tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison11439066180659882612crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -CROSSCHECK_BY SAMPLE -SECOND_INPUT /tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:57.396 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:57.396 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:57.396 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:57.396 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:57.405 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:57.405 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:57.405 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:57.405 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:57.405 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:57.405 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:57.405 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:57.405 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:57 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] SECOND_INPUT=[/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison11439066180659882612crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:57 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] SECOND_INPUT=[/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison11439066180659882612crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:57 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:54:57 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:57 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:57 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:57 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:54:57 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:57 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:54:57 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:57 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:57 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:57 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:54:57 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:57 FingerprintChecker Reading an indexed file (/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam) INFO 2024-07-02 11:54:57 FingerprintChecker Reading an indexed file (/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam) Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:57 FingerprintChecker Processed files. 27 fingerprints found in map. INFO 2024-07-02 11:54:57 FingerprintChecker Processed files. 27 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:57 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:54:57 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:57 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites ERROR 2024-07-02 11:54:57 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:57 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:57 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[18]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:57 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true) STANDARD_ERROR INFO 2024-07-02 11:54:57 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison9827547175646405432crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam -SECOND_INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -SECOND_INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam -CROSSCHECK_BY SAMPLE ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison9827547175646405432crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam -SECOND_INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -SECOND_INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam -CROSSCHECK_BY SAMPLE Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:57.950 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:57.950 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:57.950 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:57.950 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:57.951 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:57.951 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:57.951 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:57.951 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:57.951 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:57.951 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:57.951 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:57.951 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:57 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam] SECOND_INPUT=[testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison9827547175646405432crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:57 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam] SECOND_INPUT=[testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison9827547175646405432crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:57 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:54:57 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:57 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:57 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:57 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam) WARNING 2024-07-02 11:54:57 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam) Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:58 FingerprintChecker Processed files. 27 fingerprints found in map. INFO 2024-07-02 11:54:58 FingerprintChecker Processed files. 27 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:58 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:54:58 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:58 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) WARNING 2024-07-02 11:54:58 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:58 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) WARNING 2024-07-02 11:54:58 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:58 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:58 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:58 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:54:58 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:58 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites ERROR 2024-07-02 11:54:58 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:58 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:58 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:58 CrosscheckFingerprints INFO 2024-07-02 11:54:58 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison9827547175646405432crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -CROSSCHECK_BY SAMPLE -SECOND_INPUT testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam -INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison9827547175646405432crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -CROSSCHECK_BY SAMPLE -SECOND_INPUT testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam -INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -INPUT testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:58.800 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:58.800 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:58.800 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:58.800 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:58.809 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:58.809 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:58.810 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:58.810 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:58.810 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:58.810 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:58.810 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:58.810 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:58 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam] SECOND_INPUT=[testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison9827547175646405432crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:58 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam] SECOND_INPUT=[testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison9827547175646405432crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:58 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:54:58 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:58 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:54:58 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:58 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) WARNING 2024-07-02 11:54:58 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:58 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) WARNING 2024-07-02 11:54:58 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:59 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:54:59 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:59 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:54:59 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:59 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam) WARNING 2024-07-02 11:54:59 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam) Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:59 FingerprintChecker Processed files. 27 fingerprints found in map. INFO 2024-07-02 11:54:59 FingerprintChecker Processed files. 27 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:59 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:54:59 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:54:59 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites ERROR 2024-07-02 11:54:59 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:59 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:59 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[19]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], [testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam], 1, 0, CHECK_ALL_OTHERS, SAMPLE, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:59 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true) STANDARD_ERROR INFO 2024-07-02 11:54:59 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison5745591275924326797crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT /tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam -CROSSCHECK_BY READGROUP ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison5745591275924326797crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT /tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam -CROSSCHECK_BY READGROUP Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:59.172 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:59.172 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:59.172 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:59.172 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:59.176 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:59.176 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:59.176 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:59.176 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:59.176 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:59.176 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:59.176 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:59.176 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:59 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison5745591275924326797crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:59 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison5745591275924326797crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:59 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:59 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:59 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam) INFO 2024-07-02 11:54:59 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam) Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:59 FingerprintChecker Processed files. 27 fingerprints found in map. INFO 2024-07-02 11:54:59 FingerprintChecker Processed files. 27 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:59 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:59 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:59 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:59 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:59 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:54:59 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testMissingOrNoFingerprintingSites[20]([/tmp/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam7625232651990051878.bam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:59 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true) STANDARD_ERROR INFO 2024-07-02 11:54:59 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison5537380367692431985crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam -CROSSCHECK_BY READGROUP ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison5537380367692431985crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam -CROSSCHECK_BY READGROUP Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:59.462 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:59.462 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:59.462 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:59.462 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:59.463 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:59.463 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:59.463 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:59.463 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:59.463 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:59.463 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:59.463 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:59.463 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:59 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison5537380367692431985crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:59 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison5537380367692431985crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:59 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:59 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:54:59 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam) WARNING 2024-07-02 11:54:59 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam) Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:59 FingerprintChecker Processed files. 27 fingerprints found in map. INFO 2024-07-02 11:54:59 FingerprintChecker Processed files. 27 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:59 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:54:59 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:59 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:54:59 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:59 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:54:59 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testMissingOrNoFingerprintingSites[21]([testdata/picard/fingerprint/NA12891.over.fingerprints.r1.one.rg.no.fingerprint.sam], null, 0, 729, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:59 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true) STANDARD_ERROR INFO 2024-07-02 11:54:59 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison12559918439123770579crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT /tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam -CROSSCHECK_BY READGROUP ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison12559918439123770579crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT /tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam -CROSSCHECK_BY READGROUP Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:59.923 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:54:59.923 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:59.923 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:54:59.923 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:59.924 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:59.924 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:59.924 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:59.924 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:59.924 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:54:59.924 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:54:59.924 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:54:59.924 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:59 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison12559918439123770579crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:54:59 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison12559918439123770579crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:54:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:54:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:59 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:54:59 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:54:59 FingerprintChecker Reading an indexed file (/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam) INFO 2024-07-02 11:54:59 FingerprintChecker Reading an indexed file (/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam) Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 27 fingerprints found in map. INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 27 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:55:00 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:55:00 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites ERROR 2024-07-02 11:55:00 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:00 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:00 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[22]([/tmp/NA12891.not.over.fingerprints.r1.sam13247668555613234763.bam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true) STANDARD_ERROR INFO 2024-07-02 11:55:00 CrosscheckFingerprints Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison9676103145468283287crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam -CROSSCHECK_BY READGROUP ********** CrosscheckFingerprints -OUTPUT /tmp/Fingerprinting.comparison9676103145468283287crosscheck_metrics -LOD_THRESHOLD -1.0 -HAPLOTYPE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam -CROSSCHECK_BY READGROUP Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.223 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:00.223 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.223 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:00.223 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.224 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:00.224 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.224 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:00.224 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.224 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:00.224 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.224 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:00.224 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:00 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison9676103145468283287crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:00 GMT+14:00 2024] CrosscheckFingerprints INPUT=[testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting.comparison9676103145468283287crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:00 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam) WARNING 2024-07-02 11:55:00 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam) Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 27 fingerprints found in map. INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 27 fingerprints found in map. Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:55:00 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ERROR 2024-07-02 11:55:00 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites ERROR 2024-07-02 11:55:00 CrosscheckFingerprints No non-zero results found. This is likely an error. Probable cause: there are no reads or variants at fingerprinting sites Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:00 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:00 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testMissingOrNoFingerprintingSites[23]([testdata/picard/fingerprint/NA12891.not.over.fingerprints.r1.sam], null, 1, 0, CHECK_ALL_OTHERS, READGROUP, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true) STANDARD_ERROR INFO 2024-07-02 11:55:00 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting4469815178572273647test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting4469815178572273647test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.391 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:00.391 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.391 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:00.391 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.392 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:00.392 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.392 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:00.392 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.392 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:00.392 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.392 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:00.392 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:00 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting4469815178572273647test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:00 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting4469815178572273647test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:00 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:00 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:00 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:00 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:00 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testSecondInputCheckAll[0]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true) STANDARD_ERROR INFO 2024-07-02 11:55:00 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting2740914552056581034test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting2740914552056581034test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.480 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:00.480 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.480 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:00.480 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.489 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:00.489 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.489 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:00.489 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.489 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:00.489 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.489 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:00.489 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:00 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting2740914552056581034test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:00 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting2740914552056581034test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:00 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:00 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:00 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:00 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:00 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testSecondInputCheckAll[1]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true) STANDARD_ERROR INFO 2024-07-02 11:55:00 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint7004491781434766928.vcf -INPUT /tmp/fingerprint12537519721137435765.vcf -INPUT /tmp/fingerprint10061884668032474124.vcf -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting13756079198369229296test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/fingerprint7004491781434766928.vcf -INPUT /tmp/fingerprint12537519721137435765.vcf -INPUT /tmp/fingerprint10061884668032474124.vcf -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting13756079198369229296test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.552 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:00.552 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.552 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:00.552 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.561 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:00.561 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.562 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:00.562 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.562 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:00.562 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.562 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:00.562 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:00 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting13756079198369229296test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:00 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting13756079198369229296test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:00 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 3 INPUT files. INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 3 INPUT files. Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 6 fingerprints found in map. INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 6 fingerprints found in map. Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:00 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:00 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:00 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:00 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testSecondInputCheckAll[2]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false) STANDARD_ERROR INFO 2024-07-02 11:55:00 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3612930247560801544.vcf -INPUT /tmp/fingerprint3086553580626660194.vcf -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting14320681130397914886test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3612930247560801544.vcf -INPUT /tmp/fingerprint3086553580626660194.vcf -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting14320681130397914886test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.629 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:00.629 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.629 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:00.629 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.630 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:00.630 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.630 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:00.630 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.631 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:00.631 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.631 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:00.631 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:00 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting14320681130397914886test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:00 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting14320681130397914886test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:00 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:00 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:00 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:55:00 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:00 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:00 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testSecondInputCheckAll[3]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true) STANDARD_ERROR INFO 2024-07-02 11:55:00 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint6359724907451755992.vcf -SECOND_INPUT /tmp/fingerprint17481944644093970365.vcf -OUTPUT /tmp/Fingerprinting9535433605419481384test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint6359724907451755992.vcf -SECOND_INPUT /tmp/fingerprint17481944644093970365.vcf -OUTPUT /tmp/Fingerprinting9535433605419481384test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.704 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:00.704 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.704 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:00.704 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.714 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:00.714 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.714 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:00.714 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.714 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:00.714 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.714 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:00.714 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:00 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting9535433605419481384test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:00 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting9535433605419481384test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:00 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:00 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:00 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:00 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:00 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testSecondInputCheckAll[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true) STANDARD_ERROR INFO 2024-07-02 11:55:00 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/fingerprint6359724907451755992.vcf -SECOND_INPUT /tmp/fingerprint17481944644093970365.vcf -OUTPUT /tmp/Fingerprinting12021766081359294786test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/fingerprint6359724907451755992.vcf -SECOND_INPUT /tmp/fingerprint17481944644093970365.vcf -OUTPUT /tmp/Fingerprinting12021766081359294786test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.797 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:00.797 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.797 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:00.797 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.798 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:00.798 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.798 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:00.798 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.799 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:00.799 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.799 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:00.799 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:00 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting12021766081359294786test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:00 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting12021766081359294786test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:00 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:00 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:00 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:00 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:00 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testSecondInputCheckAll[5]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true) STANDARD_ERROR INFO 2024-07-02 11:55:00 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting9478251309499182849test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting9478251309499182849test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.864 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:00.864 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.864 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:00.864 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.873 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:00.873 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.873 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:00.873 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.873 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:00.873 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.873 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:00.873 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:00 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting9478251309499182849test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:00 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting9478251309499182849test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:00 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:00 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:00 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:00 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:00 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testSecondInputCheckAll[6]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false) STANDARD_ERROR INFO 2024-07-02 11:55:00 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint3612930247560801544.vcf -OUTPUT /tmp/Fingerprinting6848918713372207729test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint3612930247560801544.vcf -OUTPUT /tmp/Fingerprinting6848918713372207729test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.956 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:00.956 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.959 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:00.959 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.960 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:00.960 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.960 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:00.960 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.961 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:00.961 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:00.961 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:00.961 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:00 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting6848918713372207729test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:00 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting6848918713372207729test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:00 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:00 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:00 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:01 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:01 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:01 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:01 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:01 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:55:01 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:01 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:01 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testSecondInputCheckAll[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint3612930247560801544.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:01 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true) STANDARD_ERROR INFO 2024-07-02 11:55:01 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint7004491781434766928.vcf -INPUT /tmp/fingerprint12537519721137435765.vcf -INPUT /tmp/fingerprint10061884668032474124.vcf -SECOND_INPUT /tmp/fingerprint6359724907451755992.vcf -SECOND_INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -OUTPUT /tmp/Fingerprinting17528406811018217378test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/fingerprint7004491781434766928.vcf -INPUT /tmp/fingerprint12537519721137435765.vcf -INPUT /tmp/fingerprint10061884668032474124.vcf -SECOND_INPUT /tmp/fingerprint6359724907451755992.vcf -SECOND_INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -OUTPUT /tmp/Fingerprinting17528406811018217378test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:01.022 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:01.022 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:01.023 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:01.023 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:01.024 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:01.024 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:01.024 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:01.024 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:01.024 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:01.024 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:01.024 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:01.024 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:01 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf] SECOND_INPUT=[/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting17528406811018217378test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:01 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf] SECOND_INPUT=[/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting17528406811018217378test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:01 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:01 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:01 CrosscheckFingerprints Fingerprinting 3 INPUT files. INFO 2024-07-02 11:55:01 CrosscheckFingerprints Fingerprinting 3 INPUT files. Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:01 FingerprintChecker Processed files. 6 fingerprints found in map. INFO 2024-07-02 11:55:01 FingerprintChecker Processed files. 6 fingerprints found in map. Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:01 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:01 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:01 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:55:01 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:01 FingerprintChecker Processed files. 26 fingerprints found in map. INFO 2024-07-02 11:55:01 FingerprintChecker Processed files. 26 fingerprints found in map. Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:01 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:01 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:01 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:01 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:01 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:01 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testSecondInputCheckAll[8]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:01 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true) STANDARD_ERROR INFO 2024-07-02 11:55:01 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting15563401919337477276test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting15563401919337477276test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:01.439 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:01.439 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:01.439 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:01.439 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:01.440 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:01.440 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:01.440 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:01.440 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:01.440 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:01.440 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:01.440 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:01.440 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:01 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting15563401919337477276test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:01 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting15563401919337477276test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:01 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:01 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:01 CrosscheckFingerprints Fingerprinting 4 INPUT files. INFO 2024-07-02 11:55:01 CrosscheckFingerprints Fingerprinting 4 INPUT files. Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:01 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:55:01 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:01 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:55:01 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:01 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:55:01 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:02 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:55:02 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:02 FingerprintChecker Processed files. 104 fingerprints found in map. INFO 2024-07-02 11:55:02 FingerprintChecker Processed files. 104 fingerprints found in map. Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:02 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:02 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:02 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:02 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:02 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:02 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:02 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:02 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:02 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:55:02 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.02 minutes. Test: Test method testSecondInputCheckAll[9]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:02 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false) STANDARD_ERROR INFO 2024-07-02 11:55:02 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting9661650425249377677test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -SECOND_INPUT /tmp/fingerprint3859807643852947023.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting9661650425249377677test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:02.810 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:02.810 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:02.810 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:02.810 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:02.811 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:02.811 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:02.811 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:02.811 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:02.811 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:02.811 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:02.811 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:02.811 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:02 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting9661650425249377677test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:02 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam] SECOND_INPUT=[/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting9661650425249377677test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:02 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:02 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:02 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:02 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:02 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:55:02 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:03 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:55:03 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:03 FingerprintChecker Processed files. 54 fingerprints found in map. INFO 2024-07-02 11:55:03 FingerprintChecker Processed files. 54 fingerprints found in map. Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:03 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:03 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:03 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:03 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:03 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:03 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:03 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:55:03 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:03 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:03 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testSecondInputCheckAll[10]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint3859807643852947023.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:03 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true) STANDARD_ERROR INFO 2024-07-02 11:55:03 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/fingerprint17481944644093970365.vcf -OUTPUT /tmp/Fingerprinting12803182888708650001test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/fingerprint17481944644093970365.vcf -OUTPUT /tmp/Fingerprinting12803182888708650001test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:03.193 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:03.193 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:03.193 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:03.193 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:03.194 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:03.194 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:03.194 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:03.194 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:03.194 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:03.194 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:03.194 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:03.194 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:03 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting12803182888708650001test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:03 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting12803182888708650001test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:03 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:03 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:03 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:03 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:03 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:55:03 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:03 FingerprintChecker Processed files. 26 fingerprints found in map. INFO 2024-07-02 11:55:03 FingerprintChecker Processed files. 26 fingerprints found in map. Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:03 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:03 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:03 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:55:03 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:03 FingerprintChecker Processed files. 27 fingerprints found in map. INFO 2024-07-02 11:55:03 FingerprintChecker Processed files. 27 fingerprints found in map. Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:03 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:03 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:03 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:03 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:03 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:03 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testSecondInputCheckAll[11]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:03 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false) STANDARD_ERROR INFO 2024-07-02 11:55:03 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/fingerprint15046719082929058843.vcf -OUTPUT /tmp/Fingerprinting3098843781113154596test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/fingerprint15046719082929058843.vcf -OUTPUT /tmp/Fingerprinting3098843781113154596test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:03.670 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:03.670 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:03.670 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:03.670 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:03.671 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:03.671 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:03.671 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:03.671 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:03.671 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:03.671 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:03.671 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:03.671 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:03 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting3098843781113154596test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:03 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting3098843781113154596test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:03 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:03 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:03 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:03 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:03 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:55:03 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:03 FingerprintChecker Processed files. 28 fingerprints found in map. INFO 2024-07-02 11:55:03 FingerprintChecker Processed files. 28 fingerprints found in map. Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:03 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:03 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:03 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:55:03 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:04 FingerprintChecker Processed files. 27 fingerprints found in map. INFO 2024-07-02 11:55:04 FingerprintChecker Processed files. 27 fingerprints found in map. Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:04 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:04 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:04 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:55:04 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:04 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:04 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testSecondInputCheckAll[12]([/tmp/fingerprint3086553580626660194.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:04 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false) STANDARD_ERROR INFO 2024-07-02 11:55:04 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint6359724907451755992.vcf -SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting13638508460090844624test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint6359724907451755992.vcf -SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting13638508460090844624test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:04.062 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:04.062 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:04.062 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:04.062 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:04.063 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:04.063 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:04.063 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:04.063 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:04.063 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:04.063 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:04.063 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:04.063 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:04 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting13638508460090844624test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:04 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting13638508460090844624test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:04 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:04 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:04 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:04 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:04 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:04 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:04 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:04 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:04 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:55:04 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:04 FingerprintChecker Processed files. 28 fingerprints found in map. INFO 2024-07-02 11:55:04 FingerprintChecker Processed files. 28 fingerprints found in map. Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:04 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:04 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:04 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:55:04 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:04 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:04 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testSecondInputCheckAll[13]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:04 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false) STANDARD_ERROR INFO 2024-07-02 11:55:04 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/fingerprint6359724907451755992.vcf -SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting17288156709420613430test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/fingerprint6359724907451755992.vcf -SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting17288156709420613430test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:04.313 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:04.313 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:04.313 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:04.313 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:04.315 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:04.315 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:04.315 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:04.315 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:04.315 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:04.315 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:04.315 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:04.315 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:04 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting17288156709420613430test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:04 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting17288156709420613430test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:04 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:04 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:04 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:55:04 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:04 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:04 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:04 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:04 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:04 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:55:04 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:04 FingerprintChecker Processed files. 28 fingerprints found in map. INFO 2024-07-02 11:55:04 FingerprintChecker Processed files. 28 fingerprints found in map. Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:04 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:04 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:04 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:55:04 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:04 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:04 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testSecondInputCheckAll[14]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:04 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true) STANDARD_ERROR INFO 2024-07-02 11:55:04 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting5493023496168914376test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting5493023496168914376test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:04.586 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:04.586 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:04.587 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:04.587 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:04.588 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:04.588 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:04.588 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:04.588 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:04.588 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:04.588 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:04.588 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:04.588 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:04 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting5493023496168914376test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:04 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting5493023496168914376test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:04 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:04 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:04 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:04 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:04 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:55:04 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:04 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:55:04 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:05 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:55:05 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:05 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:05 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:05 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:55:05 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:05 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:55:05 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:05 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:55:05 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:05 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:05 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:05 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:05 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:05 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:55:05 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.02 minutes. Test: Test method testSecondInputCheckAll[15]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 2, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:05 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true) STANDARD_ERROR INFO 2024-07-02 11:55:05 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting2285991712180394801test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting2285991712180394801test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:05.849 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:05.849 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:05.850 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:05.850 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:05.851 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:05.851 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:05.851 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:05.851 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:05.851 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:05.851 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:05.851 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:05.851 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:05 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting2285991712180394801test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:05 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting2285991712180394801test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:05 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:05 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:05 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:05 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:05 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:55:05 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:06 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:55:06 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:06 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:55:06 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:06 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:55:06 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:06 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:55:06 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:06 FingerprintChecker Processed files. 26 fingerprints found in map. INFO 2024-07-02 11:55:06 FingerprintChecker Processed files. 26 fingerprints found in map. Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:06 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:06 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:06 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:06 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:06 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:55:06 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.02 minutes. Test: Test method testSecondInputCheckAll[16]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 2, 1, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:06 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true) STANDARD_ERROR INFO 2024-07-02 11:55:06 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting8239921156303185515test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting8239921156303185515test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:06.882 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:06.882 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:06.882 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:06.882 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:06.883 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:06.883 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:06.883 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:06.883 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:06.883 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:06.883 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:06.883 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:06.883 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:06 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting8239921156303185515test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:06 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting8239921156303185515test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:06 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:06 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:06 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:55:06 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:06 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:55:06 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:07 FingerprintChecker Processed files. 27 fingerprints found in map. INFO 2024-07-02 11:55:07 FingerprintChecker Processed files. 27 fingerprints found in map. Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:07 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:07 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:07 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:55:07 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:07 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:55:07 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:07 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:55:07 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:07 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:07 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:07 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:07 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:07 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:07 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testSecondInputCheckAll[17]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, true)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:07 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false) STANDARD_ERROR INFO 2024-07-02 11:55:07 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting14841528784371190704test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting14841528784371190704test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:07.578 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:07.578 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:07.578 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:07.578 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:07.579 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:07.579 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:07.579 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:07.579 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:07.579 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:07.579 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:07.579 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:07.579 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:07 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting14841528784371190704test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:07 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting14841528784371190704test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:07 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:07 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:07 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:07 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:07 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:55:07 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:07 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:55:07 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:07 FingerprintChecker Processed files. 54 fingerprints found in map. INFO 2024-07-02 11:55:07 FingerprintChecker Processed files. 54 fingerprints found in map. Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:07 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:07 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:07 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:55:07 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:08 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:55:08 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:08 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:55:08 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:08 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:08 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:08 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:55:08 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:08 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:08 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testSecondInputCheckAll[18]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:08 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false) STANDARD_ERROR INFO 2024-07-02 11:55:08 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting15152691205797472212test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting15152691205797472212test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:08.462 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:08.462 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:08.462 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:08.462 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:08.463 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:08.463 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:08.463 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:08.463 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:08.463 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:08.463 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:08.463 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:08.463 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:08 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting15152691205797472212test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:08 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting15152691205797472212test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:08 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:08 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:08 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:08 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:08 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:55:08 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:09 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:55:09 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:09 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:55:09 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:09 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:09 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:09 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:55:09 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:09 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:55:09 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:09 FingerprintChecker Processed files. 54 fingerprints found in map. INFO 2024-07-02 11:55:09 FingerprintChecker Processed files. 54 fingerprints found in map. Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:09 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:09 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:09 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:55:09 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:09 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:55:09 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.02 minutes. Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testSecondInputCheckAll[19]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:09 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false) STANDARD_ERROR INFO 2024-07-02 11:55:09 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint6454488665071355617.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting5125769247260948930test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint6454488665071355617.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting5125769247260948930test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:09.907 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:09.907 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:09.907 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:09.907 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:09.908 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:09.908 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:09.908 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:09.908 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:09.908 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:09.908 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:09.908 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:09.908 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:09 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting5125769247260948930test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:09 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting5125769247260948930test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:09 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:09 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:09 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:09 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:09 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:09 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:09 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:09 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:09 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:09 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:09 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:09 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:09 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:55:09 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:09 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:09 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testSecondInputCheckAll[20]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 1, 2, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:09 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false) STANDARD_ERROR INFO 2024-07-02 11:55:09 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting7859464275836215747test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting7859464275836215747test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:09.983 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:09.983 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:09.984 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:09.984 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:09.985 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:09.985 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:09.985 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:09.985 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:09.985 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:09.985 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:09.985 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:09.985 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:09 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting7859464275836215747test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:09 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting7859464275836215747test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:09 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:09 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:09 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:09 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:10 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:10 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:10 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:10 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testSecondInputCheckAll[21]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false) STANDARD_ERROR INFO 2024-07-02 11:55:10 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting2739459485983618246test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting2739459485983618246test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.047 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:10.047 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.047 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:10.047 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.048 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:10.048 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.048 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:10.048 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.048 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:10.048 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.048 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:10.048 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:10 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting2739459485983618246test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:10 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting2739459485983618246test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:10 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:10 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:10 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:10 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:10 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testSecondInputCheckAll[22]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false) STANDARD_ERROR INFO 2024-07-02 11:55:10 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint7004491781434766928.vcf -INPUT /tmp/fingerprint12537519721137435765.vcf -INPUT /tmp/fingerprint10061884668032474124.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting12901333966520413848test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/fingerprint7004491781434766928.vcf -INPUT /tmp/fingerprint12537519721137435765.vcf -INPUT /tmp/fingerprint10061884668032474124.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting12901333966520413848test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.142 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:10.142 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.143 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:10.143 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.143 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:10.143 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.143 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:10.143 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.144 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:10.144 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.144 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:10.144 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:10 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf] SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting12901333966520413848test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:10 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf] SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting12901333966520413848test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:10 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 3 INPUT files. INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 3 INPUT files. Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 6 fingerprints found in map. INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 6 fingerprints found in map. Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:10 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:10 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:10 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:10 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testSecondInputCheckAll[23]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false) STANDARD_ERROR INFO 2024-07-02 11:55:10 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3612930247560801544.vcf -INPUT /tmp/fingerprint3086553580626660194.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting16520321574828543224test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3612930247560801544.vcf -INPUT /tmp/fingerprint3086553580626660194.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting16520321574828543224test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.247 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:10.247 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.247 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:10.247 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.248 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:10.248 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.248 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:10.248 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.248 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:10.248 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.248 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:10.248 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:10 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf] SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting16520321574828543224test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:10 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf] SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting16520321574828543224test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:10 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:10 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:10 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:55:10 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:10 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:10 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testSecondInputCheckAll[24]([/tmp/fingerprint3612930247560801544.vcf, /tmp/fingerprint3086553580626660194.vcf], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false) STANDARD_ERROR INFO 2024-07-02 11:55:10 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint17481944644093970365.vcf -OUTPUT /tmp/Fingerprinting17645987751016864080test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint17481944644093970365.vcf -OUTPUT /tmp/Fingerprinting17645987751016864080test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.317 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:10.317 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.317 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:10.317 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.318 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:10.318 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.318 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:10.318 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.318 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:10.318 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.318 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:10.318 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:10 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint17481944644093970365.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting17645987751016864080test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:10 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint17481944644093970365.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting17645987751016864080test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:10 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:10 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:10 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:10 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:10 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testSecondInputCheckAll[25]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false) STANDARD_ERROR INFO 2024-07-02 11:55:10 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/fingerprint17481944644093970365.vcf -OUTPUT /tmp/Fingerprinting10284655705767882330test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/fingerprint17481944644093970365.vcf -OUTPUT /tmp/Fingerprinting10284655705767882330test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.375 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:10.375 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.375 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:10.375 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.376 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:10.376 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.376 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:10.376 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.376 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:10.376 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.376 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:10.376 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:10 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint17481944644093970365.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting10284655705767882330test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:10 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint17481944644093970365.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting10284655705767882330test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:10 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:10 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:10 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:10 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:10 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testSecondInputCheckAll[26]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint17481944644093970365.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false) STANDARD_ERROR INFO 2024-07-02 11:55:10 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting7874262481311805239test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting7874262481311805239test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.438 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:10.438 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.438 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:10.438 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.439 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:10.439 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.439 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:10.439 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.439 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:10.439 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.439 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:10.439 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:10 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting7874262481311805239test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:10 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting7874262481311805239test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:10 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:10 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:10 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:10 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:10 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testSecondInputCheckAll[27]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false) STANDARD_ERROR INFO 2024-07-02 11:55:10 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/fingerprint3612930247560801544.vcf -OUTPUT /tmp/Fingerprinting16720331304656435480test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/fingerprint3612930247560801544.vcf -OUTPUT /tmp/Fingerprinting16720331304656435480test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.514 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:10.514 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.514 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:10.514 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.541 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:10.541 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.541 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:10.541 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.541 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:10.541 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.541 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:10.541 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:10 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint3612930247560801544.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting16720331304656435480test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:10 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/fingerprint3612930247560801544.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting16720331304656435480test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:10 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:10 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:10 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:55:10 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:10 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:10 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testSecondInputCheckAll[28]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/fingerprint3612930247560801544.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false) STANDARD_ERROR INFO 2024-07-02 11:55:10 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint7004491781434766928.vcf -INPUT /tmp/fingerprint12537519721137435765.vcf -INPUT /tmp/fingerprint10061884668032474124.vcf -SECOND_INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -OUTPUT /tmp/Fingerprinting2648211957582770695test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/fingerprint7004491781434766928.vcf -INPUT /tmp/fingerprint12537519721137435765.vcf -INPUT /tmp/fingerprint10061884668032474124.vcf -SECOND_INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -OUTPUT /tmp/Fingerprinting2648211957582770695test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.594 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:10.594 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.595 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:10.595 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.595 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:10.595 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.596 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:10.596 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.596 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:10.596 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.596 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:10.596 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:10 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf] SECOND_INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting2648211957582770695test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:10 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf] SECOND_INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting2648211957582770695test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:10 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 3 INPUT files. INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 3 INPUT files. Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 6 fingerprints found in map. INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 6 fingerprints found in map. Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:55:10 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 25 fingerprints found in map. INFO 2024-07-02 11:55:10 FingerprintChecker Processed files. 25 fingerprints found in map. Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:10 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:10 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:10 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:10 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testSecondInputCheckAll[29]([/tmp/fingerprint7004491781434766928.vcf, /tmp/fingerprint12537519721137435765.vcf, /tmp/fingerprint10061884668032474124.vcf], [/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false) STANDARD_ERROR INFO 2024-07-02 11:55:10 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting11132572367374286578test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting11132572367374286578test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.884 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:10.884 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.884 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:10.884 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.894 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:10.894 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.894 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:10.894 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.894 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:10.894 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:10.894 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:10.894 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:10 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting11132572367374286578test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:10 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting11132572367374286578test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:10 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 4 INPUT files. INFO 2024-07-02 11:55:10 CrosscheckFingerprints Fingerprinting 4 INPUT files. Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:10 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:55:10 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:11 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:55:11 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:11 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:55:11 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:11 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:55:11 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:11 FingerprintChecker Processed files. 104 fingerprints found in map. INFO 2024-07-02 11:55:11 FingerprintChecker Processed files. 104 fingerprints found in map. Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:11 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:55:11 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:11 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:55:11 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:11 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:11 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:11 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:11 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:11 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:55:11 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.02 minutes. Test: Test method testSecondInputCheckAll[30]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam, /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], [/tmp/fingerprint10298716060568440981.vcf], 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:11 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false) STANDARD_ERROR INFO 2024-07-02 11:55:11 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting9052243324149428327test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting9052243324149428327test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:11.983 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:11.983 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:11.983 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:11.983 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:11.984 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:11.984 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:11.984 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:11.984 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:11.984 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:11.984 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:11.985 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:11.985 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:11 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam] SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting9052243324149428327test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:11 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam] SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting9052243324149428327test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:11 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:11 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:11 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:11 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:12 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:55:12 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:12 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:55:12 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:12 FingerprintChecker Processed files. 54 fingerprints found in map. INFO 2024-07-02 11:55:12 FingerprintChecker Processed files. 54 fingerprints found in map. Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:12 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:55:12 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:12 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:55:12 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:12 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:12 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:12 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:55:12 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:12 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:12 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testSecondInputCheckAll[31]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam, /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/fingerprint10298716060568440981.vcf], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:12 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false) STANDARD_ERROR INFO 2024-07-02 11:55:12 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/fingerprint17481944644093970365.vcf -OUTPUT /tmp/Fingerprinting17405702501761030440test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/fingerprint17481944644093970365.vcf -OUTPUT /tmp/Fingerprinting17405702501761030440test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:12.598 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:12.598 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:12.599 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:12.599 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:12.599 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:12.599 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:12.599 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:12.599 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:12.600 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:12.600 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:12.600 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:12.600 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:12 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting17405702501761030440test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:12 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting17405702501761030440test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:12 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:12 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:12 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:55:12 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:12 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:55:12 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:12 FingerprintChecker Processed files. 25 fingerprints found in map. INFO 2024-07-02 11:55:12 FingerprintChecker Processed files. 25 fingerprints found in map. Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:12 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:12 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:12 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:55:12 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:13 FingerprintChecker Processed files. 27 fingerprints found in map. INFO 2024-07-02 11:55:13 FingerprintChecker Processed files. 27 fingerprints found in map. Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:13 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:13 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:13 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:13 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:13 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:13 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testSecondInputCheckAll[32]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint17481944644093970365.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:13 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false) STANDARD_ERROR INFO 2024-07-02 11:55:13 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/fingerprint15046719082929058843.vcf -OUTPUT /tmp/Fingerprinting5982908693867041822test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/fingerprint15046719082929058843.vcf -OUTPUT /tmp/Fingerprinting5982908693867041822test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:13.509 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:13.509 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:13.509 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:13.509 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:13.511 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:13.511 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:13.511 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:13.511 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:13.511 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:13.511 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:13.511 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:13.511 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:13 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting5982908693867041822test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:13 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting5982908693867041822test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:13 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:13 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:13 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:55:13 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:13 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:55:13 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:13 FingerprintChecker Processed files. 27 fingerprints found in map. INFO 2024-07-02 11:55:13 FingerprintChecker Processed files. 27 fingerprints found in map. Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:13 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:13 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:13 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:55:13 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:13 FingerprintChecker Processed files. 27 fingerprints found in map. INFO 2024-07-02 11:55:13 FingerprintChecker Processed files. 27 fingerprints found in map. Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:13 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:13 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:13 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:55:13 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:13 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:13 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testSecondInputCheckAll[33]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/fingerprint15046719082929058843.vcf], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:13 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false) STANDARD_ERROR INFO 2024-07-02 11:55:13 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint6359724907451755992.vcf -SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting11408856103610114647test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint6359724907451755992.vcf -SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting11408856103610114647test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:13.933 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:13.933 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:13.933 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:13.933 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:13.934 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:13.934 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:13.934 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:13.934 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:13.934 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:13.934 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:13.934 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:13.934 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:13 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting11408856103610114647test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:13 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting11408856103610114647test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:13 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:13 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:13 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:55:13 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:13 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:55:13 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:13 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:13 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:13 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:55:13 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:14 FingerprintChecker Processed files. 28 fingerprints found in map. INFO 2024-07-02 11:55:14 FingerprintChecker Processed files. 28 fingerprints found in map. Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:14 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:14 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:14 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:55:14 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:14 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:14 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testSecondInputCheckAll[34]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6359724907451755992.vcf, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:14 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false) STANDARD_ERROR INFO 2024-07-02 11:55:14 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting11901930726650947944test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting11901930726650947944test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:14.148 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:14.148 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:14.149 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:14.149 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:14.158 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:14.158 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:14.158 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:14.158 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:14.158 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:14.158 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:14.158 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:14.158 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:14 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting11901930726650947944test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:14 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting11901930726650947944test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:14 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:14 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:14 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:55:14 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:14 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:14 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:14 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:55:14 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:14 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:55:14 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:14 FingerprintChecker Processed files. 27 fingerprints found in map. INFO 2024-07-02 11:55:14 FingerprintChecker Processed files. 27 fingerprints found in map. Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:14 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:14 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:14 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:55:14 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:14 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:14 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testSecondInputCheckAll[35]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:14 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false) STANDARD_ERROR INFO 2024-07-02 11:55:14 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting469148760655635164test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting469148760655635164test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:14.536 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:14.536 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:14.537 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:14.537 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:14.546 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:14.546 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:14.546 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:14.546 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:14.546 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:14.546 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:14.546 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:14.546 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:14 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting469148760655635164test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:14 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting469148760655635164test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:14 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:14 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:14 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:55:14 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:14 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:55:14 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:14 FingerprintChecker Processed files. 25 fingerprints found in map. INFO 2024-07-02 11:55:14 FingerprintChecker Processed files. 25 fingerprints found in map. Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:14 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:14 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:14 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:55:14 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:15 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:55:15 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:15 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:55:15 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:15 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:15 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:15 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:15 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:15 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:15 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testSecondInputCheckAll[36]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:15 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false) STANDARD_ERROR INFO 2024-07-02 11:55:15 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting12315561007380703391test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting12315561007380703391test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:15.364 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:15.364 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:15.365 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:15.365 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:15.374 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:15.374 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:15.374 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:15.374 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:15.374 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:15.374 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:15.374 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:15.374 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:15 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting12315561007380703391test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:15 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting12315561007380703391test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:15 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:15 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:15 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:55:15 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:15 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:55:15 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:15 FingerprintChecker Processed files. 25 fingerprints found in map. INFO 2024-07-02 11:55:15 FingerprintChecker Processed files. 25 fingerprints found in map. Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:15 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:55:15 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:15 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:55:15 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:15 FingerprintChecker Processed files. 26 fingerprints found in map. INFO 2024-07-02 11:55:15 FingerprintChecker Processed files. 26 fingerprints found in map. Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:15 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:15 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:15 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:15 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:15 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:15 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testSecondInputCheckAll[37]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:15 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false) STANDARD_ERROR INFO 2024-07-02 11:55:15 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting16029807832289135545test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting16029807832289135545test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:15.824 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:15.824 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:15.824 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:15.824 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:15.833 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:15.833 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:15.833 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:15.833 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:15.833 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:15.833 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:15.833 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:15.833 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:15 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam] SECOND_INPUT=[/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting16029807832289135545test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:15 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam] SECOND_INPUT=[/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting16029807832289135545test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:15 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:15 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:15 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:55:15 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:15 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:55:15 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:16 FingerprintChecker Processed files. 27 fingerprints found in map. INFO 2024-07-02 11:55:16 FingerprintChecker Processed files. 27 fingerprints found in map. Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:16 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:55:16 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:16 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:55:16 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:16 FingerprintChecker Processed files. 26 fingerprints found in map. INFO 2024-07-02 11:55:16 FingerprintChecker Processed files. 26 fingerprints found in map. Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:16 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:16 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:16 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:16 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:16 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:16 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testSecondInputCheckAll[38]([/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam], [/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:16 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false) STANDARD_ERROR INFO 2024-07-02 11:55:16 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting12875898341665926951test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting12875898341665926951test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:16.669 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:16.669 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:16.669 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:16.669 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:16.672 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:16.672 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:16.672 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:16.672 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:16.676 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:16.676 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:16.676 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:16.676 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:16 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting12875898341665926951test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:16 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting12875898341665926951test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:16 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:16 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:16 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:55:16 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:16 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:55:16 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:16 FingerprintChecker Processed files. 27 fingerprints found in map. INFO 2024-07-02 11:55:16 FingerprintChecker Processed files. 27 fingerprints found in map. Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:16 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:16 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:16 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:55:16 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:17 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:55:17 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:17 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:55:17 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:17 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:17 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:17 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:55:17 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:17 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:17 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testSecondInputCheckAll[39]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:17 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false) STANDARD_ERROR INFO 2024-07-02 11:55:17 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting488733845822933299test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam -SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting488733845822933299test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:17.229 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:17.229 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:17.234 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:17.234 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:17.234 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:17.234 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:17.234 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:17.234 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:17.235 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:17.235 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:17.235 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:17.235 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:17 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting488733845822933299test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:17 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting488733845822933299test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:17 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:17 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:17 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:55:17 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:17 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:55:17 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:17 FingerprintChecker Processed files. 25 fingerprints found in map. INFO 2024-07-02 11:55:17 FingerprintChecker Processed files. 25 fingerprints found in map. Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:17 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:17 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:17 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) INFO 2024-07-02 11:55:17 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam) Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:17 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:55:17 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:17 FingerprintChecker Processed files. 54 fingerprints found in map. INFO 2024-07-02 11:55:17 FingerprintChecker Processed files. 54 fingerprints found in map. Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:17 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:17 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:17 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:55:17 CrosscheckFingerprints 1 SAMPLEs did not relate as expected. Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:17 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:17 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testSecondInputCheckAll[40]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r1.sam11426760936722423086.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], 1, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:17 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false) STANDARD_ERROR INFO 2024-07-02 11:55:17 CrosscheckFingerprints Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint6454488665071355617.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting17105127209807102643test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint6454488665071355617.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting17105127209807102643test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:17.826 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:17.826 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:17.826 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:17.826 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:17.827 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:17.827 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:17.827 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:17.827 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:17.827 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:17.827 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:17.827 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:17.827 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:17 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting17105127209807102643test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:17 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting17105127209807102643test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:17 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:17 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:17 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:55:17 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:17 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:55:17 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:17 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:17 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:17 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:17 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:17 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:17 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:17 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:17 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:17 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:17 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testSecondInputCheckAll[41]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint6454488665071355617.vcf, /tmp/fingerprint10298716060568440981.vcf], 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:17 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAllWithFileMapping STANDARD_ERROR INFO 2024-07-02 11:55:17 CrosscheckFingerprints Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting11207015671048567105test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT_SAMPLE_FILE_MAP /tmp/map11551323632439790332.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting11207015671048567105test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT_SAMPLE_FILE_MAP /tmp/map11551323632439790332.txt Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:17.910 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:17.910 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:17.910 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:17.910 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:17.911 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:17.911 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:17.911 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:17.911 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:17.911 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:17.911 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:17.911 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:17.911 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:17 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] INPUT_SAMPLE_FILE_MAP=/tmp/map11551323632439790332.txt SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting11207015671048567105test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:17 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] INPUT_SAMPLE_FILE_MAP=/tmp/map11551323632439790332.txt SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting11207015671048567105test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:17 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:17 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:17 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:55:17 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:17 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:55:17 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:18 FingerprintChecker Processed files. 27 fingerprints found in map. INFO 2024-07-02 11:55:18 FingerprintChecker Processed files. 27 fingerprints found in map. Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:18 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:55:18 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:18 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:55:18 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:18 FingerprintChecker Processed files. 26 fingerprints found in map. INFO 2024-07-02 11:55:18 FingerprintChecker Processed files. 26 fingerprints found in map. Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:18 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:18 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:18 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:18 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:18 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:18 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testSecondInputCheckAllWithFileMapping(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:18 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false) STANDARD_ERROR INFO 2024-07-02 11:55:18 CrosscheckFingerprints Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting18296373752739803251test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NotThere_to_NA12891.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting18296373752739803251test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NotThere_to_NA12891.txt Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:18.267 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:18.267 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:18.267 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:18.267 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:18.268 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:18.268 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:18.268 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:18.268 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:18.268 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:18.268 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:18.268 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:18.268 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:18 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NotThere_to_NA12891.txt SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting18296373752739803251test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:18 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NotThere_to_NA12891.txt SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting18296373752739803251test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:18 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:18 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:18 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:55:18 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:18 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:55:18 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:18 FingerprintChecker Processed files. 25 fingerprints found in map. INFO 2024-07-02 11:55:18 FingerprintChecker Processed files. 25 fingerprints found in map. Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:18 CrosscheckFingerprints Some samples in first column in the INPUT_SAMPLE_MAP were not present as samples in fingerprinted file: [NotThere]. WARNING 2024-07-02 11:55:18 CrosscheckFingerprints Some samples in first column in the INPUT_SAMPLE_MAP were not present as samples in fingerprinted file: [NotThere]. Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:18 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:18 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:18 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:55:18 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:18 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:55:18 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:19 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:55:19 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:19 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:19 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:19 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:19 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:19 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:19 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testSecondInputCheckAllWithMapping[0]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, null, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:19 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false) STANDARD_ERROR INFO 2024-07-02 11:55:19 CrosscheckFingerprints Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting2801584429343822332test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -SECOND_INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NotThere_to_NA12891.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting2801584429343822332test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -SECOND_INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NotThere_to_NA12891.txt Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:19.094 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:19.094 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:19.094 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:19.094 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:19.095 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:19.095 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:19.095 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:19.095 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:19.096 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:19.096 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:19.096 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:19.096 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:19 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] SECOND_INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NotThere_to_NA12891.txt CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting2801584429343822332test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:19 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] SECOND_INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NotThere_to_NA12891.txt CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting2801584429343822332test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:19 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:19 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:19 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:55:19 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:19 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:55:19 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:19 FingerprintChecker Processed files. 25 fingerprints found in map. INFO 2024-07-02 11:55:19 FingerprintChecker Processed files. 25 fingerprints found in map. Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:19 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:19 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:19 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:55:19 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:19 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:55:19 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:19 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:55:19 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:19 CrosscheckFingerprints Some samples in first column in the SECOND_INPUT_SAMPLE_MAP were not present as samples in fingerprinted file: [NotThere]. WARNING 2024-07-02 11:55:19 CrosscheckFingerprints Some samples in first column in the SECOND_INPUT_SAMPLE_MAP were not present as samples in fingerprinted file: [NotThere]. Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:19 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:19 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:19 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:19 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:19 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:19 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testSecondInputCheckAllWithMapping[1]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], null, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:19 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false) STANDARD_ERROR INFO 2024-07-02 11:55:19 CrosscheckFingerprints Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting3197140079170237073test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NotThere_to_NA12891.txt -SECOND_INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NotThere_to_NA12891.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -SECOND_INPUT /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam -OUTPUT /tmp/Fingerprinting3197140079170237073test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NotThere_to_NA12891.txt -SECOND_INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NotThere_to_NA12891.txt Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:19.631 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:19.631 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:19.631 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:19.631 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:19.632 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:19.632 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:19.632 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:19.632 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:19.632 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:19.632 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:19.632 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:19.632 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:19 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NotThere_to_NA12891.txt SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] SECOND_INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NotThere_to_NA12891.txt CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting3197140079170237073test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:19 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam] INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NotThere_to_NA12891.txt SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam] SECOND_INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NotThere_to_NA12891.txt CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting3197140079170237073test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:19 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:19 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:19 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:55:19 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:19 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) INFO 2024-07-02 11:55:19 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam) Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:19 FingerprintChecker Processed files. 25 fingerprints found in map. INFO 2024-07-02 11:55:19 FingerprintChecker Processed files. 25 fingerprints found in map. Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:19 CrosscheckFingerprints Some samples in first column in the INPUT_SAMPLE_MAP were not present as samples in fingerprinted file: [NotThere]. WARNING 2024-07-02 11:55:19 CrosscheckFingerprints Some samples in first column in the INPUT_SAMPLE_MAP were not present as samples in fingerprinted file: [NotThere]. Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:19 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. INFO 2024-07-02 11:55:19 CrosscheckFingerprints Fingerprinting 2 SECOND_INPUT files. Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:19 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:55:19 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) INFO 2024-07-02 11:55:20 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam) Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:55:20 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:20 CrosscheckFingerprints Some samples in first column in the SECOND_INPUT_SAMPLE_MAP were not present as samples in fingerprinted file: [NotThere]. WARNING 2024-07-02 11:55:20 CrosscheckFingerprints Some samples in first column in the SECOND_INPUT_SAMPLE_MAP were not present as samples in fingerprinted file: [NotThere]. Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:20 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:20 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:20 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:20 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testSecondInputCheckAllWithMapping[2]([/tmp/NA12892.over.fingerprints.r1.sam18325651450656116878.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam, /tmp/NA12892.over.fingerprints.r2.sam18144097977549737082.bam], testdata/picard/fingerprint/NotThere_to_NA12891.txt, testdata/picard/fingerprint/NotThere_to_NA12891.txt, 0, 1, 2, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false) STANDARD_ERROR INFO 2024-07-02 11:55:20 CrosscheckFingerprints Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting7420672068111074551test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting7420672068111074551test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.214 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:20.214 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.214 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:20.214 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.215 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:20.215 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.215 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:20.215 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.215 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:20.215 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.216 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:20.216 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:20 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting7420672068111074551test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:20 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting7420672068111074551test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:20 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:20 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:20 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:55:20 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:55:20 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:20 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:20 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:20 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:20 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testSecondInputCheckAllWithMapping[3]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, null, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false) STANDARD_ERROR INFO 2024-07-02 11:55:20 CrosscheckFingerprints Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting7513612987530213797test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -SECOND_INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892_to_NA12891.txt ********** CrosscheckFingerprints -INPUT /tmp/fingerprint3086553580626660194.vcf -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting7513612987530213797test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -SECOND_INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892_to_NA12891.txt Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.288 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:20.288 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.288 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:20.288 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.306 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:20.306 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.306 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:20.306 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.306 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:20.306 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.306 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:20.306 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:20 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] SECOND_INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892_to_NA12891.txt CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting7513612987530213797test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:20 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf] SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] SECOND_INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892_to_NA12891.txt CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting7513612987530213797test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:20 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:20 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:20 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:55:20 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:55:20 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:20 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:20 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:55:20 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:20 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:20 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testSecondInputCheckAllWithMapping[4]([/tmp/fingerprint3086553580626660194.vcf, /tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 1, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false) STANDARD_ERROR INFO 2024-07-02 11:55:20 CrosscheckFingerprints Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting11916617919706144339test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892_to_NA12891.txt -SECOND_INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892_to_NA12891.txt ********** CrosscheckFingerprints -INPUT /tmp/fingerprint17481944644093970365.vcf -SECOND_INPUT /tmp/fingerprint10298716060568440981.vcf -OUTPUT /tmp/Fingerprinting11916617919706144339test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892_to_NA12891.txt -SECOND_INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892_to_NA12891.txt Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.356 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:20.356 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.356 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:20.356 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.370 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:20.370 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.370 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:20.370 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.370 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:20.370 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.370 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:20.370 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:20 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint17481944644093970365.vcf] INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892_to_NA12891.txt SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] SECOND_INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892_to_NA12891.txt CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting11916617919706144339test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:20 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint17481944644093970365.vcf] INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892_to_NA12891.txt SECOND_INPUT=[/tmp/fingerprint10298716060568440981.vcf] SECOND_INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892_to_NA12891.txt CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting11916617919706144339test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:20 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:55:20 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:55:20 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:55:20 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 FingerprintChecker Processed files. 1 fingerprints found in map. INFO 2024-07-02 11:55:20 FingerprintChecker Processed files. 1 fingerprints found in map. Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:20 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:20 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:20 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:20 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testSecondInputCheckAllWithMapping[5]([/tmp/fingerprint17481944644093970365.vcf], [/tmp/fingerprint10298716060568440981.vcf], testdata/picard/fingerprint/NA12892_to_NA12891.txt, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false) STANDARD_ERROR INFO 2024-07-02 11:55:20 CrosscheckFingerprints Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting8785786690236929304test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892_to_NA12891.txt ********** CrosscheckFingerprints -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -SECOND_INPUT /tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam -OUTPUT /tmp/Fingerprinting8785786690236929304test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892_to_NA12891.txt Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.429 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:20.429 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.429 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:20.429 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.431 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:20.431 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.431 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:20.431 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.431 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:20.431 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.431 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:20.431 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:20 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892_to_NA12891.txt SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting8785786690236929304test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:20 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892_to_NA12891.txt SECOND_INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam] CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting8785786690236929304test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:20 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:55:20 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:55:20 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 FingerprintChecker Processed files. 27 fingerprints found in map. INFO 2024-07-02 11:55:20 FingerprintChecker Processed files. 27 fingerprints found in map. Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:55:20 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) INFO 2024-07-02 11:55:20 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam) Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 FingerprintChecker Processed files. 26 fingerprints found in map. INFO 2024-07-02 11:55:20 FingerprintChecker Processed files. 26 fingerprints found in map. Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:20 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:20 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:20 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:20 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testSecondInputCheckAllWithMapping[6]([/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], [/tmp/NA12891.over.fingerprints.r2.sam2324680191330846890.bam], testdata/picard/fingerprint/NA12892_to_NA12891.txt, null, 0, 1, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckFingerprintsTest.testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false) STANDARD_ERROR INFO 2024-07-02 11:55:20 CrosscheckFingerprints Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting7276666621109170623test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -SECOND_INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892_to_NA12891.txt ********** CrosscheckFingerprints -INPUT /tmp/fingerprint1275962480367888787.vcf -SECOND_INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam -OUTPUT /tmp/Fingerprinting7276666621109170623test.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_BY SAMPLE -CROSSCHECK_MODE CHECK_ALL_OTHERS -SECOND_INPUT_SAMPLE_MAP /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892_to_NA12891.txt Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.864 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:20.864 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.864 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:20.864 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.878 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:20.878 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.878 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:20.878 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.878 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:20.878 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: 11:55:20.878 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:20.878 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:20 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] SECOND_INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892_to_NA12891.txt CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting7276666621109170623test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:20 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/tmp/fingerprint1275962480367888787.vcf] SECOND_INPUT=[/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam] SECOND_INPUT_SAMPLE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892_to_NA12891.txt CROSSCHECK_MODE=CHECK_ALL_OTHERS OUTPUT=/tmp/Fingerprinting7276666621109170623test.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. INFO 2024-07-02 11:55:20 CrosscheckFingerprints SECOND_INPUT is not empty, and CROSSCHECK_MODE==CHECK_ALL_OTHERS. Will compare fingerprints from INPUT against all the fingerprints in SECOND_INPUT. Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints Fingerprinting 1 INPUT files. INFO 2024-07-02 11:55:20 CrosscheckFingerprints Fingerprinting 1 INPUT files. Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 FingerprintChecker Processed files. 2 fingerprints found in map. INFO 2024-07-02 11:55:20 FingerprintChecker Processed files. 2 fingerprints found in map. Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. INFO 2024-07-02 11:55:20 CrosscheckFingerprints Fingerprinting 1 SECOND_INPUT files. Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:20 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) INFO 2024-07-02 11:55:20 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam) Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:21 FingerprintChecker Processed files. 27 fingerprints found in map. INFO 2024-07-02 11:55:21 FingerprintChecker Processed files. 27 fingerprints found in map. Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:21 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. INFO 2024-07-02 11:55:21 CrosscheckFingerprints Checking each SAMPLE in INPUT with each SAMPLE in SECOND_INPUT. Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:21 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:21 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:21 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:21 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testSecondInputCheckAllWithMapping[7]([/tmp/fingerprint1275962480367888787.vcf], [/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam6114588504314771629.bam], null, testdata/picard/fingerprint/NA12892_to_NA12891.txt, 0, 2, 1, false)(picard.fingerprint.CrosscheckFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:21 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY) STANDARD_ERROR INFO 2024-07-02 11:55:21 CrosscheckReadGroupFingerprints Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_SAMPLES true -CROSSCHECK_BY LIBRARY ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_SAMPLES true -CROSSCHECK_BY LIBRARY Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:21.455 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:21.455 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:21.455 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:21.455 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:21.456 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:55:21.456 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: USAGE: CrosscheckReadGroupFingerprints [options] USAGE: CrosscheckReadGroupFingerprints [options] Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CrosscheckReadGroupFingerprints Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CrosscheckReadGroupFingerprints Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: DEPRECATED: USE CrosscheckFingerprints. DEPRECATED: USE CrosscheckFingerprints. Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Version: null Version: null Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Options: Options: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: --help --help Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: tools. tools. Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CROSSCHECK_SAMPLES=Boolean Instead of producing the normal comparison of read-groups, roll fingerprints up to the CROSSCHECK_SAMPLES=Boolean Instead of producing the normal comparison of read-groups, roll fingerprints up to the Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: sample level and print out a sample x sample matrix with LOD scores. Default value: sample level and print out a sample x sample matrix with LOD scores. Default value: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: false. This option can be set to 'null' to clear the default value. Possible values: false. This option can be set to 'null' to clear the default value. Possible values: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: {true, false} {true, false} Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CROSSCHECK_LIBRARIES=Boolean Instead of producing the normal comparison of read-groups, roll fingerprints up to the CROSSCHECK_LIBRARIES=Boolean Instead of producing the normal comparison of read-groups, roll fingerprints up to the Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: library level and print out a library x library matrix with LOD scores. Default value: library level and print out a library x library matrix with LOD scores. Default value: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: false. This option can be set to 'null' to clear the default value. Possible values: false. This option can be set to 'null' to clear the default value. Possible values: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: {true, false} {true, false} Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXPECT_ALL_READ_GROUPS_TO_MATCH=Boolean EXPECT_ALL_READ_GROUPS_TO_MATCH=Boolean Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Expect all read groups' fingerprints to match, irrespective of their sample names. By Expect all read groups' fingerprints to match, irrespective of their sample names. By Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: default (with this value set to false), read groups with different sample names are default (with this value set to false), read groups with different sample names are Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: expected to mismatch, and those with the same sample name are expected to match. Default expected to mismatch, and those with the same sample name are expected to match. Default Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: value: false. This option can be set to 'null' to clear the default value. Possible value: false. This option can be set to 'null' to clear the default value. Possible Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: values: {true, false} Cannot be used in conjuction with option(s) values: {true, false} Cannot be used in conjuction with option(s) Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXPECT_ALL_GROUPS_TO_MATCH EXPECT_ALL_GROUPS_TO_MATCH Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INPUT=String INPUT=String Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: I=String One or more input files (or lists of files) with which to compare fingerprints. Default I=String One or more input files (or lists of files) with which to compare fingerprints. Default Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: value: null. This option must be specified at least 1 times. value: null. This option must be specified at least 1 times. Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the INPUT data (in column INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the INPUT data (in column Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 1) and the sample as it should be used for comparisons to SECOND_INPUT (in the second 1) and the sample as it should be used for comparisons to SECOND_INPUT (in the second Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: column). Need only include the samples that change. Values in column 1 should be unique. column). Need only include the samples that change. Values in column 1 should be unique. Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Values in column 2 should be unique even in union with the remaining unmapped samples. Values in column 2 should be unique even in union with the remaining unmapped samples. Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Should only be used with SECOND_INPUT. Default value: null. Cannot be used in Should only be used with SECOND_INPUT. Default value: null. Cannot be used in Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: conjuction with option(s) INPUT_SAMPLE_FILE_MAP conjuction with option(s) INPUT_SAMPLE_FILE_MAP Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INPUT_SAMPLE_FILE_MAP=File A tsv with two columns representing the sample as it should be used for comparisons to INPUT_SAMPLE_FILE_MAP=File A tsv with two columns representing the sample as it should be used for comparisons to Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT (in the first column) and the source file (in INPUT) for the fingerprint (in SECOND_INPUT (in the first column) and the source file (in INPUT) for the fingerprint (in Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: the second column). Need only to include the samples that change. Values in column 1 the second column). Need only to include the samples that change. Values in column 1 Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: should be unique even in union with the remaining unmapped samples. Values in column 2 should be unique even in union with the remaining unmapped samples. Values in column 2 Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: should be unique in the file. Will error if more than one sample is found in a file should be unique in the file. Will error if more than one sample is found in a file Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: (multi-sample VCF) pointed to in column 2. Should only be used in the presence of (multi-sample VCF) pointed to in column 2. Should only be used in the presence of Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT. Default value: null. Cannot be used in conjuction with option(s) SECOND_INPUT. Default value: null. Cannot be used in conjuction with option(s) Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INPUT_SAMPLE_MAP INPUT_SAMPLE_MAP Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT=String SECOND_INPUT=String Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SI=String A second set of input files (or lists of files) with which to compare fingerprints. If SI=String A second set of input files (or lists of files) with which to compare fingerprints. If Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: this option is provided the tool compares each sample in INPUT with the sample from this option is provided the tool compares each sample in INPUT with the sample from Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT that has the same sample ID. In addition, data will be grouped by SAMPLE SECOND_INPUT that has the same sample ID. In addition, data will be grouped by SAMPLE Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: regardless of the value of CROSSCHECK_BY. When operating in this mode, each sample in regardless of the value of CROSSCHECK_BY. When operating in this mode, each sample in Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INPUT must also have a corresponding sample in SECOND_INPUT. If this is violated, the tool INPUT must also have a corresponding sample in SECOND_INPUT. If this is violated, the tool Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: will proceed to check the matching samples, but report the missing samples and return a will proceed to check the matching samples, but report the missing samples and return a Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: non-zero error-code. Default value: null. This option may be specified 0 or more times. non-zero error-code. Default value: null. This option may be specified 0 or more times. Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Cannot be used in conjuction with option(s) MATRIX_OUTPUT (MO) Cannot be used in conjuction with option(s) MATRIX_OUTPUT (MO) Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the SECOND_INPUT data (in SECOND_INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the SECOND_INPUT data (in Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: column 1) and the sample as it should be used for comparisons to INPUT (in the second column 1) and the sample as it should be used for comparisons to INPUT (in the second Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: column). Note that in case of unrolling files (file-of-filenames) one would need to column). Note that in case of unrolling files (file-of-filenames) one would need to Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: reference the final file, i.e. the file that contains the genomic data. Need only include reference the final file, i.e. the file that contains the genomic data. Need only include Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: the samples that change. Values in column 1 should be unique. Values in column 2 should be the samples that change. Values in column 1 should be unique. Values in column 2 should be Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: unique even in union with the remaining unmapped samples. Should only be used with unique even in union with the remaining unmapped samples. Should only be used with Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT. Default value: null. SECOND_INPUT. Default value: null. Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CROSSCHECK_MODE=CrosscheckModeAn argument that controls how crosschecking with both INPUT and SECOND_INPUT should occur. CROSSCHECK_MODE=CrosscheckModeAn argument that controls how crosschecking with both INPUT and SECOND_INPUT should occur. Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Default value: CHECK_SAME_SAMPLE. This option can be set to 'null' to clear the default Default value: CHECK_SAME_SAMPLE. This option can be set to 'null' to clear the default Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: value. Possible values: { value. Possible values: { Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CHECK_SAME_SAMPLE (In this mode, each sample in INPUT will only be checked against a CHECK_SAME_SAMPLE (In this mode, each sample in INPUT will only be checked against a Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: single corresponding sample in SECOND_INPUT. If a corresponding sample cannot be found, single corresponding sample in SECOND_INPUT. If a corresponding sample cannot be found, Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: the program will proceed, but report the missing samples and return the value specified in the program will proceed, but report the missing samples and return the value specified in Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXIT_CODE_WHEN_MISMATCH. The corresponding samples are those that equal each other, after EXIT_CODE_WHEN_MISMATCH. The corresponding samples are those that equal each other, after Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: possible renaming via INPUT_SAMPLE_MAP and SECOND_INPUT_SAMPLE_MAP. In this mode possible renaming via INPUT_SAMPLE_MAP and SECOND_INPUT_SAMPLE_MAP. In this mode Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CROSSCHECK_BY must be SAMPLE.) CROSSCHECK_BY must be SAMPLE.) Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CHECK_ALL_OTHERS (In this mode, each sample in INPUT will be checked against all the CHECK_ALL_OTHERS (In this mode, each sample in INPUT will be checked against all the Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: samples in SECOND_INPUT.) samples in SECOND_INPUT.) Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: } } Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: O=File Optional output file to write metrics to. Default is to write to stdout. Default value: O=File Optional output file to write metrics to. Default is to write to stdout. Default value: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: null. null. Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: MATRIX_OUTPUT=File MATRIX_OUTPUT=File Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: MO=File Optional output file to write matrix of LOD scores to. This is less informative than the MO=File Optional output file to write matrix of LOD scores to. This is less informative than the Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: metrics output and only contains Normal-Normal LOD score (i.e. doesn't account for Loss of metrics output and only contains Normal-Normal LOD score (i.e. doesn't account for Loss of Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Heterozygosity). It is however sometimes easier to use visually. Default value: null. Heterozygosity). It is however sometimes easier to use visually. Default value: null. Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Cannot be used in conjuction with option(s) SECOND_INPUT (SI) Cannot be used in conjuction with option(s) SECOND_INPUT (SI) Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: HAPLOTYPE_MAP=File HAPLOTYPE_MAP=File Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: H=File The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for H=File The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: fingerprinting. See https://software.broadinstitute.org/gatk/documentation/article?id=9526 fingerprinting. See https://software.broadinstitute.org/gatk/documentation/article?id=9526 Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: for details. Required. for details. Required. Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: LOD_THRESHOLD=Double LOD_THRESHOLD=Double Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: LOD=Double If any two groups (with the same sample name) match with a LOD score lower than the LOD=Double If any two groups (with the same sample name) match with a LOD score lower than the Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: threshold the tool will exit with a non-zero code to indicate error. Program will also threshold the tool will exit with a non-zero code to indicate error. Program will also Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: exit with an error if it finds two groups with different sample name that match with a LOD exit with an error if it finds two groups with different sample name that match with a LOD Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: score greater than -LOD_THRESHOLD. score greater than -LOD_THRESHOLD. Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: LOD score 0 means equal likelihood that the groups match vs. come from different LOD score 0 means equal likelihood that the groups match vs. come from different Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: individuals, negative LOD score -N, mean 10^N time more likely that the groups are from individuals, negative LOD score -N, mean 10^N time more likely that the groups are from Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: different individuals, and +N means 10^N times more likely that the groups are from the different individuals, and +N means 10^N times more likely that the groups are from the Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: same individual. Default value: 0.0. This option can be set to 'null' to clear the same individual. Default value: 0.0. This option can be set to 'null' to clear the Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: default value. default value. Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CROSSCHECK_BY=DataType Specificies which data-type should be used as the basic comparison unit. Fingerprints from CROSSCHECK_BY=DataType Specificies which data-type should be used as the basic comparison unit. Fingerprints from Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: readgroups can be "rolled-up" to the LIBRARY, SAMPLE, or FILE level before being compared. readgroups can be "rolled-up" to the LIBRARY, SAMPLE, or FILE level before being compared. Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Fingerprints from VCF can be be compared by SAMPLE or FILE. Default value: READGROUP. Fingerprints from VCF can be be compared by SAMPLE or FILE. Default value: READGROUP. Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: This option can be set to 'null' to clear the default value. Possible values: {FILE, This option can be set to 'null' to clear the default value. Possible values: {FILE, Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SAMPLE, LIBRARY, READGROUP} SAMPLE, LIBRARY, READGROUP} Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: NUM_THREADS=Integer The number of threads to use to process files and generate fingerprints. Default value: NUM_THREADS=Integer The number of threads to use to process files and generate fingerprints. Default value: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 1. This option can be set to 'null' to clear the default value. 1. This option can be set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CALCULATE_TUMOR_AWARE_RESULTS=Boolean CALCULATE_TUMOR_AWARE_RESULTS=Boolean Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: specifies whether the Tumor-aware result should be calculated. These are time consuming specifies whether the Tumor-aware result should be calculated. These are time consuming Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: and can roughly double the runtime of the tool. When crosschecking many groups not and can roughly double the runtime of the tool. When crosschecking many groups not Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: calculating the tumor-aware results can result in a significant speedup. Default value: calculating the tumor-aware results can result in a significant speedup. Default value: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: true. This option can be set to 'null' to clear the default value. Possible values: {true, true. This option can be set to 'null' to clear the default value. Possible values: {true, Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: false} false} Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ALLOW_DUPLICATE_READS=Boolean Allow the use of duplicate reads in performing the comparison. Can be useful when ALLOW_DUPLICATE_READS=Boolean Allow the use of duplicate reads in performing the comparison. Can be useful when Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: duplicate marking has been overly aggressive and coverage is low. Default value: false. duplicate marking has been overly aggressive and coverage is low. Default value: false. Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: This option can be set to 'null' to clear the default value. Possible values: {true, This option can be set to 'null' to clear the default value. Possible values: {true, Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: false} false} Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: GENOTYPING_ERROR_RATE=Double Assumed genotyping error rate that provides a floor on the probability that a genotype GENOTYPING_ERROR_RATE=Double Assumed genotyping error rate that provides a floor on the probability that a genotype Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: comes from the expected sample. Must be greater than zero. Default value: 0.01. This comes from the expected sample. Must be greater than zero. Default value: 0.01. This Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: option can be set to 'null' to clear the default value. option can be set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: OUTPUT_ERRORS_ONLY=Boolean If true then only groups that do not relate to each other as expected will have their LODs OUTPUT_ERRORS_ONLY=Boolean If true then only groups that do not relate to each other as expected will have their LODs Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: reported. Default value: false. This option can be set to 'null' to clear the default reported. Default value: false. This option can be set to 'null' to clear the default Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: LOSS_OF_HET_RATE=Double The rate at which a heterozygous genotype in a normal sample turns into a homozygous (via LOSS_OF_HET_RATE=Double The rate at which a heterozygous genotype in a normal sample turns into a homozygous (via Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: loss of heterozygosity) in the tumor (model assumes independent events, so this needs to loss of heterozygosity) in the tumor (model assumes independent events, so this needs to Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: be larger than reality). Default value: 0.5. This option can be set to 'null' to clear be larger than reality). Default value: 0.5. This option can be set to 'null' to clear Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: the default value. the default value. Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXPECT_ALL_GROUPS_TO_MATCH=Boolean EXPECT_ALL_GROUPS_TO_MATCH=Boolean Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Expect all groups' fingerprints to match, irrespective of their sample names. By default Expect all groups' fingerprints to match, irrespective of their sample names. By default Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: (with this value set to false), groups (readgroups, libraries, files, or samples) with (with this value set to false), groups (readgroups, libraries, files, or samples) with Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: different sample names are expected to mismatch, and those with the same sample name are different sample names are expected to mismatch, and those with the same sample name are Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: expected to match. Default value: false. This option can be set to 'null' to clear the expected to match. Default value: false. This option can be set to 'null' to clear the Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: default value. Possible values: {true, false} default value. Possible values: {true, false} Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXIT_CODE_WHEN_MISMATCH=Integer EXIT_CODE_WHEN_MISMATCH=Integer Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: When one or more mismatches between groups is detected, exit with this value instead of 0. When one or more mismatches between groups is detected, exit with this value instead of 0. Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Default value: 1. This option can be set to 'null' to clear the default value. Default value: 1. This option can be set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXIT_CODE_WHEN_NO_VALID_CHECKS=Integer EXIT_CODE_WHEN_NO_VALID_CHECKS=Integer Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: When all LOD score are zero, exit with this value. Default value: 1. This option can be When all LOD score are zero, exit with this value. Default value: 1. This option can be Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: set to 'null' to clear the default value. set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=Double MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=Double Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Maximal effect of any single haplotype block on outcome (-log10 of maximal likelihood Maximal effect of any single haplotype block on outcome (-log10 of maximal likelihood Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: difference between the different values for the three possible genotypes). Default value: difference between the different values for the three possible genotypes). Default value: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 3.0. This option can be set to 'null' to clear the default value. 3.0. This option can be set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: TEST_INPUT_READABILITY=BooleanWhen true code will check for readability on input files (this can be slow on cloud TEST_INPUT_READABILITY=BooleanWhen true code will check for readability on input files (this can be slow on cloud Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: access) Default value: true. This option can be set to 'null' to clear the default value. access) Default value: true. This option can be set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Possible values: {true, false} Possible values: {true, false} Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: When calling CrosscheckReadGroupFingerprints, please refrain from supplying a CROSSCHECK_BY argument. (Found value LIBRARY When calling CrosscheckReadGroupFingerprints, please refrain from supplying a CROSSCHECK_BY argument. (Found value LIBRARY Test: Test method testCannotUseNewParameters[0](CROSSCHECK_BY=LIBRARY)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Use CrosscheckFingerprints if you would like to do that. Use CrosscheckFingerprints if you would like to do that. Running Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:21 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE) STANDARD_ERROR INFO 2024-07-02 11:55:21 CrosscheckReadGroupFingerprints Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_SAMPLES true -CROSSCHECK_BY SAMPLE ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_SAMPLES true -CROSSCHECK_BY SAMPLE Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:21.610 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:21.610 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:21.610 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:21.610 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:21.611 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:55:21.611 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: USAGE: CrosscheckReadGroupFingerprints [options] USAGE: CrosscheckReadGroupFingerprints [options] Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CrosscheckReadGroupFingerprints Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CrosscheckReadGroupFingerprints Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: DEPRECATED: USE CrosscheckFingerprints. DEPRECATED: USE CrosscheckFingerprints. Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Version: null Version: null Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Options: Options: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: --help --help Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: tools. tools. Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CROSSCHECK_SAMPLES=Boolean Instead of producing the normal comparison of read-groups, roll fingerprints up to the CROSSCHECK_SAMPLES=Boolean Instead of producing the normal comparison of read-groups, roll fingerprints up to the Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: sample level and print out a sample x sample matrix with LOD scores. Default value: sample level and print out a sample x sample matrix with LOD scores. Default value: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: false. This option can be set to 'null' to clear the default value. Possible values: false. This option can be set to 'null' to clear the default value. Possible values: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: {true, false} {true, false} Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CROSSCHECK_LIBRARIES=Boolean Instead of producing the normal comparison of read-groups, roll fingerprints up to the CROSSCHECK_LIBRARIES=Boolean Instead of producing the normal comparison of read-groups, roll fingerprints up to the Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: library level and print out a library x library matrix with LOD scores. Default value: library level and print out a library x library matrix with LOD scores. Default value: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: false. This option can be set to 'null' to clear the default value. Possible values: false. This option can be set to 'null' to clear the default value. Possible values: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: {true, false} {true, false} Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXPECT_ALL_READ_GROUPS_TO_MATCH=Boolean EXPECT_ALL_READ_GROUPS_TO_MATCH=Boolean Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Expect all read groups' fingerprints to match, irrespective of their sample names. By Expect all read groups' fingerprints to match, irrespective of their sample names. By Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: default (with this value set to false), read groups with different sample names are default (with this value set to false), read groups with different sample names are Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: expected to mismatch, and those with the same sample name are expected to match. Default expected to mismatch, and those with the same sample name are expected to match. Default Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: value: false. This option can be set to 'null' to clear the default value. Possible value: false. This option can be set to 'null' to clear the default value. Possible Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: values: {true, false} Cannot be used in conjuction with option(s) values: {true, false} Cannot be used in conjuction with option(s) Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXPECT_ALL_GROUPS_TO_MATCH EXPECT_ALL_GROUPS_TO_MATCH Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INPUT=String INPUT=String Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: I=String One or more input files (or lists of files) with which to compare fingerprints. Default I=String One or more input files (or lists of files) with which to compare fingerprints. Default Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: value: null. This option must be specified at least 1 times. value: null. This option must be specified at least 1 times. Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the INPUT data (in column INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the INPUT data (in column Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 1) and the sample as it should be used for comparisons to SECOND_INPUT (in the second 1) and the sample as it should be used for comparisons to SECOND_INPUT (in the second Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: column). Need only include the samples that change. Values in column 1 should be unique. column). Need only include the samples that change. Values in column 1 should be unique. Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Values in column 2 should be unique even in union with the remaining unmapped samples. Values in column 2 should be unique even in union with the remaining unmapped samples. Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Should only be used with SECOND_INPUT. Default value: null. Cannot be used in Should only be used with SECOND_INPUT. Default value: null. Cannot be used in Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: conjuction with option(s) INPUT_SAMPLE_FILE_MAP conjuction with option(s) INPUT_SAMPLE_FILE_MAP Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INPUT_SAMPLE_FILE_MAP=File A tsv with two columns representing the sample as it should be used for comparisons to INPUT_SAMPLE_FILE_MAP=File A tsv with two columns representing the sample as it should be used for comparisons to Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT (in the first column) and the source file (in INPUT) for the fingerprint (in SECOND_INPUT (in the first column) and the source file (in INPUT) for the fingerprint (in Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: the second column). Need only to include the samples that change. Values in column 1 the second column). Need only to include the samples that change. Values in column 1 Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: should be unique even in union with the remaining unmapped samples. Values in column 2 should be unique even in union with the remaining unmapped samples. Values in column 2 Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: should be unique in the file. Will error if more than one sample is found in a file should be unique in the file. Will error if more than one sample is found in a file Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: (multi-sample VCF) pointed to in column 2. Should only be used in the presence of (multi-sample VCF) pointed to in column 2. Should only be used in the presence of Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT. Default value: null. Cannot be used in conjuction with option(s) SECOND_INPUT. Default value: null. Cannot be used in conjuction with option(s) Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INPUT_SAMPLE_MAP INPUT_SAMPLE_MAP Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT=String SECOND_INPUT=String Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SI=String A second set of input files (or lists of files) with which to compare fingerprints. If SI=String A second set of input files (or lists of files) with which to compare fingerprints. If Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: this option is provided the tool compares each sample in INPUT with the sample from this option is provided the tool compares each sample in INPUT with the sample from Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT that has the same sample ID. In addition, data will be grouped by SAMPLE SECOND_INPUT that has the same sample ID. In addition, data will be grouped by SAMPLE Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: regardless of the value of CROSSCHECK_BY. When operating in this mode, each sample in regardless of the value of CROSSCHECK_BY. When operating in this mode, each sample in Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INPUT must also have a corresponding sample in SECOND_INPUT. If this is violated, the tool INPUT must also have a corresponding sample in SECOND_INPUT. If this is violated, the tool Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: will proceed to check the matching samples, but report the missing samples and return a will proceed to check the matching samples, but report the missing samples and return a Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: non-zero error-code. Default value: null. This option may be specified 0 or more times. non-zero error-code. Default value: null. This option may be specified 0 or more times. Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Cannot be used in conjuction with option(s) MATRIX_OUTPUT (MO) Cannot be used in conjuction with option(s) MATRIX_OUTPUT (MO) Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the SECOND_INPUT data (in SECOND_INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the SECOND_INPUT data (in Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: column 1) and the sample as it should be used for comparisons to INPUT (in the second column 1) and the sample as it should be used for comparisons to INPUT (in the second Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: column). Note that in case of unrolling files (file-of-filenames) one would need to column). Note that in case of unrolling files (file-of-filenames) one would need to Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: reference the final file, i.e. the file that contains the genomic data. Need only include reference the final file, i.e. the file that contains the genomic data. Need only include Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: the samples that change. Values in column 1 should be unique. Values in column 2 should be the samples that change. Values in column 1 should be unique. Values in column 2 should be Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: unique even in union with the remaining unmapped samples. Should only be used with unique even in union with the remaining unmapped samples. Should only be used with Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT. Default value: null. SECOND_INPUT. Default value: null. Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CROSSCHECK_MODE=CrosscheckModeAn argument that controls how crosschecking with both INPUT and SECOND_INPUT should occur. CROSSCHECK_MODE=CrosscheckModeAn argument that controls how crosschecking with both INPUT and SECOND_INPUT should occur. Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Default value: CHECK_SAME_SAMPLE. This option can be set to 'null' to clear the default Default value: CHECK_SAME_SAMPLE. This option can be set to 'null' to clear the default Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: value. Possible values: { value. Possible values: { Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CHECK_SAME_SAMPLE (In this mode, each sample in INPUT will only be checked against a CHECK_SAME_SAMPLE (In this mode, each sample in INPUT will only be checked against a Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: single corresponding sample in SECOND_INPUT. If a corresponding sample cannot be found, single corresponding sample in SECOND_INPUT. If a corresponding sample cannot be found, Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: the program will proceed, but report the missing samples and return the value specified in the program will proceed, but report the missing samples and return the value specified in Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXIT_CODE_WHEN_MISMATCH. The corresponding samples are those that equal each other, after EXIT_CODE_WHEN_MISMATCH. The corresponding samples are those that equal each other, after Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: possible renaming via INPUT_SAMPLE_MAP and SECOND_INPUT_SAMPLE_MAP. In this mode possible renaming via INPUT_SAMPLE_MAP and SECOND_INPUT_SAMPLE_MAP. In this mode Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CROSSCHECK_BY must be SAMPLE.) CROSSCHECK_BY must be SAMPLE.) Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CHECK_ALL_OTHERS (In this mode, each sample in INPUT will be checked against all the CHECK_ALL_OTHERS (In this mode, each sample in INPUT will be checked against all the Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: samples in SECOND_INPUT.) samples in SECOND_INPUT.) Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: } } Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: O=File Optional output file to write metrics to. Default is to write to stdout. Default value: O=File Optional output file to write metrics to. Default is to write to stdout. Default value: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: null. null. Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: MATRIX_OUTPUT=File MATRIX_OUTPUT=File Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: MO=File Optional output file to write matrix of LOD scores to. This is less informative than the MO=File Optional output file to write matrix of LOD scores to. This is less informative than the Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: metrics output and only contains Normal-Normal LOD score (i.e. doesn't account for Loss of metrics output and only contains Normal-Normal LOD score (i.e. doesn't account for Loss of Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Heterozygosity). It is however sometimes easier to use visually. Default value: null. Heterozygosity). It is however sometimes easier to use visually. Default value: null. Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Cannot be used in conjuction with option(s) SECOND_INPUT (SI) Cannot be used in conjuction with option(s) SECOND_INPUT (SI) Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: HAPLOTYPE_MAP=File HAPLOTYPE_MAP=File Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: H=File The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for H=File The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: fingerprinting. See https://software.broadinstitute.org/gatk/documentation/article?id=9526 fingerprinting. See https://software.broadinstitute.org/gatk/documentation/article?id=9526 Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: for details. Required. for details. Required. Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: LOD_THRESHOLD=Double LOD_THRESHOLD=Double Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: LOD=Double If any two groups (with the same sample name) match with a LOD score lower than the LOD=Double If any two groups (with the same sample name) match with a LOD score lower than the Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: threshold the tool will exit with a non-zero code to indicate error. Program will also threshold the tool will exit with a non-zero code to indicate error. Program will also Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: exit with an error if it finds two groups with different sample name that match with a LOD exit with an error if it finds two groups with different sample name that match with a LOD Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: score greater than -LOD_THRESHOLD. score greater than -LOD_THRESHOLD. Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: LOD score 0 means equal likelihood that the groups match vs. come from different LOD score 0 means equal likelihood that the groups match vs. come from different Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: individuals, negative LOD score -N, mean 10^N time more likely that the groups are from individuals, negative LOD score -N, mean 10^N time more likely that the groups are from Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: different individuals, and +N means 10^N times more likely that the groups are from the different individuals, and +N means 10^N times more likely that the groups are from the Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: same individual. Default value: 0.0. This option can be set to 'null' to clear the same individual. Default value: 0.0. This option can be set to 'null' to clear the Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: default value. default value. Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CROSSCHECK_BY=DataType Specificies which data-type should be used as the basic comparison unit. Fingerprints from CROSSCHECK_BY=DataType Specificies which data-type should be used as the basic comparison unit. Fingerprints from Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: readgroups can be "rolled-up" to the LIBRARY, SAMPLE, or FILE level before being compared. readgroups can be "rolled-up" to the LIBRARY, SAMPLE, or FILE level before being compared. Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Fingerprints from VCF can be be compared by SAMPLE or FILE. Default value: READGROUP. Fingerprints from VCF can be be compared by SAMPLE or FILE. Default value: READGROUP. Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: This option can be set to 'null' to clear the default value. Possible values: {FILE, This option can be set to 'null' to clear the default value. Possible values: {FILE, Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SAMPLE, LIBRARY, READGROUP} SAMPLE, LIBRARY, READGROUP} Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: NUM_THREADS=Integer The number of threads to use to process files and generate fingerprints. Default value: NUM_THREADS=Integer The number of threads to use to process files and generate fingerprints. Default value: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 1. This option can be set to 'null' to clear the default value. 1. This option can be set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CALCULATE_TUMOR_AWARE_RESULTS=Boolean CALCULATE_TUMOR_AWARE_RESULTS=Boolean Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: specifies whether the Tumor-aware result should be calculated. These are time consuming specifies whether the Tumor-aware result should be calculated. These are time consuming Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: and can roughly double the runtime of the tool. When crosschecking many groups not and can roughly double the runtime of the tool. When crosschecking many groups not Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: calculating the tumor-aware results can result in a significant speedup. Default value: calculating the tumor-aware results can result in a significant speedup. Default value: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: true. This option can be set to 'null' to clear the default value. Possible values: {true, true. This option can be set to 'null' to clear the default value. Possible values: {true, Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: false} false} Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ALLOW_DUPLICATE_READS=Boolean Allow the use of duplicate reads in performing the comparison. Can be useful when ALLOW_DUPLICATE_READS=Boolean Allow the use of duplicate reads in performing the comparison. Can be useful when Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: duplicate marking has been overly aggressive and coverage is low. Default value: false. duplicate marking has been overly aggressive and coverage is low. Default value: false. Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: This option can be set to 'null' to clear the default value. Possible values: {true, This option can be set to 'null' to clear the default value. Possible values: {true, Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: false} false} Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: GENOTYPING_ERROR_RATE=Double Assumed genotyping error rate that provides a floor on the probability that a genotype GENOTYPING_ERROR_RATE=Double Assumed genotyping error rate that provides a floor on the probability that a genotype Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: comes from the expected sample. Must be greater than zero. Default value: 0.01. This comes from the expected sample. Must be greater than zero. Default value: 0.01. This Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: option can be set to 'null' to clear the default value. option can be set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: OUTPUT_ERRORS_ONLY=Boolean If true then only groups that do not relate to each other as expected will have their LODs OUTPUT_ERRORS_ONLY=Boolean If true then only groups that do not relate to each other as expected will have their LODs Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: reported. Default value: false. This option can be set to 'null' to clear the default reported. Default value: false. This option can be set to 'null' to clear the default Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: LOSS_OF_HET_RATE=Double The rate at which a heterozygous genotype in a normal sample turns into a homozygous (via LOSS_OF_HET_RATE=Double The rate at which a heterozygous genotype in a normal sample turns into a homozygous (via Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: loss of heterozygosity) in the tumor (model assumes independent events, so this needs to loss of heterozygosity) in the tumor (model assumes independent events, so this needs to Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: be larger than reality). Default value: 0.5. This option can be set to 'null' to clear be larger than reality). Default value: 0.5. This option can be set to 'null' to clear Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: the default value. the default value. Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXPECT_ALL_GROUPS_TO_MATCH=Boolean EXPECT_ALL_GROUPS_TO_MATCH=Boolean Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Expect all groups' fingerprints to match, irrespective of their sample names. By default Expect all groups' fingerprints to match, irrespective of their sample names. By default Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: (with this value set to false), groups (readgroups, libraries, files, or samples) with (with this value set to false), groups (readgroups, libraries, files, or samples) with Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: different sample names are expected to mismatch, and those with the same sample name are different sample names are expected to mismatch, and those with the same sample name are Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: expected to match. Default value: false. This option can be set to 'null' to clear the expected to match. Default value: false. This option can be set to 'null' to clear the Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: default value. Possible values: {true, false} default value. Possible values: {true, false} Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXIT_CODE_WHEN_MISMATCH=Integer EXIT_CODE_WHEN_MISMATCH=Integer Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: When one or more mismatches between groups is detected, exit with this value instead of 0. When one or more mismatches between groups is detected, exit with this value instead of 0. Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Default value: 1. This option can be set to 'null' to clear the default value. Default value: 1. This option can be set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXIT_CODE_WHEN_NO_VALID_CHECKS=Integer EXIT_CODE_WHEN_NO_VALID_CHECKS=Integer Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: When all LOD score are zero, exit with this value. Default value: 1. This option can be When all LOD score are zero, exit with this value. Default value: 1. This option can be Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: set to 'null' to clear the default value. set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=Double MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=Double Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Maximal effect of any single haplotype block on outcome (-log10 of maximal likelihood Maximal effect of any single haplotype block on outcome (-log10 of maximal likelihood Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: difference between the different values for the three possible genotypes). Default value: difference between the different values for the three possible genotypes). Default value: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 3.0. This option can be set to 'null' to clear the default value. 3.0. This option can be set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: TEST_INPUT_READABILITY=BooleanWhen true code will check for readability on input files (this can be slow on cloud TEST_INPUT_READABILITY=BooleanWhen true code will check for readability on input files (this can be slow on cloud Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: access) Default value: true. This option can be set to 'null' to clear the default value. access) Default value: true. This option can be set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Possible values: {true, false} Possible values: {true, false} Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: When calling CrosscheckReadGroupFingerprints, please refrain from supplying a CROSSCHECK_BY argument. (Found value SAMPLE When calling CrosscheckReadGroupFingerprints, please refrain from supplying a CROSSCHECK_BY argument. (Found value SAMPLE Test: Test method testCannotUseNewParameters[1](CROSSCHECK_BY=SAMPLE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Use CrosscheckFingerprints if you would like to do that. Use CrosscheckFingerprints if you would like to do that. Running Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:21 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCannotUseNewParameters[2](CROSSCHECK_BY=FILE) STANDARD_ERROR INFO 2024-07-02 11:55:21 CrosscheckReadGroupFingerprints Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_SAMPLES true -CROSSCHECK_BY FILE ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_SAMPLES true -CROSSCHECK_BY FILE Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:21.767 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:21.767 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:21.767 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:21.767 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:21.768 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:55:21.768 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: USAGE: CrosscheckReadGroupFingerprints [options] USAGE: CrosscheckReadGroupFingerprints [options] Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CrosscheckReadGroupFingerprints Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CrosscheckReadGroupFingerprints Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: DEPRECATED: USE CrosscheckFingerprints. DEPRECATED: USE CrosscheckFingerprints. Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Version: null Version: null Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Options: Options: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: --help --help Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: tools. tools. Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CROSSCHECK_SAMPLES=Boolean Instead of producing the normal comparison of read-groups, roll fingerprints up to the CROSSCHECK_SAMPLES=Boolean Instead of producing the normal comparison of read-groups, roll fingerprints up to the Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: sample level and print out a sample x sample matrix with LOD scores. Default value: sample level and print out a sample x sample matrix with LOD scores. Default value: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: false. This option can be set to 'null' to clear the default value. Possible values: false. This option can be set to 'null' to clear the default value. Possible values: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: {true, false} {true, false} Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CROSSCHECK_LIBRARIES=Boolean Instead of producing the normal comparison of read-groups, roll fingerprints up to the CROSSCHECK_LIBRARIES=Boolean Instead of producing the normal comparison of read-groups, roll fingerprints up to the Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: library level and print out a library x library matrix with LOD scores. Default value: library level and print out a library x library matrix with LOD scores. Default value: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: false. This option can be set to 'null' to clear the default value. Possible values: false. This option can be set to 'null' to clear the default value. Possible values: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: {true, false} {true, false} Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXPECT_ALL_READ_GROUPS_TO_MATCH=Boolean EXPECT_ALL_READ_GROUPS_TO_MATCH=Boolean Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Expect all read groups' fingerprints to match, irrespective of their sample names. By Expect all read groups' fingerprints to match, irrespective of their sample names. By Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: default (with this value set to false), read groups with different sample names are default (with this value set to false), read groups with different sample names are Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: expected to mismatch, and those with the same sample name are expected to match. Default expected to mismatch, and those with the same sample name are expected to match. Default Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: value: false. This option can be set to 'null' to clear the default value. Possible value: false. This option can be set to 'null' to clear the default value. Possible Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: values: {true, false} Cannot be used in conjuction with option(s) values: {true, false} Cannot be used in conjuction with option(s) Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXPECT_ALL_GROUPS_TO_MATCH EXPECT_ALL_GROUPS_TO_MATCH Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INPUT=String INPUT=String Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: I=String One or more input files (or lists of files) with which to compare fingerprints. Default I=String One or more input files (or lists of files) with which to compare fingerprints. Default Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: value: null. This option must be specified at least 1 times. value: null. This option must be specified at least 1 times. Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the INPUT data (in column INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the INPUT data (in column Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 1) and the sample as it should be used for comparisons to SECOND_INPUT (in the second 1) and the sample as it should be used for comparisons to SECOND_INPUT (in the second Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: column). Need only include the samples that change. Values in column 1 should be unique. column). Need only include the samples that change. Values in column 1 should be unique. Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Values in column 2 should be unique even in union with the remaining unmapped samples. Values in column 2 should be unique even in union with the remaining unmapped samples. Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Should only be used with SECOND_INPUT. Default value: null. Cannot be used in Should only be used with SECOND_INPUT. Default value: null. Cannot be used in Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: conjuction with option(s) INPUT_SAMPLE_FILE_MAP conjuction with option(s) INPUT_SAMPLE_FILE_MAP Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INPUT_SAMPLE_FILE_MAP=File A tsv with two columns representing the sample as it should be used for comparisons to INPUT_SAMPLE_FILE_MAP=File A tsv with two columns representing the sample as it should be used for comparisons to Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT (in the first column) and the source file (in INPUT) for the fingerprint (in SECOND_INPUT (in the first column) and the source file (in INPUT) for the fingerprint (in Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: the second column). Need only to include the samples that change. Values in column 1 the second column). Need only to include the samples that change. Values in column 1 Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: should be unique even in union with the remaining unmapped samples. Values in column 2 should be unique even in union with the remaining unmapped samples. Values in column 2 Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: should be unique in the file. Will error if more than one sample is found in a file should be unique in the file. Will error if more than one sample is found in a file Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: (multi-sample VCF) pointed to in column 2. Should only be used in the presence of (multi-sample VCF) pointed to in column 2. Should only be used in the presence of Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT. Default value: null. Cannot be used in conjuction with option(s) SECOND_INPUT. Default value: null. Cannot be used in conjuction with option(s) Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INPUT_SAMPLE_MAP INPUT_SAMPLE_MAP Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT=String SECOND_INPUT=String Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SI=String A second set of input files (or lists of files) with which to compare fingerprints. If SI=String A second set of input files (or lists of files) with which to compare fingerprints. If Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: this option is provided the tool compares each sample in INPUT with the sample from this option is provided the tool compares each sample in INPUT with the sample from Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT that has the same sample ID. In addition, data will be grouped by SAMPLE SECOND_INPUT that has the same sample ID. In addition, data will be grouped by SAMPLE Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: regardless of the value of CROSSCHECK_BY. When operating in this mode, each sample in regardless of the value of CROSSCHECK_BY. When operating in this mode, each sample in Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INPUT must also have a corresponding sample in SECOND_INPUT. If this is violated, the tool INPUT must also have a corresponding sample in SECOND_INPUT. If this is violated, the tool Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: will proceed to check the matching samples, but report the missing samples and return a will proceed to check the matching samples, but report the missing samples and return a Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: non-zero error-code. Default value: null. This option may be specified 0 or more times. non-zero error-code. Default value: null. This option may be specified 0 or more times. Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Cannot be used in conjuction with option(s) MATRIX_OUTPUT (MO) Cannot be used in conjuction with option(s) MATRIX_OUTPUT (MO) Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the SECOND_INPUT data (in SECOND_INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the SECOND_INPUT data (in Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: column 1) and the sample as it should be used for comparisons to INPUT (in the second column 1) and the sample as it should be used for comparisons to INPUT (in the second Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: column). Note that in case of unrolling files (file-of-filenames) one would need to column). Note that in case of unrolling files (file-of-filenames) one would need to Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: reference the final file, i.e. the file that contains the genomic data. Need only include reference the final file, i.e. the file that contains the genomic data. Need only include Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: the samples that change. Values in column 1 should be unique. Values in column 2 should be the samples that change. Values in column 1 should be unique. Values in column 2 should be Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: unique even in union with the remaining unmapped samples. Should only be used with unique even in union with the remaining unmapped samples. Should only be used with Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT. Default value: null. SECOND_INPUT. Default value: null. Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CROSSCHECK_MODE=CrosscheckModeAn argument that controls how crosschecking with both INPUT and SECOND_INPUT should occur. CROSSCHECK_MODE=CrosscheckModeAn argument that controls how crosschecking with both INPUT and SECOND_INPUT should occur. Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Default value: CHECK_SAME_SAMPLE. This option can be set to 'null' to clear the default Default value: CHECK_SAME_SAMPLE. This option can be set to 'null' to clear the default Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: value. Possible values: { value. Possible values: { Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CHECK_SAME_SAMPLE (In this mode, each sample in INPUT will only be checked against a CHECK_SAME_SAMPLE (In this mode, each sample in INPUT will only be checked against a Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: single corresponding sample in SECOND_INPUT. If a corresponding sample cannot be found, single corresponding sample in SECOND_INPUT. If a corresponding sample cannot be found, Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: the program will proceed, but report the missing samples and return the value specified in the program will proceed, but report the missing samples and return the value specified in Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXIT_CODE_WHEN_MISMATCH. The corresponding samples are those that equal each other, after EXIT_CODE_WHEN_MISMATCH. The corresponding samples are those that equal each other, after Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: possible renaming via INPUT_SAMPLE_MAP and SECOND_INPUT_SAMPLE_MAP. In this mode possible renaming via INPUT_SAMPLE_MAP and SECOND_INPUT_SAMPLE_MAP. In this mode Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CROSSCHECK_BY must be SAMPLE.) CROSSCHECK_BY must be SAMPLE.) Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CHECK_ALL_OTHERS (In this mode, each sample in INPUT will be checked against all the CHECK_ALL_OTHERS (In this mode, each sample in INPUT will be checked against all the Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: samples in SECOND_INPUT.) samples in SECOND_INPUT.) Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: } } Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: O=File Optional output file to write metrics to. Default is to write to stdout. Default value: O=File Optional output file to write metrics to. Default is to write to stdout. Default value: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: null. null. Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: MATRIX_OUTPUT=File MATRIX_OUTPUT=File Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: MO=File Optional output file to write matrix of LOD scores to. This is less informative than the MO=File Optional output file to write matrix of LOD scores to. This is less informative than the Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: metrics output and only contains Normal-Normal LOD score (i.e. doesn't account for Loss of metrics output and only contains Normal-Normal LOD score (i.e. doesn't account for Loss of Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Heterozygosity). It is however sometimes easier to use visually. Default value: null. Heterozygosity). It is however sometimes easier to use visually. Default value: null. Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Cannot be used in conjuction with option(s) SECOND_INPUT (SI) Cannot be used in conjuction with option(s) SECOND_INPUT (SI) Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: HAPLOTYPE_MAP=File HAPLOTYPE_MAP=File Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: H=File The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for H=File The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: fingerprinting. See https://software.broadinstitute.org/gatk/documentation/article?id=9526 fingerprinting. See https://software.broadinstitute.org/gatk/documentation/article?id=9526 Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: for details. Required. for details. Required. Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: LOD_THRESHOLD=Double LOD_THRESHOLD=Double Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: LOD=Double If any two groups (with the same sample name) match with a LOD score lower than the LOD=Double If any two groups (with the same sample name) match with a LOD score lower than the Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: threshold the tool will exit with a non-zero code to indicate error. Program will also threshold the tool will exit with a non-zero code to indicate error. Program will also Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: exit with an error if it finds two groups with different sample name that match with a LOD exit with an error if it finds two groups with different sample name that match with a LOD Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: score greater than -LOD_THRESHOLD. score greater than -LOD_THRESHOLD. Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: LOD score 0 means equal likelihood that the groups match vs. come from different LOD score 0 means equal likelihood that the groups match vs. come from different Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: individuals, negative LOD score -N, mean 10^N time more likely that the groups are from individuals, negative LOD score -N, mean 10^N time more likely that the groups are from Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: different individuals, and +N means 10^N times more likely that the groups are from the different individuals, and +N means 10^N times more likely that the groups are from the Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: same individual. Default value: 0.0. This option can be set to 'null' to clear the same individual. Default value: 0.0. This option can be set to 'null' to clear the Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: default value. default value. Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CROSSCHECK_BY=DataType Specificies which data-type should be used as the basic comparison unit. Fingerprints from CROSSCHECK_BY=DataType Specificies which data-type should be used as the basic comparison unit. Fingerprints from Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: readgroups can be "rolled-up" to the LIBRARY, SAMPLE, or FILE level before being compared. readgroups can be "rolled-up" to the LIBRARY, SAMPLE, or FILE level before being compared. Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Fingerprints from VCF can be be compared by SAMPLE or FILE. Default value: READGROUP. Fingerprints from VCF can be be compared by SAMPLE or FILE. Default value: READGROUP. Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: This option can be set to 'null' to clear the default value. Possible values: {FILE, This option can be set to 'null' to clear the default value. Possible values: {FILE, Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SAMPLE, LIBRARY, READGROUP} SAMPLE, LIBRARY, READGROUP} Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: NUM_THREADS=Integer The number of threads to use to process files and generate fingerprints. Default value: NUM_THREADS=Integer The number of threads to use to process files and generate fingerprints. Default value: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 1. This option can be set to 'null' to clear the default value. 1. This option can be set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CALCULATE_TUMOR_AWARE_RESULTS=Boolean CALCULATE_TUMOR_AWARE_RESULTS=Boolean Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: specifies whether the Tumor-aware result should be calculated. These are time consuming specifies whether the Tumor-aware result should be calculated. These are time consuming Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: and can roughly double the runtime of the tool. When crosschecking many groups not and can roughly double the runtime of the tool. When crosschecking many groups not Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: calculating the tumor-aware results can result in a significant speedup. Default value: calculating the tumor-aware results can result in a significant speedup. Default value: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: true. This option can be set to 'null' to clear the default value. Possible values: {true, true. This option can be set to 'null' to clear the default value. Possible values: {true, Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: false} false} Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ALLOW_DUPLICATE_READS=Boolean Allow the use of duplicate reads in performing the comparison. Can be useful when ALLOW_DUPLICATE_READS=Boolean Allow the use of duplicate reads in performing the comparison. Can be useful when Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: duplicate marking has been overly aggressive and coverage is low. Default value: false. duplicate marking has been overly aggressive and coverage is low. Default value: false. Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: This option can be set to 'null' to clear the default value. Possible values: {true, This option can be set to 'null' to clear the default value. Possible values: {true, Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: false} false} Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: GENOTYPING_ERROR_RATE=Double Assumed genotyping error rate that provides a floor on the probability that a genotype GENOTYPING_ERROR_RATE=Double Assumed genotyping error rate that provides a floor on the probability that a genotype Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: comes from the expected sample. Must be greater than zero. Default value: 0.01. This comes from the expected sample. Must be greater than zero. Default value: 0.01. This Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: option can be set to 'null' to clear the default value. option can be set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: OUTPUT_ERRORS_ONLY=Boolean If true then only groups that do not relate to each other as expected will have their LODs OUTPUT_ERRORS_ONLY=Boolean If true then only groups that do not relate to each other as expected will have their LODs Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: reported. Default value: false. This option can be set to 'null' to clear the default reported. Default value: false. This option can be set to 'null' to clear the default Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: LOSS_OF_HET_RATE=Double The rate at which a heterozygous genotype in a normal sample turns into a homozygous (via LOSS_OF_HET_RATE=Double The rate at which a heterozygous genotype in a normal sample turns into a homozygous (via Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: loss of heterozygosity) in the tumor (model assumes independent events, so this needs to loss of heterozygosity) in the tumor (model assumes independent events, so this needs to Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: be larger than reality). Default value: 0.5. This option can be set to 'null' to clear be larger than reality). Default value: 0.5. This option can be set to 'null' to clear Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: the default value. the default value. Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXPECT_ALL_GROUPS_TO_MATCH=Boolean EXPECT_ALL_GROUPS_TO_MATCH=Boolean Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Expect all groups' fingerprints to match, irrespective of their sample names. By default Expect all groups' fingerprints to match, irrespective of their sample names. By default Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: (with this value set to false), groups (readgroups, libraries, files, or samples) with (with this value set to false), groups (readgroups, libraries, files, or samples) with Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: different sample names are expected to mismatch, and those with the same sample name are different sample names are expected to mismatch, and those with the same sample name are Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: expected to match. Default value: false. This option can be set to 'null' to clear the expected to match. Default value: false. This option can be set to 'null' to clear the Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: default value. Possible values: {true, false} default value. Possible values: {true, false} Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXIT_CODE_WHEN_MISMATCH=Integer EXIT_CODE_WHEN_MISMATCH=Integer Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: When one or more mismatches between groups is detected, exit with this value instead of 0. When one or more mismatches between groups is detected, exit with this value instead of 0. Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Default value: 1. This option can be set to 'null' to clear the default value. Default value: 1. This option can be set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXIT_CODE_WHEN_NO_VALID_CHECKS=Integer EXIT_CODE_WHEN_NO_VALID_CHECKS=Integer Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: When all LOD score are zero, exit with this value. Default value: 1. This option can be When all LOD score are zero, exit with this value. Default value: 1. This option can be Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: set to 'null' to clear the default value. set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=Double MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=Double Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Maximal effect of any single haplotype block on outcome (-log10 of maximal likelihood Maximal effect of any single haplotype block on outcome (-log10 of maximal likelihood Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: difference between the different values for the three possible genotypes). Default value: difference between the different values for the three possible genotypes). Default value: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 3.0. This option can be set to 'null' to clear the default value. 3.0. This option can be set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: TEST_INPUT_READABILITY=BooleanWhen true code will check for readability on input files (this can be slow on cloud TEST_INPUT_READABILITY=BooleanWhen true code will check for readability on input files (this can be slow on cloud Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: access) Default value: true. This option can be set to 'null' to clear the default value. access) Default value: true. This option can be set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Possible values: {true, false} Possible values: {true, false} Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: When calling CrosscheckReadGroupFingerprints, please refrain from supplying a CROSSCHECK_BY argument. (Found value FILE When calling CrosscheckReadGroupFingerprints, please refrain from supplying a CROSSCHECK_BY argument. (Found value FILE Test: Test method testCannotUseNewParameters[2](CROSSCHECK_BY=FILE)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Use CrosscheckFingerprints if you would like to do that. Use CrosscheckFingerprints if you would like to do that. Running Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:21 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file) STANDARD_ERROR INFO 2024-07-02 11:55:21 CrosscheckReadGroupFingerprints Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_SAMPLES true -MATRIX_OUTPUT matrix.file ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_SAMPLES true -MATRIX_OUTPUT matrix.file Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:21.935 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:21.935 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:21.935 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:21.935 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:21.935 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:55:21.935 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: USAGE: CrosscheckReadGroupFingerprints [options] USAGE: CrosscheckReadGroupFingerprints [options] Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CrosscheckReadGroupFingerprints Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CrosscheckReadGroupFingerprints Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: DEPRECATED: USE CrosscheckFingerprints. DEPRECATED: USE CrosscheckFingerprints. Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Version: null Version: null Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Options: Options: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: --help --help Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: tools. tools. Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CROSSCHECK_SAMPLES=Boolean Instead of producing the normal comparison of read-groups, roll fingerprints up to the CROSSCHECK_SAMPLES=Boolean Instead of producing the normal comparison of read-groups, roll fingerprints up to the Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: sample level and print out a sample x sample matrix with LOD scores. Default value: sample level and print out a sample x sample matrix with LOD scores. Default value: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: false. This option can be set to 'null' to clear the default value. Possible values: false. This option can be set to 'null' to clear the default value. Possible values: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: {true, false} {true, false} Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CROSSCHECK_LIBRARIES=Boolean Instead of producing the normal comparison of read-groups, roll fingerprints up to the CROSSCHECK_LIBRARIES=Boolean Instead of producing the normal comparison of read-groups, roll fingerprints up to the Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: library level and print out a library x library matrix with LOD scores. Default value: library level and print out a library x library matrix with LOD scores. Default value: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: false. This option can be set to 'null' to clear the default value. Possible values: false. This option can be set to 'null' to clear the default value. Possible values: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: {true, false} {true, false} Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXPECT_ALL_READ_GROUPS_TO_MATCH=Boolean EXPECT_ALL_READ_GROUPS_TO_MATCH=Boolean Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Expect all read groups' fingerprints to match, irrespective of their sample names. By Expect all read groups' fingerprints to match, irrespective of their sample names. By Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: default (with this value set to false), read groups with different sample names are default (with this value set to false), read groups with different sample names are Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: expected to mismatch, and those with the same sample name are expected to match. Default expected to mismatch, and those with the same sample name are expected to match. Default Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: value: false. This option can be set to 'null' to clear the default value. Possible value: false. This option can be set to 'null' to clear the default value. Possible Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: values: {true, false} Cannot be used in conjuction with option(s) values: {true, false} Cannot be used in conjuction with option(s) Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXPECT_ALL_GROUPS_TO_MATCH EXPECT_ALL_GROUPS_TO_MATCH Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INPUT=String INPUT=String Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: I=String One or more input files (or lists of files) with which to compare fingerprints. Default I=String One or more input files (or lists of files) with which to compare fingerprints. Default Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: value: null. This option must be specified at least 1 times. value: null. This option must be specified at least 1 times. Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the INPUT data (in column INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the INPUT data (in column Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 1) and the sample as it should be used for comparisons to SECOND_INPUT (in the second 1) and the sample as it should be used for comparisons to SECOND_INPUT (in the second Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: column). Need only include the samples that change. Values in column 1 should be unique. column). Need only include the samples that change. Values in column 1 should be unique. Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Values in column 2 should be unique even in union with the remaining unmapped samples. Values in column 2 should be unique even in union with the remaining unmapped samples. Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Should only be used with SECOND_INPUT. Default value: null. Cannot be used in Should only be used with SECOND_INPUT. Default value: null. Cannot be used in Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: conjuction with option(s) INPUT_SAMPLE_FILE_MAP conjuction with option(s) INPUT_SAMPLE_FILE_MAP Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INPUT_SAMPLE_FILE_MAP=File A tsv with two columns representing the sample as it should be used for comparisons to INPUT_SAMPLE_FILE_MAP=File A tsv with two columns representing the sample as it should be used for comparisons to Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT (in the first column) and the source file (in INPUT) for the fingerprint (in SECOND_INPUT (in the first column) and the source file (in INPUT) for the fingerprint (in Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: the second column). Need only to include the samples that change. Values in column 1 the second column). Need only to include the samples that change. Values in column 1 Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: should be unique even in union with the remaining unmapped samples. Values in column 2 should be unique even in union with the remaining unmapped samples. Values in column 2 Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: should be unique in the file. Will error if more than one sample is found in a file should be unique in the file. Will error if more than one sample is found in a file Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: (multi-sample VCF) pointed to in column 2. Should only be used in the presence of (multi-sample VCF) pointed to in column 2. Should only be used in the presence of Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT. Default value: null. Cannot be used in conjuction with option(s) SECOND_INPUT. Default value: null. Cannot be used in conjuction with option(s) Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INPUT_SAMPLE_MAP INPUT_SAMPLE_MAP Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT=String SECOND_INPUT=String Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SI=String A second set of input files (or lists of files) with which to compare fingerprints. If SI=String A second set of input files (or lists of files) with which to compare fingerprints. If Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: this option is provided the tool compares each sample in INPUT with the sample from this option is provided the tool compares each sample in INPUT with the sample from Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT that has the same sample ID. In addition, data will be grouped by SAMPLE SECOND_INPUT that has the same sample ID. In addition, data will be grouped by SAMPLE Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: regardless of the value of CROSSCHECK_BY. When operating in this mode, each sample in regardless of the value of CROSSCHECK_BY. When operating in this mode, each sample in Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INPUT must also have a corresponding sample in SECOND_INPUT. If this is violated, the tool INPUT must also have a corresponding sample in SECOND_INPUT. If this is violated, the tool Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: will proceed to check the matching samples, but report the missing samples and return a will proceed to check the matching samples, but report the missing samples and return a Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: non-zero error-code. Default value: null. This option may be specified 0 or more times. non-zero error-code. Default value: null. This option may be specified 0 or more times. Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Cannot be used in conjuction with option(s) MATRIX_OUTPUT (MO) Cannot be used in conjuction with option(s) MATRIX_OUTPUT (MO) Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the SECOND_INPUT data (in SECOND_INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the SECOND_INPUT data (in Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: column 1) and the sample as it should be used for comparisons to INPUT (in the second column 1) and the sample as it should be used for comparisons to INPUT (in the second Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: column). Note that in case of unrolling files (file-of-filenames) one would need to column). Note that in case of unrolling files (file-of-filenames) one would need to Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: reference the final file, i.e. the file that contains the genomic data. Need only include reference the final file, i.e. the file that contains the genomic data. Need only include Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: the samples that change. Values in column 1 should be unique. Values in column 2 should be the samples that change. Values in column 1 should be unique. Values in column 2 should be Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: unique even in union with the remaining unmapped samples. Should only be used with unique even in union with the remaining unmapped samples. Should only be used with Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT. Default value: null. SECOND_INPUT. Default value: null. Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CROSSCHECK_MODE=CrosscheckModeAn argument that controls how crosschecking with both INPUT and SECOND_INPUT should occur. CROSSCHECK_MODE=CrosscheckModeAn argument that controls how crosschecking with both INPUT and SECOND_INPUT should occur. Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Default value: CHECK_SAME_SAMPLE. This option can be set to 'null' to clear the default Default value: CHECK_SAME_SAMPLE. This option can be set to 'null' to clear the default Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: value. Possible values: { value. Possible values: { Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CHECK_SAME_SAMPLE (In this mode, each sample in INPUT will only be checked against a CHECK_SAME_SAMPLE (In this mode, each sample in INPUT will only be checked against a Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: single corresponding sample in SECOND_INPUT. If a corresponding sample cannot be found, single corresponding sample in SECOND_INPUT. If a corresponding sample cannot be found, Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: the program will proceed, but report the missing samples and return the value specified in the program will proceed, but report the missing samples and return the value specified in Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXIT_CODE_WHEN_MISMATCH. The corresponding samples are those that equal each other, after EXIT_CODE_WHEN_MISMATCH. The corresponding samples are those that equal each other, after Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: possible renaming via INPUT_SAMPLE_MAP and SECOND_INPUT_SAMPLE_MAP. In this mode possible renaming via INPUT_SAMPLE_MAP and SECOND_INPUT_SAMPLE_MAP. In this mode Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CROSSCHECK_BY must be SAMPLE.) CROSSCHECK_BY must be SAMPLE.) Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CHECK_ALL_OTHERS (In this mode, each sample in INPUT will be checked against all the CHECK_ALL_OTHERS (In this mode, each sample in INPUT will be checked against all the Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: samples in SECOND_INPUT.) samples in SECOND_INPUT.) Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: } } Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: O=File Optional output file to write metrics to. Default is to write to stdout. Default value: O=File Optional output file to write metrics to. Default is to write to stdout. Default value: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: null. null. Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: MATRIX_OUTPUT=File MATRIX_OUTPUT=File Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: MO=File Optional output file to write matrix of LOD scores to. This is less informative than the MO=File Optional output file to write matrix of LOD scores to. This is less informative than the Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: metrics output and only contains Normal-Normal LOD score (i.e. doesn't account for Loss of metrics output and only contains Normal-Normal LOD score (i.e. doesn't account for Loss of Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Heterozygosity). It is however sometimes easier to use visually. Default value: null. Heterozygosity). It is however sometimes easier to use visually. Default value: null. Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Cannot be used in conjuction with option(s) SECOND_INPUT (SI) Cannot be used in conjuction with option(s) SECOND_INPUT (SI) Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: HAPLOTYPE_MAP=File HAPLOTYPE_MAP=File Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: H=File The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for H=File The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: fingerprinting. See https://software.broadinstitute.org/gatk/documentation/article?id=9526 fingerprinting. See https://software.broadinstitute.org/gatk/documentation/article?id=9526 Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: for details. Required. for details. Required. Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: LOD_THRESHOLD=Double LOD_THRESHOLD=Double Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: LOD=Double If any two groups (with the same sample name) match with a LOD score lower than the LOD=Double If any two groups (with the same sample name) match with a LOD score lower than the Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: threshold the tool will exit with a non-zero code to indicate error. Program will also threshold the tool will exit with a non-zero code to indicate error. Program will also Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: exit with an error if it finds two groups with different sample name that match with a LOD exit with an error if it finds two groups with different sample name that match with a LOD Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: score greater than -LOD_THRESHOLD. score greater than -LOD_THRESHOLD. Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: LOD score 0 means equal likelihood that the groups match vs. come from different LOD score 0 means equal likelihood that the groups match vs. come from different Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: individuals, negative LOD score -N, mean 10^N time more likely that the groups are from individuals, negative LOD score -N, mean 10^N time more likely that the groups are from Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: different individuals, and +N means 10^N times more likely that the groups are from the different individuals, and +N means 10^N times more likely that the groups are from the Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: same individual. Default value: 0.0. This option can be set to 'null' to clear the same individual. Default value: 0.0. This option can be set to 'null' to clear the Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: default value. default value. Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CROSSCHECK_BY=DataType Specificies which data-type should be used as the basic comparison unit. Fingerprints from CROSSCHECK_BY=DataType Specificies which data-type should be used as the basic comparison unit. Fingerprints from Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: readgroups can be "rolled-up" to the LIBRARY, SAMPLE, or FILE level before being compared. readgroups can be "rolled-up" to the LIBRARY, SAMPLE, or FILE level before being compared. Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Fingerprints from VCF can be be compared by SAMPLE or FILE. Default value: READGROUP. Fingerprints from VCF can be be compared by SAMPLE or FILE. Default value: READGROUP. Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: This option can be set to 'null' to clear the default value. Possible values: {FILE, This option can be set to 'null' to clear the default value. Possible values: {FILE, Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SAMPLE, LIBRARY, READGROUP} SAMPLE, LIBRARY, READGROUP} Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: NUM_THREADS=Integer The number of threads to use to process files and generate fingerprints. Default value: NUM_THREADS=Integer The number of threads to use to process files and generate fingerprints. Default value: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 1. This option can be set to 'null' to clear the default value. 1. This option can be set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CALCULATE_TUMOR_AWARE_RESULTS=Boolean CALCULATE_TUMOR_AWARE_RESULTS=Boolean Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: specifies whether the Tumor-aware result should be calculated. These are time consuming specifies whether the Tumor-aware result should be calculated. These are time consuming Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: and can roughly double the runtime of the tool. When crosschecking many groups not and can roughly double the runtime of the tool. When crosschecking many groups not Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: calculating the tumor-aware results can result in a significant speedup. Default value: calculating the tumor-aware results can result in a significant speedup. Default value: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: true. This option can be set to 'null' to clear the default value. Possible values: {true, true. This option can be set to 'null' to clear the default value. Possible values: {true, Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: false} false} Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ALLOW_DUPLICATE_READS=Boolean Allow the use of duplicate reads in performing the comparison. Can be useful when ALLOW_DUPLICATE_READS=Boolean Allow the use of duplicate reads in performing the comparison. Can be useful when Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: duplicate marking has been overly aggressive and coverage is low. Default value: false. duplicate marking has been overly aggressive and coverage is low. Default value: false. Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: This option can be set to 'null' to clear the default value. Possible values: {true, This option can be set to 'null' to clear the default value. Possible values: {true, Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: false} false} Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: GENOTYPING_ERROR_RATE=Double Assumed genotyping error rate that provides a floor on the probability that a genotype GENOTYPING_ERROR_RATE=Double Assumed genotyping error rate that provides a floor on the probability that a genotype Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: comes from the expected sample. Must be greater than zero. Default value: 0.01. This comes from the expected sample. Must be greater than zero. Default value: 0.01. This Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: option can be set to 'null' to clear the default value. option can be set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: OUTPUT_ERRORS_ONLY=Boolean If true then only groups that do not relate to each other as expected will have their LODs OUTPUT_ERRORS_ONLY=Boolean If true then only groups that do not relate to each other as expected will have their LODs Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: reported. Default value: false. This option can be set to 'null' to clear the default reported. Default value: false. This option can be set to 'null' to clear the default Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: LOSS_OF_HET_RATE=Double The rate at which a heterozygous genotype in a normal sample turns into a homozygous (via LOSS_OF_HET_RATE=Double The rate at which a heterozygous genotype in a normal sample turns into a homozygous (via Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: loss of heterozygosity) in the tumor (model assumes independent events, so this needs to loss of heterozygosity) in the tumor (model assumes independent events, so this needs to Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: be larger than reality). Default value: 0.5. This option can be set to 'null' to clear be larger than reality). Default value: 0.5. This option can be set to 'null' to clear Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: the default value. the default value. Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXPECT_ALL_GROUPS_TO_MATCH=Boolean EXPECT_ALL_GROUPS_TO_MATCH=Boolean Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Expect all groups' fingerprints to match, irrespective of their sample names. By default Expect all groups' fingerprints to match, irrespective of their sample names. By default Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: (with this value set to false), groups (readgroups, libraries, files, or samples) with (with this value set to false), groups (readgroups, libraries, files, or samples) with Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: different sample names are expected to mismatch, and those with the same sample name are different sample names are expected to mismatch, and those with the same sample name are Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: expected to match. Default value: false. This option can be set to 'null' to clear the expected to match. Default value: false. This option can be set to 'null' to clear the Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: default value. Possible values: {true, false} default value. Possible values: {true, false} Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXIT_CODE_WHEN_MISMATCH=Integer EXIT_CODE_WHEN_MISMATCH=Integer Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: When one or more mismatches between groups is detected, exit with this value instead of 0. When one or more mismatches between groups is detected, exit with this value instead of 0. Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Default value: 1. This option can be set to 'null' to clear the default value. Default value: 1. This option can be set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXIT_CODE_WHEN_NO_VALID_CHECKS=Integer EXIT_CODE_WHEN_NO_VALID_CHECKS=Integer Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: When all LOD score are zero, exit with this value. Default value: 1. This option can be When all LOD score are zero, exit with this value. Default value: 1. This option can be Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: set to 'null' to clear the default value. set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=Double MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=Double Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Maximal effect of any single haplotype block on outcome (-log10 of maximal likelihood Maximal effect of any single haplotype block on outcome (-log10 of maximal likelihood Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: difference between the different values for the three possible genotypes). Default value: difference between the different values for the three possible genotypes). Default value: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 3.0. This option can be set to 'null' to clear the default value. 3.0. This option can be set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: TEST_INPUT_READABILITY=BooleanWhen true code will check for readability on input files (this can be slow on cloud TEST_INPUT_READABILITY=BooleanWhen true code will check for readability on input files (this can be slow on cloud Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: access) Default value: true. This option can be set to 'null' to clear the default value. access) Default value: true. This option can be set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Possible values: {true, false} Possible values: {true, false} Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: When calling CrosscheckReadGroupFingerprints, please refrain from supplying a MATRIX_OUTPUT argument. When calling CrosscheckReadGroupFingerprints, please refrain from supplying a MATRIX_OUTPUT argument. Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: (Found value matrix.file (Found value matrix.file Test: Test method testCannotUseNewParameters[3](MATRIX_OUTPUT=matrix.file)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Use CrosscheckFingerprints if you would like to do that. Use CrosscheckFingerprints if you would like to do that. Running Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:22 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin) STANDARD_ERROR INFO 2024-07-02 11:55:22 CrosscheckReadGroupFingerprints Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_SAMPLES true -SECOND_INPUT /dev/stdin ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_SAMPLES true -SECOND_INPUT /dev/stdin Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:22.110 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:22.110 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:22.110 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:22.110 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:22.111 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:55:22.111 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: USAGE: CrosscheckReadGroupFingerprints [options] USAGE: CrosscheckReadGroupFingerprints [options] Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CrosscheckReadGroupFingerprints Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#CrosscheckReadGroupFingerprints Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: DEPRECATED: USE CrosscheckFingerprints. DEPRECATED: USE CrosscheckFingerprints. Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Version: null Version: null Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Options: Options: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: --help --help Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: tools. tools. Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CROSSCHECK_SAMPLES=Boolean Instead of producing the normal comparison of read-groups, roll fingerprints up to the CROSSCHECK_SAMPLES=Boolean Instead of producing the normal comparison of read-groups, roll fingerprints up to the Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: sample level and print out a sample x sample matrix with LOD scores. Default value: sample level and print out a sample x sample matrix with LOD scores. Default value: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: false. This option can be set to 'null' to clear the default value. Possible values: false. This option can be set to 'null' to clear the default value. Possible values: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: {true, false} {true, false} Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CROSSCHECK_LIBRARIES=Boolean Instead of producing the normal comparison of read-groups, roll fingerprints up to the CROSSCHECK_LIBRARIES=Boolean Instead of producing the normal comparison of read-groups, roll fingerprints up to the Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: library level and print out a library x library matrix with LOD scores. Default value: library level and print out a library x library matrix with LOD scores. Default value: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: false. This option can be set to 'null' to clear the default value. Possible values: false. This option can be set to 'null' to clear the default value. Possible values: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: {true, false} {true, false} Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXPECT_ALL_READ_GROUPS_TO_MATCH=Boolean EXPECT_ALL_READ_GROUPS_TO_MATCH=Boolean Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Expect all read groups' fingerprints to match, irrespective of their sample names. By Expect all read groups' fingerprints to match, irrespective of their sample names. By Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: default (with this value set to false), read groups with different sample names are default (with this value set to false), read groups with different sample names are Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: expected to mismatch, and those with the same sample name are expected to match. Default expected to mismatch, and those with the same sample name are expected to match. Default Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: value: false. This option can be set to 'null' to clear the default value. Possible value: false. This option can be set to 'null' to clear the default value. Possible Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: values: {true, false} Cannot be used in conjuction with option(s) values: {true, false} Cannot be used in conjuction with option(s) Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXPECT_ALL_GROUPS_TO_MATCH EXPECT_ALL_GROUPS_TO_MATCH Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INPUT=String INPUT=String Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: I=String One or more input files (or lists of files) with which to compare fingerprints. Default I=String One or more input files (or lists of files) with which to compare fingerprints. Default Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: value: null. This option must be specified at least 1 times. value: null. This option must be specified at least 1 times. Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the INPUT data (in column INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the INPUT data (in column Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 1) and the sample as it should be used for comparisons to SECOND_INPUT (in the second 1) and the sample as it should be used for comparisons to SECOND_INPUT (in the second Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: column). Need only include the samples that change. Values in column 1 should be unique. column). Need only include the samples that change. Values in column 1 should be unique. Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Values in column 2 should be unique even in union with the remaining unmapped samples. Values in column 2 should be unique even in union with the remaining unmapped samples. Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Should only be used with SECOND_INPUT. Default value: null. Cannot be used in Should only be used with SECOND_INPUT. Default value: null. Cannot be used in Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: conjuction with option(s) INPUT_SAMPLE_FILE_MAP conjuction with option(s) INPUT_SAMPLE_FILE_MAP Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INPUT_SAMPLE_FILE_MAP=File A tsv with two columns representing the sample as it should be used for comparisons to INPUT_SAMPLE_FILE_MAP=File A tsv with two columns representing the sample as it should be used for comparisons to Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT (in the first column) and the source file (in INPUT) for the fingerprint (in SECOND_INPUT (in the first column) and the source file (in INPUT) for the fingerprint (in Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: the second column). Need only to include the samples that change. Values in column 1 the second column). Need only to include the samples that change. Values in column 1 Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: should be unique even in union with the remaining unmapped samples. Values in column 2 should be unique even in union with the remaining unmapped samples. Values in column 2 Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: should be unique in the file. Will error if more than one sample is found in a file should be unique in the file. Will error if more than one sample is found in a file Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: (multi-sample VCF) pointed to in column 2. Should only be used in the presence of (multi-sample VCF) pointed to in column 2. Should only be used in the presence of Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT. Default value: null. Cannot be used in conjuction with option(s) SECOND_INPUT. Default value: null. Cannot be used in conjuction with option(s) Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INPUT_SAMPLE_MAP INPUT_SAMPLE_MAP Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT=String SECOND_INPUT=String Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SI=String A second set of input files (or lists of files) with which to compare fingerprints. If SI=String A second set of input files (or lists of files) with which to compare fingerprints. If Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: this option is provided the tool compares each sample in INPUT with the sample from this option is provided the tool compares each sample in INPUT with the sample from Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT that has the same sample ID. In addition, data will be grouped by SAMPLE SECOND_INPUT that has the same sample ID. In addition, data will be grouped by SAMPLE Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: regardless of the value of CROSSCHECK_BY. When operating in this mode, each sample in regardless of the value of CROSSCHECK_BY. When operating in this mode, each sample in Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INPUT must also have a corresponding sample in SECOND_INPUT. If this is violated, the tool INPUT must also have a corresponding sample in SECOND_INPUT. If this is violated, the tool Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: will proceed to check the matching samples, but report the missing samples and return a will proceed to check the matching samples, but report the missing samples and return a Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: non-zero error-code. Default value: null. This option may be specified 0 or more times. non-zero error-code. Default value: null. This option may be specified 0 or more times. Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Cannot be used in conjuction with option(s) MATRIX_OUTPUT (MO) Cannot be used in conjuction with option(s) MATRIX_OUTPUT (MO) Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the SECOND_INPUT data (in SECOND_INPUT_SAMPLE_MAP=File A tsv with two columns representing the sample as it appears in the SECOND_INPUT data (in Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: column 1) and the sample as it should be used for comparisons to INPUT (in the second column 1) and the sample as it should be used for comparisons to INPUT (in the second Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: column). Note that in case of unrolling files (file-of-filenames) one would need to column). Note that in case of unrolling files (file-of-filenames) one would need to Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: reference the final file, i.e. the file that contains the genomic data. Need only include reference the final file, i.e. the file that contains the genomic data. Need only include Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: the samples that change. Values in column 1 should be unique. Values in column 2 should be the samples that change. Values in column 1 should be unique. Values in column 2 should be Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: unique even in union with the remaining unmapped samples. Should only be used with unique even in union with the remaining unmapped samples. Should only be used with Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SECOND_INPUT. Default value: null. SECOND_INPUT. Default value: null. Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CROSSCHECK_MODE=CrosscheckModeAn argument that controls how crosschecking with both INPUT and SECOND_INPUT should occur. CROSSCHECK_MODE=CrosscheckModeAn argument that controls how crosschecking with both INPUT and SECOND_INPUT should occur. Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Default value: CHECK_SAME_SAMPLE. This option can be set to 'null' to clear the default Default value: CHECK_SAME_SAMPLE. This option can be set to 'null' to clear the default Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: value. Possible values: { value. Possible values: { Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CHECK_SAME_SAMPLE (In this mode, each sample in INPUT will only be checked against a CHECK_SAME_SAMPLE (In this mode, each sample in INPUT will only be checked against a Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: single corresponding sample in SECOND_INPUT. If a corresponding sample cannot be found, single corresponding sample in SECOND_INPUT. If a corresponding sample cannot be found, Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: the program will proceed, but report the missing samples and return the value specified in the program will proceed, but report the missing samples and return the value specified in Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXIT_CODE_WHEN_MISMATCH. The corresponding samples are those that equal each other, after EXIT_CODE_WHEN_MISMATCH. The corresponding samples are those that equal each other, after Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: possible renaming via INPUT_SAMPLE_MAP and SECOND_INPUT_SAMPLE_MAP. In this mode possible renaming via INPUT_SAMPLE_MAP and SECOND_INPUT_SAMPLE_MAP. In this mode Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CROSSCHECK_BY must be SAMPLE.) CROSSCHECK_BY must be SAMPLE.) Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CHECK_ALL_OTHERS (In this mode, each sample in INPUT will be checked against all the CHECK_ALL_OTHERS (In this mode, each sample in INPUT will be checked against all the Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: samples in SECOND_INPUT.) samples in SECOND_INPUT.) Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: } } Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: O=File Optional output file to write metrics to. Default is to write to stdout. Default value: O=File Optional output file to write metrics to. Default is to write to stdout. Default value: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: null. null. Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: MATRIX_OUTPUT=File MATRIX_OUTPUT=File Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: MO=File Optional output file to write matrix of LOD scores to. This is less informative than the MO=File Optional output file to write matrix of LOD scores to. This is less informative than the Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: metrics output and only contains Normal-Normal LOD score (i.e. doesn't account for Loss of metrics output and only contains Normal-Normal LOD score (i.e. doesn't account for Loss of Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Heterozygosity). It is however sometimes easier to use visually. Default value: null. Heterozygosity). It is however sometimes easier to use visually. Default value: null. Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Cannot be used in conjuction with option(s) SECOND_INPUT (SI) Cannot be used in conjuction with option(s) SECOND_INPUT (SI) Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: HAPLOTYPE_MAP=File HAPLOTYPE_MAP=File Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: H=File The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for H=File The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: fingerprinting. See https://software.broadinstitute.org/gatk/documentation/article?id=9526 fingerprinting. See https://software.broadinstitute.org/gatk/documentation/article?id=9526 Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: for details. Required. for details. Required. Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: LOD_THRESHOLD=Double LOD_THRESHOLD=Double Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: LOD=Double If any two groups (with the same sample name) match with a LOD score lower than the LOD=Double If any two groups (with the same sample name) match with a LOD score lower than the Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: threshold the tool will exit with a non-zero code to indicate error. Program will also threshold the tool will exit with a non-zero code to indicate error. Program will also Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: exit with an error if it finds two groups with different sample name that match with a LOD exit with an error if it finds two groups with different sample name that match with a LOD Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: score greater than -LOD_THRESHOLD. score greater than -LOD_THRESHOLD. Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: LOD score 0 means equal likelihood that the groups match vs. come from different LOD score 0 means equal likelihood that the groups match vs. come from different Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: individuals, negative LOD score -N, mean 10^N time more likely that the groups are from individuals, negative LOD score -N, mean 10^N time more likely that the groups are from Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: different individuals, and +N means 10^N times more likely that the groups are from the different individuals, and +N means 10^N times more likely that the groups are from the Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: same individual. Default value: 0.0. This option can be set to 'null' to clear the same individual. Default value: 0.0. This option can be set to 'null' to clear the Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: default value. default value. Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CROSSCHECK_BY=DataType Specificies which data-type should be used as the basic comparison unit. Fingerprints from CROSSCHECK_BY=DataType Specificies which data-type should be used as the basic comparison unit. Fingerprints from Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: readgroups can be "rolled-up" to the LIBRARY, SAMPLE, or FILE level before being compared. readgroups can be "rolled-up" to the LIBRARY, SAMPLE, or FILE level before being compared. Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Fingerprints from VCF can be be compared by SAMPLE or FILE. Default value: READGROUP. Fingerprints from VCF can be be compared by SAMPLE or FILE. Default value: READGROUP. Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: This option can be set to 'null' to clear the default value. Possible values: {FILE, This option can be set to 'null' to clear the default value. Possible values: {FILE, Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: SAMPLE, LIBRARY, READGROUP} SAMPLE, LIBRARY, READGROUP} Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: NUM_THREADS=Integer The number of threads to use to process files and generate fingerprints. Default value: NUM_THREADS=Integer The number of threads to use to process files and generate fingerprints. Default value: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 1. This option can be set to 'null' to clear the default value. 1. This option can be set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: CALCULATE_TUMOR_AWARE_RESULTS=Boolean CALCULATE_TUMOR_AWARE_RESULTS=Boolean Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: specifies whether the Tumor-aware result should be calculated. These are time consuming specifies whether the Tumor-aware result should be calculated. These are time consuming Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: and can roughly double the runtime of the tool. When crosschecking many groups not and can roughly double the runtime of the tool. When crosschecking many groups not Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: calculating the tumor-aware results can result in a significant speedup. Default value: calculating the tumor-aware results can result in a significant speedup. Default value: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: true. This option can be set to 'null' to clear the default value. Possible values: {true, true. This option can be set to 'null' to clear the default value. Possible values: {true, Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: false} false} Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ALLOW_DUPLICATE_READS=Boolean Allow the use of duplicate reads in performing the comparison. Can be useful when ALLOW_DUPLICATE_READS=Boolean Allow the use of duplicate reads in performing the comparison. Can be useful when Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: duplicate marking has been overly aggressive and coverage is low. Default value: false. duplicate marking has been overly aggressive and coverage is low. Default value: false. Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: This option can be set to 'null' to clear the default value. Possible values: {true, This option can be set to 'null' to clear the default value. Possible values: {true, Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: false} false} Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: GENOTYPING_ERROR_RATE=Double Assumed genotyping error rate that provides a floor on the probability that a genotype GENOTYPING_ERROR_RATE=Double Assumed genotyping error rate that provides a floor on the probability that a genotype Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: comes from the expected sample. Must be greater than zero. Default value: 0.01. This comes from the expected sample. Must be greater than zero. Default value: 0.01. This Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: option can be set to 'null' to clear the default value. option can be set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: OUTPUT_ERRORS_ONLY=Boolean If true then only groups that do not relate to each other as expected will have their LODs OUTPUT_ERRORS_ONLY=Boolean If true then only groups that do not relate to each other as expected will have their LODs Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: reported. Default value: false. This option can be set to 'null' to clear the default reported. Default value: false. This option can be set to 'null' to clear the default Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: LOSS_OF_HET_RATE=Double The rate at which a heterozygous genotype in a normal sample turns into a homozygous (via LOSS_OF_HET_RATE=Double The rate at which a heterozygous genotype in a normal sample turns into a homozygous (via Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: loss of heterozygosity) in the tumor (model assumes independent events, so this needs to loss of heterozygosity) in the tumor (model assumes independent events, so this needs to Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: be larger than reality). Default value: 0.5. This option can be set to 'null' to clear be larger than reality). Default value: 0.5. This option can be set to 'null' to clear Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: the default value. the default value. Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXPECT_ALL_GROUPS_TO_MATCH=Boolean EXPECT_ALL_GROUPS_TO_MATCH=Boolean Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Expect all groups' fingerprints to match, irrespective of their sample names. By default Expect all groups' fingerprints to match, irrespective of their sample names. By default Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: (with this value set to false), groups (readgroups, libraries, files, or samples) with (with this value set to false), groups (readgroups, libraries, files, or samples) with Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: different sample names are expected to mismatch, and those with the same sample name are different sample names are expected to mismatch, and those with the same sample name are Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: expected to match. Default value: false. This option can be set to 'null' to clear the expected to match. Default value: false. This option can be set to 'null' to clear the Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: default value. Possible values: {true, false} default value. Possible values: {true, false} Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXIT_CODE_WHEN_MISMATCH=Integer EXIT_CODE_WHEN_MISMATCH=Integer Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: When one or more mismatches between groups is detected, exit with this value instead of 0. When one or more mismatches between groups is detected, exit with this value instead of 0. Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Default value: 1. This option can be set to 'null' to clear the default value. Default value: 1. This option can be set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: EXIT_CODE_WHEN_NO_VALID_CHECKS=Integer EXIT_CODE_WHEN_NO_VALID_CHECKS=Integer Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: When all LOD score are zero, exit with this value. Default value: 1. This option can be When all LOD score are zero, exit with this value. Default value: 1. This option can be Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: set to 'null' to clear the default value. set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=Double MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=Double Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Maximal effect of any single haplotype block on outcome (-log10 of maximal likelihood Maximal effect of any single haplotype block on outcome (-log10 of maximal likelihood Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: difference between the different values for the three possible genotypes). Default value: difference between the different values for the three possible genotypes). Default value: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 3.0. This option can be set to 'null' to clear the default value. 3.0. This option can be set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: TEST_INPUT_READABILITY=BooleanWhen true code will check for readability on input files (this can be slow on cloud TEST_INPUT_READABILITY=BooleanWhen true code will check for readability on input files (this can be slow on cloud Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: access) Default value: true. This option can be set to 'null' to clear the default value. access) Default value: true. This option can be set to 'null' to clear the default value. Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Possible values: {true, false} Possible values: {true, false} Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: When calling CrosscheckReadGroupFingerprints, please refrain from supplying a SECOND_INPUT argument. When calling CrosscheckReadGroupFingerprints, please refrain from supplying a SECOND_INPUT argument. Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: (Found value [/dev/stdin] (Found value [/dev/stdin] Test: Test method testCannotUseNewParameters[4](SECOND_INPUT=/dev/stdin)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Use CrosscheckFingerprints if you would like to do that. Use CrosscheckFingerprints if you would like to do that. Running Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:22 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true) STANDARD_ERROR INFO 2024-07-02 11:55:22 CrosscheckReadGroupFingerprints Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam -OUTPUT /tmp/Fingerprinting5353688552748124883NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_LIBRARIES true ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam -OUTPUT /tmp/Fingerprinting5353688552748124883NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_LIBRARIES true Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:22.293 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:22.293 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:22.293 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:22.293 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:22.294 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:22.294 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:22.294 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:22.294 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:22.294 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:22.294 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:22.294 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:22.294 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:22 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_LIBRARIES=true INPUT=[/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam] OUTPUT=/tmp/Fingerprinting5353688552748124883NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_SAMPLES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:22 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_LIBRARIES=true INPUT=[/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam] OUTPUT=/tmp/Fingerprinting5353688552748124883NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_SAMPLES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:22 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:22 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:22 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) INFO 2024-07-02 11:55:22 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:22 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam) INFO 2024-07-02 11:55:22 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam) Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:22 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:55:22 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:22 CrosscheckFingerprints Cross-checking all LIBRARY against each other INFO 2024-07-02 11:55:22 CrosscheckFingerprints Cross-checking all LIBRARY against each other Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:22 CrosscheckFingerprints All LIBRARYs are related as expected. INFO 2024-07-02 11:55:22 CrosscheckFingerprints All LIBRARYs are related as expected. Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:22 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:22 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckLBs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:22 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false) STANDARD_ERROR INFO 2024-07-02 11:55:22 CrosscheckReadGroupFingerprints Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam -OUTPUT /tmp/Fingerprinting3114150808354932684NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_LIBRARIES true ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam -OUTPUT /tmp/Fingerprinting3114150808354932684NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_LIBRARIES true Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:22.860 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:22.860 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:22.860 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:22.860 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:22.870 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:22.870 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:22.870 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:22.870 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:22.870 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:22.870 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:22.870 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:22.870 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:22 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_LIBRARIES=true INPUT=[/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam] OUTPUT=/tmp/Fingerprinting3114150808354932684NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_SAMPLES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:22 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_LIBRARIES=true INPUT=[/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam] OUTPUT=/tmp/Fingerprinting3114150808354932684NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_SAMPLES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:22 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:22 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:22 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) INFO 2024-07-02 11:55:22 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:23 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam) INFO 2024-07-02 11:55:23 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam) Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:23 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:55:23 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:23 CrosscheckFingerprints Cross-checking all LIBRARY against each other INFO 2024-07-02 11:55:23 CrosscheckFingerprints Cross-checking all LIBRARY against each other Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:23 CrosscheckFingerprints All LIBRARYs are related as expected. INFO 2024-07-02 11:55:23 CrosscheckFingerprints All LIBRARYs are related as expected. Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:23 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:23 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckLBs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:23 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false) STANDARD_ERROR INFO 2024-07-02 11:55:23 CrosscheckReadGroupFingerprints Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam -OUTPUT /tmp/Fingerprinting597634017976568868NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_LIBRARIES true ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam -OUTPUT /tmp/Fingerprinting597634017976568868NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_LIBRARIES true Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:23.574 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:23.574 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:23.574 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:23.574 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:23.575 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:23.575 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:23.575 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:23.575 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:23.575 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:23.575 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:23.575 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:23.575 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:23 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_LIBRARIES=true INPUT=[/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam] OUTPUT=/tmp/Fingerprinting597634017976568868NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_SAMPLES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:23 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_LIBRARIES=true INPUT=[/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam] OUTPUT=/tmp/Fingerprinting597634017976568868NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_SAMPLES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:23 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:23 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:23 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam) INFO 2024-07-02 11:55:23 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam) Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:23 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam) INFO 2024-07-02 11:55:23 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam) Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:23 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:55:23 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:23 CrosscheckFingerprints Cross-checking all LIBRARY against each other INFO 2024-07-02 11:55:23 CrosscheckFingerprints Cross-checking all LIBRARY against each other Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:23 CrosscheckFingerprints All LIBRARYs are related as expected. INFO 2024-07-02 11:55:23 CrosscheckFingerprints All LIBRARYs are related as expected. Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:23 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:23 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckLBs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:23 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false) STANDARD_ERROR INFO 2024-07-02 11:55:23 CrosscheckReadGroupFingerprints Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -OUTPUT /tmp/Fingerprinting224987885189315632NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_LIBRARIES true ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -OUTPUT /tmp/Fingerprinting224987885189315632NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_LIBRARIES true Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:23.962 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:23.962 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:23.962 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:23.962 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:23.964 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:23.964 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:23.964 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:23.964 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:23.964 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:23.964 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:23.964 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:23.964 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:23 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_LIBRARIES=true INPUT=[/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam] OUTPUT=/tmp/Fingerprinting224987885189315632NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_SAMPLES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:23 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_LIBRARIES=true INPUT=[/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam] OUTPUT=/tmp/Fingerprinting224987885189315632NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_SAMPLES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:23 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:23 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:24 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam) INFO 2024-07-02 11:55:24 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam) Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:24 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) INFO 2024-07-02 11:55:24 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:24 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:55:24 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:24 CrosscheckFingerprints Cross-checking all LIBRARY against each other INFO 2024-07-02 11:55:24 CrosscheckFingerprints Cross-checking all LIBRARY against each other Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:24 CrosscheckFingerprints All LIBRARYs are related as expected. INFO 2024-07-02 11:55:24 CrosscheckFingerprints All LIBRARYs are related as expected. Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:24 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:24 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckLBs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, 0, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:24 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true) STANDARD_ERROR INFO 2024-07-02 11:55:24 CrosscheckReadGroupFingerprints Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam -OUTPUT /tmp/Fingerprinting11855374356812719910NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_LIBRARIES true ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam -OUTPUT /tmp/Fingerprinting11855374356812719910NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_LIBRARIES true Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:24.417 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:24.417 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:24.417 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:24.417 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:24.418 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:24.418 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:24.418 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:24.418 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:24.418 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:24.418 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:24.418 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:24.418 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:24 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_LIBRARIES=true INPUT=[/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam] OUTPUT=/tmp/Fingerprinting11855374356812719910NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_SAMPLES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:24 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_LIBRARIES=true INPUT=[/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam] OUTPUT=/tmp/Fingerprinting11855374356812719910NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_SAMPLES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:24 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:24 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:24 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) INFO 2024-07-02 11:55:24 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:24 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam) WARNING 2024-07-02 11:55:24 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam) Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:24 FingerprintChecker Processed files. 54 fingerprints found in map. INFO 2024-07-02 11:55:24 FingerprintChecker Processed files. 54 fingerprints found in map. Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:24 CrosscheckFingerprints Cross-checking all LIBRARY against each other INFO 2024-07-02 11:55:24 CrosscheckFingerprints Cross-checking all LIBRARY against each other Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:24 CrosscheckFingerprints 2 LIBRARYs did not relate as expected. WARNING 2024-07-02 11:55:24 CrosscheckFingerprints 2 LIBRARYs did not relate as expected. Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:24 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:24 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testCrossCheckLBs[4](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:24 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false) STANDARD_ERROR INFO 2024-07-02 11:55:24 CrosscheckReadGroupFingerprints Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam -OUTPUT /tmp/Fingerprinting13544682875305126262NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_LIBRARIES true ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam -OUTPUT /tmp/Fingerprinting13544682875305126262NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_LIBRARIES true Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:24.894 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:24.894 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:24.895 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:24.895 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:24.895 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:24.895 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:24.895 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:24.895 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:24.895 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:24.895 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:24.895 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:24.895 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:24 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_LIBRARIES=true INPUT=[/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam] OUTPUT=/tmp/Fingerprinting13544682875305126262NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_SAMPLES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:24 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_LIBRARIES=true INPUT=[/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam] OUTPUT=/tmp/Fingerprinting13544682875305126262NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_SAMPLES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:24 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:24 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:24 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam) INFO 2024-07-02 11:55:24 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam) Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:25 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam) WARNING 2024-07-02 11:55:25 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam) Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:25 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:55:25 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:25 CrosscheckFingerprints Cross-checking all LIBRARY against each other INFO 2024-07-02 11:55:25 CrosscheckFingerprints Cross-checking all LIBRARY against each other Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:25 CrosscheckFingerprints 2 LIBRARYs did not relate as expected. WARNING 2024-07-02 11:55:25 CrosscheckFingerprints 2 LIBRARYs did not relate as expected. Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:25 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:25 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testCrossCheckLBs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:25 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true) STANDARD_ERROR INFO 2024-07-02 11:55:25 CrosscheckReadGroupFingerprints Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam -OUTPUT /tmp/Fingerprinting8884877091638949619NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_LIBRARIES true ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam -OUTPUT /tmp/Fingerprinting8884877091638949619NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_LIBRARIES true Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:25.521 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:25.521 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:25.533 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:25.533 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:25.534 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:25.534 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:25.534 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:25.534 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:25.534 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:25.534 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:25.534 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:25.534 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:25 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_LIBRARIES=true INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam] OUTPUT=/tmp/Fingerprinting8884877091638949619NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_SAMPLES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:25 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_LIBRARIES=true INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam] OUTPUT=/tmp/Fingerprinting8884877091638949619NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_SAMPLES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:25 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:25 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:25 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam) INFO 2024-07-02 11:55:25 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam) Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:25 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam) WARNING 2024-07-02 11:55:25 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam) Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:26 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:55:26 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:26 CrosscheckFingerprints Cross-checking all LIBRARY against each other INFO 2024-07-02 11:55:26 CrosscheckFingerprints Cross-checking all LIBRARY against each other Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:26 CrosscheckFingerprints 2 LIBRARYs did not relate as expected. WARNING 2024-07-02 11:55:26 CrosscheckFingerprints 2 LIBRARYs did not relate as expected. Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:26 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:26 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testCrossCheckLBs[6](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:26 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false) STANDARD_ERROR INFO 2024-07-02 11:55:26 CrosscheckReadGroupFingerprints Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam -OUTPUT /tmp/Fingerprinting7958971715281611241NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_LIBRARIES true ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam -OUTPUT /tmp/Fingerprinting7958971715281611241NA1291.LB.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_LIBRARIES true Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:26.227 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:26.227 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:26.227 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:26.227 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:26.227 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:26.227 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:26.227 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:26.227 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:26.227 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:26.227 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:26.228 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:26.228 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:26 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_LIBRARIES=true INPUT=[/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam] OUTPUT=/tmp/Fingerprinting7958971715281611241NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_SAMPLES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:26 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_LIBRARIES=true INPUT=[/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam] OUTPUT=/tmp/Fingerprinting7958971715281611241NA1291.LB.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_SAMPLES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:26 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:26 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:26 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam) INFO 2024-07-02 11:55:26 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam) Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:26 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam) WARNING 2024-07-02 11:55:26 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam) Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:26 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:55:26 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:26 CrosscheckFingerprints Cross-checking all LIBRARY against each other INFO 2024-07-02 11:55:26 CrosscheckFingerprints Cross-checking all LIBRARY against each other Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:26 CrosscheckFingerprints 2 LIBRARYs did not relate as expected. WARNING 2024-07-02 11:55:26 CrosscheckFingerprints 2 LIBRARYs did not relate as expected. Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:26 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:26 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testCrossCheckLBs[7](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, testdata/picard/fingerprint/NA12891_named_NA12892.over.fingerprints.r1.sam, 1, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:26 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53) STANDARD_ERROR INFO 2024-07-02 11:55:26 CrosscheckReadGroupFingerprints Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam -OUTPUT /tmp/Fingerprinting2291435850880574030NA1291.RG.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam -OUTPUT /tmp/Fingerprinting2291435850880574030NA1291.RG.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:26.850 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:26.850 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:26.850 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:26.850 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:26.851 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:26.851 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:26.851 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:26.851 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:26.851 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:26.851 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:26.851 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:26.851 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:26 GMT+14:00 2024] CrosscheckReadGroupFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam] OUTPUT=/tmp/Fingerprinting2291435850880574030NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false CROSSCHECK_SAMPLES=false CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:26 GMT+14:00 2024] CrosscheckReadGroupFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam] OUTPUT=/tmp/Fingerprinting2291435850880574030NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false CROSSCHECK_SAMPLES=false CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:26 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:26 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:26 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) INFO 2024-07-02 11:55:26 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:27 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam) INFO 2024-07-02 11:55:27 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam) Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:27 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:55:27 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:27 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:55:27 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:27 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:55:27 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:27 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:27 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:27 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52) STANDARD_ERROR INFO 2024-07-02 11:55:27 CrosscheckReadGroupFingerprints Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam -OUTPUT /tmp/Fingerprinting6323481332228360050NA1291.RG.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam -OUTPUT /tmp/Fingerprinting6323481332228360050NA1291.RG.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:27.630 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:27.630 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:27.630 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:27.630 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:27.631 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:27.631 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:27.631 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:27.631 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:27.631 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:27.631 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:27.631 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:27.631 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:27 GMT+14:00 2024] CrosscheckReadGroupFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam] OUTPUT=/tmp/Fingerprinting6323481332228360050NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false CROSSCHECK_SAMPLES=false CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:27 GMT+14:00 2024] CrosscheckReadGroupFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam] OUTPUT=/tmp/Fingerprinting6323481332228360050NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false CROSSCHECK_SAMPLES=false CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:27 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:27 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:27 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) INFO 2024-07-02 11:55:27 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:27 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam) INFO 2024-07-02 11:55:27 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam) Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:28 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:55:28 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:28 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:55:28 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:28 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:55:28 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:28 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:28 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:28 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53) STANDARD_ERROR INFO 2024-07-02 11:55:28 CrosscheckReadGroupFingerprints Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam -OUTPUT /tmp/Fingerprinting12310632496501880023NA1291.RG.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam -OUTPUT /tmp/Fingerprinting12310632496501880023NA1291.RG.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:28.187 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:28.187 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:28.187 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:28.187 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:28.188 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:28.188 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:28.188 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:28.188 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:28.188 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:28.188 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:28.188 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:28.188 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:28 GMT+14:00 2024] CrosscheckReadGroupFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam] OUTPUT=/tmp/Fingerprinting12310632496501880023NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false CROSSCHECK_SAMPLES=false CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:28 GMT+14:00 2024] CrosscheckReadGroupFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam] OUTPUT=/tmp/Fingerprinting12310632496501880023NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false CROSSCHECK_SAMPLES=false CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:28 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:28 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:28 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) INFO 2024-07-02 11:55:28 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:28 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam) INFO 2024-07-02 11:55:28 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam) Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:28 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:55:28 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:28 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:55:28 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:28 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:55:28 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:28 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:28 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[2](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:28 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51) STANDARD_ERROR INFO 2024-07-02 11:55:28 CrosscheckReadGroupFingerprints Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam -OUTPUT /tmp/Fingerprinting1033371143069595847NA1291.RG.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam -OUTPUT /tmp/Fingerprinting1033371143069595847NA1291.RG.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:28.709 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:28.709 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:28.710 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:28.710 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:28.710 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:28.710 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:28.710 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:28.710 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:28.710 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:28.710 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:28.710 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:28.710 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:28 GMT+14:00 2024] CrosscheckReadGroupFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam] OUTPUT=/tmp/Fingerprinting1033371143069595847NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false CROSSCHECK_SAMPLES=false CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:28 GMT+14:00 2024] CrosscheckReadGroupFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam] OUTPUT=/tmp/Fingerprinting1033371143069595847NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false CROSSCHECK_SAMPLES=false CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:28 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:28 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:28 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam) INFO 2024-07-02 11:55:28 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam) Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:29 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam) INFO 2024-07-02 11:55:29 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam) Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:29 FingerprintChecker Processed files. 51 fingerprints found in map. INFO 2024-07-02 11:55:29 FingerprintChecker Processed files. 51 fingerprints found in map. Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:29 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:55:29 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:29 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:55:29 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:29 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:29 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[3](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, false, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:29 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52) STANDARD_ERROR INFO 2024-07-02 11:55:29 CrosscheckReadGroupFingerprints Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam -OUTPUT /tmp/Fingerprinting11644484694001127243NA1291.RG.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam -OUTPUT /tmp/Fingerprinting11644484694001127243NA1291.RG.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:29.514 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:29.514 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:29.514 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:29.514 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:29.515 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:29.515 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:29.515 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:29.515 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:29.515 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:29.515 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:29.515 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:29.515 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:29 GMT+14:00 2024] CrosscheckReadGroupFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam] OUTPUT=/tmp/Fingerprinting11644484694001127243NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false CROSSCHECK_SAMPLES=false CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:29 GMT+14:00 2024] CrosscheckReadGroupFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam] OUTPUT=/tmp/Fingerprinting11644484694001127243NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false CROSSCHECK_SAMPLES=false CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:29 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:29 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:29 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam) INFO 2024-07-02 11:55:29 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam) Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:29 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam) INFO 2024-07-02 11:55:29 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam) Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:30 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:55:30 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:30 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:55:30 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:30 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:55:30 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:30 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:30 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[4](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, false, 0, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:30 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53) STANDARD_ERROR INFO 2024-07-02 11:55:30 CrosscheckReadGroupFingerprints Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -OUTPUT /tmp/Fingerprinting11835933136223267630NA1291.RG.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -OUTPUT /tmp/Fingerprinting11835933136223267630NA1291.RG.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH false Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:30.246 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:30.246 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:30.246 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:30.246 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:30.247 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:30.247 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:30.247 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:30.247 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:30.247 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:30.247 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:30.247 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:30.247 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:30 GMT+14:00 2024] CrosscheckReadGroupFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam] OUTPUT=/tmp/Fingerprinting11835933136223267630NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false CROSSCHECK_SAMPLES=false CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:30 GMT+14:00 2024] CrosscheckReadGroupFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam] OUTPUT=/tmp/Fingerprinting11835933136223267630NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=false CROSSCHECK_SAMPLES=false CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:30 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:30 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:30 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam) INFO 2024-07-02 11:55:30 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam) Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:30 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) INFO 2024-07-02 11:55:30 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:30 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:55:30 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:30 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:55:30 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:30 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:55:30 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:30 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:30 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[5](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, false, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:30 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53) STANDARD_ERROR INFO 2024-07-02 11:55:30 CrosscheckReadGroupFingerprints Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam -OUTPUT /tmp/Fingerprinting6940560247129110586NA1291.RG.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam -OUTPUT /tmp/Fingerprinting6940560247129110586NA1291.RG.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:30.747 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:30.747 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:30.747 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:30.747 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:30.748 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:30.748 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:30.748 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:30.748 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:30.748 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:30.748 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:30.748 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:30.748 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:30 GMT+14:00 2024] CrosscheckReadGroupFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam] OUTPUT=/tmp/Fingerprinting6940560247129110586NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true CROSSCHECK_SAMPLES=false CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:30 GMT+14:00 2024] CrosscheckReadGroupFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam] OUTPUT=/tmp/Fingerprinting6940560247129110586NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true CROSSCHECK_SAMPLES=false CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:30 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:30 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:30 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) INFO 2024-07-02 11:55:30 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:30 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam) INFO 2024-07-02 11:55:30 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam) Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:30 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:55:30 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:30 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:55:30 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:30 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:55:30 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:30 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:30 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCrossCheckRGs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 0, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:31 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52) STANDARD_ERROR INFO 2024-07-02 11:55:31 CrosscheckReadGroupFingerprints Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam -OUTPUT /tmp/Fingerprinting16205359293901315924NA1291.RG.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam -OUTPUT /tmp/Fingerprinting16205359293901315924NA1291.RG.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:31.028 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:31.028 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:31.028 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:31.028 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:31.029 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:31.029 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:31.029 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:31.029 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:31.029 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:31.029 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:31.029 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:31.029 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:31 GMT+14:00 2024] CrosscheckReadGroupFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam] OUTPUT=/tmp/Fingerprinting16205359293901315924NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true CROSSCHECK_SAMPLES=false CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:31 GMT+14:00 2024] CrosscheckReadGroupFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam] OUTPUT=/tmp/Fingerprinting16205359293901315924NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true CROSSCHECK_SAMPLES=false CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:31 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:31 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:31 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) INFO 2024-07-02 11:55:31 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:31 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam) INFO 2024-07-02 11:55:31 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam) Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:31 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:55:31 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:31 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:55:31 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:31 CrosscheckFingerprints 84 READGROUPs did not relate as expected. WARNING 2024-07-02 11:55:31 CrosscheckFingerprints 84 READGROUPs did not relate as expected. Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:31 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:31 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testCrossCheckRGs[7](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:31 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53) STANDARD_ERROR INFO 2024-07-02 11:55:31 CrosscheckReadGroupFingerprints Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam -OUTPUT /tmp/Fingerprinting18077931505142210026NA1291.RG.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam -OUTPUT /tmp/Fingerprinting18077931505142210026NA1291.RG.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:31.855 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:31.855 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:31.855 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:31.855 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:31.862 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:31.862 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:31.862 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:31.862 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:31.862 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:31.862 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:31.862 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:31.862 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:31 GMT+14:00 2024] CrosscheckReadGroupFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam] OUTPUT=/tmp/Fingerprinting18077931505142210026NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true CROSSCHECK_SAMPLES=false CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:31 GMT+14:00 2024] CrosscheckReadGroupFingerprints INPUT=[/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam] OUTPUT=/tmp/Fingerprinting18077931505142210026NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true CROSSCHECK_SAMPLES=false CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:31 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:31 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:31 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) INFO 2024-07-02 11:55:31 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:32 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam) INFO 2024-07-02 11:55:32 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam) Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:32 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:55:32 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:32 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:55:32 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:32 CrosscheckFingerprints 138 READGROUPs did not relate as expected. WARNING 2024-07-02 11:55:32 CrosscheckFingerprints 138 READGROUPs did not relate as expected. Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:32 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:32 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testCrossCheckRGs[8](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:32 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51) STANDARD_ERROR INFO 2024-07-02 11:55:32 CrosscheckReadGroupFingerprints Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam -OUTPUT /tmp/Fingerprinting9085417490060260792NA1291.RG.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam -INPUT /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam -OUTPUT /tmp/Fingerprinting9085417490060260792NA1291.RG.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:32.803 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:32.803 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:32.803 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:32.803 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:32.804 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:32.804 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:32.804 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:32.804 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:32.805 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:32.805 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:32.805 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:32.805 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:32 GMT+14:00 2024] CrosscheckReadGroupFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam] OUTPUT=/tmp/Fingerprinting9085417490060260792NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true CROSSCHECK_SAMPLES=false CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:32 GMT+14:00 2024] CrosscheckReadGroupFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam] OUTPUT=/tmp/Fingerprinting9085417490060260792NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true CROSSCHECK_SAMPLES=false CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:32 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:32 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:32 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam) INFO 2024-07-02 11:55:32 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam) Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:32 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam) INFO 2024-07-02 11:55:32 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam) Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:32 FingerprintChecker Processed files. 51 fingerprints found in map. INFO 2024-07-02 11:55:32 FingerprintChecker Processed files. 51 fingerprints found in map. Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:32 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:55:32 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:33 CrosscheckFingerprints All READGROUPs are related as expected. INFO 2024-07-02 11:55:33 CrosscheckFingerprints All READGROUPs are related as expected. Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:33 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:33 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.00 minutes. Test: Test method testCrossCheckRGs[9](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, true, 0, 51)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:33 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52) STANDARD_ERROR INFO 2024-07-02 11:55:33 CrosscheckReadGroupFingerprints Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam -OUTPUT /tmp/Fingerprinting1943361617221993479NA1291.RG.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam -OUTPUT /tmp/Fingerprinting1943361617221993479NA1291.RG.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:33.108 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:33.108 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:33.108 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:33.108 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:33.110 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:33.110 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:33.110 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:33.110 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:33.111 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:33.111 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:33.111 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:33.111 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:33 GMT+14:00 2024] CrosscheckReadGroupFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam] OUTPUT=/tmp/Fingerprinting1943361617221993479NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true CROSSCHECK_SAMPLES=false CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:33 GMT+14:00 2024] CrosscheckReadGroupFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam] OUTPUT=/tmp/Fingerprinting1943361617221993479NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true CROSSCHECK_SAMPLES=false CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:33 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:33 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:33 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam) INFO 2024-07-02 11:55:33 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam) Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:33 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam) INFO 2024-07-02 11:55:33 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam) Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:33 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:55:33 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:33 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:55:33 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:33 CrosscheckFingerprints 188 READGROUPs did not relate as expected. WARNING 2024-07-02 11:55:33 CrosscheckFingerprints 188 READGROUPs did not relate as expected. Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:33 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:33 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testCrossCheckRGs[10](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, true, 1, 52)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:34 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53) STANDARD_ERROR INFO 2024-07-02 11:55:34 CrosscheckReadGroupFingerprints Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -OUTPUT /tmp/Fingerprinting10682364864867457872NA1291.RG.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -OUTPUT /tmp/Fingerprinting10682364864867457872NA1291.RG.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -2.0 -EXPECT_ALL_GROUPS_TO_MATCH true Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:34.079 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:34.079 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:34.079 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:34.079 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:34.080 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:34.080 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:34.080 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:34.080 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:34.093 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:34.093 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:34.093 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:34.093 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:34 GMT+14:00 2024] CrosscheckReadGroupFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam] OUTPUT=/tmp/Fingerprinting10682364864867457872NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true CROSSCHECK_SAMPLES=false CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:34 GMT+14:00 2024] CrosscheckReadGroupFingerprints INPUT=[/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam] OUTPUT=/tmp/Fingerprinting10682364864867457872NA1291.RG.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-2.0 EXPECT_ALL_GROUPS_TO_MATCH=true CROSSCHECK_SAMPLES=false CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:34 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:34 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:34 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam) INFO 2024-07-02 11:55:34 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam) Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:34 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) INFO 2024-07-02 11:55:34 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:34 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:55:34 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:34 CrosscheckFingerprints Cross-checking all READGROUP against each other INFO 2024-07-02 11:55:34 CrosscheckFingerprints Cross-checking all READGROUP against each other Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:34 CrosscheckFingerprints 138 READGROUPs did not relate as expected. WARNING 2024-07-02 11:55:34 CrosscheckFingerprints 138 READGROUPs did not relate as expected. Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:34 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:34 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testCrossCheckRGs[11](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, true, 1, 53)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:34 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true) STANDARD_ERROR INFO 2024-07-02 11:55:34 CrosscheckReadGroupFingerprints Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam -OUTPUT /tmp/Fingerprinting4980954260689365847NA1291.SM.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_SAMPLES true ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam -OUTPUT /tmp/Fingerprinting4980954260689365847NA1291.SM.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_SAMPLES true Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:34.802 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:34.802 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:34.802 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:34.802 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:34.804 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:34.804 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:34.804 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:34.804 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:34.804 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:34.804 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:34.804 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:34.804 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:34 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_SAMPLES=true INPUT=[/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam] OUTPUT=/tmp/Fingerprinting4980954260689365847NA1291.SM.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:34 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_SAMPLES=true INPUT=[/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam] OUTPUT=/tmp/Fingerprinting4980954260689365847NA1291.SM.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:34 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:34 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:34 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) INFO 2024-07-02 11:55:34 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:35 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam) INFO 2024-07-02 11:55:35 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam) Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:35 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:55:35 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:35 CrosscheckFingerprints Cross-checking all SAMPLE against each other INFO 2024-07-02 11:55:35 CrosscheckFingerprints Cross-checking all SAMPLE against each other Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:35 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:35 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:35 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:35 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckSMs[0](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:35 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false) STANDARD_ERROR INFO 2024-07-02 11:55:35 CrosscheckReadGroupFingerprints Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam -OUTPUT /tmp/Fingerprinting7618706601608191784NA1291.SM.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_SAMPLES true ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam -OUTPUT /tmp/Fingerprinting7618706601608191784NA1291.SM.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_SAMPLES true Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:35.386 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:35.386 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:35.386 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:35.386 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:35.387 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:35.387 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:35.387 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:35.387 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:35.388 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:35.388 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:35.388 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:35.388 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:35 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_SAMPLES=true INPUT=[/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam] OUTPUT=/tmp/Fingerprinting7618706601608191784NA1291.SM.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:35 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_SAMPLES=true INPUT=[/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam] OUTPUT=/tmp/Fingerprinting7618706601608191784NA1291.SM.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:35 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:35 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:35 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) INFO 2024-07-02 11:55:35 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:35 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam) INFO 2024-07-02 11:55:35 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam) Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:35 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:55:35 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:35 CrosscheckFingerprints Cross-checking all SAMPLE against each other INFO 2024-07-02 11:55:35 CrosscheckFingerprints Cross-checking all SAMPLE against each other Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:35 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:35 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:35 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:35 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckSMs[1](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:35 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false) STANDARD_ERROR INFO 2024-07-02 11:55:35 CrosscheckReadGroupFingerprints Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam -OUTPUT /tmp/Fingerprinting12899446132689717188NA1291.SM.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_SAMPLES true ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam -INPUT /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam -OUTPUT /tmp/Fingerprinting12899446132689717188NA1291.SM.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_SAMPLES true Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:35.714 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:35.714 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:35.714 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:35.714 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:35.715 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:35.715 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:35.715 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:35.715 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:35.715 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:35.715 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:35.716 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:35.716 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:35 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_SAMPLES=true INPUT=[/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam] OUTPUT=/tmp/Fingerprinting12899446132689717188NA1291.SM.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:35 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_SAMPLES=true INPUT=[/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam] OUTPUT=/tmp/Fingerprinting12899446132689717188NA1291.SM.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:35 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:35 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:35 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam) INFO 2024-07-02 11:55:35 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam) Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:35 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam) INFO 2024-07-02 11:55:35 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam) Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:36 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:55:36 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:36 CrosscheckFingerprints Cross-checking all SAMPLE against each other INFO 2024-07-02 11:55:36 CrosscheckFingerprints Cross-checking all SAMPLE against each other Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:36 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:36 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:36 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:36 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckSMs[2](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, 0, 2, false)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:36 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true) STANDARD_ERROR INFO 2024-07-02 11:55:36 CrosscheckReadGroupFingerprints Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam -OUTPUT /tmp/Fingerprinting15090519151148818878NA1291.SM.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_SAMPLES true ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam -OUTPUT /tmp/Fingerprinting15090519151148818878NA1291.SM.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_SAMPLES true Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:36.219 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:36.219 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:36.219 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:36.219 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:36.220 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:36.220 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:36.220 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:36.220 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:36.220 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:36.220 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:36.220 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:36.220 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:36 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_SAMPLES=true INPUT=[/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam] OUTPUT=/tmp/Fingerprinting15090519151148818878NA1291.SM.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:36 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_SAMPLES=true INPUT=[/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam] OUTPUT=/tmp/Fingerprinting15090519151148818878NA1291.SM.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:36 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:36 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:36 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam) INFO 2024-07-02 11:55:36 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam) Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:36 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam) INFO 2024-07-02 11:55:36 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam) Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:36 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:55:36 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:36 CrosscheckFingerprints Cross-checking all SAMPLE against each other INFO 2024-07-02 11:55:36 CrosscheckFingerprints Cross-checking all SAMPLE against each other Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:36 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:36 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:36 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:36 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckSMs[3](/tmp/NA12892.over.fingerprints.r2.sam10182470599059181622.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:36 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true) STANDARD_ERROR INFO 2024-07-02 11:55:36 CrosscheckReadGroupFingerprints Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam -OUTPUT /tmp/Fingerprinting9780485274712481738NA1291.SM.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_SAMPLES true ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam -OUTPUT /tmp/Fingerprinting9780485274712481738NA1291.SM.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_SAMPLES true Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:36.990 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:36.990 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:36.990 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:36.990 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:36.991 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:36.991 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:36.991 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:36.991 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:36.991 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:36.991 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:36.991 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:36.991 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:36 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_SAMPLES=true INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam] OUTPUT=/tmp/Fingerprinting9780485274712481738NA1291.SM.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:36 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_SAMPLES=true INPUT=[/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam] OUTPUT=/tmp/Fingerprinting9780485274712481738NA1291.SM.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:37 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:37 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:37 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam) INFO 2024-07-02 11:55:37 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam) Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:37 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam) INFO 2024-07-02 11:55:37 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam) Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:37 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:55:37 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:37 CrosscheckFingerprints Cross-checking all SAMPLE against each other INFO 2024-07-02 11:55:37 CrosscheckFingerprints Cross-checking all SAMPLE against each other Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:37 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:55:37 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:37 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:37 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testCrossCheckSMs[4](/tmp/NA12891.over.fingerprints.r2.sam2929363863420764352.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:37 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true) STANDARD_ERROR INFO 2024-07-02 11:55:37 CrosscheckReadGroupFingerprints Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam -OUTPUT /tmp/Fingerprinting13655362976400798970NA1291.SM.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_SAMPLES true ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam -OUTPUT /tmp/Fingerprinting13655362976400798970NA1291.SM.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_SAMPLES true Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:37.538 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:37.538 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:37.538 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:37.538 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:37.539 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:37.539 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:37.539 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:37.539 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:37.540 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:37.540 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:37.540 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:37.540 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:37 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_SAMPLES=true INPUT=[/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam] OUTPUT=/tmp/Fingerprinting13655362976400798970NA1291.SM.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:37 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_SAMPLES=true INPUT=[/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam] OUTPUT=/tmp/Fingerprinting13655362976400798970NA1291.SM.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:37 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:37 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:37 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam) INFO 2024-07-02 11:55:37 FingerprintChecker Reading an indexed file (/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam) Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:37 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam) INFO 2024-07-02 11:55:37 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam) Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:38 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:55:38 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:38 CrosscheckFingerprints Cross-checking all SAMPLE against each other INFO 2024-07-02 11:55:38 CrosscheckFingerprints Cross-checking all SAMPLE against each other Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:38 CrosscheckFingerprints All SAMPLEs are related as expected. INFO 2024-07-02 11:55:38 CrosscheckFingerprints All SAMPLEs are related as expected. Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:38 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:38 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckSMs[5](/tmp/NA12892.over.fingerprints.r1.sam12029866391796830641.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 0, 1, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:38 CrosscheckReadGroupFingerprints Gradle suite > Gradle test > picard.fingerprint.CrosscheckReadGroupFingerprintsTest.testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true) STANDARD_ERROR INFO 2024-07-02 11:55:38 CrosscheckReadGroupFingerprints Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam -OUTPUT /tmp/Fingerprinting3594177547499243110NA1291.SM.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_SAMPLES true ********** CrosscheckReadGroupFingerprints -INPUT /tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam -INPUT /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam -OUTPUT /tmp/Fingerprinting3594177547499243110NA1291.SM.crosscheck_metrics -HAPLOTYPE_MAP testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -LOD_THRESHOLD -1.0 -CROSSCHECK_SAMPLES true Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: ********** ********** Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:38.081 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:55:38.081 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:38.081 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:55:38.081 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:38.082 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:38.082 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:38.083 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:38.083 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:38.083 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:38.083 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: 11:55:38.083 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:38.083 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:38 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_SAMPLES=true INPUT=[/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam] OUTPUT=/tmp/Fingerprinting3594177547499243110NA1291.SM.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:38 GMT+14:00 2024] CrosscheckReadGroupFingerprints CROSSCHECK_SAMPLES=true INPUT=[/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam] OUTPUT=/tmp/Fingerprinting3594177547499243110NA1291.SM.crosscheck_metrics HAPLOTYPE_MAP=testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_LIBRARIES=false EXPECT_ALL_READ_GROUPS_TO_MATCH=false CROSSCHECK_MODE=CHECK_SAME_SAMPLE CROSSCHECK_BY=READGROUP NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXPECT_ALL_GROUPS_TO_MATCH=false EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:38 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:55:38 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:38 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) INFO 2024-07-02 11:55:38 FingerprintChecker Reading an indexed file (/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam) Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:38 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam) INFO 2024-07-02 11:55:38 FingerprintChecker Reading an indexed file (/tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam) Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:38 FingerprintChecker Processed files. 54 fingerprints found in map. INFO 2024-07-02 11:55:38 FingerprintChecker Processed files. 54 fingerprints found in map. Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: INFO 2024-07-02 11:55:38 CrosscheckFingerprints Cross-checking all SAMPLE against each other INFO 2024-07-02 11:55:38 CrosscheckFingerprints Cross-checking all SAMPLE against each other Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: WARNING 2024-07-02 11:55:38 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. WARNING 2024-07-02 11:55:38 CrosscheckFingerprints 2 SAMPLEs did not relate as expected. Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: [Tue Jul 02 11:55:38 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:38 GMT+14:00 2024] picard.fingerprint.CrosscheckReadGroupFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testCrossCheckSMs[6](/tmp/NA12891.over.fingerprints.r1.sam7648435695179897805.bam, /tmp/NA12891_named_NA12892.over.fingerprints.r1.sam3027855844115582249.bam, 1, 2, true)(picard.fingerprint.CrosscheckReadGroupFingerprintsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method basicParsingTest(picard.util.DelimitedTextFileWithHeaderIteratorTest) Running Test: Test method parsingWithColumnHeadersTest(picard.util.DelimitedTextFileWithHeaderIteratorTest) Running Test: Test method testDistances[0](picard.util.BarcodeEditDistanceQuery@3a4807a0, LENIENT_HAMMING, 0)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[1](picard.util.BarcodeEditDistanceQuery@3a4807a0, HAMMING, 0)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[2](picard.util.BarcodeEditDistanceQuery@3a4807a0, FREE, 0)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[3](picard.util.BarcodeEditDistanceQuery@5b9588d2, LENIENT_HAMMING, 1)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[4](picard.util.BarcodeEditDistanceQuery@5b9588d2, HAMMING, 1)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[5](picard.util.BarcodeEditDistanceQuery@5b9588d2, FREE, 1)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[6](picard.util.BarcodeEditDistanceQuery@265892f9, LENIENT_HAMMING, 1)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[7](picard.util.BarcodeEditDistanceQuery@265892f9, HAMMING, 1)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[8](picard.util.BarcodeEditDistanceQuery@265892f9, FREE, 1)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[9](picard.util.BarcodeEditDistanceQuery@44d0e997, LENIENT_HAMMING, 3)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[10](picard.util.BarcodeEditDistanceQuery@44d0e997, HAMMING, 3)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[11](picard.util.BarcodeEditDistanceQuery@44d0e997, FREE, 1)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[12](picard.util.BarcodeEditDistanceQuery@3393f17d, LENIENT_HAMMING, 2)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[13](picard.util.BarcodeEditDistanceQuery@3393f17d, HAMMING, 2)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[14](picard.util.BarcodeEditDistanceQuery@3393f17d, FREE, 1)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[15](picard.util.BarcodeEditDistanceQuery@61daa142, LENIENT_HAMMING, 3)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[16](picard.util.BarcodeEditDistanceQuery@61daa142, HAMMING, 3)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[17](picard.util.BarcodeEditDistanceQuery@61daa142, FREE, 3)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[18](picard.util.BarcodeEditDistanceQuery@4dd79ad4, LENIENT_HAMMING, 2)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[19](picard.util.BarcodeEditDistanceQuery@4dd79ad4, HAMMING, 2)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[20](picard.util.BarcodeEditDistanceQuery@4dd79ad4, FREE, 2)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[21](picard.util.BarcodeEditDistanceQuery@26eb610c, LENIENT_HAMMING, 0)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[22](picard.util.BarcodeEditDistanceQuery@26eb610c, HAMMING, 1)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[23](picard.util.BarcodeEditDistanceQuery@26eb610c, FREE, 0)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[24](picard.util.BarcodeEditDistanceQuery@2e6c3bd8, LENIENT_HAMMING, 0)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[25](picard.util.BarcodeEditDistanceQuery@2e6c3bd8, HAMMING, 1)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[26](picard.util.BarcodeEditDistanceQuery@2e6c3bd8, FREE, 0)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[27](picard.util.BarcodeEditDistanceQuery@1834d975, LENIENT_HAMMING, 0)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[28](picard.util.BarcodeEditDistanceQuery@1834d975, HAMMING, 0)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[29](picard.util.BarcodeEditDistanceQuery@1834d975, FREE, 0)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[30](picard.util.BarcodeEditDistanceQuery@592b5de0, LENIENT_HAMMING, 3)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[31](picard.util.BarcodeEditDistanceQuery@592b5de0, HAMMING, 3)(picard.illumina.DistanceMetricTest) Running Test: Test method testDistances[32](picard.util.BarcodeEditDistanceQuery@592b5de0, FREE, 3)(picard.illumina.DistanceMetricTest) Running Test: Test method testDownsampleStrategies[0](0.3, HighAccuracy, 1)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[0](0.3, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:38 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[0](0.3, HighAccuracy, 1) STANDARD_ERROR INFO 2024-07-02 11:55:38 DownsampleSam Test: Test method testDownsampleStrategies[0](0.3, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[0](0.3, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[0](0.3, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[0](0.3, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[0](0.3, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[0](0.3, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[0](0.3, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[0](0.3, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[0](0.3, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6297477354191831125.bam -PROBABILITY 0.3 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6297477354191831125.bam -PROBABILITY 0.3 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testDownsampleStrategies[0](0.3, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[0](0.3, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[0](0.3, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[0](0.3, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:38.622 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:38.622 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[0](0.3, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:38.622 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:38.622 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[0](0.3, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:38.622 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:38.622 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[0](0.3, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:38.622 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:38.622 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[0](0.3, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:38 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6297477354191831125.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.3 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:38 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6297477354191831125.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.3 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[0](0.3, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[0](0.3, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:38 DownsampleSam Finished downsampling. INFO 2024-07-02 11:55:38 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[0](0.3, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:38 DownsampleSam Kept 6000 out of 20000 reads (30.00%). INFO 2024-07-02 11:55:38 DownsampleSam Kept 6000 out of 20000 reads (30.00%). Test: Test method testDownsampleStrategies[0](0.3, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:38 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:55:38 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testDownsampleStrategies[0](0.3, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[0](0.3, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:55:38 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:55:38 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[0](0.3, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[0](0.3, HighAccuracy, 1) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[1](0.4, HighAccuracy, 1)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[1](0.4, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:39 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[1](0.4, HighAccuracy, 1) STANDARD_ERROR INFO 2024-07-02 11:55:39 DownsampleSam Test: Test method testDownsampleStrategies[1](0.4, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[1](0.4, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[1](0.4, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[1](0.4, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[1](0.4, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[1](0.4, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[1](0.4, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[1](0.4, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[1](0.4, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6458270514675293361.bam -PROBABILITY 0.4 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6458270514675293361.bam -PROBABILITY 0.4 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testDownsampleStrategies[1](0.4, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[1](0.4, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[1](0.4, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[1](0.4, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:39.210 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:39.210 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[1](0.4, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:39.210 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:39.210 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[1](0.4, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:39.211 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:39.211 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[1](0.4, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:39.211 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:39.211 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[1](0.4, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:39 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6458270514675293361.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.4 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:39 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6458270514675293361.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.4 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[1](0.4, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[1](0.4, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:39 DownsampleSam Finished downsampling. INFO 2024-07-02 11:55:39 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[1](0.4, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:39 DownsampleSam Kept 8000 out of 20000 reads (40.00%). INFO 2024-07-02 11:55:39 DownsampleSam Kept 8000 out of 20000 reads (40.00%). Test: Test method testDownsampleStrategies[1](0.4, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:39 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:39 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[1](0.4, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[1](0.4, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:55:39 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:55:39 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[1](0.4, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[1](0.4, HighAccuracy, 1) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[2](0.5, HighAccuracy, 1)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[2](0.5, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:40 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[2](0.5, HighAccuracy, 1) STANDARD_ERROR INFO 2024-07-02 11:55:40 DownsampleSam Test: Test method testDownsampleStrategies[2](0.5, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[2](0.5, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[2](0.5, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[2](0.5, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[2](0.5, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[2](0.5, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[2](0.5, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[2](0.5, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[2](0.5, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5384187541317452710.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5384187541317452710.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testDownsampleStrategies[2](0.5, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[2](0.5, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[2](0.5, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[2](0.5, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:40.187 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:40.187 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[2](0.5, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:40.187 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:40.187 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[2](0.5, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:40.188 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:40.188 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[2](0.5, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:40.188 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:40.188 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[2](0.5, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:40 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5384187541317452710.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:40 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5384187541317452710.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[2](0.5, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[2](0.5, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:40 DownsampleSam Finished downsampling. INFO 2024-07-02 11:55:40 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[2](0.5, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:40 DownsampleSam Kept 10000 out of 20000 reads (50.00%). INFO 2024-07-02 11:55:40 DownsampleSam Kept 10000 out of 20000 reads (50.00%). Test: Test method testDownsampleStrategies[2](0.5, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:40 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:40 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[2](0.5, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[2](0.5, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:55:40 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:55:40 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[2](0.5, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[2](0.5, HighAccuracy, 1) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[3](0.6, HighAccuracy, 1)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[3](0.6, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:41 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[3](0.6, HighAccuracy, 1) STANDARD_ERROR INFO 2024-07-02 11:55:41 DownsampleSam Test: Test method testDownsampleStrategies[3](0.6, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[3](0.6, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[3](0.6, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[3](0.6, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[3](0.6, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[3](0.6, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[3](0.6, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[3](0.6, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[3](0.6, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6029823884133749644.bam -PROBABILITY 0.6 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6029823884133749644.bam -PROBABILITY 0.6 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testDownsampleStrategies[3](0.6, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[3](0.6, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[3](0.6, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[3](0.6, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:41.032 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:41.032 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[3](0.6, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:41.032 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:41.032 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[3](0.6, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:41.032 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:41.032 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[3](0.6, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:41.032 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:41.032 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[3](0.6, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:41 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6029823884133749644.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.6 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:41 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6029823884133749644.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.6 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[3](0.6, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[3](0.6, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:41 DownsampleSam Finished downsampling. INFO 2024-07-02 11:55:41 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[3](0.6, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:41 DownsampleSam Kept 12000 out of 20000 reads (60.00%). INFO 2024-07-02 11:55:41 DownsampleSam Kept 12000 out of 20000 reads (60.00%). Test: Test method testDownsampleStrategies[3](0.6, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:41 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:41 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[3](0.6, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[3](0.6, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:55:41 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:55:41 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[3](0.6, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[3](0.6, HighAccuracy, 1) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[4](0.7, HighAccuracy, 1)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[4](0.7, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:41 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[4](0.7, HighAccuracy, 1) STANDARD_ERROR INFO 2024-07-02 11:55:41 DownsampleSam Test: Test method testDownsampleStrategies[4](0.7, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[4](0.7, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[4](0.7, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[4](0.7, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[4](0.7, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[4](0.7, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[4](0.7, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[4](0.7, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[4](0.7, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1908762312371486621.bam -PROBABILITY 0.7 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1908762312371486621.bam -PROBABILITY 0.7 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testDownsampleStrategies[4](0.7, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[4](0.7, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[4](0.7, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[4](0.7, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:41.850 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:41.850 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[4](0.7, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:41.851 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:41.851 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[4](0.7, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:41.851 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:41.851 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[4](0.7, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:41.851 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:41.851 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[4](0.7, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:41 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1908762312371486621.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.7 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:41 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1908762312371486621.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.7 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[4](0.7, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[4](0.7, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:42 DownsampleSam Finished downsampling. INFO 2024-07-02 11:55:42 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[4](0.7, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:42 DownsampleSam Kept 14000 out of 20000 reads (70.00%). INFO 2024-07-02 11:55:42 DownsampleSam Kept 14000 out of 20000 reads (70.00%). Test: Test method testDownsampleStrategies[4](0.7, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:42 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:42 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[4](0.7, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[4](0.7, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:55:42 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:55:42 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[4](0.7, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[4](0.7, HighAccuracy, 1) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:42 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1) STANDARD_ERROR INFO 2024-07-02 11:55:42 DownsampleSam Test: Test method testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam9725034256340739.bam -PROBABILITY 0.7999999999999999 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam9725034256340739.bam -PROBABILITY 0.7999999999999999 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:42.711 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:42.711 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:42.711 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:42.711 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:42.711 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:42.711 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:42.711 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:42.711 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:42 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam9725034256340739.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.7999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:42 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam9725034256340739.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.7999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:43 DownsampleSam Finished downsampling. INFO 2024-07-02 11:55:43 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:43 DownsampleSam Kept 15998 out of 20000 reads (79.99%). INFO 2024-07-02 11:55:43 DownsampleSam Kept 15998 out of 20000 reads (79.99%). Test: Test method testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:43 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:43 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:55:43 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:55:43 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[5](0.7999999999999999, HighAccuracy, 1) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:43 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1) STANDARD_ERROR INFO 2024-07-02 11:55:43 DownsampleSam Test: Test method testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14821227719209064253.bam -PROBABILITY 0.8999999999999999 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14821227719209064253.bam -PROBABILITY 0.8999999999999999 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:43.638 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:43.638 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:43.638 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:43.638 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:43.639 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:43.639 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:43.639 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:43.639 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:43 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14821227719209064253.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.8999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:43 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14821227719209064253.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.8999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:44 DownsampleSam Finished downsampling. INFO 2024-07-02 11:55:44 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:44 DownsampleSam Kept 18000 out of 20000 reads (90.00%). INFO 2024-07-02 11:55:44 DownsampleSam Kept 18000 out of 20000 reads (90.00%). Test: Test method testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:44 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:44 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:55:44 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:55:44 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[6](0.8999999999999999, HighAccuracy, 1) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:44 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1) STANDARD_ERROR INFO 2024-07-02 11:55:44 DownsampleSam Test: Test method testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6269661777743155650.bam -PROBABILITY 0.9999999999999999 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6269661777743155650.bam -PROBABILITY 0.9999999999999999 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:44.981 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:44.981 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:44.981 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:44.981 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:44.982 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:44.982 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:44.982 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:44.982 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:44 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6269661777743155650.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.9999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:44 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6269661777743155650.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.9999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:45 DownsampleSam Finished downsampling. INFO 2024-07-02 11:55:45 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:45 DownsampleSam Kept 19998 out of 20000 reads (99.99%). INFO 2024-07-02 11:55:45 DownsampleSam Kept 19998 out of 20000 reads (99.99%). Test: Test method testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:45 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:45 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:55:45 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:55:45 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[7](0.9999999999999999, HighAccuracy, 1) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[8](0.3, HighAccuracy, null)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[8](0.3, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:46 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[8](0.3, HighAccuracy, null) STANDARD_ERROR INFO 2024-07-02 11:55:46 DownsampleSam Test: Test method testDownsampleStrategies[8](0.3, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[8](0.3, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[8](0.3, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[8](0.3, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[8](0.3, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[8](0.3, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[8](0.3, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[8](0.3, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[8](0.3, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1488127787624188376.bam -PROBABILITY 0.3 -STRATEGY HighAccuracy -RANDOM_SEED null -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1488127787624188376.bam -PROBABILITY 0.3 -STRATEGY HighAccuracy -RANDOM_SEED null -CREATE_INDEX true Test: Test method testDownsampleStrategies[8](0.3, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[8](0.3, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[8](0.3, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[8](0.3, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:46.586 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:46.586 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[8](0.3, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:46.586 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:46.586 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[8](0.3, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:46.586 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:46.586 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[8](0.3, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:46.586 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:46.586 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[8](0.3, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:46 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1488127787624188376.bam STRATEGY=HighAccuracy RANDOM_SEED=null PROBABILITY=0.3 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:46 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1488127787624188376.bam STRATEGY=HighAccuracy RANDOM_SEED=null PROBABILITY=0.3 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[8](0.3, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[8](0.3, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:55:46 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -673097432 to reproduce these results in the future. WARNING 2024-07-02 11:55:46 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -673097432 to reproduce these results in the future. Test: Test method testDownsampleStrategies[8](0.3, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:46 DownsampleSam Finished downsampling. INFO 2024-07-02 11:55:46 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[8](0.3, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:46 DownsampleSam Kept 6000 out of 20000 reads (30.00%). INFO 2024-07-02 11:55:46 DownsampleSam Kept 6000 out of 20000 reads (30.00%). Test: Test method testDownsampleStrategies[8](0.3, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:46 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:46 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[8](0.3, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[8](0.3, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:55:46 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:55:46 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[8](0.3, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[8](0.3, HighAccuracy, null) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[9](0.4, HighAccuracy, null)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[9](0.4, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:47 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[9](0.4, HighAccuracy, null) STANDARD_ERROR INFO 2024-07-02 11:55:47 DownsampleSam Test: Test method testDownsampleStrategies[9](0.4, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[9](0.4, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[9](0.4, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[9](0.4, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[9](0.4, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[9](0.4, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[9](0.4, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[9](0.4, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[9](0.4, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14469995765079269809.bam -PROBABILITY 0.4 -STRATEGY HighAccuracy -RANDOM_SEED null -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14469995765079269809.bam -PROBABILITY 0.4 -STRATEGY HighAccuracy -RANDOM_SEED null -CREATE_INDEX true Test: Test method testDownsampleStrategies[9](0.4, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[9](0.4, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[9](0.4, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[9](0.4, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:47.060 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:47.060 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[9](0.4, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:47.060 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:47.060 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[9](0.4, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:47.060 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:47.060 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[9](0.4, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:47.060 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:47.060 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[9](0.4, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:47 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14469995765079269809.bam STRATEGY=HighAccuracy RANDOM_SEED=null PROBABILITY=0.4 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:47 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14469995765079269809.bam STRATEGY=HighAccuracy RANDOM_SEED=null PROBABILITY=0.4 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[9](0.4, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[9](0.4, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:55:47 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -1321058396 to reproduce these results in the future. WARNING 2024-07-02 11:55:47 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -1321058396 to reproduce these results in the future. Test: Test method testDownsampleStrategies[9](0.4, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:47 DownsampleSam Finished downsampling. INFO 2024-07-02 11:55:47 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[9](0.4, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:47 DownsampleSam Kept 8000 out of 20000 reads (40.00%). INFO 2024-07-02 11:55:47 DownsampleSam Kept 8000 out of 20000 reads (40.00%). Test: Test method testDownsampleStrategies[9](0.4, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:47 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:47 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[9](0.4, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[9](0.4, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:55:47 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:55:47 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[9](0.4, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[9](0.4, HighAccuracy, null) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[10](0.5, HighAccuracy, null)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[10](0.5, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:48 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[10](0.5, HighAccuracy, null) STANDARD_ERROR INFO 2024-07-02 11:55:48 DownsampleSam Test: Test method testDownsampleStrategies[10](0.5, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[10](0.5, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[10](0.5, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[10](0.5, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[10](0.5, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[10](0.5, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[10](0.5, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[10](0.5, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[10](0.5, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam17611557775436290152.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED null -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam17611557775436290152.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED null -CREATE_INDEX true Test: Test method testDownsampleStrategies[10](0.5, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[10](0.5, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[10](0.5, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[10](0.5, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:48.049 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:48.049 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[10](0.5, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:48.049 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:48.049 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[10](0.5, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:48.050 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:48.050 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[10](0.5, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:48.050 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:48.050 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[10](0.5, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:48 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam17611557775436290152.bam STRATEGY=HighAccuracy RANDOM_SEED=null PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:48 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam17611557775436290152.bam STRATEGY=HighAccuracy RANDOM_SEED=null PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[10](0.5, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[10](0.5, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:55:48 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -297733286 to reproduce these results in the future. WARNING 2024-07-02 11:55:48 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -297733286 to reproduce these results in the future. Test: Test method testDownsampleStrategies[10](0.5, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:48 DownsampleSam Finished downsampling. INFO 2024-07-02 11:55:48 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[10](0.5, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:48 DownsampleSam Kept 10000 out of 20000 reads (50.00%). INFO 2024-07-02 11:55:48 DownsampleSam Kept 10000 out of 20000 reads (50.00%). Test: Test method testDownsampleStrategies[10](0.5, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:48 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:48 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[10](0.5, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[10](0.5, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:55:48 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:55:48 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[10](0.5, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[10](0.5, HighAccuracy, null) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[11](0.6, HighAccuracy, null)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[11](0.6, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:49 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[11](0.6, HighAccuracy, null) STANDARD_ERROR INFO 2024-07-02 11:55:49 DownsampleSam Test: Test method testDownsampleStrategies[11](0.6, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[11](0.6, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[11](0.6, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[11](0.6, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[11](0.6, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[11](0.6, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[11](0.6, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[11](0.6, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[11](0.6, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam4347316442276194036.bam -PROBABILITY 0.6 -STRATEGY HighAccuracy -RANDOM_SEED null -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam4347316442276194036.bam -PROBABILITY 0.6 -STRATEGY HighAccuracy -RANDOM_SEED null -CREATE_INDEX true Test: Test method testDownsampleStrategies[11](0.6, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[11](0.6, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[11](0.6, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[11](0.6, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:49.191 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:49.191 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[11](0.6, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:49.191 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:49.191 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[11](0.6, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:49.191 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:49.191 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[11](0.6, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:49.191 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:49.191 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[11](0.6, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:49 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam4347316442276194036.bam STRATEGY=HighAccuracy RANDOM_SEED=null PROBABILITY=0.6 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:49 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam4347316442276194036.bam STRATEGY=HighAccuracy RANDOM_SEED=null PROBABILITY=0.6 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[11](0.6, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[11](0.6, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:55:49 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -369934372 to reproduce these results in the future. WARNING 2024-07-02 11:55:49 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -369934372 to reproduce these results in the future. Test: Test method testDownsampleStrategies[11](0.6, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:49 DownsampleSam Finished downsampling. INFO 2024-07-02 11:55:49 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[11](0.6, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:49 DownsampleSam Kept 12000 out of 20000 reads (60.00%). INFO 2024-07-02 11:55:49 DownsampleSam Kept 12000 out of 20000 reads (60.00%). Test: Test method testDownsampleStrategies[11](0.6, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:49 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:49 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[11](0.6, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[11](0.6, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:55:50 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:55:50 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[11](0.6, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[11](0.6, HighAccuracy, null) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[12](0.7, HighAccuracy, null)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[12](0.7, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:50 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[12](0.7, HighAccuracy, null) STANDARD_ERROR INFO 2024-07-02 11:55:50 DownsampleSam Test: Test method testDownsampleStrategies[12](0.7, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[12](0.7, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[12](0.7, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[12](0.7, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[12](0.7, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[12](0.7, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[12](0.7, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[12](0.7, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[12](0.7, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam3570526087888941027.bam -PROBABILITY 0.7 -STRATEGY HighAccuracy -RANDOM_SEED null -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam3570526087888941027.bam -PROBABILITY 0.7 -STRATEGY HighAccuracy -RANDOM_SEED null -CREATE_INDEX true Test: Test method testDownsampleStrategies[12](0.7, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[12](0.7, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[12](0.7, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[12](0.7, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:50.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:50.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[12](0.7, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:50.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:50.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[12](0.7, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:50.493 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:50.493 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[12](0.7, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:50.493 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:50.493 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[12](0.7, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:50 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam3570526087888941027.bam STRATEGY=HighAccuracy RANDOM_SEED=null PROBABILITY=0.7 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:50 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam3570526087888941027.bam STRATEGY=HighAccuracy RANDOM_SEED=null PROBABILITY=0.7 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[12](0.7, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[12](0.7, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:55:50 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -1635570710 to reproduce these results in the future. WARNING 2024-07-02 11:55:50 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -1635570710 to reproduce these results in the future. Test: Test method testDownsampleStrategies[12](0.7, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:51 DownsampleSam Finished downsampling. INFO 2024-07-02 11:55:51 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[12](0.7, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:51 DownsampleSam Kept 14000 out of 20000 reads (70.00%). INFO 2024-07-02 11:55:51 DownsampleSam Kept 14000 out of 20000 reads (70.00%). Test: Test method testDownsampleStrategies[12](0.7, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:51 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:51 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[12](0.7, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[12](0.7, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:55:51 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:55:51 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[12](0.7, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[12](0.7, HighAccuracy, null) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:51 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null) STANDARD_ERROR INFO 2024-07-02 11:55:51 DownsampleSam Test: Test method testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8331825031376893192.bam -PROBABILITY 0.7999999999999999 -STRATEGY HighAccuracy -RANDOM_SEED null -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8331825031376893192.bam -PROBABILITY 0.7999999999999999 -STRATEGY HighAccuracy -RANDOM_SEED null -CREATE_INDEX true Test: Test method testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:51.940 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:51.940 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:51.940 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:51.940 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:51.940 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:51.940 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:51.940 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:51.940 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:51 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8331825031376893192.bam STRATEGY=HighAccuracy RANDOM_SEED=null PROBABILITY=0.7999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:51 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8331825031376893192.bam STRATEGY=HighAccuracy RANDOM_SEED=null PROBABILITY=0.7999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:55:51 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to 1685940446 to reproduce these results in the future. WARNING 2024-07-02 11:55:51 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to 1685940446 to reproduce these results in the future. Test: Test method testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:52 DownsampleSam Finished downsampling. INFO 2024-07-02 11:55:52 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:52 DownsampleSam Kept 15998 out of 20000 reads (79.99%). INFO 2024-07-02 11:55:52 DownsampleSam Kept 15998 out of 20000 reads (79.99%). Test: Test method testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:52 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:52 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:55:52 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:55:52 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[13](0.7999999999999999, HighAccuracy, null) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:52 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null) STANDARD_ERROR INFO 2024-07-02 11:55:52 DownsampleSam Test: Test method testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam10698327550017707527.bam -PROBABILITY 0.8999999999999999 -STRATEGY HighAccuracy -RANDOM_SEED null -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam10698327550017707527.bam -PROBABILITY 0.8999999999999999 -STRATEGY HighAccuracy -RANDOM_SEED null -CREATE_INDEX true Test: Test method testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:52.938 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:52.938 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:52.938 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:52.938 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:52.938 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:52.938 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:52.938 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:52.938 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:52 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam10698327550017707527.bam STRATEGY=HighAccuracy RANDOM_SEED=null PROBABILITY=0.8999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:52 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam10698327550017707527.bam STRATEGY=HighAccuracy RANDOM_SEED=null PROBABILITY=0.8999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:55:52 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to 1114421903 to reproduce these results in the future. WARNING 2024-07-02 11:55:52 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to 1114421903 to reproduce these results in the future. Test: Test method testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:53 DownsampleSam Finished downsampling. INFO 2024-07-02 11:55:53 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:53 DownsampleSam Kept 18000 out of 20000 reads (90.00%). INFO 2024-07-02 11:55:53 DownsampleSam Kept 18000 out of 20000 reads (90.00%). Test: Test method testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:53 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:55:53 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.02 minutes. Test: Test method testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:55:53 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:55:53 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[14](0.8999999999999999, HighAccuracy, null) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:54 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null) STANDARD_ERROR INFO 2024-07-02 11:55:54 DownsampleSam Test: Test method testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2977719891657599235.bam -PROBABILITY 0.9999999999999999 -STRATEGY HighAccuracy -RANDOM_SEED null -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2977719891657599235.bam -PROBABILITY 0.9999999999999999 -STRATEGY HighAccuracy -RANDOM_SEED null -CREATE_INDEX true Test: Test method testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:54.687 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:54.687 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:54.687 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:54.687 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:54.687 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:54.687 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:54.687 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:54.687 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:54 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2977719891657599235.bam STRATEGY=HighAccuracy RANDOM_SEED=null PROBABILITY=0.9999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:54 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2977719891657599235.bam STRATEGY=HighAccuracy RANDOM_SEED=null PROBABILITY=0.9999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:55:54 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -1260601116 to reproduce these results in the future. WARNING 2024-07-02 11:55:54 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -1260601116 to reproduce these results in the future. Test: Test method testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:55 DownsampleSam Finished downsampling. INFO 2024-07-02 11:55:55 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:55 DownsampleSam Kept 19998 out of 20000 reads (99.99%). INFO 2024-07-02 11:55:55 DownsampleSam Kept 19998 out of 20000 reads (99.99%). Test: Test method testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:55 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:55 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:55:55 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:55:55 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[15](0.9999999999999999, HighAccuracy, null) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[16](0.3, ConstantMemory, 1)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[16](0.3, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:55 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[16](0.3, ConstantMemory, 1) STANDARD_ERROR INFO 2024-07-02 11:55:55 DownsampleSam Test: Test method testDownsampleStrategies[16](0.3, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[16](0.3, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[16](0.3, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[16](0.3, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[16](0.3, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[16](0.3, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[16](0.3, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[16](0.3, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[16](0.3, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14709043926033298726.bam -PROBABILITY 0.3 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14709043926033298726.bam -PROBABILITY 0.3 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testDownsampleStrategies[16](0.3, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[16](0.3, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[16](0.3, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[16](0.3, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:55.726 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:55.726 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[16](0.3, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:55.726 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:55.726 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[16](0.3, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:55.726 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:55.726 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[16](0.3, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:55.726 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:55.726 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[16](0.3, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:55 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14709043926033298726.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.3 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:55 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14709043926033298726.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.3 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[16](0.3, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[16](0.3, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:56 DownsampleSam Finished downsampling. INFO 2024-07-02 11:55:56 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[16](0.3, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:56 DownsampleSam Kept 6026 out of 20000 reads (30.13%). INFO 2024-07-02 11:55:56 DownsampleSam Kept 6026 out of 20000 reads (30.13%). Test: Test method testDownsampleStrategies[16](0.3, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:56 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:56 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[16](0.3, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[16](0.3, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:55:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:55:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[16](0.3, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[16](0.3, ConstantMemory, 1) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[17](0.4, ConstantMemory, 1)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[17](0.4, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:56 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[17](0.4, ConstantMemory, 1) STANDARD_ERROR INFO 2024-07-02 11:55:56 DownsampleSam Test: Test method testDownsampleStrategies[17](0.4, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[17](0.4, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[17](0.4, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[17](0.4, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[17](0.4, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[17](0.4, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[17](0.4, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[17](0.4, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[17](0.4, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam11858015913312396825.bam -PROBABILITY 0.4 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam11858015913312396825.bam -PROBABILITY 0.4 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testDownsampleStrategies[17](0.4, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[17](0.4, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[17](0.4, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[17](0.4, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:56.604 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:56.604 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[17](0.4, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:56.604 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:56.604 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[17](0.4, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:56.604 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:56.604 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[17](0.4, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:56.604 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:56.604 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[17](0.4, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:56 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam11858015913312396825.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.4 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:56 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam11858015913312396825.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.4 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[17](0.4, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[17](0.4, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:57 DownsampleSam Finished downsampling. INFO 2024-07-02 11:55:57 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[17](0.4, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:57 DownsampleSam Kept 8002 out of 20000 reads (40.01%). INFO 2024-07-02 11:55:57 DownsampleSam Kept 8002 out of 20000 reads (40.01%). Test: Test method testDownsampleStrategies[17](0.4, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:57 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:57 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[17](0.4, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[17](0.4, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:55:57 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:55:57 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[17](0.4, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[17](0.4, ConstantMemory, 1) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[18](0.5, ConstantMemory, 1)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[18](0.5, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:57 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[18](0.5, ConstantMemory, 1) STANDARD_ERROR INFO 2024-07-02 11:55:57 DownsampleSam Test: Test method testDownsampleStrategies[18](0.5, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[18](0.5, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[18](0.5, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[18](0.5, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[18](0.5, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[18](0.5, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[18](0.5, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[18](0.5, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[18](0.5, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1877177710140879420.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1877177710140879420.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testDownsampleStrategies[18](0.5, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[18](0.5, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[18](0.5, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[18](0.5, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:57.338 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:57.338 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[18](0.5, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:57.338 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:57.338 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[18](0.5, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:57.338 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:57.338 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[18](0.5, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:57.338 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:57.338 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[18](0.5, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:57 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1877177710140879420.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:57 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1877177710140879420.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[18](0.5, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[18](0.5, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:57 DownsampleSam Finished downsampling. INFO 2024-07-02 11:55:57 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[18](0.5, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:57 DownsampleSam Kept 10018 out of 20000 reads (50.09%). INFO 2024-07-02 11:55:57 DownsampleSam Kept 10018 out of 20000 reads (50.09%). Test: Test method testDownsampleStrategies[18](0.5, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:57 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:57 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[18](0.5, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[18](0.5, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:55:57 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:55:57 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[18](0.5, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[18](0.5, ConstantMemory, 1) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[19](0.6, ConstantMemory, 1)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[19](0.6, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:58 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[19](0.6, ConstantMemory, 1) STANDARD_ERROR INFO 2024-07-02 11:55:58 DownsampleSam Test: Test method testDownsampleStrategies[19](0.6, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[19](0.6, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[19](0.6, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[19](0.6, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[19](0.6, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[19](0.6, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[19](0.6, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[19](0.6, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[19](0.6, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13799308162394194131.bam -PROBABILITY 0.6 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13799308162394194131.bam -PROBABILITY 0.6 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testDownsampleStrategies[19](0.6, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[19](0.6, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[19](0.6, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[19](0.6, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:58.338 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:58.338 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[19](0.6, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:58.338 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:58.338 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[19](0.6, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:58.339 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:58.339 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[19](0.6, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:58.339 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:58.339 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[19](0.6, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:58 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13799308162394194131.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.6 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:58 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13799308162394194131.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.6 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[19](0.6, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[19](0.6, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:59 DownsampleSam Finished downsampling. INFO 2024-07-02 11:55:59 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[19](0.6, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:59 DownsampleSam Kept 12002 out of 20000 reads (60.01%). INFO 2024-07-02 11:55:59 DownsampleSam Kept 12002 out of 20000 reads (60.01%). Test: Test method testDownsampleStrategies[19](0.6, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:59 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:55:59 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[19](0.6, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[19](0.6, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:55:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:55:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[19](0.6, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[19](0.6, ConstantMemory, 1) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[20](0.7, ConstantMemory, 1)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[20](0.7, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:55:59 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[20](0.7, ConstantMemory, 1) STANDARD_ERROR INFO 2024-07-02 11:55:59 DownsampleSam Test: Test method testDownsampleStrategies[20](0.7, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[20](0.7, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[20](0.7, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[20](0.7, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[20](0.7, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[20](0.7, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[20](0.7, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[20](0.7, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[20](0.7, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam7315943487644812100.bam -PROBABILITY 0.7 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam7315943487644812100.bam -PROBABILITY 0.7 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testDownsampleStrategies[20](0.7, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[20](0.7, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[20](0.7, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[20](0.7, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:59.755 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:59.755 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[20](0.7, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:59.755 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:59.755 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[20](0.7, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:59.755 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:55:59.755 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[20](0.7, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:55:59.755 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:55:59.755 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[20](0.7, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:59 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam7315943487644812100.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.7 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:55:59 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam7315943487644812100.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.7 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[20](0.7, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:55:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:55:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[20](0.7, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:00 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:00 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[20](0.7, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:00 DownsampleSam Kept 14018 out of 20000 reads (70.09%). INFO 2024-07-02 11:56:00 DownsampleSam Kept 14018 out of 20000 reads (70.09%). Test: Test method testDownsampleStrategies[20](0.7, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:00 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:00 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[20](0.7, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[20](0.7, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[20](0.7, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[20](0.7, ConstantMemory, 1) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:01 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1) STANDARD_ERROR INFO 2024-07-02 11:56:01 DownsampleSam Test: Test method testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13301908843147928364.bam -PROBABILITY 0.7999999999999999 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13301908843147928364.bam -PROBABILITY 0.7999999999999999 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:01.032 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:01.032 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:01.032 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:01.032 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:01.049 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:01.049 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:01.049 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:01.049 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:01 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13301908843147928364.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.7999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:01 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13301908843147928364.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.7999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:01 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:01 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:01 DownsampleSam Kept 15972 out of 20000 reads (79.86%). INFO 2024-07-02 11:56:01 DownsampleSam Kept 15972 out of 20000 reads (79.86%). Test: Test method testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:01 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:01 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[21](0.7999999999999999, ConstantMemory, 1) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:02 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1) STANDARD_ERROR INFO 2024-07-02 11:56:02 DownsampleSam Test: Test method testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5901321311145319784.bam -PROBABILITY 0.8999999999999999 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5901321311145319784.bam -PROBABILITY 0.8999999999999999 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:02.270 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:02.270 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:02.270 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:02.270 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:02.270 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:02.270 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:02.270 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:02.270 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:02 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5901321311145319784.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.8999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:02 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5901321311145319784.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.8999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:02 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:02 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:02 DownsampleSam Kept 18038 out of 20000 reads (90.19%). INFO 2024-07-02 11:56:02 DownsampleSam Kept 18038 out of 20000 reads (90.19%). Test: Test method testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:02 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:02 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[22](0.8999999999999999, ConstantMemory, 1) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:02 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1) STANDARD_ERROR INFO 2024-07-02 11:56:02 DownsampleSam Test: Test method testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam10676373838960161851.bam -PROBABILITY 0.9999999999999999 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam10676373838960161851.bam -PROBABILITY 0.9999999999999999 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:02.947 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:02.947 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:02.947 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:02.947 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:02.947 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:02.947 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:02.947 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:02.947 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:02 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam10676373838960161851.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.9999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:02 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam10676373838960161851.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.9999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:03 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:03 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:03 DownsampleSam Kept 20000 out of 20000 reads (100.00%). INFO 2024-07-02 11:56:03 DownsampleSam Kept 20000 out of 20000 reads (100.00%). Test: Test method testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:03 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:03 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[23](0.9999999999999999, ConstantMemory, 1) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[24](0.3, ConstantMemory, null)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[24](0.3, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:03 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[24](0.3, ConstantMemory, null) STANDARD_ERROR INFO 2024-07-02 11:56:03 DownsampleSam Test: Test method testDownsampleStrategies[24](0.3, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[24](0.3, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[24](0.3, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[24](0.3, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[24](0.3, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[24](0.3, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[24](0.3, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[24](0.3, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[24](0.3, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16570507789366191345.bam -PROBABILITY 0.3 -STRATEGY ConstantMemory -RANDOM_SEED null -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16570507789366191345.bam -PROBABILITY 0.3 -STRATEGY ConstantMemory -RANDOM_SEED null -CREATE_INDEX true Test: Test method testDownsampleStrategies[24](0.3, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[24](0.3, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[24](0.3, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[24](0.3, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:03.788 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:03.788 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[24](0.3, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:03.788 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:03.788 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[24](0.3, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:03.797 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:03.797 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[24](0.3, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:03.797 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:03.797 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[24](0.3, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:03 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16570507789366191345.bam STRATEGY=ConstantMemory RANDOM_SEED=null PROBABILITY=0.3 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:03 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16570507789366191345.bam STRATEGY=ConstantMemory RANDOM_SEED=null PROBABILITY=0.3 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[24](0.3, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[24](0.3, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:03 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to 336948433 to reproduce these results in the future. WARNING 2024-07-02 11:56:03 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to 336948433 to reproduce these results in the future. Test: Test method testDownsampleStrategies[24](0.3, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:03 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:03 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[24](0.3, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:03 DownsampleSam Kept 5876 out of 20000 reads (29.38%). INFO 2024-07-02 11:56:03 DownsampleSam Kept 5876 out of 20000 reads (29.38%). Test: Test method testDownsampleStrategies[24](0.3, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:03 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:03 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testDownsampleStrategies[24](0.3, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[24](0.3, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[24](0.3, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[24](0.3, ConstantMemory, null) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[25](0.4, ConstantMemory, null)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[25](0.4, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:04 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[25](0.4, ConstantMemory, null) STANDARD_ERROR INFO 2024-07-02 11:56:04 DownsampleSam Test: Test method testDownsampleStrategies[25](0.4, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[25](0.4, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[25](0.4, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[25](0.4, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[25](0.4, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[25](0.4, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[25](0.4, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[25](0.4, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[25](0.4, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam9082419240525716129.bam -PROBABILITY 0.4 -STRATEGY ConstantMemory -RANDOM_SEED null -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam9082419240525716129.bam -PROBABILITY 0.4 -STRATEGY ConstantMemory -RANDOM_SEED null -CREATE_INDEX true Test: Test method testDownsampleStrategies[25](0.4, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[25](0.4, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[25](0.4, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[25](0.4, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:04.126 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:04.126 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[25](0.4, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:04.126 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:04.126 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[25](0.4, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:04.126 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:04.126 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[25](0.4, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:04.126 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:04.126 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[25](0.4, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:04 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam9082419240525716129.bam STRATEGY=ConstantMemory RANDOM_SEED=null PROBABILITY=0.4 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:04 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam9082419240525716129.bam STRATEGY=ConstantMemory RANDOM_SEED=null PROBABILITY=0.4 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[25](0.4, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[25](0.4, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:04 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -102352565 to reproduce these results in the future. WARNING 2024-07-02 11:56:04 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -102352565 to reproduce these results in the future. Test: Test method testDownsampleStrategies[25](0.4, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:04 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:04 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[25](0.4, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:04 DownsampleSam Kept 7966 out of 20000 reads (39.83%). INFO 2024-07-02 11:56:04 DownsampleSam Kept 7966 out of 20000 reads (39.83%). Test: Test method testDownsampleStrategies[25](0.4, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:04 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:04 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testDownsampleStrategies[25](0.4, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[25](0.4, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[25](0.4, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[25](0.4, ConstantMemory, null) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[26](0.5, ConstantMemory, null)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[26](0.5, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:04 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[26](0.5, ConstantMemory, null) STANDARD_ERROR INFO 2024-07-02 11:56:04 DownsampleSam Test: Test method testDownsampleStrategies[26](0.5, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[26](0.5, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[26](0.5, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[26](0.5, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[26](0.5, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[26](0.5, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[26](0.5, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[26](0.5, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[26](0.5, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam11215037484327514260.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED null -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam11215037484327514260.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED null -CREATE_INDEX true Test: Test method testDownsampleStrategies[26](0.5, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[26](0.5, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[26](0.5, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[26](0.5, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:04.529 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:04.529 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[26](0.5, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:04.529 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:04.529 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[26](0.5, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:04.529 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:04.529 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[26](0.5, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:04.529 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:04.529 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[26](0.5, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:04 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam11215037484327514260.bam STRATEGY=ConstantMemory RANDOM_SEED=null PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:04 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam11215037484327514260.bam STRATEGY=ConstantMemory RANDOM_SEED=null PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[26](0.5, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[26](0.5, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:04 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -310254627 to reproduce these results in the future. WARNING 2024-07-02 11:56:04 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -310254627 to reproduce these results in the future. Test: Test method testDownsampleStrategies[26](0.5, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:04 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:04 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[26](0.5, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:04 DownsampleSam Kept 9640 out of 20000 reads (48.20%). INFO 2024-07-02 11:56:04 DownsampleSam Kept 9640 out of 20000 reads (48.20%). Test: Test method testDownsampleStrategies[26](0.5, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:04 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:04 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testDownsampleStrategies[26](0.5, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[26](0.5, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[26](0.5, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[26](0.5, ConstantMemory, null) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[27](0.6, ConstantMemory, null)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[27](0.6, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:04 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[27](0.6, ConstantMemory, null) STANDARD_ERROR INFO 2024-07-02 11:56:04 DownsampleSam Test: Test method testDownsampleStrategies[27](0.6, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[27](0.6, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[27](0.6, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[27](0.6, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[27](0.6, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[27](0.6, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[27](0.6, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[27](0.6, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[27](0.6, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam17739386999334267154.bam -PROBABILITY 0.6 -STRATEGY ConstantMemory -RANDOM_SEED null -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam17739386999334267154.bam -PROBABILITY 0.6 -STRATEGY ConstantMemory -RANDOM_SEED null -CREATE_INDEX true Test: Test method testDownsampleStrategies[27](0.6, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[27](0.6, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[27](0.6, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[27](0.6, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:04.931 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:04.931 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[27](0.6, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:04.931 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:04.931 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[27](0.6, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:04.931 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:04.931 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[27](0.6, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:04.931 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:04.931 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[27](0.6, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:04 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam17739386999334267154.bam STRATEGY=ConstantMemory RANDOM_SEED=null PROBABILITY=0.6 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:04 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam17739386999334267154.bam STRATEGY=ConstantMemory RANDOM_SEED=null PROBABILITY=0.6 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[27](0.6, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[27](0.6, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:04 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -871692896 to reproduce these results in the future. WARNING 2024-07-02 11:56:04 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -871692896 to reproduce these results in the future. Test: Test method testDownsampleStrategies[27](0.6, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:05 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:05 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[27](0.6, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:05 DownsampleSam Kept 11978 out of 20000 reads (59.89%). INFO 2024-07-02 11:56:05 DownsampleSam Kept 11978 out of 20000 reads (59.89%). Test: Test method testDownsampleStrategies[27](0.6, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:05 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:05 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testDownsampleStrategies[27](0.6, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[27](0.6, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:05 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:05 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[27](0.6, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[27](0.6, ConstantMemory, null) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[28](0.7, ConstantMemory, null)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[28](0.7, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:05 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[28](0.7, ConstantMemory, null) STANDARD_ERROR INFO 2024-07-02 11:56:05 DownsampleSam Test: Test method testDownsampleStrategies[28](0.7, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[28](0.7, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[28](0.7, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[28](0.7, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[28](0.7, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[28](0.7, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[28](0.7, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[28](0.7, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[28](0.7, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam17820500712687752233.bam -PROBABILITY 0.7 -STRATEGY ConstantMemory -RANDOM_SEED null -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam17820500712687752233.bam -PROBABILITY 0.7 -STRATEGY ConstantMemory -RANDOM_SEED null -CREATE_INDEX true Test: Test method testDownsampleStrategies[28](0.7, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[28](0.7, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[28](0.7, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[28](0.7, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:05.430 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:05.430 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[28](0.7, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:05.430 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:05.430 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[28](0.7, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:05.431 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:05.431 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[28](0.7, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:05.431 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:05.431 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[28](0.7, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:05 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam17820500712687752233.bam STRATEGY=ConstantMemory RANDOM_SEED=null PROBABILITY=0.7 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:05 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam17820500712687752233.bam STRATEGY=ConstantMemory RANDOM_SEED=null PROBABILITY=0.7 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[28](0.7, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[28](0.7, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:05 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to 1808017912 to reproduce these results in the future. WARNING 2024-07-02 11:56:05 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to 1808017912 to reproduce these results in the future. Test: Test method testDownsampleStrategies[28](0.7, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:05 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:05 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[28](0.7, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:05 DownsampleSam Kept 14114 out of 20000 reads (70.57%). INFO 2024-07-02 11:56:05 DownsampleSam Kept 14114 out of 20000 reads (70.57%). Test: Test method testDownsampleStrategies[28](0.7, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:05 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:05 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[28](0.7, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[28](0.7, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:05 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:05 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[28](0.7, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[28](0.7, ConstantMemory, null) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:06 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null) STANDARD_ERROR INFO 2024-07-02 11:56:06 DownsampleSam Test: Test method testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam17501125893036665444.bam -PROBABILITY 0.7999999999999999 -STRATEGY ConstantMemory -RANDOM_SEED null -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam17501125893036665444.bam -PROBABILITY 0.7999999999999999 -STRATEGY ConstantMemory -RANDOM_SEED null -CREATE_INDEX true Test: Test method testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:06.010 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:06.010 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:06.010 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:06.010 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:06.010 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:06.010 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:06.010 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:06.010 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:06 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam17501125893036665444.bam STRATEGY=ConstantMemory RANDOM_SEED=null PROBABILITY=0.7999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:06 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam17501125893036665444.bam STRATEGY=ConstantMemory RANDOM_SEED=null PROBABILITY=0.7999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:06 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -1052856330 to reproduce these results in the future. WARNING 2024-07-02 11:56:06 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -1052856330 to reproduce these results in the future. Test: Test method testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:06 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:06 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:06 DownsampleSam Kept 15792 out of 20000 reads (78.96%). INFO 2024-07-02 11:56:06 DownsampleSam Kept 15792 out of 20000 reads (78.96%). Test: Test method testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:06 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:06 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:06 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:06 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[29](0.7999999999999999, ConstantMemory, null) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:06 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null) STANDARD_ERROR INFO 2024-07-02 11:56:06 DownsampleSam Test: Test method testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam668733661332367109.bam -PROBABILITY 0.8999999999999999 -STRATEGY ConstantMemory -RANDOM_SEED null -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam668733661332367109.bam -PROBABILITY 0.8999999999999999 -STRATEGY ConstantMemory -RANDOM_SEED null -CREATE_INDEX true Test: Test method testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:06.675 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:06.675 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:06.675 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:06.675 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:06.675 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:06.675 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:06.675 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:06.675 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:06 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam668733661332367109.bam STRATEGY=ConstantMemory RANDOM_SEED=null PROBABILITY=0.8999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:06 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam668733661332367109.bam STRATEGY=ConstantMemory RANDOM_SEED=null PROBABILITY=0.8999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:06 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -1748240071 to reproduce these results in the future. WARNING 2024-07-02 11:56:06 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -1748240071 to reproduce these results in the future. Test: Test method testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:07 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:07 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:07 DownsampleSam Kept 18000 out of 20000 reads (90.00%). INFO 2024-07-02 11:56:07 DownsampleSam Kept 18000 out of 20000 reads (90.00%). Test: Test method testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:07 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:07 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[30](0.8999999999999999, ConstantMemory, null) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:07 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null) STANDARD_ERROR INFO 2024-07-02 11:56:07 DownsampleSam Test: Test method testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2724946708823957522.bam -PROBABILITY 0.9999999999999999 -STRATEGY ConstantMemory -RANDOM_SEED null -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2724946708823957522.bam -PROBABILITY 0.9999999999999999 -STRATEGY ConstantMemory -RANDOM_SEED null -CREATE_INDEX true Test: Test method testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:07.823 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:07.823 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:07.823 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:07.823 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:07.823 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:07.823 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:07.823 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:07.823 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:07 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2724946708823957522.bam STRATEGY=ConstantMemory RANDOM_SEED=null PROBABILITY=0.9999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:07 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2724946708823957522.bam STRATEGY=ConstantMemory RANDOM_SEED=null PROBABILITY=0.9999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:07 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -1335195081 to reproduce these results in the future. WARNING 2024-07-02 11:56:07 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -1335195081 to reproduce these results in the future. Test: Test method testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:08 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:08 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:08 DownsampleSam Kept 20000 out of 20000 reads (100.00%). INFO 2024-07-02 11:56:08 DownsampleSam Kept 20000 out of 20000 reads (100.00%). Test: Test method testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:08 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:08 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:08 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:08 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[31](0.9999999999999999, ConstantMemory, null) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[32](0.3, Chained, 1)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[32](0.3, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:09 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[32](0.3, Chained, 1) STANDARD_ERROR INFO 2024-07-02 11:56:09 DownsampleSam Test: Test method testDownsampleStrategies[32](0.3, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[32](0.3, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[32](0.3, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[32](0.3, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[32](0.3, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[32](0.3, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[32](0.3, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[32](0.3, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[32](0.3, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam12289148353386629549.bam -PROBABILITY 0.3 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam12289148353386629549.bam -PROBABILITY 0.3 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testDownsampleStrategies[32](0.3, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[32](0.3, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[32](0.3, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[32](0.3, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:09.344 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:09.344 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[32](0.3, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:09.344 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:09.344 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[32](0.3, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:09.344 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:09.344 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[32](0.3, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:09.344 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:09.344 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[32](0.3, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:09 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam12289148353386629549.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.3 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:09 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam12289148353386629549.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.3 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[32](0.3, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[32](0.3, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:09 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:09 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[32](0.3, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:09 DownsampleSam Kept 5998 out of 20000 reads (29.99%). INFO 2024-07-02 11:56:09 DownsampleSam Kept 5998 out of 20000 reads (29.99%). Test: Test method testDownsampleStrategies[32](0.3, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:09 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:09 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[32](0.3, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[32](0.3, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[32](0.3, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[32](0.3, Chained, 1) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[33](0.4, Chained, 1)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[33](0.4, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:09 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[33](0.4, Chained, 1) STANDARD_ERROR INFO 2024-07-02 11:56:09 DownsampleSam Test: Test method testDownsampleStrategies[33](0.4, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[33](0.4, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[33](0.4, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[33](0.4, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[33](0.4, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[33](0.4, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[33](0.4, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[33](0.4, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[33](0.4, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14016514560735991158.bam -PROBABILITY 0.4 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14016514560735991158.bam -PROBABILITY 0.4 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testDownsampleStrategies[33](0.4, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[33](0.4, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[33](0.4, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[33](0.4, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:09.970 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:09.970 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[33](0.4, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:09.970 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:09.970 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[33](0.4, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:09.970 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:09.970 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[33](0.4, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:09.970 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:09.970 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[33](0.4, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:09 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14016514560735991158.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.4 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:09 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14016514560735991158.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.4 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[33](0.4, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[33](0.4, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:10 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:10 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[33](0.4, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:10 DownsampleSam Kept 7998 out of 20000 reads (39.99%). INFO 2024-07-02 11:56:10 DownsampleSam Kept 7998 out of 20000 reads (39.99%). Test: Test method testDownsampleStrategies[33](0.4, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:10 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:10 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[33](0.4, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[33](0.4, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:10 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:10 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[33](0.4, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[33](0.4, Chained, 1) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[34](0.5, Chained, 1)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[34](0.5, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:11 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[34](0.5, Chained, 1) STANDARD_ERROR INFO 2024-07-02 11:56:11 DownsampleSam Test: Test method testDownsampleStrategies[34](0.5, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[34](0.5, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[34](0.5, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[34](0.5, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[34](0.5, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[34](0.5, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[34](0.5, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[34](0.5, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[34](0.5, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1087051278563548357.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1087051278563548357.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testDownsampleStrategies[34](0.5, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[34](0.5, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[34](0.5, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[34](0.5, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:11.083 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:11.083 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[34](0.5, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:11.083 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:11.083 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[34](0.5, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:11.083 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:11.083 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[34](0.5, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:11.083 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:11.083 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[34](0.5, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:11 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1087051278563548357.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:11 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1087051278563548357.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[34](0.5, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[34](0.5, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:11 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:11 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[34](0.5, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:11 DownsampleSam Kept 9998 out of 20000 reads (49.99%). INFO 2024-07-02 11:56:11 DownsampleSam Kept 9998 out of 20000 reads (49.99%). Test: Test method testDownsampleStrategies[34](0.5, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:11 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:11 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[34](0.5, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[34](0.5, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:11 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:11 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[34](0.5, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[34](0.5, Chained, 1) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[35](0.6, Chained, 1)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[35](0.6, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:12 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[35](0.6, Chained, 1) STANDARD_ERROR INFO 2024-07-02 11:56:12 DownsampleSam Test: Test method testDownsampleStrategies[35](0.6, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[35](0.6, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[35](0.6, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[35](0.6, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[35](0.6, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[35](0.6, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[35](0.6, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[35](0.6, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[35](0.6, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2202054096483993292.bam -PROBABILITY 0.6 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2202054096483993292.bam -PROBABILITY 0.6 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testDownsampleStrategies[35](0.6, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[35](0.6, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[35](0.6, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[35](0.6, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:12.239 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:12.239 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[35](0.6, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:12.239 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:12.239 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[35](0.6, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:12.239 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:12.239 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[35](0.6, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:12.239 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:12.239 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[35](0.6, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:12 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2202054096483993292.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.6 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:12 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2202054096483993292.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.6 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[35](0.6, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[35](0.6, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:12 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:12 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[35](0.6, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:12 DownsampleSam Kept 11998 out of 20000 reads (59.99%). INFO 2024-07-02 11:56:12 DownsampleSam Kept 11998 out of 20000 reads (59.99%). Test: Test method testDownsampleStrategies[35](0.6, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:12 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:12 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[35](0.6, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[35](0.6, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:12 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:12 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[35](0.6, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[35](0.6, Chained, 1) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[36](0.7, Chained, 1)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[36](0.7, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:13 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[36](0.7, Chained, 1) STANDARD_ERROR INFO 2024-07-02 11:56:13 DownsampleSam Test: Test method testDownsampleStrategies[36](0.7, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[36](0.7, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[36](0.7, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[36](0.7, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[36](0.7, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[36](0.7, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[36](0.7, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[36](0.7, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[36](0.7, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam218534824940997731.bam -PROBABILITY 0.7 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam218534824940997731.bam -PROBABILITY 0.7 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testDownsampleStrategies[36](0.7, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[36](0.7, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[36](0.7, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[36](0.7, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:13.371 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:13.371 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[36](0.7, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:13.371 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:13.371 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[36](0.7, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:13.372 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:13.372 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[36](0.7, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:13.372 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:13.372 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[36](0.7, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:13 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam218534824940997731.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.7 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:13 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam218534824940997731.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.7 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[36](0.7, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[36](0.7, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:13 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:13 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[36](0.7, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:13 DownsampleSam Kept 14000 out of 20000 reads (70.00%). INFO 2024-07-02 11:56:13 DownsampleSam Kept 14000 out of 20000 reads (70.00%). Test: Test method testDownsampleStrategies[36](0.7, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:13 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:13 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[36](0.7, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[36](0.7, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:13 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:13 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[36](0.7, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[36](0.7, Chained, 1) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[37](0.7999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[37](0.7999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:14 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[37](0.7999999999999999, Chained, 1) STANDARD_ERROR INFO 2024-07-02 11:56:14 DownsampleSam Test: Test method testDownsampleStrategies[37](0.7999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[37](0.7999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[37](0.7999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[37](0.7999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[37](0.7999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[37](0.7999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[37](0.7999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[37](0.7999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[37](0.7999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8900406147398583229.bam -PROBABILITY 0.7999999999999999 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8900406147398583229.bam -PROBABILITY 0.7999999999999999 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testDownsampleStrategies[37](0.7999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[37](0.7999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[37](0.7999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[37](0.7999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:14.157 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:14.157 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[37](0.7999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:14.157 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:14.157 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[37](0.7999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:14.157 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:14.157 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[37](0.7999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:14.158 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:14.158 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[37](0.7999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:14 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8900406147398583229.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.7999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:14 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8900406147398583229.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.7999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[37](0.7999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[37](0.7999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:14 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:14 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[37](0.7999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:14 DownsampleSam Kept 15998 out of 20000 reads (79.99%). INFO 2024-07-02 11:56:14 DownsampleSam Kept 15998 out of 20000 reads (79.99%). Test: Test method testDownsampleStrategies[37](0.7999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:14 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:14 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[37](0.7999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[37](0.7999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:14 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:14 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[37](0.7999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[37](0.7999999999999999, Chained, 1) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[38](0.8999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[38](0.8999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:15 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[38](0.8999999999999999, Chained, 1) STANDARD_ERROR INFO 2024-07-02 11:56:15 DownsampleSam Test: Test method testDownsampleStrategies[38](0.8999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[38](0.8999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[38](0.8999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[38](0.8999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[38](0.8999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[38](0.8999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[38](0.8999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[38](0.8999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[38](0.8999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2802788757872875710.bam -PROBABILITY 0.8999999999999999 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2802788757872875710.bam -PROBABILITY 0.8999999999999999 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testDownsampleStrategies[38](0.8999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[38](0.8999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[38](0.8999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[38](0.8999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:15.546 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:15.546 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[38](0.8999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:15.546 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:15.546 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[38](0.8999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:15.546 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:15.546 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[38](0.8999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:15.546 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:15.546 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[38](0.8999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:15 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2802788757872875710.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.8999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:15 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2802788757872875710.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.8999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[38](0.8999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[38](0.8999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:16 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:16 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[38](0.8999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:16 DownsampleSam Kept 18000 out of 20000 reads (90.00%). INFO 2024-07-02 11:56:16 DownsampleSam Kept 18000 out of 20000 reads (90.00%). Test: Test method testDownsampleStrategies[38](0.8999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:16 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:16 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[38](0.8999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[38](0.8999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:16 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:16 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[38](0.8999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[38](0.8999999999999999, Chained, 1) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[39](0.9999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[39](0.9999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:16 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[39](0.9999999999999999, Chained, 1) STANDARD_ERROR INFO 2024-07-02 11:56:16 DownsampleSam Test: Test method testDownsampleStrategies[39](0.9999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[39](0.9999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[39](0.9999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[39](0.9999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[39](0.9999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[39](0.9999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[39](0.9999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[39](0.9999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[39](0.9999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8146770597654535772.bam -PROBABILITY 0.9999999999999999 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8146770597654535772.bam -PROBABILITY 0.9999999999999999 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testDownsampleStrategies[39](0.9999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[39](0.9999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[39](0.9999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[39](0.9999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:16.486 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:16.486 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[39](0.9999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:16.486 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:16.486 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[39](0.9999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:16.487 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:16.487 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[39](0.9999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:16.487 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:16.487 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[39](0.9999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:16 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8146770597654535772.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.9999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:16 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8146770597654535772.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.9999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[39](0.9999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[39](0.9999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:16 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:16 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[39](0.9999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:16 DownsampleSam Kept 19998 out of 20000 reads (99.99%). INFO 2024-07-02 11:56:16 DownsampleSam Kept 19998 out of 20000 reads (99.99%). Test: Test method testDownsampleStrategies[39](0.9999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:16 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:16 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[39](0.9999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[39](0.9999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:16 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:16 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[39](0.9999999999999999, Chained, 1)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[39](0.9999999999999999, Chained, 1) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[40](0.3, Chained, null)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[40](0.3, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:17 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[40](0.3, Chained, null) STANDARD_ERROR INFO 2024-07-02 11:56:17 DownsampleSam Test: Test method testDownsampleStrategies[40](0.3, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[40](0.3, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[40](0.3, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[40](0.3, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[40](0.3, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[40](0.3, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[40](0.3, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[40](0.3, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[40](0.3, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam11643080825904651813.bam -PROBABILITY 0.3 -STRATEGY Chained -RANDOM_SEED null -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam11643080825904651813.bam -PROBABILITY 0.3 -STRATEGY Chained -RANDOM_SEED null -CREATE_INDEX true Test: Test method testDownsampleStrategies[40](0.3, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[40](0.3, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[40](0.3, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[40](0.3, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:17.254 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:17.254 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[40](0.3, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:17.254 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:17.254 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[40](0.3, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:17.254 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:17.254 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[40](0.3, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:17.254 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:17.254 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[40](0.3, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:17 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam11643080825904651813.bam STRATEGY=Chained RANDOM_SEED=null PROBABILITY=0.3 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:17 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam11643080825904651813.bam STRATEGY=Chained RANDOM_SEED=null PROBABILITY=0.3 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[40](0.3, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[40](0.3, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:17 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to 582383163 to reproduce these results in the future. WARNING 2024-07-02 11:56:17 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to 582383163 to reproduce these results in the future. Test: Test method testDownsampleStrategies[40](0.3, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:17 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:17 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[40](0.3, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:17 DownsampleSam Kept 5998 out of 20000 reads (29.99%). INFO 2024-07-02 11:56:17 DownsampleSam Kept 5998 out of 20000 reads (29.99%). Test: Test method testDownsampleStrategies[40](0.3, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:17 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:17 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[40](0.3, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[40](0.3, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:17 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:17 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[40](0.3, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[40](0.3, Chained, null) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[41](0.4, Chained, null)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[41](0.4, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:17 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[41](0.4, Chained, null) STANDARD_ERROR INFO 2024-07-02 11:56:17 DownsampleSam Test: Test method testDownsampleStrategies[41](0.4, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[41](0.4, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[41](0.4, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[41](0.4, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[41](0.4, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[41](0.4, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[41](0.4, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[41](0.4, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[41](0.4, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam10058883986338425503.bam -PROBABILITY 0.4 -STRATEGY Chained -RANDOM_SEED null -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam10058883986338425503.bam -PROBABILITY 0.4 -STRATEGY Chained -RANDOM_SEED null -CREATE_INDEX true Test: Test method testDownsampleStrategies[41](0.4, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[41](0.4, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[41](0.4, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[41](0.4, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:17.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:17.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[41](0.4, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:17.743 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:17.743 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[41](0.4, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:17.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:17.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[41](0.4, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:17.743 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:17.743 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[41](0.4, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:17 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam10058883986338425503.bam STRATEGY=Chained RANDOM_SEED=null PROBABILITY=0.4 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:17 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam10058883986338425503.bam STRATEGY=Chained RANDOM_SEED=null PROBABILITY=0.4 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[41](0.4, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[41](0.4, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:17 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to 149007660 to reproduce these results in the future. WARNING 2024-07-02 11:56:17 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to 149007660 to reproduce these results in the future. Test: Test method testDownsampleStrategies[41](0.4, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:18 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:18 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[41](0.4, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:18 DownsampleSam Kept 7998 out of 20000 reads (39.99%). INFO 2024-07-02 11:56:18 DownsampleSam Kept 7998 out of 20000 reads (39.99%). Test: Test method testDownsampleStrategies[41](0.4, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:18 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:18 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[41](0.4, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[41](0.4, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:18 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:18 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[41](0.4, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[41](0.4, Chained, null) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[42](0.5, Chained, null)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[42](0.5, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:18 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[42](0.5, Chained, null) STANDARD_ERROR INFO 2024-07-02 11:56:18 DownsampleSam Test: Test method testDownsampleStrategies[42](0.5, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[42](0.5, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[42](0.5, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[42](0.5, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[42](0.5, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[42](0.5, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[42](0.5, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[42](0.5, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[42](0.5, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13642403502677257131.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED null -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13642403502677257131.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED null -CREATE_INDEX true Test: Test method testDownsampleStrategies[42](0.5, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[42](0.5, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[42](0.5, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[42](0.5, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:18.231 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:18.231 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[42](0.5, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:18.231 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:18.231 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[42](0.5, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:18.231 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:18.231 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[42](0.5, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:18.231 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:18.231 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[42](0.5, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:18 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13642403502677257131.bam STRATEGY=Chained RANDOM_SEED=null PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:18 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13642403502677257131.bam STRATEGY=Chained RANDOM_SEED=null PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[42](0.5, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[42](0.5, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:18 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to 1511860938 to reproduce these results in the future. WARNING 2024-07-02 11:56:18 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to 1511860938 to reproduce these results in the future. Test: Test method testDownsampleStrategies[42](0.5, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:18 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:18 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[42](0.5, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:18 DownsampleSam Kept 10000 out of 20000 reads (50.00%). INFO 2024-07-02 11:56:18 DownsampleSam Kept 10000 out of 20000 reads (50.00%). Test: Test method testDownsampleStrategies[42](0.5, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:18 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:18 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testDownsampleStrategies[42](0.5, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[42](0.5, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:18 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:18 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[42](0.5, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[42](0.5, Chained, null) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[43](0.6, Chained, null)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[43](0.6, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:18 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[43](0.6, Chained, null) STANDARD_ERROR INFO 2024-07-02 11:56:18 DownsampleSam Test: Test method testDownsampleStrategies[43](0.6, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[43](0.6, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[43](0.6, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[43](0.6, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[43](0.6, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[43](0.6, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[43](0.6, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[43](0.6, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[43](0.6, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8659218804339869167.bam -PROBABILITY 0.6 -STRATEGY Chained -RANDOM_SEED null -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8659218804339869167.bam -PROBABILITY 0.6 -STRATEGY Chained -RANDOM_SEED null -CREATE_INDEX true Test: Test method testDownsampleStrategies[43](0.6, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[43](0.6, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[43](0.6, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[43](0.6, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:18.779 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:18.779 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[43](0.6, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:18.779 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:18.779 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[43](0.6, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:18.779 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:18.779 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[43](0.6, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:18.779 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:18.779 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[43](0.6, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:18 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8659218804339869167.bam STRATEGY=Chained RANDOM_SEED=null PROBABILITY=0.6 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:18 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8659218804339869167.bam STRATEGY=Chained RANDOM_SEED=null PROBABILITY=0.6 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[43](0.6, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[43](0.6, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:18 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -424832793 to reproduce these results in the future. WARNING 2024-07-02 11:56:18 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -424832793 to reproduce these results in the future. Test: Test method testDownsampleStrategies[43](0.6, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:19 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:19 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[43](0.6, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:19 DownsampleSam Kept 12000 out of 20000 reads (60.00%). INFO 2024-07-02 11:56:19 DownsampleSam Kept 12000 out of 20000 reads (60.00%). Test: Test method testDownsampleStrategies[43](0.6, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:19 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:19 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[43](0.6, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[43](0.6, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:19 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:19 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[43](0.6, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[43](0.6, Chained, null) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[44](0.7, Chained, null)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[44](0.7, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:19 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[44](0.7, Chained, null) STANDARD_ERROR INFO 2024-07-02 11:56:19 DownsampleSam Test: Test method testDownsampleStrategies[44](0.7, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[44](0.7, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[44](0.7, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[44](0.7, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[44](0.7, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[44](0.7, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[44](0.7, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[44](0.7, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[44](0.7, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam9958108650546517044.bam -PROBABILITY 0.7 -STRATEGY Chained -RANDOM_SEED null -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam9958108650546517044.bam -PROBABILITY 0.7 -STRATEGY Chained -RANDOM_SEED null -CREATE_INDEX true Test: Test method testDownsampleStrategies[44](0.7, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[44](0.7, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[44](0.7, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[44](0.7, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:19.780 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:19.780 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[44](0.7, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:19.780 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:19.780 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[44](0.7, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:19.780 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:19.780 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[44](0.7, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:19.780 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:19.780 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[44](0.7, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:19 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam9958108650546517044.bam STRATEGY=Chained RANDOM_SEED=null PROBABILITY=0.7 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:19 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam9958108650546517044.bam STRATEGY=Chained RANDOM_SEED=null PROBABILITY=0.7 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[44](0.7, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[44](0.7, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:19 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -1787439650 to reproduce these results in the future. WARNING 2024-07-02 11:56:19 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -1787439650 to reproduce these results in the future. Test: Test method testDownsampleStrategies[44](0.7, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:20 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:20 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[44](0.7, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:20 DownsampleSam Kept 14000 out of 20000 reads (70.00%). INFO 2024-07-02 11:56:20 DownsampleSam Kept 14000 out of 20000 reads (70.00%). Test: Test method testDownsampleStrategies[44](0.7, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:20 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:20 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[44](0.7, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[44](0.7, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:20 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:20 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[44](0.7, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[44](0.7, Chained, null) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[45](0.7999999999999999, Chained, null)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[45](0.7999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:20 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[45](0.7999999999999999, Chained, null) STANDARD_ERROR INFO 2024-07-02 11:56:20 DownsampleSam Test: Test method testDownsampleStrategies[45](0.7999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[45](0.7999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[45](0.7999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[45](0.7999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[45](0.7999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[45](0.7999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[45](0.7999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[45](0.7999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[45](0.7999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13891115054193507426.bam -PROBABILITY 0.7999999999999999 -STRATEGY Chained -RANDOM_SEED null -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13891115054193507426.bam -PROBABILITY 0.7999999999999999 -STRATEGY Chained -RANDOM_SEED null -CREATE_INDEX true Test: Test method testDownsampleStrategies[45](0.7999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[45](0.7999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[45](0.7999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[45](0.7999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:20.964 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:20.964 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[45](0.7999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:20.964 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:20.964 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[45](0.7999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:20.964 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:20.964 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[45](0.7999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:20.964 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:20.964 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[45](0.7999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:20 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13891115054193507426.bam STRATEGY=Chained RANDOM_SEED=null PROBABILITY=0.7999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:20 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13891115054193507426.bam STRATEGY=Chained RANDOM_SEED=null PROBABILITY=0.7999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[45](0.7999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[45](0.7999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:20 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -312603348 to reproduce these results in the future. WARNING 2024-07-02 11:56:20 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -312603348 to reproduce these results in the future. Test: Test method testDownsampleStrategies[45](0.7999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:21 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:21 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[45](0.7999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:21 DownsampleSam Kept 16000 out of 20000 reads (80.00%). INFO 2024-07-02 11:56:21 DownsampleSam Kept 16000 out of 20000 reads (80.00%). Test: Test method testDownsampleStrategies[45](0.7999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:21 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:21 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[45](0.7999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[45](0.7999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:21 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:21 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[45](0.7999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[45](0.7999999999999999, Chained, null) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[46](0.8999999999999999, Chained, null)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[46](0.8999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:22 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[46](0.8999999999999999, Chained, null) STANDARD_ERROR INFO 2024-07-02 11:56:22 DownsampleSam Test: Test method testDownsampleStrategies[46](0.8999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[46](0.8999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[46](0.8999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[46](0.8999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[46](0.8999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[46](0.8999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[46](0.8999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[46](0.8999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[46](0.8999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam9182416039093750148.bam -PROBABILITY 0.8999999999999999 -STRATEGY Chained -RANDOM_SEED null -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam9182416039093750148.bam -PROBABILITY 0.8999999999999999 -STRATEGY Chained -RANDOM_SEED null -CREATE_INDEX true Test: Test method testDownsampleStrategies[46](0.8999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[46](0.8999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[46](0.8999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[46](0.8999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:22.119 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:22.119 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[46](0.8999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:22.119 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:22.119 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[46](0.8999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:22.119 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:22.119 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[46](0.8999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:22.119 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:22.119 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[46](0.8999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:22 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam9182416039093750148.bam STRATEGY=Chained RANDOM_SEED=null PROBABILITY=0.8999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:22 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam9182416039093750148.bam STRATEGY=Chained RANDOM_SEED=null PROBABILITY=0.8999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[46](0.8999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[46](0.8999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:22 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -1309142631 to reproduce these results in the future. WARNING 2024-07-02 11:56:22 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -1309142631 to reproduce these results in the future. Test: Test method testDownsampleStrategies[46](0.8999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:23 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:23 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[46](0.8999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:23 DownsampleSam Kept 17998 out of 20000 reads (89.99%). INFO 2024-07-02 11:56:23 DownsampleSam Kept 17998 out of 20000 reads (89.99%). Test: Test method testDownsampleStrategies[46](0.8999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:23 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:56:23 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.02 minutes. Test: Test method testDownsampleStrategies[46](0.8999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[46](0.8999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:23 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:23 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[46](0.8999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[46](0.8999999999999999, Chained, null) STANDARD_OUT No errors found Running Test: Test method testDownsampleStrategies[47](0.9999999999999999, Chained, null)(picard.sam.DownsampleSamTest) Test: Test method testDownsampleStrategies[47](0.9999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:23 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[47](0.9999999999999999, Chained, null) STANDARD_ERROR INFO 2024-07-02 11:56:23 DownsampleSam Test: Test method testDownsampleStrategies[47](0.9999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[47](0.9999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleStrategies[47](0.9999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[47](0.9999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleStrategies[47](0.9999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleStrategies[47](0.9999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[47](0.9999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleStrategies[47](0.9999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[47](0.9999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam9251576474666724098.bam -PROBABILITY 0.9999999999999999 -STRATEGY Chained -RANDOM_SEED null -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam9251576474666724098.bam -PROBABILITY 0.9999999999999999 -STRATEGY Chained -RANDOM_SEED null -CREATE_INDEX true Test: Test method testDownsampleStrategies[47](0.9999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleStrategies[47](0.9999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[47](0.9999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testDownsampleStrategies[47](0.9999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:23.610 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:23.610 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[47](0.9999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:23.610 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:23.610 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[47](0.9999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:23.610 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:23.610 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleStrategies[47](0.9999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:23.610 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:23.610 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleStrategies[47](0.9999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:23 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam9251576474666724098.bam STRATEGY=Chained RANDOM_SEED=null PROBABILITY=0.9999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:23 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam9251576474666724098.bam STRATEGY=Chained RANDOM_SEED=null PROBABILITY=0.9999999999999999 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleStrategies[47](0.9999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleStrategies[47](0.9999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:23 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -2136734705 to reproduce these results in the future. WARNING 2024-07-02 11:56:23 DownsampleSam Drawing a random seed because RANDOM_SEED was not set. Set RANDOM_SEED to -2136734705 to reproduce these results in the future. Test: Test method testDownsampleStrategies[47](0.9999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:24 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:24 DownsampleSam Finished downsampling. Test: Test method testDownsampleStrategies[47](0.9999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:24 DownsampleSam Kept 19998 out of 20000 reads (99.99%). INFO 2024-07-02 11:56:24 DownsampleSam Kept 19998 out of 20000 reads (99.99%). Test: Test method testDownsampleStrategies[47](0.9999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:24 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:24 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleStrategies[47](0.9999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testDownsampleStrategies[47](0.9999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:24 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:24 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleStrategies[47](0.9999999999999999, Chained, null)(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testDownsampleStrategies[47](0.9999999999999999, Chained, null) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:25 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:25 DownsampleSam Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5499632263725646352.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5499632263725646352.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:25.016 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:25.016 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:25.016 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:25.016 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:25.016 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:25.016 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:25.016 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:25.016 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:25 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5499632263725646352.bam STRATEGY=ConstantMemory RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:25 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5499632263725646352.bam STRATEGY=ConstantMemory RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:25 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:25 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:25 DownsampleSam Kept 10030 out of 20000 reads (50.15%). INFO 2024-07-02 11:56:25 DownsampleSam Kept 10030 out of 20000 reads (50.15%). Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:25 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:25 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:25 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:25 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:25 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:25 DownsampleSam Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5499632263725646352.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam4019377588909195563.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5499632263725646352.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam4019377588909195563.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:25.670 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:25.670 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:25.670 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:25.670 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:25.670 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:25.670 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:25.670 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:25.670 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:25 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5499632263725646352.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam4019377588909195563.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:25 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5499632263725646352.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam4019377588909195563.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:25 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:25 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:25 DownsampleSam Kept 4968 out of 10030 reads (49.53%). INFO 2024-07-02 11:56:25 DownsampleSam Kept 4968 out of 10030 reads (49.53%). Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:25 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:25 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:25 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:25 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[0]([ConstantMemory, ConstantMemory], [2, 1]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:26 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0]) STANDARD_ERROR INFO 2024-07-02 11:56:26 DownsampleSam Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5047543742838175604.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5047543742838175604.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:26.166 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:26.166 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:26.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:26.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:26.166 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:26.166 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:26.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:26.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:26 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5047543742838175604.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:26 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5047543742838175604.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:26 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:26 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:26 DownsampleSam Kept 10142 out of 20000 reads (50.71%). INFO 2024-07-02 11:56:26 DownsampleSam Kept 10142 out of 20000 reads (50.71%). Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:26 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:26 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:26 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:26 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:27 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0]) STANDARD_ERROR INFO 2024-07-02 11:56:27 DownsampleSam Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5047543742838175604.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1941456161975004054.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5047543742838175604.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1941456161975004054.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:27.105 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:27.105 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:27.105 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:27.105 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:27.105 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:27.105 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:27.105 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:27.105 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:27 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5047543742838175604.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1941456161975004054.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:27 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5047543742838175604.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1941456161975004054.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:27 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:56:27 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:27 DownsampleSam RANDOM_SEED has been changed to -1155484576. WARNING 2024-07-02 11:56:27 DownsampleSam RANDOM_SEED has been changed to -1155484576. Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:27 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:27 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:27 DownsampleSam Kept 4988 out of 10142 reads (49.18%). INFO 2024-07-02 11:56:27 DownsampleSam Kept 4988 out of 10142 reads (49.18%). Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:27 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:27 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:27 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:27 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[1]([ConstantMemory, ConstantMemory], [0, 0]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:27 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647]) STANDARD_ERROR INFO 2024-07-02 11:56:27 DownsampleSam Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6409208042573952071.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2147483647 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6409208042573952071.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2147483647 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:27.680 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:27.680 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:27.680 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:27.680 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:27.680 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:27.680 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:27.680 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:27.680 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:27 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6409208042573952071.bam STRATEGY=ConstantMemory RANDOM_SEED=2147483647 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:27 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6409208042573952071.bam STRATEGY=ConstantMemory RANDOM_SEED=2147483647 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:28 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:28 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:28 DownsampleSam Kept 10000 out of 20000 reads (50.00%). INFO 2024-07-02 11:56:28 DownsampleSam Kept 10000 out of 20000 reads (50.00%). Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:28 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:28 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:28 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:28 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:28 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647]) STANDARD_ERROR INFO 2024-07-02 11:56:28 DownsampleSam Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6409208042573952071.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam17569520168205204760.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2147483647 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6409208042573952071.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam17569520168205204760.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2147483647 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:28.552 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:28.552 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:28.552 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:28.552 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:28.552 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:28.552 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:28.552 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:28.552 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:28 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6409208042573952071.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam17569520168205204760.bam STRATEGY=ConstantMemory RANDOM_SEED=2147483647 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:28 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6409208042573952071.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam17569520168205204760.bam STRATEGY=ConstantMemory RANDOM_SEED=2147483647 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:28 DownsampleSam DownsampleSam has been run before on this data with the seed -1631654733. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:56:28 DownsampleSam DownsampleSam has been run before on this data with the seed -1631654733. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:28 DownsampleSam RANDOM_SEED has been changed to -1631654733. WARNING 2024-07-02 11:56:28 DownsampleSam RANDOM_SEED has been changed to -1631654733. Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:28 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:28 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:28 DownsampleSam Kept 4918 out of 10000 reads (49.18%). INFO 2024-07-02 11:56:28 DownsampleSam Kept 4918 out of 10000 reads (49.18%). Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:28 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:28 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:28 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:28 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[2]([ConstantMemory, ConstantMemory], [2147483647, 2147483647]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:29 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648]) STANDARD_ERROR INFO 2024-07-02 11:56:29 DownsampleSam Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam17530618653207870137.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED -2147483648 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam17530618653207870137.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED -2147483648 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:29.056 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:29.056 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:29.056 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:29.056 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:29.056 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:29.056 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:29.056 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:29.056 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:29 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam17530618653207870137.bam STRATEGY=ConstantMemory RANDOM_SEED=-2147483648 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:29 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam17530618653207870137.bam STRATEGY=ConstantMemory RANDOM_SEED=-2147483648 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:29 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:29 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:29 DownsampleSam Kept 9966 out of 20000 reads (49.83%). INFO 2024-07-02 11:56:29 DownsampleSam Kept 9966 out of 20000 reads (49.83%). Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:29 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:29 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:29 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:29 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:29 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648]) STANDARD_ERROR INFO 2024-07-02 11:56:29 DownsampleSam Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam17530618653207870137.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5860909773871496543.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED -2147483648 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam17530618653207870137.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5860909773871496543.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED -2147483648 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:29.910 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:29.910 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:29.910 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:29.910 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:29.911 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:29.911 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:29.911 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:29.911 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:29 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam17530618653207870137.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5860909773871496543.bam STRATEGY=ConstantMemory RANDOM_SEED=-2147483648 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:29 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam17530618653207870137.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5860909773871496543.bam STRATEGY=ConstantMemory RANDOM_SEED=-2147483648 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:29 DownsampleSam DownsampleSam has been run before on this data with the seed 1631269984. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:56:29 DownsampleSam DownsampleSam has been run before on this data with the seed 1631269984. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:29 DownsampleSam RANDOM_SEED has been changed to 1631269984. WARNING 2024-07-02 11:56:29 DownsampleSam RANDOM_SEED has been changed to 1631269984. Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:30 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:30 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:30 DownsampleSam Kept 5034 out of 9966 reads (50.51%). INFO 2024-07-02 11:56:30 DownsampleSam Kept 5034 out of 9966 reads (50.51%). Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:30 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:30 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:30 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:30 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[3]([ConstantMemory, ConstantMemory], [-2147483648, -2147483648]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:30 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647]) STANDARD_ERROR INFO 2024-07-02 11:56:30 DownsampleSam Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16197514948792464658.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED -2147483648 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16197514948792464658.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED -2147483648 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:30.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:30.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:30.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:30.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:30.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:30.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:30.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:30.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:30 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16197514948792464658.bam STRATEGY=ConstantMemory RANDOM_SEED=-2147483648 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:30 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16197514948792464658.bam STRATEGY=ConstantMemory RANDOM_SEED=-2147483648 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:30 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:30 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:30 DownsampleSam Kept 9966 out of 20000 reads (49.83%). INFO 2024-07-02 11:56:30 DownsampleSam Kept 9966 out of 20000 reads (49.83%). Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:30 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:30 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:30 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:30 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:30 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647]) STANDARD_ERROR INFO 2024-07-02 11:56:30 DownsampleSam Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16197514948792464658.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14500684271712761576.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2147483647 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16197514948792464658.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14500684271712761576.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2147483647 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:30.900 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:30.900 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:30.900 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:30.900 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:30.900 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:30.900 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:30.900 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:30.900 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:30 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16197514948792464658.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14500684271712761576.bam STRATEGY=ConstantMemory RANDOM_SEED=2147483647 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:30 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16197514948792464658.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14500684271712761576.bam STRATEGY=ConstantMemory RANDOM_SEED=2147483647 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:30 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:30 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:30 DownsampleSam Kept 4940 out of 9966 reads (49.57%). INFO 2024-07-02 11:56:30 DownsampleSam Kept 4940 out of 9966 reads (49.57%). Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:30 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:30 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:30 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:30 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[4]([ConstantMemory, ConstantMemory], [-2147483648, 2147483647]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:31 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0]) STANDARD_ERROR INFO 2024-07-02 11:56:31 DownsampleSam Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13193500137052146509.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2147483647 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13193500137052146509.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2147483647 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:31.088 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:31.088 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:31.088 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:31.088 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:31.088 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:31.088 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:31.088 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:31.088 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:31 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13193500137052146509.bam STRATEGY=ConstantMemory RANDOM_SEED=2147483647 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:31 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13193500137052146509.bam STRATEGY=ConstantMemory RANDOM_SEED=2147483647 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:31 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:31 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:31 DownsampleSam Kept 10000 out of 20000 reads (50.00%). INFO 2024-07-02 11:56:31 DownsampleSam Kept 10000 out of 20000 reads (50.00%). Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:31 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:31 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:31 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:31 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:31 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0]) STANDARD_ERROR INFO 2024-07-02 11:56:31 DownsampleSam Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13193500137052146509.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam11583015752188248672.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13193500137052146509.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam11583015752188248672.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:31.411 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:31.411 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:31.411 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:31.411 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:31.411 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:31.411 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:31.411 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:31.411 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:31 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13193500137052146509.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam11583015752188248672.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:31 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13193500137052146509.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam11583015752188248672.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:31 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:31 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:31 DownsampleSam Kept 5052 out of 10000 reads (50.52%). INFO 2024-07-02 11:56:31 DownsampleSam Kept 5052 out of 10000 reads (50.52%). Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:31 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:31 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:31 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:31 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[5]([ConstantMemory, ConstantMemory], [2147483647, 0]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:31 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:31 DownsampleSam Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam12859451651562593262.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam12859451651562593262.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:31.895 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:31.895 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:31.895 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:31.895 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:31.895 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:31.895 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:31.895 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:31.895 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:31 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam12859451651562593262.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:31 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam12859451651562593262.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:32 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:32 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:32 DownsampleSam Kept 10018 out of 20000 reads (50.09%). INFO 2024-07-02 11:56:32 DownsampleSam Kept 10018 out of 20000 reads (50.09%). Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:32 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:32 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:32 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:32 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:32 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:32 DownsampleSam Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam12859451651562593262.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam9563583532490800503.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam12859451651562593262.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam9563583532490800503.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:32.897 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:32.897 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:32.897 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:32.897 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:32.897 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:32.897 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:32.897 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:32.897 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:32 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam12859451651562593262.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam9563583532490800503.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:32 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam12859451651562593262.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam9563583532490800503.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:32 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:56:32 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:32 DownsampleSam RANDOM_SEED has been changed to -1155869325. WARNING 2024-07-02 11:56:32 DownsampleSam RANDOM_SEED has been changed to -1155869325. Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:33 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:33 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:33 DownsampleSam Kept 5108 out of 10018 reads (50.99%). INFO 2024-07-02 11:56:33 DownsampleSam Kept 5108 out of 10018 reads (50.99%). Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:33 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:33 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:33 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:33 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[6]([ConstantMemory, ConstantMemory], [1, 1]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:33 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:33 DownsampleSam Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam11748902310941831757.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam11748902310941831757.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:33.386 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:33.386 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:33.386 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:33.386 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:33.386 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:33.386 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:33.386 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:33.386 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:33 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam11748902310941831757.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:33 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam11748902310941831757.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:33 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:33 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:33 DownsampleSam Kept 9998 out of 20000 reads (49.99%). INFO 2024-07-02 11:56:33 DownsampleSam Kept 9998 out of 20000 reads (49.99%). Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:33 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:33 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:33 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:33 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:34 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:34 DownsampleSam Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam11748902310941831757.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam488937926190635479.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam11748902310941831757.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam488937926190635479.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:34.044 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:34.044 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:34.044 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:34.044 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:34.044 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:34.044 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:34.044 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:34.044 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:34 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam11748902310941831757.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam488937926190635479.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:34 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam11748902310941831757.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam488937926190635479.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:34 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:56:34 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:34 DownsampleSam RANDOM_SEED has been changed to -1155869325. WARNING 2024-07-02 11:56:34 DownsampleSam RANDOM_SEED has been changed to -1155869325. Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:34 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:34 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:34 DownsampleSam Kept 5102 out of 9998 reads (51.03%). INFO 2024-07-02 11:56:34 DownsampleSam Kept 5102 out of 9998 reads (51.03%). Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:34 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:34 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[7]([Chained, ConstantMemory], [1, 1]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:34 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3]) STANDARD_ERROR INFO 2024-07-02 11:56:34 DownsampleSam Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16642919542004914978.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16642919542004914978.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:34.435 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:34.435 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:34.435 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:34.435 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:34.435 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:34.435 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:34.435 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:34.435 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:34 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16642919542004914978.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:34 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16642919542004914978.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:34 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:34 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:34 DownsampleSam Kept 9998 out of 20000 reads (49.99%). INFO 2024-07-02 11:56:34 DownsampleSam Kept 9998 out of 20000 reads (49.99%). Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:34 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:34 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:35 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3]) STANDARD_ERROR INFO 2024-07-02 11:56:35 DownsampleSam Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16642919542004914978.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5119076609865337240.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 3 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16642919542004914978.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5119076609865337240.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 3 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:35.072 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:35.072 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:35.073 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:35.073 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:35.081 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:35.081 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:35.081 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:35.081 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:35 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16642919542004914978.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5119076609865337240.bam STRATEGY=ConstantMemory RANDOM_SEED=3 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:35 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16642919542004914978.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5119076609865337240.bam STRATEGY=ConstantMemory RANDOM_SEED=3 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:35 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:35 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:35 DownsampleSam Kept 4932 out of 9998 reads (49.33%). INFO 2024-07-02 11:56:35 DownsampleSam Kept 4932 out of 9998 reads (49.33%). Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:35 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:35 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:35 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:35 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[8]([Chained, ConstantMemory], [1, 3]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:35 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:35 DownsampleSam Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8189832923695169728.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8189832923695169728.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:35.652 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:35.652 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:35.652 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:35.652 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:35.652 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:35.652 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:35.652 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:35.652 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:35 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8189832923695169728.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:35 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8189832923695169728.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:36 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:36 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:36 DownsampleSam Kept 10018 out of 20000 reads (50.09%). INFO 2024-07-02 11:56:36 DownsampleSam Kept 10018 out of 20000 reads (50.09%). Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:36 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:36 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:36 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:36 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:36 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:36 DownsampleSam Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8189832923695169728.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam7721312888301313706.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8189832923695169728.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam7721312888301313706.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:36.770 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:36.770 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:36.770 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:36.770 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:36.770 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:36.770 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:36.770 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:36.770 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:36 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8189832923695169728.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam7721312888301313706.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:36 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8189832923695169728.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam7721312888301313706.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:36 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:56:36 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:36 DownsampleSam RANDOM_SEED has been changed to -1155869325. WARNING 2024-07-02 11:56:36 DownsampleSam RANDOM_SEED has been changed to -1155869325. Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:37 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:37 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:37 DownsampleSam Kept 5008 out of 10018 reads (49.99%). INFO 2024-07-02 11:56:37 DownsampleSam Kept 5008 out of 10018 reads (49.99%). Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:37 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:37 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:37 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:37 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[9]([ConstantMemory, Chained], [1, 1]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:37 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:37 DownsampleSam Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8508704096449541826.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8508704096449541826.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:37.359 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:37.359 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:37.360 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:37.360 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:37.360 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:37.360 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:37.360 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:37.360 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:37 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8508704096449541826.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:37 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8508704096449541826.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:37 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:37 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:37 DownsampleSam Kept 10000 out of 20000 reads (50.00%). INFO 2024-07-02 11:56:37 DownsampleSam Kept 10000 out of 20000 reads (50.00%). Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:37 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:37 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:37 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:37 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:38 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:38 DownsampleSam Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8508704096449541826.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13565005952012750717.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8508704096449541826.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13565005952012750717.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:38.372 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:38.372 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:38.372 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:38.372 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:38.385 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:38.385 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:38.385 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:38.385 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:38 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8508704096449541826.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13565005952012750717.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:38 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8508704096449541826.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13565005952012750717.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:38 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:56:38 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:38 DownsampleSam RANDOM_SEED has been changed to -1155869325. WARNING 2024-07-02 11:56:38 DownsampleSam RANDOM_SEED has been changed to -1155869325. Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:38 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:38 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:38 DownsampleSam Kept 4920 out of 10000 reads (49.20%). INFO 2024-07-02 11:56:38 DownsampleSam Kept 4920 out of 10000 reads (49.20%). Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:38 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:38 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:38 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:38 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[10]([HighAccuracy, ConstantMemory], [1, 1]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:38 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:38 DownsampleSam Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam18408440982733879478.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam18408440982733879478.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:38.858 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:38.858 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:38.858 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:38.858 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:38.858 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:38.858 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:38.858 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:38.858 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:38 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam18408440982733879478.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:38 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam18408440982733879478.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:39 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:39 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:39 DownsampleSam Kept 10018 out of 20000 reads (50.09%). INFO 2024-07-02 11:56:39 DownsampleSam Kept 10018 out of 20000 reads (50.09%). Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:39 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:39 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:39 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:39 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:39 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:39 DownsampleSam Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam18408440982733879478.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8564966954117107554.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam18408440982733879478.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8564966954117107554.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:39.480 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:39.480 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:39.480 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:39.480 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:39.480 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:39.480 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:39.480 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:39.480 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:39 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam18408440982733879478.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8564966954117107554.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:39 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam18408440982733879478.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8564966954117107554.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:39 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:39 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:39 DownsampleSam Kept 5008 out of 10018 reads (49.99%). INFO 2024-07-02 11:56:39 DownsampleSam Kept 5008 out of 10018 reads (49.99%). Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:39 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:39 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:39 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:39 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[11]([ConstantMemory, HighAccuracy], [1, 1]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:39 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[12]([Chained, Chained], [1, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:39 DownsampleSam Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14906881582946704121.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14906881582946704121.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:39.930 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:39.930 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:39.930 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:39.930 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:39.930 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:39.930 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:39.930 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:39.930 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:39 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14906881582946704121.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:39 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14906881582946704121.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:40 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:40 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:40 DownsampleSam Kept 9998 out of 20000 reads (49.99%). INFO 2024-07-02 11:56:40 DownsampleSam Kept 9998 out of 20000 reads (49.99%). Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:40 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:40 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:40 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:40 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[12]([Chained, Chained], [1, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:40 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[12]([Chained, Chained], [1, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:40 DownsampleSam Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14906881582946704121.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14947701462688801547.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14906881582946704121.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14947701462688801547.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:40.824 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:40.824 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:40.824 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:40.824 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:40.824 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:40.824 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:40.824 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:40.824 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:40 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14906881582946704121.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14947701462688801547.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:40 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14906881582946704121.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14947701462688801547.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:40 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:56:40 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:40 DownsampleSam RANDOM_SEED has been changed to -1155869325. WARNING 2024-07-02 11:56:40 DownsampleSam RANDOM_SEED has been changed to -1155869325. Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:41 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:41 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:41 DownsampleSam Kept 4998 out of 9998 reads (49.99%). INFO 2024-07-02 11:56:41 DownsampleSam Kept 4998 out of 9998 reads (49.99%). Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:41 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:41 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:41 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:41 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[12]([Chained, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[12]([Chained, Chained], [1, 1]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:41 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:41 DownsampleSam Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14499422680406702686.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14499422680406702686.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:41.194 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:41.194 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:41.194 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:41.194 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:41.195 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:41.195 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:41.195 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:41.195 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:41 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14499422680406702686.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:41 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14499422680406702686.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:41 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:41 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:41 DownsampleSam Kept 10000 out of 20000 reads (50.00%). INFO 2024-07-02 11:56:41 DownsampleSam Kept 10000 out of 20000 reads (50.00%). Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:41 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:41 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:41 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:41 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:42 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:42 DownsampleSam Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14499422680406702686.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8092894304758906382.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14499422680406702686.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8092894304758906382.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:42.150 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:42.150 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:42.150 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:42.150 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:42.151 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:42.151 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:42.151 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:42.151 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:42 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14499422680406702686.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8092894304758906382.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:42 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14499422680406702686.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8092894304758906382.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:42 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:56:42 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:42 DownsampleSam RANDOM_SEED has been changed to -1155869325. WARNING 2024-07-02 11:56:42 DownsampleSam RANDOM_SEED has been changed to -1155869325. Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:42 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:42 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:42 DownsampleSam Kept 5000 out of 10000 reads (50.00%). INFO 2024-07-02 11:56:42 DownsampleSam Kept 5000 out of 10000 reads (50.00%). Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:42 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:42 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:42 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:42 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[13]([HighAccuracy, Chained], [1, 1]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:42 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:42 DownsampleSam Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8832725820537021443.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8832725820537021443.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:42.721 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:42.721 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:42.721 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:42.721 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:42.721 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:42.721 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:42.721 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:42.721 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:42 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8832725820537021443.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:42 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8832725820537021443.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:43 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:43 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:43 DownsampleSam Kept 10000 out of 20000 reads (50.00%). INFO 2024-07-02 11:56:43 DownsampleSam Kept 10000 out of 20000 reads (50.00%). Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:43 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:43 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:43 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:43 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:43 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:43 DownsampleSam Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8832725820537021443.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam7317304991444248884.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8832725820537021443.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam7317304991444248884.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:43.456 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:43.456 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:43.456 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:43.456 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:43.456 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:43.456 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:43.456 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:43.456 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:43 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8832725820537021443.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam7317304991444248884.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:43 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8832725820537021443.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam7317304991444248884.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:43 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:43 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:43 DownsampleSam Kept 5000 out of 10000 reads (50.00%). INFO 2024-07-02 11:56:43 DownsampleSam Kept 5000 out of 10000 reads (50.00%). Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:43 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:43 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:43 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:43 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[14]([HighAccuracy, HighAccuracy], [1, 1]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:43 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:43 DownsampleSam Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam11776018046728483310.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam11776018046728483310.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:43.622 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:43.622 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:43.622 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:43.622 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:43.623 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:43.623 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:43.623 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:43.623 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:43 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam11776018046728483310.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:43 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam11776018046728483310.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:43 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:43 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:43 DownsampleSam Kept 9998 out of 20000 reads (49.99%). INFO 2024-07-02 11:56:43 DownsampleSam Kept 9998 out of 20000 reads (49.99%). Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:43 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:43 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:43 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:43 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:43 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:43 DownsampleSam Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam11776018046728483310.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam3875053472239018742.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam11776018046728483310.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam3875053472239018742.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:43.926 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:43.926 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:43.926 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:43.926 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:43.926 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:43.926 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:43.926 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:43.926 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:43 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam11776018046728483310.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam3875053472239018742.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:43 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam11776018046728483310.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam3875053472239018742.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:44 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:44 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:44 DownsampleSam Kept 4998 out of 9998 reads (49.99%). INFO 2024-07-02 11:56:44 DownsampleSam Kept 4998 out of 9998 reads (49.99%). Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:44 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:44 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:44 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:44 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[15]([Chained, HighAccuracy], [1, 1]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:44 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:44 DownsampleSam Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16128142092093182971.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16128142092093182971.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:44.201 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:44.201 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:44.201 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:44.201 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:44.202 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:44.202 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:44.202 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:44.202 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:44 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16128142092093182971.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:44 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16128142092093182971.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:44 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:44 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:44 DownsampleSam Kept 10018 out of 20000 reads (50.09%). INFO 2024-07-02 11:56:44 DownsampleSam Kept 10018 out of 20000 reads (50.09%). Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:44 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:44 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:44 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:44 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:44 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:44 DownsampleSam Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16128142092093182971.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1471130133832340546.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16128142092093182971.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1471130133832340546.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:44.493 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:44.493 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:44.493 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:44.493 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:44.493 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:44.493 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:44.493 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:44.493 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:44 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16128142092093182971.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1471130133832340546.bam STRATEGY=HighAccuracy RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:44 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16128142092093182971.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1471130133832340546.bam STRATEGY=HighAccuracy RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:44 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:44 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:44 DownsampleSam Kept 5008 out of 10018 reads (49.99%). INFO 2024-07-02 11:56:44 DownsampleSam Kept 5008 out of 10018 reads (49.99%). Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:44 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:44 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:44 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:44 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:44 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:44 DownsampleSam Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1471130133832340546.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2865907378165055620.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1471130133832340546.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2865907378165055620.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:44.637 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:44.637 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:44.637 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:44.637 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:44.638 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:44.638 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:44.638 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:44.638 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:44 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1471130133832340546.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2865907378165055620.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:44 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1471130133832340546.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2865907378165055620.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:44 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:56:44 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:44 DownsampleSam RANDOM_SEED has been changed to -1155869325. WARNING 2024-07-02 11:56:44 DownsampleSam RANDOM_SEED has been changed to -1155869325. Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:44 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:44 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:44 DownsampleSam Kept 2526 out of 5008 reads (50.44%). INFO 2024-07-02 11:56:44 DownsampleSam Kept 2526 out of 5008 reads (50.44%). Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:44 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:44 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:44 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:44 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:44 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:44 DownsampleSam Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2865907378165055620.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2039347002078891769.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2865907378165055620.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2039347002078891769.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:44.802 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:44.802 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:44.802 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:44.802 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:44.802 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:44.802 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:44.802 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:44.802 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:44 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2865907378165055620.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2039347002078891769.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:44 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2865907378165055620.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2039347002078891769.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:44 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:44 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:44 DownsampleSam Kept 1262 out of 2526 reads (49.96%). INFO 2024-07-02 11:56:44 DownsampleSam Kept 1262 out of 2526 reads (49.96%). Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:44 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:44 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:44 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:44 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:44 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:44 DownsampleSam Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2039347002078891769.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2660805090138597989.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2039347002078891769.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2660805090138597989.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:44.916 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:44.916 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:44.916 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:44.916 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:44.925 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:44.925 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:44.925 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:44.925 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:44 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2039347002078891769.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2660805090138597989.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:44 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2039347002078891769.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2660805090138597989.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:44 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:44 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:44 DownsampleSam Kept 630 out of 1262 reads (49.92%). INFO 2024-07-02 11:56:44 DownsampleSam Kept 630 out of 1262 reads (49.92%). Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:44 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:44 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:44 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:44 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[16]([ConstantMemory, HighAccuracy, ConstantMemory, HighAccuracy, HighAccuracy], [1, 0, 1, 1, 1]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:45 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2]) STANDARD_ERROR INFO 2024-07-02 11:56:45 DownsampleSam Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1009584270534525276.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1009584270534525276.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:45.024 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:45.024 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:45.024 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:45.024 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:45.024 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:45.024 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:45.024 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:45.024 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:45 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1009584270534525276.bam STRATEGY=HighAccuracy RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:45 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1009584270534525276.bam STRATEGY=HighAccuracy RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:45 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:45 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:45 DownsampleSam Kept 10000 out of 20000 reads (50.00%). INFO 2024-07-02 11:56:45 DownsampleSam Kept 10000 out of 20000 reads (50.00%). Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:45 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:45 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:45 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:45 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:45 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2]) STANDARD_ERROR INFO 2024-07-02 11:56:45 DownsampleSam Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1009584270534525276.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16586950058390037837.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1009584270534525276.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16586950058390037837.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:45.492 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:45.492 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:45.492 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:45.492 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:45.497 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:45.497 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:45.497 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:45.497 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:45 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1009584270534525276.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16586950058390037837.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:45 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1009584270534525276.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16586950058390037837.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:45 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:45 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:45 DownsampleSam Kept 4970 out of 10000 reads (49.70%). INFO 2024-07-02 11:56:45 DownsampleSam Kept 4970 out of 10000 reads (49.70%). Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:45 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:45 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:45 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:45 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:45 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2]) STANDARD_ERROR INFO 2024-07-02 11:56:45 DownsampleSam Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16586950058390037837.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam871365430903193300.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16586950058390037837.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam871365430903193300.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:45.753 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:45.753 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:45.753 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:45.753 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:45.753 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:45.753 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:45.753 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:45.753 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:45 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16586950058390037837.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam871365430903193300.bam STRATEGY=ConstantMemory RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:45 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16586950058390037837.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam871365430903193300.bam STRATEGY=ConstantMemory RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:45 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:56:45 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:45 DownsampleSam RANDOM_SEED has been changed to -1154715079. WARNING 2024-07-02 11:56:45 DownsampleSam RANDOM_SEED has been changed to -1154715079. Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:45 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:45 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:45 DownsampleSam Kept 2510 out of 4970 reads (50.50%). INFO 2024-07-02 11:56:45 DownsampleSam Kept 2510 out of 4970 reads (50.50%). Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:45 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:45 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:45 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:45 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:45 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2]) STANDARD_ERROR INFO 2024-07-02 11:56:45 DownsampleSam Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam871365430903193300.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam11251312788448763648.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam871365430903193300.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam11251312788448763648.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:45.927 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:45.927 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:45.927 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:45.927 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:45.927 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:45.927 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:45.927 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:45.927 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:45 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam871365430903193300.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam11251312788448763648.bam STRATEGY=ConstantMemory RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:45 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam871365430903193300.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam11251312788448763648.bam STRATEGY=ConstantMemory RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:45 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:56:45 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:45 DownsampleSam DownsampleSam has been run before on this data with the seed 1260042744. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:56:45 DownsampleSam DownsampleSam has been run before on this data with the seed 1260042744. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:45 DownsampleSam RANDOM_SEED has been changed to 1260042744. WARNING 2024-07-02 11:56:45 DownsampleSam RANDOM_SEED has been changed to 1260042744. Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:45 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:45 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:45 DownsampleSam Kept 1298 out of 2510 reads (51.71%). INFO 2024-07-02 11:56:45 DownsampleSam Kept 1298 out of 2510 reads (51.71%). Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:45 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:45 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:45 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:45 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:46 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2]) STANDARD_ERROR INFO 2024-07-02 11:56:46 DownsampleSam Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam11251312788448763648.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5105317314568267374.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam11251312788448763648.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5105317314568267374.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:46.053 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:46.053 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:46.053 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:46.053 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:46.054 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:46.054 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:46.054 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:46.054 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:46 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam11251312788448763648.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5105317314568267374.bam STRATEGY=HighAccuracy RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:46 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam11251312788448763648.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5105317314568267374.bam STRATEGY=HighAccuracy RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:46 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:46 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:46 DownsampleSam Kept 648 out of 1298 reads (49.92%). INFO 2024-07-02 11:56:46 DownsampleSam Kept 648 out of 1298 reads (49.92%). Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:46 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:46 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:46 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:46 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[17]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, HighAccuracy], [2, 1, 2, 2, 2]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:46 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2]) STANDARD_ERROR INFO 2024-07-02 11:56:46 DownsampleSam Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6879286698386504242.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6879286698386504242.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:46.164 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:46.164 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:46.164 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:46.164 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:46.164 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:46.164 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:46.164 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:46.164 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:46 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6879286698386504242.bam STRATEGY=ConstantMemory RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:46 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6879286698386504242.bam STRATEGY=ConstantMemory RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:46 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:46 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:46 DownsampleSam Kept 10030 out of 20000 reads (50.15%). INFO 2024-07-02 11:56:46 DownsampleSam Kept 10030 out of 20000 reads (50.15%). Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:46 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:46 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:46 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:46 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:46 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2]) STANDARD_ERROR INFO 2024-07-02 11:56:46 DownsampleSam Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6879286698386504242.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2333660991970337963.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6879286698386504242.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2333660991970337963.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:46.439 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:46.439 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:46.439 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:46.439 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:46.439 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:46.439 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:46.439 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:46.439 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:46 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6879286698386504242.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2333660991970337963.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:46 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6879286698386504242.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2333660991970337963.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:46 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:46 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:46 DownsampleSam Kept 4968 out of 10030 reads (49.53%). INFO 2024-07-02 11:56:46 DownsampleSam Kept 4968 out of 10030 reads (49.53%). Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:46 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:46 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:46 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:46 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:46 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2]) STANDARD_ERROR INFO 2024-07-02 11:56:46 DownsampleSam Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2333660991970337963.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5797453983984860791.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2333660991970337963.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5797453983984860791.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:46.796 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:46.796 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:46.796 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:46.796 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:46.805 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:46.805 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:46.805 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:46.805 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:46 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2333660991970337963.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5797453983984860791.bam STRATEGY=HighAccuracy RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:46 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2333660991970337963.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5797453983984860791.bam STRATEGY=HighAccuracy RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:46 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:46 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:46 DownsampleSam Kept 2484 out of 4968 reads (50.00%). INFO 2024-07-02 11:56:46 DownsampleSam Kept 2484 out of 4968 reads (50.00%). Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:46 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:46 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:46 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:46 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:47 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2]) STANDARD_ERROR INFO 2024-07-02 11:56:47 DownsampleSam Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5797453983984860791.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6010564387158790741.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5797453983984860791.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6010564387158790741.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:47.080 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:47.080 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:47.080 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:47.080 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:47.080 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:47.080 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:47.080 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:47.080 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:47 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5797453983984860791.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6010564387158790741.bam STRATEGY=Chained RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:47 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5797453983984860791.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6010564387158790741.bam STRATEGY=Chained RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:47 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:56:47 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:47 DownsampleSam RANDOM_SEED has been changed to -1154715079. WARNING 2024-07-02 11:56:47 DownsampleSam RANDOM_SEED has been changed to -1154715079. Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:47 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:47 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:47 DownsampleSam Kept 1242 out of 2484 reads (50.00%). INFO 2024-07-02 11:56:47 DownsampleSam Kept 1242 out of 2484 reads (50.00%). Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:47 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:47 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:47 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:47 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:47 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2]) STANDARD_ERROR INFO 2024-07-02 11:56:47 DownsampleSam Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6010564387158790741.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam541586544935999595.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6010564387158790741.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam541586544935999595.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:47.223 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:47.223 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:47.223 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:47.223 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:47.223 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:47.223 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:47.223 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:47.223 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:47 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6010564387158790741.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam541586544935999595.bam STRATEGY=HighAccuracy RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:47 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6010564387158790741.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam541586544935999595.bam STRATEGY=HighAccuracy RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:47 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:47 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:47 DownsampleSam Kept 620 out of 1242 reads (49.92%). INFO 2024-07-02 11:56:47 DownsampleSam Kept 620 out of 1242 reads (49.92%). Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:47 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:47 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:47 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:47 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[18]([ConstantMemory, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [2, 1, 2, 2, 2]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:47 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:47 DownsampleSam Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2233022735586524376.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2233022735586524376.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:47.399 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:47.399 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:47.400 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:47.400 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:47.400 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:47.400 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:47.400 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:47.400 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:47 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2233022735586524376.bam STRATEGY=Chained RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:47 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2233022735586524376.bam STRATEGY=Chained RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:47 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:47 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:47 DownsampleSam Kept 10000 out of 20000 reads (50.00%). INFO 2024-07-02 11:56:47 DownsampleSam Kept 10000 out of 20000 reads (50.00%). Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:47 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:47 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:47 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:47 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:48 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:48 DownsampleSam Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2233022735586524376.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam747162706762224354.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2233022735586524376.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam747162706762224354.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:48.103 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:48.103 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:48.103 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:48.103 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:48.103 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:48.103 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:48.103 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:48.103 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:48 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2233022735586524376.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam747162706762224354.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:48 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2233022735586524376.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam747162706762224354.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:48 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:56:48 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:48 DownsampleSam RANDOM_SEED has been changed to -1155484576. WARNING 2024-07-02 11:56:48 DownsampleSam RANDOM_SEED has been changed to -1155484576. Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:48 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:48 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:48 DownsampleSam Kept 4920 out of 10000 reads (49.20%). INFO 2024-07-02 11:56:48 DownsampleSam Kept 4920 out of 10000 reads (49.20%). Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:48 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:48 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:48 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:48 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:48 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:48 DownsampleSam Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam747162706762224354.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2341118303290803999.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam747162706762224354.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2341118303290803999.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:48.727 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:48.727 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:48.727 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:48.727 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:48.728 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:48.728 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:48.728 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:48.728 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:48 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam747162706762224354.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2341118303290803999.bam STRATEGY=Chained RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:48 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam747162706762224354.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2341118303290803999.bam STRATEGY=Chained RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:48 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:48 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:48 DownsampleSam Kept 2458 out of 4920 reads (49.96%). INFO 2024-07-02 11:56:48 DownsampleSam Kept 2458 out of 4920 reads (49.96%). Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:48 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:48 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:48 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:48 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:49 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:49 DownsampleSam Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2341118303290803999.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8988500454636442118.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2341118303290803999.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8988500454636442118.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:49.212 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:49.212 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:49.212 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:49.212 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:49.212 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:49.212 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:49.212 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:49.212 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:49 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2341118303290803999.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8988500454636442118.bam STRATEGY=HighAccuracy RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:49 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2341118303290803999.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8988500454636442118.bam STRATEGY=HighAccuracy RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:49 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:49 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:49 DownsampleSam Kept 1228 out of 2458 reads (49.96%). INFO 2024-07-02 11:56:49 DownsampleSam Kept 1228 out of 2458 reads (49.96%). Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:49 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:49 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:49 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:49 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:49 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:49 DownsampleSam Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8988500454636442118.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6995093282595958618.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8988500454636442118.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6995093282595958618.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:49.541 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:49.541 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:49.542 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:49.542 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:49.542 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:49.542 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:49.542 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:49.542 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:49 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8988500454636442118.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6995093282595958618.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:49 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8988500454636442118.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6995093282595958618.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:49 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:49 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:49 DownsampleSam Kept 544 out of 1228 reads (44.30%). INFO 2024-07-02 11:56:49 DownsampleSam Kept 544 out of 1228 reads (44.30%). Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:49 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:49 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:49 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:49 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[19]([Chained, ConstantMemory, Chained, HighAccuracy, ConstantMemory], [0, 0, 2, 2, 1]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:49 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2]) STANDARD_ERROR INFO 2024-07-02 11:56:49 DownsampleSam Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1795663469921113550.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1795663469921113550.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:49.759 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:49.759 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:49.759 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:49.759 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:49.759 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:49.759 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:49.759 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:49.759 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:49 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1795663469921113550.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:49 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1795663469921113550.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:50 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:50 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:50 DownsampleSam Kept 10142 out of 20000 reads (50.71%). INFO 2024-07-02 11:56:50 DownsampleSam Kept 10142 out of 20000 reads (50.71%). Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:50 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:50 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:50 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:50 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:50 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2]) STANDARD_ERROR INFO 2024-07-02 11:56:50 DownsampleSam Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1795663469921113550.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam7181610578520118727.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1795663469921113550.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam7181610578520118727.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:50.871 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:50.871 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:50.872 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:50.872 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:50.872 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:50.872 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:50.872 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:50.872 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:50 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1795663469921113550.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam7181610578520118727.bam STRATEGY=Chained RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:50 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1795663469921113550.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam7181610578520118727.bam STRATEGY=Chained RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:50 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:50 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:56:50 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:50 DownsampleSam RANDOM_SEED has been changed to -1155484576. WARNING 2024-07-02 11:56:50 DownsampleSam RANDOM_SEED has been changed to -1155484576. Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:51 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:51 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:51 DownsampleSam Kept 5070 out of 10142 reads (49.99%). INFO 2024-07-02 11:56:51 DownsampleSam Kept 5070 out of 10142 reads (49.99%). Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:51 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:51 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:51 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:51 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:51 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2]) STANDARD_ERROR INFO 2024-07-02 11:56:51 DownsampleSam Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam7181610578520118727.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam7587064730235937980.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam7181610578520118727.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam7587064730235937980.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:51.591 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:51.591 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:51.591 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:51.591 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:51.591 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:51.591 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:51.591 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:51.591 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:51 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam7181610578520118727.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam7587064730235937980.bam STRATEGY=ConstantMemory RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:51 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam7181610578520118727.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam7587064730235937980.bam STRATEGY=ConstantMemory RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:51 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:51 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:51 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:51 DownsampleSam Kept 2562 out of 5070 reads (50.53%). INFO 2024-07-02 11:56:51 DownsampleSam Kept 2562 out of 5070 reads (50.53%). Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:51 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:51 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:51 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:51 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:52 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2]) STANDARD_ERROR INFO 2024-07-02 11:56:52 DownsampleSam Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam7587064730235937980.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5983698541245246160.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam7587064730235937980.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5983698541245246160.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:52.038 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:52.038 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:52.038 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:52.038 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:52.038 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:52.038 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:52.038 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:52.038 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:52 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam7587064730235937980.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5983698541245246160.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:52 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam7587064730235937980.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5983698541245246160.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:52 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:56:52 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:52 DownsampleSam DownsampleSam has been run before on this data with the seed -723955400. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:56:52 DownsampleSam DownsampleSam has been run before on this data with the seed -723955400. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:52 DownsampleSam RANDOM_SEED has been changed to -723955400. WARNING 2024-07-02 11:56:52 DownsampleSam RANDOM_SEED has been changed to -723955400. Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:52 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:52 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:52 DownsampleSam Kept 1304 out of 2562 reads (50.90%). INFO 2024-07-02 11:56:52 DownsampleSam Kept 1304 out of 2562 reads (50.90%). Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:52 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:52 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:52 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:52 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:52 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2]) STANDARD_ERROR INFO 2024-07-02 11:56:52 DownsampleSam Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5983698541245246160.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam10236732670509682529.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5983698541245246160.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam10236732670509682529.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:52.356 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:52.356 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:52.356 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:52.356 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:52.356 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:52.356 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:52.356 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:52.356 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:52 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5983698541245246160.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam10236732670509682529.bam STRATEGY=HighAccuracy RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:52 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5983698541245246160.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam10236732670509682529.bam STRATEGY=HighAccuracy RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:52 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:52 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:52 DownsampleSam Kept 652 out of 1304 reads (50.00%). INFO 2024-07-02 11:56:52 DownsampleSam Kept 652 out of 1304 reads (50.00%). Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:52 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:52 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:52 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:52 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[20]([ConstantMemory, Chained, ConstantMemory, ConstantMemory, HighAccuracy], [0, 0, 2, 0, 2]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:52 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:52 DownsampleSam Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5478589208949175541.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5478589208949175541.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:52.658 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:52.658 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:52.659 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:52.659 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:52.659 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:52.659 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:52.659 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:52.659 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:52 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5478589208949175541.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:52 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5478589208949175541.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:53 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:53 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:53 DownsampleSam Kept 10142 out of 20000 reads (50.71%). INFO 2024-07-02 11:56:53 DownsampleSam Kept 10142 out of 20000 reads (50.71%). Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:53 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:53 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:53 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:53 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:53 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:53 DownsampleSam Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5478589208949175541.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2960880826055378946.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5478589208949175541.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2960880826055378946.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:53.691 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:53.691 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:53.691 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:53.691 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:53.691 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:53.691 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:53.691 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:53.691 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:53 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5478589208949175541.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2960880826055378946.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:53 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5478589208949175541.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2960880826055378946.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:53 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:56:53 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:53 DownsampleSam RANDOM_SEED has been changed to -1155484576. WARNING 2024-07-02 11:56:53 DownsampleSam RANDOM_SEED has been changed to -1155484576. Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:53 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:53 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:53 DownsampleSam Kept 4988 out of 10142 reads (49.18%). INFO 2024-07-02 11:56:53 DownsampleSam Kept 4988 out of 10142 reads (49.18%). Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:53 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:53 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:53 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:53 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:54 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:54 DownsampleSam Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2960880826055378946.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam4274774949833881557.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2960880826055378946.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam4274774949833881557.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:54.335 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:54.335 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:54.335 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:54.335 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:54.335 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:54.335 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:54.335 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:54.335 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:54 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2960880826055378946.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam4274774949833881557.bam STRATEGY=HighAccuracy RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:54 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2960880826055378946.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam4274774949833881557.bam STRATEGY=HighAccuracy RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:54 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:54 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:54 DownsampleSam Kept 2494 out of 4988 reads (50.00%). INFO 2024-07-02 11:56:54 DownsampleSam Kept 2494 out of 4988 reads (50.00%). Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:54 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:54 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:54 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:54 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:54 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:54 DownsampleSam Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam4274774949833881557.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14959030119730262732.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam4274774949833881557.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14959030119730262732.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:54.714 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:54.714 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:54.715 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:54.715 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:54.715 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:54.715 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:54.715 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:54.715 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:54 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam4274774949833881557.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14959030119730262732.bam STRATEGY=HighAccuracy RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:54 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam4274774949833881557.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14959030119730262732.bam STRATEGY=HighAccuracy RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:54 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:54 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:54 DownsampleSam Kept 1246 out of 2494 reads (49.96%). INFO 2024-07-02 11:56:54 DownsampleSam Kept 1246 out of 2494 reads (49.96%). Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:54 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:54 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:54 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:54 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:54 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1]) STANDARD_ERROR INFO 2024-07-02 11:56:54 DownsampleSam Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14959030119730262732.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam3760987695326316837.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14959030119730262732.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam3760987695326316837.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:54.980 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:54.980 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:54.980 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:54.980 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:54.980 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:54.980 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:54.980 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:54.980 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:54 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14959030119730262732.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam3760987695326316837.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:54 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14959030119730262732.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam3760987695326316837.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:55 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:55 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:55 DownsampleSam Kept 622 out of 1246 reads (49.92%). INFO 2024-07-02 11:56:55 DownsampleSam Kept 622 out of 1246 reads (49.92%). Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:55 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:55 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:55 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:55 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[21]([ConstantMemory, ConstantMemory, HighAccuracy, HighAccuracy, HighAccuracy], [0, 0, 2, 2, 1]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:55 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0]) STANDARD_ERROR INFO 2024-07-02 11:56:55 DownsampleSam Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam4800764365192875969.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam4800764365192875969.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:55.204 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:55.204 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:55.204 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:55.204 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:55.204 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:55.204 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:55.204 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:55.204 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:55 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam4800764365192875969.bam STRATEGY=HighAccuracy RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:55 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam4800764365192875969.bam STRATEGY=HighAccuracy RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:55 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:55 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:55 DownsampleSam Kept 10000 out of 20000 reads (50.00%). INFO 2024-07-02 11:56:55 DownsampleSam Kept 10000 out of 20000 reads (50.00%). Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:55 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:55 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:55 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:55 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:56 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0]) STANDARD_ERROR INFO 2024-07-02 11:56:56 DownsampleSam Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam4800764365192875969.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam3803212589805209715.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam4800764365192875969.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam3803212589805209715.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:56.277 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:56.277 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:56.277 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:56.277 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:56.277 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:56.277 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:56.277 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:56.277 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:56 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam4800764365192875969.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam3803212589805209715.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:56 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam4800764365192875969.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam3803212589805209715.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:56 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:56 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:56 DownsampleSam Kept 4998 out of 10000 reads (49.98%). INFO 2024-07-02 11:56:56 DownsampleSam Kept 4998 out of 10000 reads (49.98%). Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:56 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:56 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:56 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0]) STANDARD_ERROR INFO 2024-07-02 11:56:56 DownsampleSam Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam3803212589805209715.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam15328251200331571562.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam3803212589805209715.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam15328251200331571562.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:56.682 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:56.682 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:56.682 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:56.682 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:56.682 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:56.682 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:56.682 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:56.682 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:56 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam3803212589805209715.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam15328251200331571562.bam STRATEGY=ConstantMemory RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:56 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam3803212589805209715.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam15328251200331571562.bam STRATEGY=ConstantMemory RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:56 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:56 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:56 DownsampleSam Kept 2516 out of 4998 reads (50.34%). INFO 2024-07-02 11:56:56 DownsampleSam Kept 2516 out of 4998 reads (50.34%). Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:56 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:56 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:56 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0]) STANDARD_ERROR INFO 2024-07-02 11:56:56 DownsampleSam Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam15328251200331571562.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam17858651195146998499.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam15328251200331571562.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam17858651195146998499.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:56.917 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:56.917 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:56.921 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:56.921 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:56.921 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:56.921 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:56.921 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:56.921 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:56 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam15328251200331571562.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam17858651195146998499.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:56 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam15328251200331571562.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam17858651195146998499.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:56 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:56:56 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:56 DownsampleSam RANDOM_SEED has been changed to -1155484576. WARNING 2024-07-02 11:56:56 DownsampleSam RANDOM_SEED has been changed to -1155484576. Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:56 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:56 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:56 DownsampleSam Kept 1214 out of 2516 reads (48.25%). INFO 2024-07-02 11:56:56 DownsampleSam Kept 1214 out of 2516 reads (48.25%). Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:56 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:56 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:57 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0]) STANDARD_ERROR INFO 2024-07-02 11:56:57 DownsampleSam Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam17858651195146998499.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam9191639357605227904.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam17858651195146998499.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam9191639357605227904.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:57.086 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:57.086 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:57.086 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:57.086 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:57.086 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:57.086 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:57.086 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:57.086 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:57 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam17858651195146998499.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam9191639357605227904.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:57 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam17858651195146998499.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam9191639357605227904.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:57 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:56:57 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:57 DownsampleSam DownsampleSam has been run before on this data with the seed -723955400. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:56:57 DownsampleSam DownsampleSam has been run before on this data with the seed -723955400. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:57 DownsampleSam RANDOM_SEED has been changed to -723955400. WARNING 2024-07-02 11:56:57 DownsampleSam RANDOM_SEED has been changed to -723955400. Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:57 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:57 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:57 DownsampleSam Kept 626 out of 1214 reads (51.57%). INFO 2024-07-02 11:56:57 DownsampleSam Kept 626 out of 1214 reads (51.57%). Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:57 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:57 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:57 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:57 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[22]([HighAccuracy, ConstantMemory, ConstantMemory, ConstantMemory, ConstantMemory], [0, 1, 2, 0, 0]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:57 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2]) STANDARD_ERROR INFO 2024-07-02 11:56:57 DownsampleSam Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5674096236382415785.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5674096236382415785.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:57.224 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:57.224 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:57.233 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:57.233 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:57.233 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:57.233 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:57.233 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:57.233 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:57 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5674096236382415785.bam STRATEGY=Chained RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:57 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5674096236382415785.bam STRATEGY=Chained RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:57 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:57 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:57 DownsampleSam Kept 9998 out of 20000 reads (49.99%). INFO 2024-07-02 11:56:57 DownsampleSam Kept 9998 out of 20000 reads (49.99%). Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:57 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:57 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:57 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:57 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:57 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2]) STANDARD_ERROR INFO 2024-07-02 11:56:57 DownsampleSam Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5674096236382415785.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam3273588350711935010.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5674096236382415785.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam3273588350711935010.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:57.891 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:57.891 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:57.891 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:57.891 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:57.891 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:57.891 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:57.891 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:57.891 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:57 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5674096236382415785.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam3273588350711935010.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:57 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5674096236382415785.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam3273588350711935010.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:58 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:58 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:58 DownsampleSam Kept 4972 out of 9998 reads (49.73%). INFO 2024-07-02 11:56:58 DownsampleSam Kept 4972 out of 9998 reads (49.73%). Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:58 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:58 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:58 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:58 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:58 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2]) STANDARD_ERROR INFO 2024-07-02 11:56:58 DownsampleSam Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam3273588350711935010.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6708643471822115182.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam3273588350711935010.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6708643471822115182.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:58.479 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:58.479 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:58.479 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:58.479 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:58.480 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:58.480 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:58.480 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:58.480 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:58 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam3273588350711935010.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6708643471822115182.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:58 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam3273588350711935010.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6708643471822115182.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:58 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:58 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:58 DownsampleSam Kept 2486 out of 4972 reads (50.00%). INFO 2024-07-02 11:56:58 DownsampleSam Kept 2486 out of 4972 reads (50.00%). Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:58 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:58 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:58 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:58 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:58 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2]) STANDARD_ERROR INFO 2024-07-02 11:56:58 DownsampleSam Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6708643471822115182.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam4780163107456594897.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6708643471822115182.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam4780163107456594897.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:58.874 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:58.874 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:58.875 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:58.875 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:58.875 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:58.875 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:58.875 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:58.875 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:58 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6708643471822115182.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam4780163107456594897.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:58 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6708643471822115182.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam4780163107456594897.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:58 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:58 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:58 DownsampleSam Kept 1276 out of 2486 reads (51.33%). INFO 2024-07-02 11:56:58 DownsampleSam Kept 1276 out of 2486 reads (51.33%). Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:58 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:58 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:58 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:58 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:59 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2]) STANDARD_ERROR INFO 2024-07-02 11:56:59 DownsampleSam Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam4780163107456594897.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam12368347822099506409.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam4780163107456594897.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam12368347822099506409.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:59.078 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:59.078 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:59.078 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:59.078 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:59.079 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:59.079 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:59.079 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:59.079 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:59 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam4780163107456594897.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam12368347822099506409.bam STRATEGY=ConstantMemory RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:59 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam4780163107456594897.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam12368347822099506409.bam STRATEGY=ConstantMemory RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:59 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:56:59 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:59 DownsampleSam RANDOM_SEED has been changed to -1154715079. WARNING 2024-07-02 11:56:59 DownsampleSam RANDOM_SEED has been changed to -1154715079. Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:59 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:59 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:59 DownsampleSam Kept 646 out of 1276 reads (50.63%). INFO 2024-07-02 11:56:59 DownsampleSam Kept 646 out of 1276 reads (50.63%). Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:59 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:56:59 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[23]([Chained, ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory], [2, 1, 1, 0, 2]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:59 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2]) STANDARD_ERROR INFO 2024-07-02 11:56:59 DownsampleSam Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam510863830543061902.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam510863830543061902.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:59.228 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:59.228 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:59.228 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:59.228 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:59.229 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:59.229 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:59.229 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:59.229 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:59 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam510863830543061902.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:59 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam510863830543061902.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:59 DownsampleSam Finished downsampling. INFO 2024-07-02 11:56:59 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:59 DownsampleSam Kept 10142 out of 20000 reads (50.71%). INFO 2024-07-02 11:56:59 DownsampleSam Kept 10142 out of 20000 reads (50.71%). Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:59 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:56:59 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:56:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:56:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:56:59 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2]) STANDARD_ERROR INFO 2024-07-02 11:56:59 DownsampleSam Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam510863830543061902.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam904267305134173415.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam510863830543061902.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam904267305134173415.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:59.910 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:59.910 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:59.910 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:59.910 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:59.910 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:56:59.910 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:56:59.910 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:56:59.910 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:59 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam510863830543061902.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam904267305134173415.bam STRATEGY=HighAccuracy RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:56:59 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam510863830543061902.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam904267305134173415.bam STRATEGY=HighAccuracy RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:56:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:56:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:00 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:00 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:00 DownsampleSam Kept 5070 out of 10142 reads (49.99%). INFO 2024-07-02 11:57:00 DownsampleSam Kept 5070 out of 10142 reads (49.99%). Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:00 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:57:00 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:00 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2]) STANDARD_ERROR INFO 2024-07-02 11:57:00 DownsampleSam Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam904267305134173415.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5706976641559110685.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam904267305134173415.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5706976641559110685.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:00.481 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:00.481 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:00.482 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:00.482 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:00.482 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:00.482 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:00.482 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:00.482 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:00 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam904267305134173415.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5706976641559110685.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:00 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam904267305134173415.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5706976641559110685.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:00 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:57:00 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:00 DownsampleSam RANDOM_SEED has been changed to -1155484576. WARNING 2024-07-02 11:57:00 DownsampleSam RANDOM_SEED has been changed to -1155484576. Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:00 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:00 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:00 DownsampleSam Kept 2506 out of 5070 reads (49.43%). INFO 2024-07-02 11:57:00 DownsampleSam Kept 2506 out of 5070 reads (49.43%). Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:00 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:00 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:00 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2]) STANDARD_ERROR INFO 2024-07-02 11:57:00 DownsampleSam Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5706976641559110685.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam3940092447911534718.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5706976641559110685.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam3940092447911534718.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:00.755 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:00.755 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:00.755 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:00.755 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:00.756 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:00.756 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:00.756 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:00.756 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:00 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5706976641559110685.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam3940092447911534718.bam STRATEGY=Chained RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:00 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5706976641559110685.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam3940092447911534718.bam STRATEGY=Chained RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:00 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:57:00 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:00 DownsampleSam DownsampleSam has been run before on this data with the seed -723955400. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:57:00 DownsampleSam DownsampleSam has been run before on this data with the seed -723955400. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:00 DownsampleSam RANDOM_SEED has been changed to -723955400. WARNING 2024-07-02 11:57:00 DownsampleSam RANDOM_SEED has been changed to -723955400. Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:00 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:00 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:00 DownsampleSam Kept 1238 out of 2506 reads (49.40%). INFO 2024-07-02 11:57:00 DownsampleSam Kept 1238 out of 2506 reads (49.40%). Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:00 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:00 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:00 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2]) STANDARD_ERROR INFO 2024-07-02 11:57:00 DownsampleSam Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam3940092447911534718.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam7191477850422516011.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam3940092447911534718.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam7191477850422516011.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:00.936 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:00.936 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:00.937 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:00.937 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:00.949 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:00.949 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:00.949 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:00.949 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:00 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam3940092447911534718.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam7191477850422516011.bam STRATEGY=ConstantMemory RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:00 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam3940092447911534718.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam7191477850422516011.bam STRATEGY=ConstantMemory RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:00 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:00 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:00 DownsampleSam Kept 642 out of 1238 reads (51.86%). INFO 2024-07-02 11:57:00 DownsampleSam Kept 642 out of 1238 reads (51.86%). Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:00 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:00 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[24]([ConstantMemory, HighAccuracy, ConstantMemory, Chained, ConstantMemory], [0, 0, 0, 0, 2]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:01 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0]) STANDARD_ERROR INFO 2024-07-02 11:57:01 DownsampleSam Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1172000407694451142.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1172000407694451142.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:01.162 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:01.162 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:01.162 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:01.162 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:01.163 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:01.163 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:01.163 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:01.163 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:01 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1172000407694451142.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:01 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1172000407694451142.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:01 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:01 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:01 DownsampleSam Kept 10018 out of 20000 reads (50.09%). INFO 2024-07-02 11:57:01 DownsampleSam Kept 10018 out of 20000 reads (50.09%). Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:01 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:57:01 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:01 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0]) STANDARD_ERROR INFO 2024-07-02 11:57:01 DownsampleSam Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1172000407694451142.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16781589288900075204.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1172000407694451142.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16781589288900075204.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:01.868 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:01.868 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:01.868 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:01.868 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:01.868 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:01.868 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:01.868 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:01.868 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:01 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1172000407694451142.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16781589288900075204.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:01 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1172000407694451142.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16781589288900075204.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:02 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:02 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:02 DownsampleSam Kept 5008 out of 10018 reads (49.99%). INFO 2024-07-02 11:57:02 DownsampleSam Kept 5008 out of 10018 reads (49.99%). Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:02 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:57:02 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:02 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0]) STANDARD_ERROR INFO 2024-07-02 11:57:02 DownsampleSam Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16781589288900075204.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14495341955441848122.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16781589288900075204.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14495341955441848122.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:02.457 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:02.457 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:02.457 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:02.457 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:02.458 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:02.458 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:02.458 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:02.458 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:02 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16781589288900075204.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14495341955441848122.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:02 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16781589288900075204.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14495341955441848122.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:02 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:02 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:02 DownsampleSam Kept 2504 out of 5008 reads (50.00%). INFO 2024-07-02 11:57:02 DownsampleSam Kept 2504 out of 5008 reads (50.00%). Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:02 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:02 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:02 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0]) STANDARD_ERROR INFO 2024-07-02 11:57:02 DownsampleSam Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14495341955441848122.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8949817919241723361.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14495341955441848122.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8949817919241723361.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:02.658 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:02.658 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:02.659 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:02.659 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:02.659 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:02.659 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:02.659 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:02.659 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:02 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14495341955441848122.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8949817919241723361.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:02 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14495341955441848122.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8949817919241723361.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:02 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:57:02 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:02 DownsampleSam RANDOM_SEED has been changed to -1155869325. WARNING 2024-07-02 11:57:02 DownsampleSam RANDOM_SEED has been changed to -1155869325. Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:02 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:02 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:02 DownsampleSam Kept 1250 out of 2504 reads (49.92%). INFO 2024-07-02 11:57:02 DownsampleSam Kept 1250 out of 2504 reads (49.92%). Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:02 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:02 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:02 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0]) STANDARD_ERROR INFO 2024-07-02 11:57:02 DownsampleSam Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8949817919241723361.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13855490641694875147.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8949817919241723361.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13855490641694875147.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:02.766 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:02.766 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:02.766 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:02.766 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:02.766 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:02.766 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:02.766 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:02.766 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:02 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8949817919241723361.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13855490641694875147.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:02 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8949817919241723361.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13855490641694875147.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:02 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:02 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:02 DownsampleSam Kept 610 out of 1250 reads (48.80%). INFO 2024-07-02 11:57:02 DownsampleSam Kept 610 out of 1250 reads (48.80%). Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:02 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:02 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:02 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[25]([ConstantMemory, HighAccuracy, HighAccuracy, Chained, ConstantMemory], [1, 1, 1, 1, 0]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:02 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0]) STANDARD_ERROR INFO 2024-07-02 11:57:02 DownsampleSam Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam18412227728595681635.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam18412227728595681635.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:02.880 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:02.880 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:02.880 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:02.880 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:02.880 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:02.880 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:02.880 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:02.880 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:02 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam18412227728595681635.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:02 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam18412227728595681635.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:03 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:03 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:03 DownsampleSam Kept 10018 out of 20000 reads (50.09%). INFO 2024-07-02 11:57:03 DownsampleSam Kept 10018 out of 20000 reads (50.09%). Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:03 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:57:03 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:03 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:03 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0]) STANDARD_ERROR INFO 2024-07-02 11:57:03 DownsampleSam Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam18412227728595681635.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2957477839783369213.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam18412227728595681635.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2957477839783369213.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:03.630 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:03.630 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:03.630 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:03.630 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:03.631 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:03.631 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:03.631 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:03.631 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:03 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam18412227728595681635.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2957477839783369213.bam STRATEGY=Chained RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:03 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam18412227728595681635.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2957477839783369213.bam STRATEGY=Chained RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:04 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:04 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:04 DownsampleSam Kept 5008 out of 10018 reads (49.99%). INFO 2024-07-02 11:57:04 DownsampleSam Kept 5008 out of 10018 reads (49.99%). Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:04 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:57:04 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:04 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0]) STANDARD_ERROR INFO 2024-07-02 11:57:04 DownsampleSam Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2957477839783369213.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam7920031930281985137.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2957477839783369213.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam7920031930281985137.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:04.307 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:04.307 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:04.307 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:04.307 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:04.307 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:04.307 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:04.307 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:04.307 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:04 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2957477839783369213.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam7920031930281985137.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:04 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2957477839783369213.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam7920031930281985137.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:04 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:57:04 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:04 DownsampleSam RANDOM_SEED has been changed to -1155869325. WARNING 2024-07-02 11:57:04 DownsampleSam RANDOM_SEED has been changed to -1155869325. Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:04 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:04 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:04 DownsampleSam Kept 2552 out of 5008 reads (50.96%). INFO 2024-07-02 11:57:04 DownsampleSam Kept 2552 out of 5008 reads (50.96%). Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:04 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:04 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:04 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0]) STANDARD_ERROR INFO 2024-07-02 11:57:04 DownsampleSam Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam7920031930281985137.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6024139070367384454.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam7920031930281985137.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6024139070367384454.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:04.662 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:04.662 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:04.662 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:04.662 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:04.662 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:04.662 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:04.662 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:04.662 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:04 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam7920031930281985137.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6024139070367384454.bam STRATEGY=HighAccuracy RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:04 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam7920031930281985137.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6024139070367384454.bam STRATEGY=HighAccuracy RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:04 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:04 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:04 DownsampleSam Kept 1276 out of 2552 reads (50.00%). INFO 2024-07-02 11:57:04 DownsampleSam Kept 1276 out of 2552 reads (50.00%). Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:04 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:04 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:04 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0]) STANDARD_ERROR INFO 2024-07-02 11:57:04 DownsampleSam Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6024139070367384454.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6684479209101519683.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6024139070367384454.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6684479209101519683.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:04.938 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:04.938 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:04.938 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:04.938 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:04.938 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:04.938 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:04.938 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:04.938 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:04 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6024139070367384454.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6684479209101519683.bam STRATEGY=Chained RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:04 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6024139070367384454.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6684479209101519683.bam STRATEGY=Chained RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:04 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:57:04 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:04 DownsampleSam RANDOM_SEED has been changed to -1155484576. WARNING 2024-07-02 11:57:04 DownsampleSam RANDOM_SEED has been changed to -1155484576. Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:04 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:04 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:04 DownsampleSam Kept 638 out of 1276 reads (50.00%). INFO 2024-07-02 11:57:04 DownsampleSam Kept 638 out of 1276 reads (50.00%). Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:04 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:04 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[26]([ConstantMemory, Chained, ConstantMemory, HighAccuracy, Chained], [1, 0, 1, 2, 0]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:05 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2]) STANDARD_ERROR INFO 2024-07-02 11:57:05 DownsampleSam Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13562358235899131205.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13562358235899131205.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:05.166 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:05.166 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:05.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:05.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:05.166 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:05.166 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:05.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:05.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:05 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13562358235899131205.bam STRATEGY=HighAccuracy RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:05 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13562358235899131205.bam STRATEGY=HighAccuracy RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:05 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:05 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:05 DownsampleSam Kept 10000 out of 20000 reads (50.00%). INFO 2024-07-02 11:57:05 DownsampleSam Kept 10000 out of 20000 reads (50.00%). Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:05 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:57:05 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:05 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:05 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:06 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2]) STANDARD_ERROR INFO 2024-07-02 11:57:06 DownsampleSam Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13562358235899131205.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam12495291383734246250.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13562358235899131205.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam12495291383734246250.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:06.214 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:06.214 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:06.214 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:06.214 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:06.214 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:06.214 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:06.214 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:06.214 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:06 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13562358235899131205.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam12495291383734246250.bam STRATEGY=Chained RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:06 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13562358235899131205.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam12495291383734246250.bam STRATEGY=Chained RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:06 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:57:06 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:06 DownsampleSam RANDOM_SEED has been changed to -1154715079. WARNING 2024-07-02 11:57:06 DownsampleSam RANDOM_SEED has been changed to -1154715079. Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:06 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:06 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:06 DownsampleSam Kept 4998 out of 10000 reads (49.98%). INFO 2024-07-02 11:57:06 DownsampleSam Kept 4998 out of 10000 reads (49.98%). Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:06 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:57:06 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:06 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:06 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:06 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2]) STANDARD_ERROR INFO 2024-07-02 11:57:06 DownsampleSam Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam12495291383734246250.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8763515183155547534.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam12495291383734246250.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8763515183155547534.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:06.839 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:06.839 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:06.839 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:06.839 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:06.839 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:06.839 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:06.839 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:06.839 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:06 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam12495291383734246250.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8763515183155547534.bam STRATEGY=Chained RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:06 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam12495291383734246250.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8763515183155547534.bam STRATEGY=Chained RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:06 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:06 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:06 DownsampleSam Kept 2498 out of 4998 reads (49.98%). INFO 2024-07-02 11:57:06 DownsampleSam Kept 2498 out of 4998 reads (49.98%). Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:06 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:06 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:06 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:06 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:07 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2]) STANDARD_ERROR INFO 2024-07-02 11:57:07 DownsampleSam Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8763515183155547534.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6317099263679456817.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8763515183155547534.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6317099263679456817.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:07.080 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:07.080 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:07.080 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:07.080 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:07.090 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:07.090 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:07.090 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:07.090 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:07 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8763515183155547534.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6317099263679456817.bam STRATEGY=HighAccuracy RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:07 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8763515183155547534.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6317099263679456817.bam STRATEGY=HighAccuracy RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:07 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:07 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:07 DownsampleSam Kept 1248 out of 2498 reads (49.96%). INFO 2024-07-02 11:57:07 DownsampleSam Kept 1248 out of 2498 reads (49.96%). Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:07 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:07 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:07 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2]) STANDARD_ERROR INFO 2024-07-02 11:57:07 DownsampleSam Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6317099263679456817.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8948562085915282833.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6317099263679456817.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8948562085915282833.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:07.259 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:07.259 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:07.259 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:07.259 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:07.259 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:07.259 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:07.259 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:07.259 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:07 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6317099263679456817.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8948562085915282833.bam STRATEGY=HighAccuracy RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:07 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6317099263679456817.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8948562085915282833.bam STRATEGY=HighAccuracy RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:07 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:07 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:07 DownsampleSam Kept 624 out of 1248 reads (50.00%). INFO 2024-07-02 11:57:07 DownsampleSam Kept 624 out of 1248 reads (50.00%). Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:07 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:07 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[27]([HighAccuracy, Chained, Chained, HighAccuracy, HighAccuracy], [2, 2, 0, 2, 2]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:07 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1]) STANDARD_ERROR INFO 2024-07-02 11:57:07 DownsampleSam Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5784303695849309093.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5784303695849309093.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:07.424 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:07.424 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:07.424 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:07.424 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:07.424 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:07.424 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:07.424 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:07.424 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:07 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5784303695849309093.bam STRATEGY=ConstantMemory RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:07 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5784303695849309093.bam STRATEGY=ConstantMemory RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:07 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:07 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:07 DownsampleSam Kept 10030 out of 20000 reads (50.15%). INFO 2024-07-02 11:57:07 DownsampleSam Kept 10030 out of 20000 reads (50.15%). Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:07 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:57:07 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:08 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1]) STANDARD_ERROR INFO 2024-07-02 11:57:08 DownsampleSam Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5784303695849309093.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam15906929409816365209.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5784303695849309093.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam15906929409816365209.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:08.206 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:08.206 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:08.206 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:08.206 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:08.206 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:08.206 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:08.206 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:08.206 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:08 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5784303695849309093.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam15906929409816365209.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:08 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5784303695849309093.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam15906929409816365209.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:08 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:08 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:08 DownsampleSam Kept 5014 out of 10030 reads (49.99%). INFO 2024-07-02 11:57:08 DownsampleSam Kept 5014 out of 10030 reads (49.99%). Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:08 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:08 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:08 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:08 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:08 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1]) STANDARD_ERROR INFO 2024-07-02 11:57:08 DownsampleSam Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam15906929409816365209.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5132975749633329484.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam15906929409816365209.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5132975749633329484.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:08.434 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:08.434 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:08.434 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:08.434 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:08.434 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:08.434 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:08.434 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:08.434 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:08 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam15906929409816365209.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5132975749633329484.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:08 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam15906929409816365209.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5132975749633329484.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:08 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:08 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:08 DownsampleSam Kept 2506 out of 5014 reads (49.98%). INFO 2024-07-02 11:57:08 DownsampleSam Kept 2506 out of 5014 reads (49.98%). Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:08 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:08 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:08 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:08 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:08 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1]) STANDARD_ERROR INFO 2024-07-02 11:57:08 DownsampleSam Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5132975749633329484.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam7445623667795399959.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5132975749633329484.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam7445623667795399959.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:08.782 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:08.782 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:08.782 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:08.782 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:08.782 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:08.782 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:08.782 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:08.782 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:08 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5132975749633329484.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam7445623667795399959.bam STRATEGY=ConstantMemory RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:08 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5132975749633329484.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam7445623667795399959.bam STRATEGY=ConstantMemory RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:08 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:57:08 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:08 DownsampleSam RANDOM_SEED has been changed to -1154715079. WARNING 2024-07-02 11:57:08 DownsampleSam RANDOM_SEED has been changed to -1154715079. Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:08 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:08 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:08 DownsampleSam Kept 1236 out of 2506 reads (49.32%). INFO 2024-07-02 11:57:08 DownsampleSam Kept 1236 out of 2506 reads (49.32%). Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:08 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:08 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:08 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:08 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:08 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1]) STANDARD_ERROR INFO 2024-07-02 11:57:08 DownsampleSam Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam7445623667795399959.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6087409141045312158.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam7445623667795399959.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6087409141045312158.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:08.944 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:08.944 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:08.944 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:08.944 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:08.944 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:08.944 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:08.944 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:08.944 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:08 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam7445623667795399959.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6087409141045312158.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:08 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam7445623667795399959.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6087409141045312158.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:08 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:08 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:08 DownsampleSam Kept 618 out of 1236 reads (50.00%). INFO 2024-07-02 11:57:08 DownsampleSam Kept 618 out of 1236 reads (50.00%). Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:08 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:08 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:08 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:08 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[28]([ConstantMemory, Chained, HighAccuracy, ConstantMemory, HighAccuracy], [2, 1, 1, 2, 1]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:09 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2]) STANDARD_ERROR INFO 2024-07-02 11:57:09 DownsampleSam Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16206197088332763013.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16206197088332763013.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:09.117 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:09.117 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:09.117 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:09.117 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:09.117 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:09.117 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:09.117 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:09.117 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:09 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16206197088332763013.bam STRATEGY=HighAccuracy RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:09 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16206197088332763013.bam STRATEGY=HighAccuracy RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:09 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:09 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:09 DownsampleSam Kept 10000 out of 20000 reads (50.00%). INFO 2024-07-02 11:57:09 DownsampleSam Kept 10000 out of 20000 reads (50.00%). Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:09 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:57:09 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:09 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2]) STANDARD_ERROR INFO 2024-07-02 11:57:09 DownsampleSam Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16206197088332763013.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16957427798942465283.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16206197088332763013.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16957427798942465283.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:09.647 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:09.647 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:09.647 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:09.647 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:09.648 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:09.648 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:09.648 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:09.648 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:09 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16206197088332763013.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16957427798942465283.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:09 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16206197088332763013.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16957427798942465283.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:09 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:09 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:09 DownsampleSam Kept 5044 out of 10000 reads (50.44%). INFO 2024-07-02 11:57:09 DownsampleSam Kept 5044 out of 10000 reads (50.44%). Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:09 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:09 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:09 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2]) STANDARD_ERROR INFO 2024-07-02 11:57:09 DownsampleSam Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16957427798942465283.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8812095559748312179.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16957427798942465283.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8812095559748312179.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:09.818 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:09.818 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:09.818 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:09.818 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:09.819 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:09.819 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:09.819 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:09.819 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:09 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16957427798942465283.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8812095559748312179.bam STRATEGY=Chained RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:09 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16957427798942465283.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8812095559748312179.bam STRATEGY=Chained RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:09 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:57:09 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:09 DownsampleSam RANDOM_SEED has been changed to -1154715079. WARNING 2024-07-02 11:57:09 DownsampleSam RANDOM_SEED has been changed to -1154715079. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:09 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:09 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:09 DownsampleSam Kept 2520 out of 5044 reads (49.96%). INFO 2024-07-02 11:57:09 DownsampleSam Kept 2520 out of 5044 reads (49.96%). Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:09 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:09 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:10 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2]) STANDARD_ERROR INFO 2024-07-02 11:57:10 DownsampleSam Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8812095559748312179.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam798196077461261851.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam8812095559748312179.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam798196077461261851.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:10.022 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:10.022 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:10.022 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:10.022 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:10.022 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:10.022 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:10.022 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:10.022 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:10 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8812095559748312179.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam798196077461261851.bam STRATEGY=ConstantMemory RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:10 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam8812095559748312179.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam798196077461261851.bam STRATEGY=ConstantMemory RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:10 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:57:10 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:10 DownsampleSam DownsampleSam has been run before on this data with the seed 1260042744. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:57:10 DownsampleSam DownsampleSam has been run before on this data with the seed 1260042744. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:10 DownsampleSam RANDOM_SEED has been changed to 1260042744. WARNING 2024-07-02 11:57:10 DownsampleSam RANDOM_SEED has been changed to 1260042744. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:10 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:10 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:10 DownsampleSam Kept 1292 out of 2520 reads (51.27%). INFO 2024-07-02 11:57:10 DownsampleSam Kept 1292 out of 2520 reads (51.27%). Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:10 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:10 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:10 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:10 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:10 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2]) STANDARD_ERROR INFO 2024-07-02 11:57:10 DownsampleSam Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam798196077461261851.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam15537044205305907778.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam798196077461261851.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam15537044205305907778.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:10.281 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:10.281 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:10.293 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:10.293 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:10.293 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:10.293 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:10.293 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:10.293 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:10 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam798196077461261851.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam15537044205305907778.bam STRATEGY=Chained RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:10 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam798196077461261851.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam15537044205305907778.bam STRATEGY=Chained RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:10 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:57:10 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:10 DownsampleSam DownsampleSam has been run before on this data with the seed 1260042744. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:57:10 DownsampleSam DownsampleSam has been run before on this data with the seed 1260042744. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:10 DownsampleSam DownsampleSam has been run before on this data with the seed -423279216. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:57:10 DownsampleSam DownsampleSam has been run before on this data with the seed -423279216. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:10 DownsampleSam RANDOM_SEED has been changed to -423279216. WARNING 2024-07-02 11:57:10 DownsampleSam RANDOM_SEED has been changed to -423279216. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:10 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:10 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:10 DownsampleSam Kept 644 out of 1292 reads (49.85%). INFO 2024-07-02 11:57:10 DownsampleSam Kept 644 out of 1292 reads (49.85%). Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:10 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:10 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:10 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:10 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[29]([HighAccuracy, ConstantMemory, Chained, ConstantMemory, Chained], [2, 0, 2, 2, 2]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:10 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2]) STANDARD_ERROR INFO 2024-07-02 11:57:10 DownsampleSam Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13514101735600693666.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13514101735600693666.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:10.417 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:10.417 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:10.417 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:10.417 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:10.418 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:10.418 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:10.418 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:10.418 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:10 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13514101735600693666.bam STRATEGY=Chained RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:10 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13514101735600693666.bam STRATEGY=Chained RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:10 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:10 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:10 DownsampleSam Kept 9998 out of 20000 reads (49.99%). INFO 2024-07-02 11:57:10 DownsampleSam Kept 9998 out of 20000 reads (49.99%). Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:10 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:10 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:10 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:10 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:10 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2]) STANDARD_ERROR INFO 2024-07-02 11:57:10 DownsampleSam Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13514101735600693666.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam9583022740334408316.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13514101735600693666.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam9583022740334408316.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:10.877 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:10.877 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:10.877 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:10.877 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:10.877 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:10.877 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:10.877 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:10.877 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:10 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13514101735600693666.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam9583022740334408316.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:10 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13514101735600693666.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam9583022740334408316.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:11 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:11 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:11 DownsampleSam Kept 4998 out of 9998 reads (49.99%). INFO 2024-07-02 11:57:11 DownsampleSam Kept 4998 out of 9998 reads (49.99%). Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:11 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:57:11 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:11 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:11 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:11 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2]) STANDARD_ERROR INFO 2024-07-02 11:57:11 DownsampleSam Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam9583022740334408316.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5116548565727120956.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam9583022740334408316.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5116548565727120956.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:11.740 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:11.740 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:11.740 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:11.740 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:11.753 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:11.753 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:11.753 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:11.753 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:11 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam9583022740334408316.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5116548565727120956.bam STRATEGY=Chained RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:11 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam9583022740334408316.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5116548565727120956.bam STRATEGY=Chained RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:11 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:57:11 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:11 DownsampleSam RANDOM_SEED has been changed to -1154715079. WARNING 2024-07-02 11:57:11 DownsampleSam RANDOM_SEED has been changed to -1154715079. Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:11 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:11 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:11 DownsampleSam Kept 2466 out of 4998 reads (49.34%). INFO 2024-07-02 11:57:11 DownsampleSam Kept 2466 out of 4998 reads (49.34%). Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:11 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:11 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:11 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:11 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:12 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2]) STANDARD_ERROR INFO 2024-07-02 11:57:12 DownsampleSam Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5116548565727120956.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14477874500224980424.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5116548565727120956.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14477874500224980424.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:12.331 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:12.331 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:12.331 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:12.331 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:12.331 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:12.331 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:12.331 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:12.331 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:12 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5116548565727120956.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14477874500224980424.bam STRATEGY=Chained RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:12 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5116548565727120956.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14477874500224980424.bam STRATEGY=Chained RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:12 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:12 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:12 DownsampleSam Kept 1232 out of 2466 reads (49.96%). INFO 2024-07-02 11:57:12 DownsampleSam Kept 1232 out of 2466 reads (49.96%). Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:12 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:12 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:12 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:12 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:12 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2]) STANDARD_ERROR INFO 2024-07-02 11:57:12 DownsampleSam Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14477874500224980424.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6413581917167322066.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14477874500224980424.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6413581917167322066.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:12.653 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:12.653 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:12.653 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:12.653 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:12.653 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:12.653 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:12.653 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:12.653 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:12 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14477874500224980424.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6413581917167322066.bam STRATEGY=Chained RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:12 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14477874500224980424.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6413581917167322066.bam STRATEGY=Chained RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:12 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:57:12 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:12 DownsampleSam DownsampleSam has been run before on this data with the seed 1260042744. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:57:12 DownsampleSam DownsampleSam has been run before on this data with the seed 1260042744. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:12 DownsampleSam RANDOM_SEED has been changed to 1260042744. WARNING 2024-07-02 11:57:12 DownsampleSam RANDOM_SEED has been changed to 1260042744. Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:12 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:12 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:12 DownsampleSam Kept 616 out of 1232 reads (50.00%). INFO 2024-07-02 11:57:12 DownsampleSam Kept 616 out of 1232 reads (50.00%). Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:12 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:12 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:12 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:12 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[30]([Chained, HighAccuracy, Chained, Chained, Chained], [2, 1, 2, 0, 2]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:12 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0]) STANDARD_ERROR INFO 2024-07-02 11:57:12 DownsampleSam Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13300407214685479358.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13300407214685479358.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:12.876 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:12.876 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:12.876 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:12.876 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:12.876 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:12.876 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:12.876 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:12.876 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:12 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13300407214685479358.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:12 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13300407214685479358.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:12 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:13 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:13 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:13 DownsampleSam Kept 10000 out of 20000 reads (50.00%). INFO 2024-07-02 11:57:13 DownsampleSam Kept 10000 out of 20000 reads (50.00%). Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:13 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:57:13 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:13 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:13 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:13 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0]) STANDARD_ERROR INFO 2024-07-02 11:57:13 DownsampleSam Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13300407214685479358.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam15413134872587189867.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13300407214685479358.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam15413134872587189867.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:13.770 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:13.770 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:13.770 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:13.770 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:13.771 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:13.771 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:13.771 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:13.771 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:13 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13300407214685479358.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam15413134872587189867.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:13 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13300407214685479358.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam15413134872587189867.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:14 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:14 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:14 DownsampleSam Kept 5080 out of 10000 reads (50.80%). INFO 2024-07-02 11:57:14 DownsampleSam Kept 5080 out of 10000 reads (50.80%). Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:14 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:57:14 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:14 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:14 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:14 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0]) STANDARD_ERROR INFO 2024-07-02 11:57:14 DownsampleSam Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam15413134872587189867.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1140375998688502439.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam15413134872587189867.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1140375998688502439.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:14.466 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:14.466 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:14.466 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:14.466 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:14.467 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:14.467 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:14.467 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:14.467 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:14 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam15413134872587189867.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1140375998688502439.bam STRATEGY=HighAccuracy RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:14 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam15413134872587189867.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1140375998688502439.bam STRATEGY=HighAccuracy RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:15 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:15 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:15 DownsampleSam Kept 2540 out of 5080 reads (50.00%). INFO 2024-07-02 11:57:15 DownsampleSam Kept 2540 out of 5080 reads (50.00%). Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:15 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:57:15 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:15 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:15 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:15 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0]) STANDARD_ERROR INFO 2024-07-02 11:57:15 DownsampleSam Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1140375998688502439.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam15998289227168373640.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1140375998688502439.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam15998289227168373640.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:15.379 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:15.379 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:15.380 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:15.380 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:15.380 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:15.380 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:15.380 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:15.380 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:15 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1140375998688502439.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam15998289227168373640.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:15 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1140375998688502439.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam15998289227168373640.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:15 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:57:15 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:15 DownsampleSam RANDOM_SEED has been changed to -1155869325. WARNING 2024-07-02 11:57:15 DownsampleSam RANDOM_SEED has been changed to -1155869325. Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:15 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:15 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:15 DownsampleSam Kept 1270 out of 2540 reads (50.00%). INFO 2024-07-02 11:57:15 DownsampleSam Kept 1270 out of 2540 reads (50.00%). Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:15 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:15 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:15 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:15 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:15 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0]) STANDARD_ERROR INFO 2024-07-02 11:57:15 DownsampleSam Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam15998289227168373640.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6214192127820417634.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam15998289227168373640.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6214192127820417634.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:15.764 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:15.764 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:15.764 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:15.764 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:15.764 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:15.764 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:15.764 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:15.764 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:15 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam15998289227168373640.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6214192127820417634.bam STRATEGY=HighAccuracy RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:15 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam15998289227168373640.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6214192127820417634.bam STRATEGY=HighAccuracy RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:16 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:16 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:16 DownsampleSam Kept 634 out of 1270 reads (49.92%). INFO 2024-07-02 11:57:16 DownsampleSam Kept 634 out of 1270 reads (49.92%). Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:16 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:16 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:16 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:16 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[31]([HighAccuracy, ConstantMemory, HighAccuracy, Chained, HighAccuracy], [1, 0, 0, 1, 0]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:16 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0]) STANDARD_ERROR INFO 2024-07-02 11:57:16 DownsampleSam Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam17234485039483566889.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam17234485039483566889.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:16.397 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:16.397 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:16.397 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:16.397 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:16.397 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:16.397 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:16.397 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:16.397 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:16 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam17234485039483566889.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:16 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam17234485039483566889.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:17 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:17 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:17 DownsampleSam Kept 10142 out of 20000 reads (50.71%). INFO 2024-07-02 11:57:17 DownsampleSam Kept 10142 out of 20000 reads (50.71%). Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:17 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:57:17 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.02 minutes. Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:17 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:17 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:17 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0]) STANDARD_ERROR INFO 2024-07-02 11:57:17 DownsampleSam Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam17234485039483566889.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2149510862056817585.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam17234485039483566889.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2149510862056817585.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:17.584 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:17.584 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:17.584 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:17.584 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:17.584 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:17.584 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:17.584 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:17.584 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:17 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam17234485039483566889.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2149510862056817585.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:17 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam17234485039483566889.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2149510862056817585.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:17 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:17 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:17 DownsampleSam Kept 5070 out of 10142 reads (49.99%). INFO 2024-07-02 11:57:17 DownsampleSam Kept 5070 out of 10142 reads (49.99%). Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:17 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:57:17 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:17 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:17 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:18 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0]) STANDARD_ERROR INFO 2024-07-02 11:57:18 DownsampleSam Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2149510862056817585.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6750320589013319984.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam2149510862056817585.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6750320589013319984.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:18.099 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:18.099 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:18.099 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:18.099 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:18.099 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:18.099 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:18.099 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:18.099 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:18 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2149510862056817585.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6750320589013319984.bam STRATEGY=HighAccuracy RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:18 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam2149510862056817585.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6750320589013319984.bam STRATEGY=HighAccuracy RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:18 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:18 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:18 DownsampleSam Kept 2534 out of 5070 reads (49.98%). INFO 2024-07-02 11:57:18 DownsampleSam Kept 2534 out of 5070 reads (49.98%). Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:18 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:18 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:18 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:18 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:18 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0]) STANDARD_ERROR INFO 2024-07-02 11:57:18 DownsampleSam Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6750320589013319984.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5851750530709160890.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6750320589013319984.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5851750530709160890.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:18.438 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:18.438 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:18.438 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:18.438 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:18.438 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:18.438 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:18.438 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:18.438 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:18 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6750320589013319984.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5851750530709160890.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:18 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6750320589013319984.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5851750530709160890.bam STRATEGY=Chained RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:18 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:57:18 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:18 DownsampleSam RANDOM_SEED has been changed to -1155869325. WARNING 2024-07-02 11:57:18 DownsampleSam RANDOM_SEED has been changed to -1155869325. Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:18 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:18 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:18 DownsampleSam Kept 1266 out of 2534 reads (49.96%). INFO 2024-07-02 11:57:18 DownsampleSam Kept 1266 out of 2534 reads (49.96%). Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:18 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:18 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:18 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:18 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:18 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0]) STANDARD_ERROR INFO 2024-07-02 11:57:18 DownsampleSam Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5851750530709160890.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13882887946032746107.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam5851750530709160890.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13882887946032746107.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:18.733 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:18.733 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:18.733 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:18.733 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:18.733 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:18.733 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:18.733 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:18.733 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:18 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5851750530709160890.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13882887946032746107.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:18 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam5851750530709160890.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13882887946032746107.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:18 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:57:18 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:18 DownsampleSam RANDOM_SEED has been changed to -1155484576. WARNING 2024-07-02 11:57:18 DownsampleSam RANDOM_SEED has been changed to -1155484576. Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:18 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:18 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:18 DownsampleSam Kept 592 out of 1266 reads (46.76%). INFO 2024-07-02 11:57:18 DownsampleSam Kept 592 out of 1266 reads (46.76%). Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:18 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:18 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:18 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:18 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[32]([ConstantMemory, Chained, HighAccuracy, Chained, ConstantMemory], [0, 1, 0, 1, 0]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:18 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1]) STANDARD_ERROR INFO 2024-07-02 11:57:18 DownsampleSam Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13386388557873885657.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13386388557873885657.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:18.986 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:18.986 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:18.986 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:18.986 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:18.986 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:18.986 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:18.986 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:18.986 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:18 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13386388557873885657.bam STRATEGY=ConstantMemory RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:18 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13386388557873885657.bam STRATEGY=ConstantMemory RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:19 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:19 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:19 DownsampleSam Kept 10030 out of 20000 reads (50.15%). INFO 2024-07-02 11:57:19 DownsampleSam Kept 10030 out of 20000 reads (50.15%). Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:19 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:57:19 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:19 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:19 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:19 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1]) STANDARD_ERROR INFO 2024-07-02 11:57:19 DownsampleSam Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13386388557873885657.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam9404195324576551322.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13386388557873885657.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam9404195324576551322.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:19.764 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:19.764 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:19.764 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:19.764 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:19.764 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:19.764 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:19.764 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:19.764 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:19 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13386388557873885657.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam9404195324576551322.bam STRATEGY=HighAccuracy RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:19 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13386388557873885657.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam9404195324576551322.bam STRATEGY=HighAccuracy RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:19 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:19 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:19 DownsampleSam Kept 5014 out of 10030 reads (49.99%). INFO 2024-07-02 11:57:19 DownsampleSam Kept 5014 out of 10030 reads (49.99%). Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:19 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:19 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:19 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:19 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:20 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1]) STANDARD_ERROR INFO 2024-07-02 11:57:20 DownsampleSam Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam9404195324576551322.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam4826917503735470730.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam9404195324576551322.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam4826917503735470730.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:20.144 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:20.144 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:20.144 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:20.144 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:20.144 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:20.144 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:20.144 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:20.144 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:20 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam9404195324576551322.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam4826917503735470730.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:20 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam9404195324576551322.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam4826917503735470730.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:20 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:57:20 DownsampleSam DownsampleSam has been run before on this data with the seed -1155484576. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:20 DownsampleSam RANDOM_SEED has been changed to -1155484576. WARNING 2024-07-02 11:57:20 DownsampleSam RANDOM_SEED has been changed to -1155484576. Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:20 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:20 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:20 DownsampleSam Kept 2420 out of 5014 reads (48.26%). INFO 2024-07-02 11:57:20 DownsampleSam Kept 2420 out of 5014 reads (48.26%). Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:20 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:20 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:20 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:20 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:20 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1]) STANDARD_ERROR INFO 2024-07-02 11:57:20 DownsampleSam Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam4826917503735470730.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14982460378932893339.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam4826917503735470730.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14982460378932893339.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:20.264 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:20.264 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:20.264 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:20.264 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:20.264 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:20.264 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:20.264 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:20.264 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:20 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam4826917503735470730.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14982460378932893339.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:20 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam4826917503735470730.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14982460378932893339.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:20 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:20 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:20 DownsampleSam Kept 1198 out of 2420 reads (49.50%). INFO 2024-07-02 11:57:20 DownsampleSam Kept 1198 out of 2420 reads (49.50%). Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:20 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:20 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:20 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:20 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:20 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1]) STANDARD_ERROR INFO 2024-07-02 11:57:20 DownsampleSam Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14982460378932893339.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam10369372114846517011.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam14982460378932893339.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam10369372114846517011.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:20.549 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:20.549 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:20.549 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:20.549 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:20.549 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:20.549 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:20.549 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:20.549 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:20 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14982460378932893339.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam10369372114846517011.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:20 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam14982460378932893339.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam10369372114846517011.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:20 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:20 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:20 DownsampleSam Kept 598 out of 1198 reads (49.92%). INFO 2024-07-02 11:57:20 DownsampleSam Kept 598 out of 1198 reads (49.92%). Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:20 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:57:20 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:20 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:20 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[33]([ConstantMemory, HighAccuracy, ConstantMemory, ConstantMemory, HighAccuracy], [2, 0, 0, 1, 1]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:21 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1]) STANDARD_ERROR INFO 2024-07-02 11:57:21 DownsampleSam Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam7971472855838799117.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam7971472855838799117.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:21.125 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:21.125 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:21.125 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:21.125 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:21.125 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:21.125 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:21.125 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:21.125 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:21 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam7971472855838799117.bam STRATEGY=Chained RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:21 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam7971472855838799117.bam STRATEGY=Chained RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:21 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:21 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:21 DownsampleSam Kept 10000 out of 20000 reads (50.00%). INFO 2024-07-02 11:57:21 DownsampleSam Kept 10000 out of 20000 reads (50.00%). Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:21 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:57:21 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:21 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:21 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:21 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1]) STANDARD_ERROR INFO 2024-07-02 11:57:21 DownsampleSam Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam7971472855838799117.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13417749872730142750.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam7971472855838799117.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13417749872730142750.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:21.938 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:21.938 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:21.938 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:21.938 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:21.938 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:21.938 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:21.938 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:21.938 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:21 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam7971472855838799117.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13417749872730142750.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:21 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam7971472855838799117.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13417749872730142750.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:22 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:22 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:22 DownsampleSam Kept 5000 out of 10000 reads (50.00%). INFO 2024-07-02 11:57:22 DownsampleSam Kept 5000 out of 10000 reads (50.00%). Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:22 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:22 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:22 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:22 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:22 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1]) STANDARD_ERROR INFO 2024-07-02 11:57:22 DownsampleSam Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13417749872730142750.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16159742911289868759.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13417749872730142750.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16159742911289868759.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:22.251 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:22.251 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:22.251 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:22.251 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:22.251 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:22.251 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:22.251 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:22.251 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:22 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13417749872730142750.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16159742911289868759.bam STRATEGY=ConstantMemory RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:22 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13417749872730142750.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16159742911289868759.bam STRATEGY=ConstantMemory RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:22 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:22 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:22 DownsampleSam Kept 2544 out of 5000 reads (50.88%). INFO 2024-07-02 11:57:22 DownsampleSam Kept 2544 out of 5000 reads (50.88%). Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:22 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:22 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:22 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:22 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:22 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1]) STANDARD_ERROR INFO 2024-07-02 11:57:22 DownsampleSam Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16159742911289868759.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam18159382611248317774.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16159742911289868759.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam18159382611248317774.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:22.491 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:22.491 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:22.491 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:22.491 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:22.491 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:22.491 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:22.491 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:22.491 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:22 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16159742911289868759.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam18159382611248317774.bam STRATEGY=HighAccuracy RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:22 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16159742911289868759.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam18159382611248317774.bam STRATEGY=HighAccuracy RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:22 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:22 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:22 DownsampleSam Kept 1272 out of 2544 reads (50.00%). INFO 2024-07-02 11:57:22 DownsampleSam Kept 1272 out of 2544 reads (50.00%). Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:22 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:22 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:22 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:22 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:22 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1]) STANDARD_ERROR INFO 2024-07-02 11:57:22 DownsampleSam Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam18159382611248317774.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16411428513356377738.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam18159382611248317774.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam16411428513356377738.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:22.674 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:22.674 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:22.674 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:22.674 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:22.674 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:22.674 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:22.674 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:22.674 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:22 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam18159382611248317774.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16411428513356377738.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:22 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam18159382611248317774.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam16411428513356377738.bam STRATEGY=ConstantMemory RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:22 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:57:22 DownsampleSam DownsampleSam has been run before on this data with the seed -1155869325. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:22 DownsampleSam RANDOM_SEED has been changed to -1155869325. WARNING 2024-07-02 11:57:22 DownsampleSam RANDOM_SEED has been changed to -1155869325. Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:22 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:22 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:22 DownsampleSam Kept 630 out of 1272 reads (49.53%). INFO 2024-07-02 11:57:22 DownsampleSam Kept 630 out of 1272 reads (49.53%). Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:22 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:22 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:22 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:22 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[34]([Chained, HighAccuracy, ConstantMemory, HighAccuracy, ConstantMemory], [0, 1, 2, 0, 1]) STANDARD_OUT No errors found Running Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:22 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2]) STANDARD_ERROR INFO 2024-07-02 11:57:22 DownsampleSam Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13751576571438546251.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13751576571438546251.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:22.742 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:22.742 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:22.742 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:22.742 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:22.742 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:22.742 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:22.742 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:22.742 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:22 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13751576571438546251.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:22 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6759554851736902246.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13751576571438546251.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:22 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:22 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:22 DownsampleSam Kept 10000 out of 20000 reads (50.00%). INFO 2024-07-02 11:57:22 DownsampleSam Kept 10000 out of 20000 reads (50.00%). Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:22 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:22 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:22 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:22 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:23 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2]) STANDARD_ERROR INFO 2024-07-02 11:57:23 DownsampleSam Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13751576571438546251.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1081190975914680209.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam13751576571438546251.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1081190975914680209.bam -PROBABILITY 0.5 -STRATEGY HighAccuracy -RANDOM_SEED 1 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:23.052 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:23.052 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:23.052 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:23.052 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:23.052 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:23.052 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:23.052 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:23.052 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:23 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13751576571438546251.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1081190975914680209.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:23 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam13751576571438546251.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1081190975914680209.bam STRATEGY=HighAccuracy RANDOM_SEED=1 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:23 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:23 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:23 DownsampleSam Kept 5000 out of 10000 reads (50.00%). INFO 2024-07-02 11:57:23 DownsampleSam Kept 5000 out of 10000 reads (50.00%). Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:23 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:23 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:23 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:23 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:23 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2]) STANDARD_ERROR INFO 2024-07-02 11:57:23 DownsampleSam Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1081190975914680209.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam4235650315021711806.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam1081190975914680209.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam4235650315021711806.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:23.248 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:23.248 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:23.248 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:23.248 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:23.248 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:23.248 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:23.248 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:23.248 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:23 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1081190975914680209.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam4235650315021711806.bam STRATEGY=ConstantMemory RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:23 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam1081190975914680209.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam4235650315021711806.bam STRATEGY=ConstantMemory RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:23 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:23 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:23 DownsampleSam Kept 2434 out of 5000 reads (48.68%). INFO 2024-07-02 11:57:23 DownsampleSam Kept 2434 out of 5000 reads (48.68%). Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:23 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:23 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:23 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:23 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:23 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2]) STANDARD_ERROR INFO 2024-07-02 11:57:23 DownsampleSam Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam4235650315021711806.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam17348282032758171790.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam4235650315021711806.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam17348282032758171790.bam -PROBABILITY 0.5 -STRATEGY ConstantMemory -RANDOM_SEED 0 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:23.474 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:23.474 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:23.474 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:23.474 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:23.474 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:23.474 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:23.474 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:23.474 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:23 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam4235650315021711806.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam17348282032758171790.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:23 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam4235650315021711806.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam17348282032758171790.bam STRATEGY=ConstantMemory RANDOM_SEED=0 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:23 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:23 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:23 DownsampleSam Kept 1256 out of 2434 reads (51.60%). INFO 2024-07-02 11:57:23 DownsampleSam Kept 1256 out of 2434 reads (51.60%). Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:23 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:23 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:23 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:23 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2]) STANDARD_OUT No errors found Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:23 DownsampleSam Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2]) STANDARD_ERROR INFO 2024-07-02 11:57:23 DownsampleSam Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam17348282032758171790.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6108957638143818996.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 2 -CREATE_INDEX true ********** DownsampleSam -INPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam17348282032758171790.bam -OUTPUT /tmp/ds_test7972657326771054700Downsampling/DownsampleSam6108957638143818996.bam -PROBABILITY 0.5 -STRATEGY Chained -RANDOM_SEED 2 -CREATE_INDEX true Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:23.723 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:23.723 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:23.724 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:23.724 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:23.724 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:23.724 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: 11:57:23.724 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:23.724 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:23 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam17348282032758171790.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6108957638143818996.bam STRATEGY=Chained RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:23 GMT+14:00 2024] DownsampleSam INPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam17348282032758171790.bam OUTPUT=/tmp/ds_test7972657326771054700Downsampling/DownsampleSam6108957638143818996.bam STRATEGY=Chained RANDOM_SEED=2 PROBABILITY=0.5 CREATE_INDEX=true ACCURACY=1.0E-4 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:23 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. WARNING 2024-07-02 11:57:23 DownsampleSam DownsampleSam has been run before on this data with the seed -1154715079. The random seed will be changed to avoid using the same seed as previously. Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:23 DownsampleSam RANDOM_SEED has been changed to -1154715079. WARNING 2024-07-02 11:57:23 DownsampleSam RANDOM_SEED has been changed to -1154715079. Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:23 DownsampleSam Finished downsampling. INFO 2024-07-02 11:57:23 DownsampleSam Finished downsampling. Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: INFO 2024-07-02 11:57:23 DownsampleSam Kept 614 out of 1256 reads (48.89%). INFO 2024-07-02 11:57:23 DownsampleSam Kept 614 out of 1256 reads (48.89%). Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: [Tue Jul 02 11:57:23 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:23 GMT+14:00 2024] picard.sam.DownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: WARNING 2024-07-02 11:57:23 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 11:57:23 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2])(picard.sam.DownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.DownsampleSamTest.testRepeatedDownsampling[35]([HighAccuracy, HighAccuracy, ConstantMemory, ConstantMemory, Chained], [1, 1, 2, 0, 2]) STANDARD_OUT No errors found Running Test: Test method infiniteLoopFromGithub_1146(picard.sam.DuplicationMetricsTest) Running Test: Test method testEmptyDuplicationMetricsDerivation(picard.sam.DuplicationMetricsTest) Running Test: Test method testMerge[0](LIBRARY LIBRARY UNPAIRED_READS_EXAMINED 0 READ_PAIRS_EXAMINED 0 SECONDARY_OR_SUPPLEMENTARY_RDS 0 UNMAPPED_READS 0 UNPAIRED_READ_DUPLICATES 0 READ_PAIR_DUPLICATES 0 READ_PAIR_OPTICAL_DUPLICATES 0 PERCENT_DUPLICATION 0 ESTIMATED_LIBRARY_SIZE , LIBRARY LIBRARY UNPAIRED_READS_EXAMINED 0 READ_PAIRS_EXAMINED 0 SECONDARY_OR_SUPPLEMENTARY_RDS 0 UNMAPPED_READS 0 UNPAIRED_READ_DUPLICATES 0 READ_PAIR_DUPLICATES 0 READ_PAIR_OPTICAL_DUPLICATES 0 PERCENT_DUPLICATION 0 ESTIMATED_LIBRARY_SIZE , LIBRARY LIBRARY UNPAIRED_READS_EXAMINED 0 READ_PAIRS_EXAMINED 0 SECONDARY_OR_SUPPLEMENTARY_RDS 0 UNMAPPED_READS 0 UNPAIRED_READ_DUPLICATES 0 READ_PAIR_DUPLICATES 0 READ_PAIR_OPTICAL_DUPLICATES 0 PERCENT_DUPLICATION 0 ESTIMATED_LIBRARY_SIZE )(picard.sam.DuplicationMetricsTest) Running Test: Test method testMerge[1](LIBRARY LIBRARY UNPAIRED_READS_EXAMINED 0 READ_PAIRS_EXAMINED 0 SECONDARY_OR_SUPPLEMENTARY_RDS 0 UNMAPPED_READS 0 UNPAIRED_READ_DUPLICATES 0 READ_PAIR_DUPLICATES 0 READ_PAIR_OPTICAL_DUPLICATES 0 PERCENT_DUPLICATION 0 ESTIMATED_LIBRARY_SIZE , LIBRARY LIBRARY UNPAIRED_READS_EXAMINED 1000 READ_PAIRS_EXAMINED 1000 SECONDARY_OR_SUPPLEMENTARY_RDS 1 UNMAPPED_READS 10 UNPAIRED_READ_DUPLICATES 100 READ_PAIR_DUPLICATES 110 READ_PAIR_OPTICAL_DUPLICATES 10 PERCENT_DUPLICATION 0.106667 ESTIMATED_LIBRARY_SIZE 4564 , LIBRARY LIBRARY UNPAIRED_READS_EXAMINED 1000 READ_PAIRS_EXAMINED 1000 SECONDARY_OR_SUPPLEMENTARY_RDS 1 UNMAPPED_READS 10 UNPAIRED_READ_DUPLICATES 100 READ_PAIR_DUPLICATES 110 READ_PAIR_OPTICAL_DUPLICATES 10 PERCENT_DUPLICATION 0.106667 ESTIMATED_LIBRARY_SIZE 4564 )(picard.sam.DuplicationMetricsTest) Running Test: Test method testMerge[2](LIBRARY LIBRARY UNPAIRED_READS_EXAMINED 1000 READ_PAIRS_EXAMINED 1000 SECONDARY_OR_SUPPLEMENTARY_RDS 1 UNMAPPED_READS 10 UNPAIRED_READ_DUPLICATES 100 READ_PAIR_DUPLICATES 110 READ_PAIR_OPTICAL_DUPLICATES 10 PERCENT_DUPLICATION 0.106667 ESTIMATED_LIBRARY_SIZE 4564 , LIBRARY LIBRARY UNPAIRED_READS_EXAMINED 0 READ_PAIRS_EXAMINED 0 SECONDARY_OR_SUPPLEMENTARY_RDS 0 UNMAPPED_READS 0 UNPAIRED_READ_DUPLICATES 0 READ_PAIR_DUPLICATES 0 READ_PAIR_OPTICAL_DUPLICATES 0 PERCENT_DUPLICATION 0 ESTIMATED_LIBRARY_SIZE , LIBRARY LIBRARY UNPAIRED_READS_EXAMINED 1000 READ_PAIRS_EXAMINED 1000 SECONDARY_OR_SUPPLEMENTARY_RDS 1 UNMAPPED_READS 10 UNPAIRED_READ_DUPLICATES 100 READ_PAIR_DUPLICATES 110 READ_PAIR_OPTICAL_DUPLICATES 10 PERCENT_DUPLICATION 0.106667 ESTIMATED_LIBRARY_SIZE 4564 )(picard.sam.DuplicationMetricsTest) Running Test: Test method testMerge[3](LIBRARY LIBRARY UNPAIRED_READS_EXAMINED 1000 READ_PAIRS_EXAMINED 1000 SECONDARY_OR_SUPPLEMENTARY_RDS 1 UNMAPPED_READS 10 UNPAIRED_READ_DUPLICATES 100 READ_PAIR_DUPLICATES 110 READ_PAIR_OPTICAL_DUPLICATES 10 PERCENT_DUPLICATION 0.106667 ESTIMATED_LIBRARY_SIZE 4564 , LIBRARY LIBRARY UNPAIRED_READS_EXAMINED 1000 READ_PAIRS_EXAMINED 1000 SECONDARY_OR_SUPPLEMENTARY_RDS 1 UNMAPPED_READS 10 UNPAIRED_READ_DUPLICATES 100 READ_PAIR_DUPLICATES 110 READ_PAIR_OPTICAL_DUPLICATES 10 PERCENT_DUPLICATION 0.106667 ESTIMATED_LIBRARY_SIZE 4564 , LIBRARY LIBRARY UNPAIRED_READS_EXAMINED 2000 READ_PAIRS_EXAMINED 2000 SECONDARY_OR_SUPPLEMENTARY_RDS 2 UNMAPPED_READS 20 UNPAIRED_READ_DUPLICATES 200 READ_PAIR_DUPLICATES 220 READ_PAIR_OPTICAL_DUPLICATES 20 PERCENT_DUPLICATION 0.106667 ESTIMATED_LIBRARY_SIZE 9129 )(picard.sam.DuplicationMetricsTest) Running Test: Test method testMerge[4](LIBRARY LIBRARY UNPAIRED_READS_EXAMINED 1000 READ_PAIRS_EXAMINED 1000 SECONDARY_OR_SUPPLEMENTARY_RDS 1 UNMAPPED_READS 10 UNPAIRED_READ_DUPLICATES 100 READ_PAIR_DUPLICATES 110 READ_PAIR_OPTICAL_DUPLICATES 10 PERCENT_DUPLICATION 0.106667 ESTIMATED_LIBRARY_SIZE 4564 , LIBRARY LIBRARY UNPAIRED_READS_EXAMINED 2000 READ_PAIRS_EXAMINED 2000 SECONDARY_OR_SUPPLEMENTARY_RDS 2 UNMAPPED_READS 20 UNPAIRED_READ_DUPLICATES 200 READ_PAIR_DUPLICATES 220 READ_PAIR_OPTICAL_DUPLICATES 20 PERCENT_DUPLICATION 0.106667 ESTIMATED_LIBRARY_SIZE 9129 , LIBRARY LIBRARY UNPAIRED_READS_EXAMINED 3000 READ_PAIRS_EXAMINED 3000 SECONDARY_OR_SUPPLEMENTARY_RDS 3 UNMAPPED_READS 30 UNPAIRED_READ_DUPLICATES 300 READ_PAIR_DUPLICATES 330 READ_PAIR_OPTICAL_DUPLICATES 30 PERCENT_DUPLICATION 0.106667 ESTIMATED_LIBRARY_SIZE 13693 )(picard.sam.DuplicationMetricsTest) Running Test: Test method levenshteinDistanceTest[0](one, ont, 3, 1)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceTest[1](o-e, oe-, 3, 1)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceTest[2](on-e, one-, 3, 1)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceTest[3](o-ne, one-, 3, 1)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceTest[4](o-nce, once-, 3, 1)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceTest[5](on-ce, once-, 3, 1)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceTest[6](on-ce, onc-e, 3, 2)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceTest[7](n-ce, nc-e, 3, 2)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceTest[8](, , 2, 0)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceTest[9](ABCA-CABC, ABCACABC-, 2, 1)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceTest[10](BC AB- ABC, -BC AB ABC, 2, 2)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceTest[11](HELLO!, HELLO!, 2, 0)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceTest[12](very large distances are not measured well, so this should return the threshold plus 1, 5, 6)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceTest[13](-ELLO, ELLO-, 3, 1)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceTest[14](ont, one, 3, 1)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceTest[15](oe-, o-e, 3, 1)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceTest[16](one-, on-e, 3, 1)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceTest[17](one-, o-ne, 3, 1)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceTest[18](once-, o-nce, 3, 1)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceTest[19](once-, on-ce, 3, 1)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceTest[20](onc-e, on-ce, 3, 2)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceTest[21](nc-e, n-ce, 3, 2)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceTest[22](, , 2, 0)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceTest[23](ABCACABC-, ABCA-CABC, 2, 1)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceTest[24](-BC AB ABC, BC AB- ABC, 2, 2)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceTest[25](HELLO!, HELLO!, 2, 0)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceTest[26](so this should return the threshold plus 1, very large distances are not measured well, 5, 6)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceTest[27](ELLO-, -ELLO, 3, 1)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceWithNocallsTest[0](one, .ne, 0)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceWithNocallsTest[1](any, ..., 0)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceWithNocallsTest[2](hello, hell., 0)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceWithNocallsTest[3](TCTGCAAGGCCAGAAG, T.TGCAAGGCCAGAAG, 0)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceWithNocallsTest[4](CGCCTTCC, C.CCcTCC, 1)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceWithNocallsTest[5](AATCGCTG, A.cCGCTG, 1)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceWithNocallsTest[6](goodbye--, good.bye-, 1)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceWithNocallsTest[7](goodddbye, good.bye-, 1)(picard.util.EditDistanceQueriesTest) Running Test: Test method levenshteinDistanceWithNocallsTest[8](--goodbye, good.bye-, 3)(picard.util.EditDistanceQueriesTest) Running Test: Test method testFillHistogram[0](picard.sam.markduplicates.ElcHashBasedDuplicatesFinder@704eddce, {}, {}, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@1c55ddcb, [], 1, 0, 0)(picard.sam.markduplicates.ElcHashBasedDuplicatesFinderTest) Running Test: Test method testFillHistogram[1](picard.sam.markduplicates.ElcHashBasedDuplicatesFinder@704eddce, {}, {}, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@3586671, [picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@5fe6b79, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@37f75588, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@5801be38, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@18aa20a7, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@6ef92568, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@63af762a, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@368ae419, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@7f6c5577, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@5899ed97, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@401fde88], 11, 0, 0)(picard.sam.markduplicates.ElcHashBasedDuplicatesFinderTest) Running Test: Test method testFillHistogram[2](picard.sam.markduplicates.ElcHashBasedDuplicatesFinder@704eddce, {}, {}, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@3c0e7e1e, [picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@2b6cc95d, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@15b9b926, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@166bda9f, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@595aa8c2, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@1431b495, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@4c995fbc, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@46ecb92, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@87e6f65, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@11f2e7e3, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@17103ede], 11, 11, 10)(picard.sam.markduplicates.ElcHashBasedDuplicatesFinderTest) Running Test: Test method testSearchDuplicates[0](picard.sam.markduplicates.ElcHashBasedDuplicatesFinder@704eddce, {}, {}, [picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@1eae1b7d], 1, 0, 0)(picard.sam.markduplicates.ElcHashBasedDuplicatesFinderTest) Running Test: Test method testSearchDuplicates[1](picard.sam.markduplicates.ElcHashBasedDuplicatesFinder@704eddce, {}, {}, [picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@690d9262, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@71609cd, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@36172311, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@10a96cba, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@15b2724f, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@22dd5955, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@2d5de9b4, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@76ca9c19, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@70ecb885, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@38b3503c], 10, 0, 0)(picard.sam.markduplicates.ElcHashBasedDuplicatesFinderTest) Running Test: Test method testSearchDuplicates[2](picard.sam.markduplicates.ElcHashBasedDuplicatesFinder@704eddce, {}, {}, [picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@58696fd6, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@4d54ccce, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@6fc457e8, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@1d21fb71, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@ea520dc, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@65fcaf7a, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@28cacf3a, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@3aa24321, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@1d263769, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@1d21dcc8], 9, 0, 0)(picard.sam.markduplicates.ElcHashBasedDuplicatesFinderTest) Running Test: Test method testSearchDuplicates[3](picard.sam.markduplicates.ElcHashBasedDuplicatesFinder@704eddce, {}, {}, [picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@4bff8f5e, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@67ce7437, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@741a239a, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@746c606b, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@43de94c7, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@57a53f47, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@7206c0da, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@657e89c9, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@52b1410d, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@2c90131b], 10, 10, 9)(picard.sam.markduplicates.ElcHashBasedDuplicatesFinderTest) Running Test: Test method testSearchDuplicates[4](picard.sam.markduplicates.ElcHashBasedDuplicatesFinder@704eddce, {}, {}, [picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@7975ea41, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@2114654b, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@db0a2b9, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@459ecb52, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@13ef1642, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@11530749, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@19fecab0, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@2a095686, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@41bf0883, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@485f36b2], 9, 9, 8)(picard.sam.markduplicates.ElcHashBasedDuplicatesFinderTest) Running Test: Test method testFillHistogram[0](picard.sam.markduplicates.ElcIdenticalBasesDuplicatesFinder@7e04e22b, {}, {}, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@4f5fb1ff, [], 1, 0, 0)(picard.sam.markduplicates.ElcIdenticalBasesDuplicatesFinderTest) Running Test: Test method testFillHistogram[1](picard.sam.markduplicates.ElcIdenticalBasesDuplicatesFinder@7e04e22b, {}, {}, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@4174cc19, [picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@18b87ba6, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@2adae107, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@60e398d2, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@79094d3, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@5c2eaacc, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@2181aa97, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@5d58837d, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@5e6da209, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@773c0bc2, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@5bc5d2a0], 11, 0, 0)(picard.sam.markduplicates.ElcIdenticalBasesDuplicatesFinderTest) Running Test: Test method testFillHistogram[2](picard.sam.markduplicates.ElcIdenticalBasesDuplicatesFinder@7e04e22b, {}, {}, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@71516e7e, [picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@6624198d, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@1381973b, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@2e2d8514, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@54f52c31, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@125bbf53, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@dfcca6c, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@4f3bfbe2, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@3252c290, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@7d3c52ae, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@16f858cf], 11, 11, 10)(picard.sam.markduplicates.ElcIdenticalBasesDuplicatesFinderTest) Running Test: Test method testSearchDuplicates[0](picard.sam.markduplicates.ElcIdenticalBasesDuplicatesFinder@7e04e22b, {}, {}, [picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@22ee411a], 1, 0, 0)(picard.sam.markduplicates.ElcIdenticalBasesDuplicatesFinderTest) Running Test: Test method testSearchDuplicates[1](picard.sam.markduplicates.ElcIdenticalBasesDuplicatesFinder@7e04e22b, {}, {}, [picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@6932c79f, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@df2633d, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@5dc41508, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@2611a6fd, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@5960939f, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@4715f805, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@3a84d9ba, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@1109b659, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@4ca8338c, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@24152fcc], 10, 0, 0)(picard.sam.markduplicates.ElcIdenticalBasesDuplicatesFinderTest) Running Test: Test method testSearchDuplicates[2](picard.sam.markduplicates.ElcIdenticalBasesDuplicatesFinder@7e04e22b, {}, {}, [picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@6427a9d2, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@699ec289, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@64f8fb39, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@5fdcebc8, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@6ecb0d8, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@1979b006, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@3a7ba123, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@2418f0f, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@614885ef, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@3565e040], 10, 10, 9)(picard.sam.markduplicates.ElcIdenticalBasesDuplicatesFinderTest) Running Test: Test method testSearchDuplicates[3](picard.sam.markduplicates.ElcIdenticalBasesDuplicatesFinder@7e04e22b, {}, {}, [picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@5c47f9d0, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@7985684a, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@63f8f0da, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@3030ea4e, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@53da0ce1, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@1cfe9e8, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@2595b72b, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@12c04b4d, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@117ef0f0, picard.sam.markduplicates.EstimateLibraryComplexity$PairedReadSequence@6f80db9e], 9, 9, 8)(picard.sam.markduplicates.ElcIdenticalBasesDuplicatesFinderTest) Running Test: Test method testDefaultMinGroupCount[0](dupes.sam, 0, 0)(picard.sam.markduplicates.EstimateLibraryComplexityTest) Test: Test method testDefaultMinGroupCount[0](dupes.sam, 0, 0)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:24 EstimateLibraryComplexity Gradle suite > Gradle test > picard.sam.markduplicates.EstimateLibraryComplexityTest.testDefaultMinGroupCount[0](dupes.sam, 0, 0) STANDARD_ERROR INFO 2024-07-02 11:57:24 EstimateLibraryComplexity Test: Test method testDefaultMinGroupCount[0](dupes.sam, 0, 0)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testDefaultMinGroupCount[0](dupes.sam, 0, 0)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDefaultMinGroupCount[0](dupes.sam, 0, 0)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testDefaultMinGroupCount[0](dupes.sam, 0, 0)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDefaultMinGroupCount[0](dupes.sam, 0, 0)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDefaultMinGroupCount[0](dupes.sam, 0, 0)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testDefaultMinGroupCount[0](dupes.sam, 0, 0)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDefaultMinGroupCount[0](dupes.sam, 0, 0)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testDefaultMinGroupCount[0](dupes.sam, 0, 0)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** EstimateLibraryComplexity -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/dupes.sam -OUTPUT /tmp/estimateLibraryComplexity11896690183748873970.els_metrics ********** EstimateLibraryComplexity -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/dupes.sam -OUTPUT /tmp/estimateLibraryComplexity11896690183748873970.els_metrics Test: Test method testDefaultMinGroupCount[0](dupes.sam, 0, 0)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testDefaultMinGroupCount[0](dupes.sam, 0, 0)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testDefaultMinGroupCount[0](dupes.sam, 0, 0)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testDefaultMinGroupCount[0](dupes.sam, 0, 0)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:24.081 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:24.081 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDefaultMinGroupCount[0](dupes.sam, 0, 0)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:24.081 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:24.081 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDefaultMinGroupCount[0](dupes.sam, 0, 0)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:24.081 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:24.081 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDefaultMinGroupCount[0](dupes.sam, 0, 0)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:24.081 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:24.081 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDefaultMinGroupCount[0](dupes.sam, 0, 0)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:24 GMT+14:00 2024] EstimateLibraryComplexity INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/dupes.sam] OUTPUT=/tmp/estimateLibraryComplexity11896690183748873970.els_metrics MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 MAX_READ_LENGTH=0 MIN_GROUP_COUNT=2 READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:24 GMT+14:00 2024] EstimateLibraryComplexity INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/dupes.sam] OUTPUT=/tmp/estimateLibraryComplexity11896690183748873970.els_metrics MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 MAX_READ_LENGTH=0 MIN_GROUP_COUNT=2 READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDefaultMinGroupCount[0](dupes.sam, 0, 0)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDefaultMinGroupCount[0](dupes.sam, 0, 0)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:24 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting. INFO 2024-07-02 11:57:24 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting. Test: Test method testDefaultMinGroupCount[0](dupes.sam, 0, 0)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:24 EstimateLibraryComplexity Finished reading - read 4 records - moving on to scanning for duplicates. INFO 2024-07-02 11:57:24 EstimateLibraryComplexity Finished reading - read 4 records - moving on to scanning for duplicates. Test: Test method testDefaultMinGroupCount[0](dupes.sam, 0, 0)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:24 GMT+14:00 2024] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:24 GMT+14:00 2024] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes. Test: Test method testDefaultMinGroupCount[0](dupes.sam, 0, 0)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testDefaultMinGroupCount[1](big_dupes.sam, 8, 497)(picard.sam.markduplicates.EstimateLibraryComplexityTest) Test: Test method testDefaultMinGroupCount[1](big_dupes.sam, 8, 497)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:24 EstimateLibraryComplexity Gradle suite > Gradle test > picard.sam.markduplicates.EstimateLibraryComplexityTest.testDefaultMinGroupCount[1](big_dupes.sam, 8, 497) STANDARD_ERROR INFO 2024-07-02 11:57:24 EstimateLibraryComplexity Test: Test method testDefaultMinGroupCount[1](big_dupes.sam, 8, 497)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testDefaultMinGroupCount[1](big_dupes.sam, 8, 497)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDefaultMinGroupCount[1](big_dupes.sam, 8, 497)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testDefaultMinGroupCount[1](big_dupes.sam, 8, 497)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDefaultMinGroupCount[1](big_dupes.sam, 8, 497)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDefaultMinGroupCount[1](big_dupes.sam, 8, 497)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testDefaultMinGroupCount[1](big_dupes.sam, 8, 497)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDefaultMinGroupCount[1](big_dupes.sam, 8, 497)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testDefaultMinGroupCount[1](big_dupes.sam, 8, 497)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** EstimateLibraryComplexity -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/big_dupes.sam -OUTPUT /tmp/estimateLibraryComplexity14100200855208115012.els_metrics ********** EstimateLibraryComplexity -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/big_dupes.sam -OUTPUT /tmp/estimateLibraryComplexity14100200855208115012.els_metrics Test: Test method testDefaultMinGroupCount[1](big_dupes.sam, 8, 497)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testDefaultMinGroupCount[1](big_dupes.sam, 8, 497)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testDefaultMinGroupCount[1](big_dupes.sam, 8, 497)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testDefaultMinGroupCount[1](big_dupes.sam, 8, 497)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:24.221 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:24.221 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDefaultMinGroupCount[1](big_dupes.sam, 8, 497)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:24.237 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:24.237 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDefaultMinGroupCount[1](big_dupes.sam, 8, 497)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:24.237 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:24.237 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDefaultMinGroupCount[1](big_dupes.sam, 8, 497)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:24.237 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:24.237 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDefaultMinGroupCount[1](big_dupes.sam, 8, 497)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:24 GMT+14:00 2024] EstimateLibraryComplexity INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/big_dupes.sam] OUTPUT=/tmp/estimateLibraryComplexity14100200855208115012.els_metrics MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 MAX_READ_LENGTH=0 MIN_GROUP_COUNT=2 READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:24 GMT+14:00 2024] EstimateLibraryComplexity INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/big_dupes.sam] OUTPUT=/tmp/estimateLibraryComplexity14100200855208115012.els_metrics MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 MAX_READ_LENGTH=0 MIN_GROUP_COUNT=2 READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDefaultMinGroupCount[1](big_dupes.sam, 8, 497)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDefaultMinGroupCount[1](big_dupes.sam, 8, 497)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:24 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting. INFO 2024-07-02 11:57:24 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting. Test: Test method testDefaultMinGroupCount[1](big_dupes.sam, 8, 497)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: WARNING 2024-07-02 11:57:24 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name 'H06HDADXX130110:2:1101:10781:2344:1984'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. WARNING 2024-07-02 11:57:24 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name 'H06HDADXX130110:2:1101:10781:2344:1984'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. Test: Test method testDefaultMinGroupCount[1](big_dupes.sam, 8, 497)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:24 EstimateLibraryComplexity Finished reading - read 1000 records - moving on to scanning for duplicates. INFO 2024-07-02 11:57:24 EstimateLibraryComplexity Finished reading - read 1000 records - moving on to scanning for duplicates. Test: Test method testDefaultMinGroupCount[1](big_dupes.sam, 8, 497)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:25 GMT+14:00 2024] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:57:25 GMT+14:00 2024] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.02 minutes. Test: Test method testDefaultMinGroupCount[1](big_dupes.sam, 8, 497)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testMaxDiffRate[0](dupes.sam, 0, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) Test: Test method testMaxDiffRate[0](dupes.sam, 0, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:25 EstimateLibraryComplexity Gradle suite > Gradle test > picard.sam.markduplicates.EstimateLibraryComplexityTest.testMaxDiffRate[0](dupes.sam, 0, 2) STANDARD_ERROR INFO 2024-07-02 11:57:25 EstimateLibraryComplexity Test: Test method testMaxDiffRate[0](dupes.sam, 0, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testMaxDiffRate[0](dupes.sam, 0, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMaxDiffRate[0](dupes.sam, 0, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testMaxDiffRate[0](dupes.sam, 0, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMaxDiffRate[0](dupes.sam, 0, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMaxDiffRate[0](dupes.sam, 0, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testMaxDiffRate[0](dupes.sam, 0, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMaxDiffRate[0](dupes.sam, 0, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testMaxDiffRate[0](dupes.sam, 0, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** EstimateLibraryComplexity -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/dupes.sam -OUTPUT /tmp/estimateLibraryComplexity13817351645811390254.els_metrics -MAX_DIFF_RATE 0.0 -MIN_GROUP_COUNT 1 ********** EstimateLibraryComplexity -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/dupes.sam -OUTPUT /tmp/estimateLibraryComplexity13817351645811390254.els_metrics -MAX_DIFF_RATE 0.0 -MIN_GROUP_COUNT 1 Test: Test method testMaxDiffRate[0](dupes.sam, 0, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testMaxDiffRate[0](dupes.sam, 0, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testMaxDiffRate[0](dupes.sam, 0, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testMaxDiffRate[0](dupes.sam, 0, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:25.708 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:25.708 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMaxDiffRate[0](dupes.sam, 0, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:25.708 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:25.708 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMaxDiffRate[0](dupes.sam, 0, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:25.708 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:25.708 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMaxDiffRate[0](dupes.sam, 0, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:25.708 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:25.708 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMaxDiffRate[0](dupes.sam, 0, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:25 GMT+14:00 2024] EstimateLibraryComplexity INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/dupes.sam] OUTPUT=/tmp/estimateLibraryComplexity13817351645811390254.els_metrics MAX_DIFF_RATE=0.0 MIN_GROUP_COUNT=1 MIN_IDENTICAL_BASES=5 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 MAX_READ_LENGTH=0 READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:25 GMT+14:00 2024] EstimateLibraryComplexity INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/dupes.sam] OUTPUT=/tmp/estimateLibraryComplexity13817351645811390254.els_metrics MAX_DIFF_RATE=0.0 MIN_GROUP_COUNT=1 MIN_IDENTICAL_BASES=5 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 MAX_READ_LENGTH=0 READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMaxDiffRate[0](dupes.sam, 0, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMaxDiffRate[0](dupes.sam, 0, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:25 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting. INFO 2024-07-02 11:57:25 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting. Test: Test method testMaxDiffRate[0](dupes.sam, 0, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:25 EstimateLibraryComplexity Finished reading - read 4 records - moving on to scanning for duplicates. INFO 2024-07-02 11:57:25 EstimateLibraryComplexity Finished reading - read 4 records - moving on to scanning for duplicates. Test: Test method testMaxDiffRate[0](dupes.sam, 0, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:25 GMT+14:00 2024] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:25 GMT+14:00 2024] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes. Test: Test method testMaxDiffRate[0](dupes.sam, 0, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testMaxDiffRate[1](big_dupes.sam, 8, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) Test: Test method testMaxDiffRate[1](big_dupes.sam, 8, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:25 EstimateLibraryComplexity Gradle suite > Gradle test > picard.sam.markduplicates.EstimateLibraryComplexityTest.testMaxDiffRate[1](big_dupes.sam, 8, 500) STANDARD_ERROR INFO 2024-07-02 11:57:25 EstimateLibraryComplexity Test: Test method testMaxDiffRate[1](big_dupes.sam, 8, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testMaxDiffRate[1](big_dupes.sam, 8, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMaxDiffRate[1](big_dupes.sam, 8, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testMaxDiffRate[1](big_dupes.sam, 8, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMaxDiffRate[1](big_dupes.sam, 8, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMaxDiffRate[1](big_dupes.sam, 8, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testMaxDiffRate[1](big_dupes.sam, 8, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMaxDiffRate[1](big_dupes.sam, 8, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testMaxDiffRate[1](big_dupes.sam, 8, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** EstimateLibraryComplexity -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/big_dupes.sam -OUTPUT /tmp/estimateLibraryComplexity15741360447318819620.els_metrics -MAX_DIFF_RATE 0.0 -MIN_GROUP_COUNT 1 ********** EstimateLibraryComplexity -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/big_dupes.sam -OUTPUT /tmp/estimateLibraryComplexity15741360447318819620.els_metrics -MAX_DIFF_RATE 0.0 -MIN_GROUP_COUNT 1 Test: Test method testMaxDiffRate[1](big_dupes.sam, 8, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testMaxDiffRate[1](big_dupes.sam, 8, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testMaxDiffRate[1](big_dupes.sam, 8, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testMaxDiffRate[1](big_dupes.sam, 8, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:25.759 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:25.759 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMaxDiffRate[1](big_dupes.sam, 8, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:25.759 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:25.759 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMaxDiffRate[1](big_dupes.sam, 8, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:25.759 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:25.759 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMaxDiffRate[1](big_dupes.sam, 8, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:25.759 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:25.759 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMaxDiffRate[1](big_dupes.sam, 8, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:25 GMT+14:00 2024] EstimateLibraryComplexity INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/big_dupes.sam] OUTPUT=/tmp/estimateLibraryComplexity15741360447318819620.els_metrics MAX_DIFF_RATE=0.0 MIN_GROUP_COUNT=1 MIN_IDENTICAL_BASES=5 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 MAX_READ_LENGTH=0 READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:25 GMT+14:00 2024] EstimateLibraryComplexity INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/big_dupes.sam] OUTPUT=/tmp/estimateLibraryComplexity15741360447318819620.els_metrics MAX_DIFF_RATE=0.0 MIN_GROUP_COUNT=1 MIN_IDENTICAL_BASES=5 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 MAX_READ_LENGTH=0 READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMaxDiffRate[1](big_dupes.sam, 8, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMaxDiffRate[1](big_dupes.sam, 8, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:25 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting. INFO 2024-07-02 11:57:25 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting. Test: Test method testMaxDiffRate[1](big_dupes.sam, 8, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: WARNING 2024-07-02 11:57:25 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name 'H06HDADXX130110:2:1101:10781:2344:1984'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. WARNING 2024-07-02 11:57:25 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name 'H06HDADXX130110:2:1101:10781:2344:1984'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. Test: Test method testMaxDiffRate[1](big_dupes.sam, 8, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:25 EstimateLibraryComplexity Finished reading - read 1000 records - moving on to scanning for duplicates. INFO 2024-07-02 11:57:25 EstimateLibraryComplexity Finished reading - read 1000 records - moving on to scanning for duplicates. Test: Test method testMaxDiffRate[1](big_dupes.sam, 8, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:25 GMT+14:00 2024] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:25 GMT+14:00 2024] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes. Test: Test method testMaxDiffRate[1](big_dupes.sam, 8, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSimpleDuplicate[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) Test: Test method testSimpleDuplicate[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:25 EstimateLibraryComplexity Gradle suite > Gradle test > picard.sam.markduplicates.EstimateLibraryComplexityTest.testSimpleDuplicate[0](dupes.sam, 2, 2) STANDARD_ERROR INFO 2024-07-02 11:57:25 EstimateLibraryComplexity Test: Test method testSimpleDuplicate[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testSimpleDuplicate[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSimpleDuplicate[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testSimpleDuplicate[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSimpleDuplicate[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSimpleDuplicate[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testSimpleDuplicate[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSimpleDuplicate[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testSimpleDuplicate[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** EstimateLibraryComplexity -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/dupes.sam -OUTPUT /tmp/estimateLibraryComplexity18364758252020884331.els_metrics -MIN_GROUP_COUNT 1 ********** EstimateLibraryComplexity -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/dupes.sam -OUTPUT /tmp/estimateLibraryComplexity18364758252020884331.els_metrics -MIN_GROUP_COUNT 1 Test: Test method testSimpleDuplicate[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testSimpleDuplicate[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testSimpleDuplicate[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testSimpleDuplicate[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:25.875 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:25.875 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSimpleDuplicate[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:25.875 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:25.875 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSimpleDuplicate[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:25.875 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:25.875 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSimpleDuplicate[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:25.875 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:25.875 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSimpleDuplicate[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:25 GMT+14:00 2024] EstimateLibraryComplexity INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/dupes.sam] OUTPUT=/tmp/estimateLibraryComplexity18364758252020884331.els_metrics MIN_GROUP_COUNT=1 MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 MAX_READ_LENGTH=0 READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:25 GMT+14:00 2024] EstimateLibraryComplexity INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/dupes.sam] OUTPUT=/tmp/estimateLibraryComplexity18364758252020884331.els_metrics MIN_GROUP_COUNT=1 MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 MAX_READ_LENGTH=0 READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSimpleDuplicate[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSimpleDuplicate[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:25 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting. INFO 2024-07-02 11:57:25 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting. Test: Test method testSimpleDuplicate[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:25 EstimateLibraryComplexity Finished reading - read 4 records - moving on to scanning for duplicates. INFO 2024-07-02 11:57:25 EstimateLibraryComplexity Finished reading - read 4 records - moving on to scanning for duplicates. Test: Test method testSimpleDuplicate[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:25 GMT+14:00 2024] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:25 GMT+14:00 2024] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes. Test: Test method testSimpleDuplicate[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSimpleDuplicate[1](big_dupes.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) Test: Test method testSimpleDuplicate[1](big_dupes.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:25 EstimateLibraryComplexity Gradle suite > Gradle test > picard.sam.markduplicates.EstimateLibraryComplexityTest.testSimpleDuplicate[1](big_dupes.sam, 12, 500) STANDARD_ERROR INFO 2024-07-02 11:57:25 EstimateLibraryComplexity Test: Test method testSimpleDuplicate[1](big_dupes.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testSimpleDuplicate[1](big_dupes.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSimpleDuplicate[1](big_dupes.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testSimpleDuplicate[1](big_dupes.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSimpleDuplicate[1](big_dupes.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSimpleDuplicate[1](big_dupes.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testSimpleDuplicate[1](big_dupes.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSimpleDuplicate[1](big_dupes.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testSimpleDuplicate[1](big_dupes.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** EstimateLibraryComplexity -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/big_dupes.sam -OUTPUT /tmp/estimateLibraryComplexity8514874373709831665.els_metrics -MIN_GROUP_COUNT 1 ********** EstimateLibraryComplexity -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/big_dupes.sam -OUTPUT /tmp/estimateLibraryComplexity8514874373709831665.els_metrics -MIN_GROUP_COUNT 1 Test: Test method testSimpleDuplicate[1](big_dupes.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testSimpleDuplicate[1](big_dupes.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testSimpleDuplicate[1](big_dupes.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testSimpleDuplicate[1](big_dupes.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:25.922 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:25.922 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSimpleDuplicate[1](big_dupes.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:25.923 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:25.923 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSimpleDuplicate[1](big_dupes.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:25.923 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:25.923 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSimpleDuplicate[1](big_dupes.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:25.923 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:25.923 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSimpleDuplicate[1](big_dupes.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:25 GMT+14:00 2024] EstimateLibraryComplexity INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/big_dupes.sam] OUTPUT=/tmp/estimateLibraryComplexity8514874373709831665.els_metrics MIN_GROUP_COUNT=1 MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 MAX_READ_LENGTH=0 READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:25 GMT+14:00 2024] EstimateLibraryComplexity INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/big_dupes.sam] OUTPUT=/tmp/estimateLibraryComplexity8514874373709831665.els_metrics MIN_GROUP_COUNT=1 MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 MAX_READ_LENGTH=0 READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSimpleDuplicate[1](big_dupes.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSimpleDuplicate[1](big_dupes.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:25 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting. INFO 2024-07-02 11:57:25 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting. Test: Test method testSimpleDuplicate[1](big_dupes.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: WARNING 2024-07-02 11:57:25 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name 'H06HDADXX130110:2:1101:10781:2344:1984'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. WARNING 2024-07-02 11:57:25 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name 'H06HDADXX130110:2:1101:10781:2344:1984'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. Test: Test method testSimpleDuplicate[1](big_dupes.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:25 EstimateLibraryComplexity Finished reading - read 1000 records - moving on to scanning for duplicates. INFO 2024-07-02 11:57:25 EstimateLibraryComplexity Finished reading - read 1000 records - moving on to scanning for duplicates. Test: Test method testSimpleDuplicate[1](big_dupes.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:27 GMT+14:00 2024] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:57:27 GMT+14:00 2024] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.02 minutes. Test: Test method testSimpleDuplicate[1](big_dupes.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSimpleDuplicateWithMaxReadLength[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) Test: Test method testSimpleDuplicateWithMaxReadLength[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:27 EstimateLibraryComplexity Gradle suite > Gradle test > picard.sam.markduplicates.EstimateLibraryComplexityTest.testSimpleDuplicateWithMaxReadLength[0](dupes.sam, 2, 2) STANDARD_ERROR INFO 2024-07-02 11:57:27 EstimateLibraryComplexity Test: Test method testSimpleDuplicateWithMaxReadLength[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testSimpleDuplicateWithMaxReadLength[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSimpleDuplicateWithMaxReadLength[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testSimpleDuplicateWithMaxReadLength[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSimpleDuplicateWithMaxReadLength[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSimpleDuplicateWithMaxReadLength[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testSimpleDuplicateWithMaxReadLength[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSimpleDuplicateWithMaxReadLength[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testSimpleDuplicateWithMaxReadLength[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** EstimateLibraryComplexity -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/dupes.sam -OUTPUT /tmp/estimateLibraryComplexity13199926092028423840.els_metrics -MAX_DIFF_RATE 0.0 -MIN_GROUP_COUNT 1 -MAX_READ_LENGTH 10 ********** EstimateLibraryComplexity -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/dupes.sam -OUTPUT /tmp/estimateLibraryComplexity13199926092028423840.els_metrics -MAX_DIFF_RATE 0.0 -MIN_GROUP_COUNT 1 -MAX_READ_LENGTH 10 Test: Test method testSimpleDuplicateWithMaxReadLength[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testSimpleDuplicateWithMaxReadLength[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testSimpleDuplicateWithMaxReadLength[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testSimpleDuplicateWithMaxReadLength[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:27.266 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:27.266 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSimpleDuplicateWithMaxReadLength[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:27.266 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:27.266 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSimpleDuplicateWithMaxReadLength[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:27.267 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:27.267 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSimpleDuplicateWithMaxReadLength[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:27.267 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:27.267 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSimpleDuplicateWithMaxReadLength[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:27 GMT+14:00 2024] EstimateLibraryComplexity INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/dupes.sam] OUTPUT=/tmp/estimateLibraryComplexity13199926092028423840.els_metrics MAX_DIFF_RATE=0.0 MAX_READ_LENGTH=10 MIN_GROUP_COUNT=1 MIN_IDENTICAL_BASES=5 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:27 GMT+14:00 2024] EstimateLibraryComplexity INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/dupes.sam] OUTPUT=/tmp/estimateLibraryComplexity13199926092028423840.els_metrics MAX_DIFF_RATE=0.0 MAX_READ_LENGTH=10 MIN_GROUP_COUNT=1 MIN_IDENTICAL_BASES=5 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSimpleDuplicateWithMaxReadLength[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSimpleDuplicateWithMaxReadLength[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:27 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting. INFO 2024-07-02 11:57:27 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting. Test: Test method testSimpleDuplicateWithMaxReadLength[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:27 EstimateLibraryComplexity Finished reading - read 4 records - moving on to scanning for duplicates. INFO 2024-07-02 11:57:27 EstimateLibraryComplexity Finished reading - read 4 records - moving on to scanning for duplicates. Test: Test method testSimpleDuplicateWithMaxReadLength[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:27 GMT+14:00 2024] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:27 GMT+14:00 2024] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes. Test: Test method testSimpleDuplicateWithMaxReadLength[0](dupes.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSimpleDuplicateWithMaxReadLength[1](big_dupes.sam, 512, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) Test: Test method testSimpleDuplicateWithMaxReadLength[1](big_dupes.sam, 512, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:27 EstimateLibraryComplexity Gradle suite > Gradle test > picard.sam.markduplicates.EstimateLibraryComplexityTest.testSimpleDuplicateWithMaxReadLength[1](big_dupes.sam, 512, 500) STANDARD_ERROR INFO 2024-07-02 11:57:27 EstimateLibraryComplexity Test: Test method testSimpleDuplicateWithMaxReadLength[1](big_dupes.sam, 512, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testSimpleDuplicateWithMaxReadLength[1](big_dupes.sam, 512, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSimpleDuplicateWithMaxReadLength[1](big_dupes.sam, 512, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testSimpleDuplicateWithMaxReadLength[1](big_dupes.sam, 512, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSimpleDuplicateWithMaxReadLength[1](big_dupes.sam, 512, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSimpleDuplicateWithMaxReadLength[1](big_dupes.sam, 512, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testSimpleDuplicateWithMaxReadLength[1](big_dupes.sam, 512, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSimpleDuplicateWithMaxReadLength[1](big_dupes.sam, 512, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testSimpleDuplicateWithMaxReadLength[1](big_dupes.sam, 512, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** EstimateLibraryComplexity -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/big_dupes.sam -OUTPUT /tmp/estimateLibraryComplexity4304140797522969283.els_metrics -MAX_DIFF_RATE 0.0 -MIN_GROUP_COUNT 1 -MAX_READ_LENGTH 10 ********** EstimateLibraryComplexity -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/big_dupes.sam -OUTPUT /tmp/estimateLibraryComplexity4304140797522969283.els_metrics -MAX_DIFF_RATE 0.0 -MIN_GROUP_COUNT 1 -MAX_READ_LENGTH 10 Test: Test method testSimpleDuplicateWithMaxReadLength[1](big_dupes.sam, 512, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testSimpleDuplicateWithMaxReadLength[1](big_dupes.sam, 512, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testSimpleDuplicateWithMaxReadLength[1](big_dupes.sam, 512, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testSimpleDuplicateWithMaxReadLength[1](big_dupes.sam, 512, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:27.356 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:27.356 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSimpleDuplicateWithMaxReadLength[1](big_dupes.sam, 512, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:27.356 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:27.356 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSimpleDuplicateWithMaxReadLength[1](big_dupes.sam, 512, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:27.356 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:27.356 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSimpleDuplicateWithMaxReadLength[1](big_dupes.sam, 512, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:27.356 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:27.356 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSimpleDuplicateWithMaxReadLength[1](big_dupes.sam, 512, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:27 GMT+14:00 2024] EstimateLibraryComplexity INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/big_dupes.sam] OUTPUT=/tmp/estimateLibraryComplexity4304140797522969283.els_metrics MAX_DIFF_RATE=0.0 MAX_READ_LENGTH=10 MIN_GROUP_COUNT=1 MIN_IDENTICAL_BASES=5 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:27 GMT+14:00 2024] EstimateLibraryComplexity INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/big_dupes.sam] OUTPUT=/tmp/estimateLibraryComplexity4304140797522969283.els_metrics MAX_DIFF_RATE=0.0 MAX_READ_LENGTH=10 MIN_GROUP_COUNT=1 MIN_IDENTICAL_BASES=5 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSimpleDuplicateWithMaxReadLength[1](big_dupes.sam, 512, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSimpleDuplicateWithMaxReadLength[1](big_dupes.sam, 512, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:27 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting. INFO 2024-07-02 11:57:27 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting. Test: Test method testSimpleDuplicateWithMaxReadLength[1](big_dupes.sam, 512, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: WARNING 2024-07-02 11:57:27 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name 'H06HDADXX130110:2:1101:10781:2344:1984'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. WARNING 2024-07-02 11:57:27 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name 'H06HDADXX130110:2:1101:10781:2344:1984'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. Test: Test method testSimpleDuplicateWithMaxReadLength[1](big_dupes.sam, 512, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:27 EstimateLibraryComplexity Finished reading - read 1000 records - moving on to scanning for duplicates. INFO 2024-07-02 11:57:27 EstimateLibraryComplexity Finished reading - read 1000 records - moving on to scanning for duplicates. Test: Test method testSimpleDuplicateWithMaxReadLength[1](big_dupes.sam, 512, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:27 GMT+14:00 2024] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:27 GMT+14:00 2024] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes. Test: Test method testSimpleDuplicateWithMaxReadLength[1](big_dupes.sam, 512, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[0](dupes_with_sos.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[0](dupes_with_sos.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:27 EstimateLibraryComplexity Gradle suite > Gradle test > picard.sam.markduplicates.EstimateLibraryComplexityTest.testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[0](dupes_with_sos.sam, 2, 2) STANDARD_ERROR INFO 2024-07-02 11:57:27 EstimateLibraryComplexity Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[0](dupes_with_sos.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[0](dupes_with_sos.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[0](dupes_with_sos.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[0](dupes_with_sos.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[0](dupes_with_sos.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[0](dupes_with_sos.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[0](dupes_with_sos.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[0](dupes_with_sos.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[0](dupes_with_sos.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** EstimateLibraryComplexity -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/dupes_with_sos.sam -OUTPUT /tmp/estimateLibraryComplexity18006180158033364363.els_metrics -MIN_GROUP_COUNT 1 ********** EstimateLibraryComplexity -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/dupes_with_sos.sam -OUTPUT /tmp/estimateLibraryComplexity18006180158033364363.els_metrics -MIN_GROUP_COUNT 1 Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[0](dupes_with_sos.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[0](dupes_with_sos.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[0](dupes_with_sos.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[0](dupes_with_sos.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:27.546 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:27.546 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[0](dupes_with_sos.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:27.546 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:27.546 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[0](dupes_with_sos.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:27.546 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:27.546 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[0](dupes_with_sos.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:27.546 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:27.546 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[0](dupes_with_sos.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:27 GMT+14:00 2024] EstimateLibraryComplexity INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/dupes_with_sos.sam] OUTPUT=/tmp/estimateLibraryComplexity18006180158033364363.els_metrics MIN_GROUP_COUNT=1 MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 MAX_READ_LENGTH=0 READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:27 GMT+14:00 2024] EstimateLibraryComplexity INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/dupes_with_sos.sam] OUTPUT=/tmp/estimateLibraryComplexity18006180158033364363.els_metrics MIN_GROUP_COUNT=1 MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 MAX_READ_LENGTH=0 READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[0](dupes_with_sos.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[0](dupes_with_sos.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:27 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting. INFO 2024-07-02 11:57:27 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting. Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[0](dupes_with_sos.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:27 EstimateLibraryComplexity Finished reading - read 4 records - moving on to scanning for duplicates. INFO 2024-07-02 11:57:27 EstimateLibraryComplexity Finished reading - read 4 records - moving on to scanning for duplicates. Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[0](dupes_with_sos.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:27 GMT+14:00 2024] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:27 GMT+14:00 2024] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes. Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[0](dupes_with_sos.sam, 2, 2)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[1](big_dupes_with_sos.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[1](big_dupes_with_sos.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:27 EstimateLibraryComplexity Gradle suite > Gradle test > picard.sam.markduplicates.EstimateLibraryComplexityTest.testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[1](big_dupes_with_sos.sam, 12, 500) STANDARD_ERROR INFO 2024-07-02 11:57:27 EstimateLibraryComplexity Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[1](big_dupes_with_sos.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[1](big_dupes_with_sos.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[1](big_dupes_with_sos.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[1](big_dupes_with_sos.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[1](big_dupes_with_sos.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[1](big_dupes_with_sos.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[1](big_dupes_with_sos.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[1](big_dupes_with_sos.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[1](big_dupes_with_sos.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** EstimateLibraryComplexity -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/big_dupes_with_sos.sam -OUTPUT /tmp/estimateLibraryComplexity13037520652213322079.els_metrics -MIN_GROUP_COUNT 1 ********** EstimateLibraryComplexity -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/big_dupes_with_sos.sam -OUTPUT /tmp/estimateLibraryComplexity13037520652213322079.els_metrics -MIN_GROUP_COUNT 1 Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[1](big_dupes_with_sos.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: ********** ********** Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[1](big_dupes_with_sos.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[1](big_dupes_with_sos.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[1](big_dupes_with_sos.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:27.674 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:27.674 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[1](big_dupes_with_sos.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:27.675 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:27.675 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[1](big_dupes_with_sos.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:27.675 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:27.675 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[1](big_dupes_with_sos.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: 11:57:27.675 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:27.675 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[1](big_dupes_with_sos.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:27 GMT+14:00 2024] EstimateLibraryComplexity INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/big_dupes_with_sos.sam] OUTPUT=/tmp/estimateLibraryComplexity13037520652213322079.els_metrics MIN_GROUP_COUNT=1 MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 MAX_READ_LENGTH=0 READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:27 GMT+14:00 2024] EstimateLibraryComplexity INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/EstimateLibraryComplexity/big_dupes_with_sos.sam] OUTPUT=/tmp/estimateLibraryComplexity13037520652213322079.els_metrics MIN_GROUP_COUNT=1 MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 MAX_READ_LENGTH=0 READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[1](big_dupes_with_sos.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[1](big_dupes_with_sos.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:27 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting. INFO 2024-07-02 11:57:27 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting. Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[1](big_dupes_with_sos.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: WARNING 2024-07-02 11:57:27 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name 'H06HDADXX130110:2:1101:10781:2344:1984'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. WARNING 2024-07-02 11:57:27 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '' did not match read name 'H06HDADXX130110:2:1101:10781:2344:1984'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex. Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[1](big_dupes_with_sos.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: INFO 2024-07-02 11:57:27 EstimateLibraryComplexity Finished reading - read 1000 records - moving on to scanning for duplicates. INFO 2024-07-02 11:57:27 EstimateLibraryComplexity Finished reading - read 1000 records - moving on to scanning for duplicates. Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[1](big_dupes_with_sos.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: [Tue Jul 02 11:57:28 GMT+14:00 2024] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:57:28 GMT+14:00 2024] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.02 minutes. Test: Test method testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[1](big_dupes_with_sos.sam, 12, 500)(picard.sam.markduplicates.EstimateLibraryComplexityTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testBarcodeMatching(picard.illumina.ExtractIlluminaBarcodesTest) Test: Test method testBarcodeMatching(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:28 ExtractIlluminaBarcodes Gradle suite > Gradle test > picard.illumina.ExtractIlluminaBarcodesTest.testBarcodeMatching STANDARD_ERROR INFO 2024-07-02 11:57:28 ExtractIlluminaBarcodes Test: Test method testBarcodeMatching(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testBarcodeMatching(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBarcodeMatching(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testBarcodeMatching(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBarcodeMatching(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBarcodeMatching(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testBarcodeMatching(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBarcodeMatching(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testBarcodeMatching(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ExtractIlluminaBarcodes -BASECALLS_DIR /tmp/eib.3548948540762354946.tmp -LANE 1 -READ_STRUCTURE 25T8B25T -METRICS_FILE /tmp/eib.8698735777523268910.metrics -BARCODE CAACTCTC -BARCODE CAACTCTG -BARCODE ACAGGTAT -BARCODE GACCGTTG -BARCODE ATTATCAA -BARCODE TGCTGCTG -BARCODE AACAATGG -BARCODE TGTAATCA -BARCODE GCCGTCGA -BARCODE GTCCACAG -BARCODE TTGTCTAT -BARCODE GTGGAGAC -BARCODE TTGCAAAT ********** ExtractIlluminaBarcodes -BASECALLS_DIR /tmp/eib.3548948540762354946.tmp -LANE 1 -READ_STRUCTURE 25T8B25T -METRICS_FILE /tmp/eib.8698735777523268910.metrics -BARCODE CAACTCTC -BARCODE CAACTCTG -BARCODE ACAGGTAT -BARCODE GACCGTTG -BARCODE ATTATCAA -BARCODE TGCTGCTG -BARCODE AACAATGG -BARCODE TGTAATCA -BARCODE GCCGTCGA -BARCODE GTCCACAG -BARCODE TTGTCTAT -BARCODE GTGGAGAC -BARCODE TTGCAAAT Test: Test method testBarcodeMatching(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testBarcodeMatching(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testBarcodeMatching(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testBarcodeMatching(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:29.057 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:29.057 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBarcodeMatching(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:29.057 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:29.057 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBarcodeMatching(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:29.058 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:29.058 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBarcodeMatching(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:29.058 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:29.058 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBarcodeMatching(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:29 GMT+14:00 2024] ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib.3548948540762354946.tmp LANE=1 READ_STRUCTURE=25T8B25T BARCODE=[CAACTCTC, CAACTCTG, ACAGGTAT, GACCGTTG, ATTATCAA, TGCTGCTG, AACAATGG, TGTAATCA, GCCGTCGA, GTCCACAG, TTGTCTAT, GTGGAGAC, TTGCAAAT] METRICS_FILE=/tmp/eib.8698735777523268910.metrics MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 DISTANCE_MODE=HAMMING VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:29 GMT+14:00 2024] ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib.3548948540762354946.tmp LANE=1 READ_STRUCTURE=25T8B25T BARCODE=[CAACTCTC, CAACTCTG, ACAGGTAT, GACCGTTG, ATTATCAA, TGCTGCTG, AACAATGG, TGTAATCA, GCCGTCGA, GTCCACAG, TTGTCTAT, GTGGAGAC, TTGCAAAT] METRICS_FILE=/tmp/eib.8698735777523268910.metrics MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 DISTANCE_MODE=HAMMING VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBarcodeMatching(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBarcodeMatching(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:29 ExtractIlluminaBarcodes Processing with 1 PerTileBarcodeExtractor(s). INFO 2024-07-02 11:57:29 ExtractIlluminaBarcodes Processing with 1 PerTileBarcodeExtractor(s). Test: Test method testBarcodeMatching(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:29 ExtractIlluminaBarcodes Extracting barcodes for tile 1101 INFO 2024-07-02 11:57:29 ExtractIlluminaBarcodes Extracting barcodes for tile 1101 Test: Test method testBarcodeMatching(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:29 ExtractIlluminaBarcodes Extracting barcodes for tile 1201 INFO 2024-07-02 11:57:29 ExtractIlluminaBarcodes Extracting barcodes for tile 1201 Test: Test method testBarcodeMatching(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:29 ExtractIlluminaBarcodes Extracting barcodes for tile 2101 INFO 2024-07-02 11:57:29 ExtractIlluminaBarcodes Extracting barcodes for tile 2101 Test: Test method testBarcodeMatching(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:29 ExtractIlluminaBarcodes Processed 3 tiles. INFO 2024-07-02 11:57:29 ExtractIlluminaBarcodes Processed 3 tiles. Test: Test method testBarcodeMatching(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:29 GMT+14:00 2024] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:29 GMT+14:00 2024] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes. Test: Test method testBarcodeMatching(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testCbclDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) Test: Test method testCbclDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:29 ExtractIlluminaBarcodes Gradle suite > Gradle test > picard.illumina.ExtractIlluminaBarcodesTest.testCbclDualBarcodes STANDARD_ERROR INFO 2024-07-02 11:57:29 ExtractIlluminaBarcodes Test: Test method testCbclDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testCbclDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCbclDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testCbclDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCbclDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCbclDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testCbclDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCbclDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testCbclDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ExtractIlluminaBarcodes -BASECALLS_DIR /tmp/eib_cbcl12229771432099575892.tmp/BaseCalls -LANE 1 -METRICS_FILE /tmp/cbcl.14481553499193271216.metrics -READ_STRUCTURE 151T8B8B151T -BARCODE CACCTAGTACTCGAGT ********** ExtractIlluminaBarcodes -BASECALLS_DIR /tmp/eib_cbcl12229771432099575892.tmp/BaseCalls -LANE 1 -METRICS_FILE /tmp/cbcl.14481553499193271216.metrics -READ_STRUCTURE 151T8B8B151T -BARCODE CACCTAGTACTCGAGT Test: Test method testCbclDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testCbclDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testCbclDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testCbclDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:29.584 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:29.584 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCbclDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:29.593 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:29.593 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCbclDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:29.593 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:29.593 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCbclDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:29.593 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:29.593 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCbclDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:29 GMT+14:00 2024] ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib_cbcl12229771432099575892.tmp/BaseCalls LANE=1 READ_STRUCTURE=151T8B8B151T BARCODE=[CACCTAGTACTCGAGT] METRICS_FILE=/tmp/cbcl.14481553499193271216.metrics MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 DISTANCE_MODE=HAMMING VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:29 GMT+14:00 2024] ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib_cbcl12229771432099575892.tmp/BaseCalls LANE=1 READ_STRUCTURE=151T8B8B151T BARCODE=[CACCTAGTACTCGAGT] METRICS_FILE=/tmp/cbcl.14481553499193271216.metrics MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 DISTANCE_MODE=HAMMING VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCbclDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCbclDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:29 ExtractIlluminaBarcodes Processing with 1 PerTileBarcodeExtractor(s). INFO 2024-07-02 11:57:29 ExtractIlluminaBarcodes Processing with 1 PerTileBarcodeExtractor(s). Test: Test method testCbclDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:31 CbclReader Processing tile 1101 INFO 2024-07-02 11:57:31 CbclReader Processing tile 1101 Test: Test method testCbclDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:31 ExtractIlluminaBarcodes Extracting barcodes for tile 1101 INFO 2024-07-02 11:57:31 ExtractIlluminaBarcodes Extracting barcodes for tile 1101 Test: Test method testCbclDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:31 CbclReader Processing tile 1102 INFO 2024-07-02 11:57:31 CbclReader Processing tile 1102 Test: Test method testCbclDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:31 ExtractIlluminaBarcodes Extracting barcodes for tile 1102 INFO 2024-07-02 11:57:31 ExtractIlluminaBarcodes Extracting barcodes for tile 1102 Test: Test method testCbclDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:31 ExtractIlluminaBarcodes Processed 2 tiles. INFO 2024-07-02 11:57:31 ExtractIlluminaBarcodes Processed 2 tiles. Test: Test method testCbclDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:31 GMT+14:00 2024] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.04 minutes. [Tue Jul 02 11:57:31 GMT+14:00 2024] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.04 minutes. Test: Test method testCbclDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testDelta[0]([Ljava.lang.String;@7b5ce46, [Ljava.lang.String;@9e32af1, 2, 5)(picard.illumina.ExtractIlluminaBarcodesTest) Running Test: Test method testDelta[1]([Ljava.lang.String;@4ecd4c30, [Ljava.lang.String;@644cc939, 5, 5)(picard.illumina.ExtractIlluminaBarcodesTest) Running Test: Test method testDelta[2]([Ljava.lang.String;@3c40e309, [Ljava.lang.String;@1848947d, 0, 5)(picard.illumina.ExtractIlluminaBarcodesTest) Running Test: Test method testDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) Test: Test method testDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:31 ExtractIlluminaBarcodes Gradle suite > Gradle test > picard.illumina.ExtractIlluminaBarcodesTest.testDualBarcodes STANDARD_ERROR INFO 2024-07-02 11:57:31 ExtractIlluminaBarcodes Test: Test method testDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ExtractIlluminaBarcodes -BASECALLS_DIR /tmp/eib_dual3084723418794809468.tmp -LANE 1 -METRICS_FILE /tmp/dual.7315928554985060898.metrics -READ_STRUCTURE 25T8B8B25T -BARCODE CAATAGTCCGACTCTC ********** ExtractIlluminaBarcodes -BASECALLS_DIR /tmp/eib_dual3084723418794809468.tmp -LANE 1 -METRICS_FILE /tmp/dual.7315928554985060898.metrics -READ_STRUCTURE 25T8B8B25T -BARCODE CAATAGTCCGACTCTC Test: Test method testDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:31.795 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:31.795 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:31.796 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:31.796 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:31.796 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:31.796 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:31.796 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:31.796 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:31 GMT+14:00 2024] ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib_dual3084723418794809468.tmp LANE=1 READ_STRUCTURE=25T8B8B25T BARCODE=[CAATAGTCCGACTCTC] METRICS_FILE=/tmp/dual.7315928554985060898.metrics MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 DISTANCE_MODE=HAMMING VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:31 GMT+14:00 2024] ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib_dual3084723418794809468.tmp LANE=1 READ_STRUCTURE=25T8B8B25T BARCODE=[CAATAGTCCGACTCTC] METRICS_FILE=/tmp/dual.7315928554985060898.metrics MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 DISTANCE_MODE=HAMMING VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:31 ExtractIlluminaBarcodes Processing with 1 PerTileBarcodeExtractor(s). INFO 2024-07-02 11:57:31 ExtractIlluminaBarcodes Processing with 1 PerTileBarcodeExtractor(s). Test: Test method testDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:31 ExtractIlluminaBarcodes Extracting barcodes for tile 1101 INFO 2024-07-02 11:57:31 ExtractIlluminaBarcodes Extracting barcodes for tile 1101 Test: Test method testDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:31 ExtractIlluminaBarcodes Processed 1 tiles. INFO 2024-07-02 11:57:31 ExtractIlluminaBarcodes Processed 1 tiles. Test: Test method testDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:32 GMT+14:00 2024] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:32 GMT+14:00 2024] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes. Test: Test method testDualBarcodes(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testNoLocsSymlink(picard.illumina.ExtractIlluminaBarcodesTest) Test: Test method testNoLocsSymlink(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Gradle suite > Gradle test > picard.illumina.ExtractIlluminaBarcodesTest.testNoLocsSymlink STANDARD_ERROR INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Test: Test method testNoLocsSymlink(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testNoLocsSymlink(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testNoLocsSymlink(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testNoLocsSymlink(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testNoLocsSymlink(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testNoLocsSymlink(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testNoLocsSymlink(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testNoLocsSymlink(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testNoLocsSymlink(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ExtractIlluminaBarcodes -BASECALLS_DIR /tmp/eib_nosymlink11757899304754412107.tmp -LANE 1 -METRICS_FILE /tmp/dual.7377650946433479007.metrics -READ_STRUCTURE 25T8B8B25T -BARCODE CAATAGTCCGACTCTC ********** ExtractIlluminaBarcodes -BASECALLS_DIR /tmp/eib_nosymlink11757899304754412107.tmp -LANE 1 -METRICS_FILE /tmp/dual.7377650946433479007.metrics -READ_STRUCTURE 25T8B8B25T -BARCODE CAATAGTCCGACTCTC Test: Test method testNoLocsSymlink(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testNoLocsSymlink(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testNoLocsSymlink(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testNoLocsSymlink(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:32.090 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:32.090 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoLocsSymlink(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:32.090 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:32.090 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoLocsSymlink(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:32.090 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:32.090 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoLocsSymlink(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:32.090 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:32.090 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoLocsSymlink(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:32 GMT+14:00 2024] ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib_nosymlink11757899304754412107.tmp LANE=1 READ_STRUCTURE=25T8B8B25T BARCODE=[CAATAGTCCGACTCTC] METRICS_FILE=/tmp/dual.7377650946433479007.metrics MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 DISTANCE_MODE=HAMMING VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:32 GMT+14:00 2024] ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib_nosymlink11757899304754412107.tmp LANE=1 READ_STRUCTURE=25T8B8B25T BARCODE=[CAATAGTCCGACTCTC] METRICS_FILE=/tmp/dual.7377650946433479007.metrics MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 DISTANCE_MODE=HAMMING VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testNoLocsSymlink(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testNoLocsSymlink(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Processing with 1 PerTileBarcodeExtractor(s). INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Processing with 1 PerTileBarcodeExtractor(s). Test: Test method testNoLocsSymlink(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Extracting barcodes for tile 1101 INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Extracting barcodes for tile 1101 Test: Test method testNoLocsSymlink(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Extracting barcodes for tile 1102 INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Extracting barcodes for tile 1102 Test: Test method testNoLocsSymlink(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Processed 2 tiles. INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Processed 2 tiles. Test: Test method testNoLocsSymlink(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:32 GMT+14:00 2024] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:32 GMT+14:00 2024] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes. Test: Test method testNoLocsSymlink(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testPairedEndWithBarcodeAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) Test: Test method testPairedEndWithBarcodeAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Gradle suite > Gradle test > picard.illumina.ExtractIlluminaBarcodesTest.testPairedEndWithBarcodeAndMolecularIndicies STANDARD_ERROR INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Test: Test method testPairedEndWithBarcodeAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testPairedEndWithBarcodeAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedEndWithBarcodeAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testPairedEndWithBarcodeAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedEndWithBarcodeAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedEndWithBarcodeAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testPairedEndWithBarcodeAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedEndWithBarcodeAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testPairedEndWithBarcodeAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ExtractIlluminaBarcodes -BASECALLS_DIR /tmp/eib.3548948540762354946.tmp -LANE 1 -READ_STRUCTURE 4M21T8B21T4M -METRICS_FILE /tmp/eib.1737819509291665955.metrics -BARCODE CAACTCTC -BARCODE CAACTCTG -BARCODE ACAGGTAT -BARCODE GACCGTTG -BARCODE ATTATCAA -BARCODE TGCTGCTG -BARCODE AACAATGG -BARCODE TGTAATCA -BARCODE GCCGTCGA -BARCODE GTCCACAG -BARCODE TTGTCTAT -BARCODE GTGGAGAC -BARCODE TTGCAAAT ********** ExtractIlluminaBarcodes -BASECALLS_DIR /tmp/eib.3548948540762354946.tmp -LANE 1 -READ_STRUCTURE 4M21T8B21T4M -METRICS_FILE /tmp/eib.1737819509291665955.metrics -BARCODE CAACTCTC -BARCODE CAACTCTG -BARCODE ACAGGTAT -BARCODE GACCGTTG -BARCODE ATTATCAA -BARCODE TGCTGCTG -BARCODE AACAATGG -BARCODE TGTAATCA -BARCODE GCCGTCGA -BARCODE GTCCACAG -BARCODE TTGTCTAT -BARCODE GTGGAGAC -BARCODE TTGCAAAT Test: Test method testPairedEndWithBarcodeAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testPairedEndWithBarcodeAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testPairedEndWithBarcodeAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testPairedEndWithBarcodeAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:32.296 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:32.296 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedEndWithBarcodeAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:32.296 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:32.296 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedEndWithBarcodeAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:32.296 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:32.296 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedEndWithBarcodeAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:32.296 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:32.296 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedEndWithBarcodeAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:32 GMT+14:00 2024] ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib.3548948540762354946.tmp LANE=1 READ_STRUCTURE=4M21T8B21T4M BARCODE=[CAACTCTC, CAACTCTG, ACAGGTAT, GACCGTTG, ATTATCAA, TGCTGCTG, AACAATGG, TGTAATCA, GCCGTCGA, GTCCACAG, TTGTCTAT, GTGGAGAC, TTGCAAAT] METRICS_FILE=/tmp/eib.1737819509291665955.metrics MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 DISTANCE_MODE=HAMMING VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:32 GMT+14:00 2024] ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib.3548948540762354946.tmp LANE=1 READ_STRUCTURE=4M21T8B21T4M BARCODE=[CAACTCTC, CAACTCTG, ACAGGTAT, GACCGTTG, ATTATCAA, TGCTGCTG, AACAATGG, TGTAATCA, GCCGTCGA, GTCCACAG, TTGTCTAT, GTGGAGAC, TTGCAAAT] METRICS_FILE=/tmp/eib.1737819509291665955.metrics MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 DISTANCE_MODE=HAMMING VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedEndWithBarcodeAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedEndWithBarcodeAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Processing with 1 PerTileBarcodeExtractor(s). INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Processing with 1 PerTileBarcodeExtractor(s). Test: Test method testPairedEndWithBarcodeAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Extracting barcodes for tile 1101 INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Extracting barcodes for tile 1101 Test: Test method testPairedEndWithBarcodeAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Extracting barcodes for tile 1201 INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Extracting barcodes for tile 1201 Test: Test method testPairedEndWithBarcodeAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Extracting barcodes for tile 2101 INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Extracting barcodes for tile 2101 Test: Test method testPairedEndWithBarcodeAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Processed 3 tiles. INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Processed 3 tiles. Test: Test method testPairedEndWithBarcodeAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:32 GMT+14:00 2024] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:32 GMT+14:00 2024] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes. Test: Test method testPairedEndWithBarcodeAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testPairedEndWithBarcodeOnFirstEnd(picard.illumina.ExtractIlluminaBarcodesTest) Test: Test method testPairedEndWithBarcodeOnFirstEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Gradle suite > Gradle test > picard.illumina.ExtractIlluminaBarcodesTest.testPairedEndWithBarcodeOnFirstEnd STANDARD_ERROR INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Test: Test method testPairedEndWithBarcodeOnFirstEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testPairedEndWithBarcodeOnFirstEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedEndWithBarcodeOnFirstEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testPairedEndWithBarcodeOnFirstEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedEndWithBarcodeOnFirstEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedEndWithBarcodeOnFirstEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testPairedEndWithBarcodeOnFirstEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedEndWithBarcodeOnFirstEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testPairedEndWithBarcodeOnFirstEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ExtractIlluminaBarcodes -BASECALLS_DIR /tmp/eib.3548948540762354946.tmp -LANE 1 -READ_STRUCTURE 25T8B25T -METRICS_FILE /tmp/eib.4186183814005981536.metrics -BARCODE CAACTCTC -BARCODE CAACTCTG -BARCODE ACAGGTAT -BARCODE GACCGTTG -BARCODE ATTATCAA -BARCODE TGCTGCTG -BARCODE AACAATGG -BARCODE TGTAATCA -BARCODE GCCGTCGA -BARCODE GTCCACAG -BARCODE TTGTCTAT -BARCODE GTGGAGAC -BARCODE TTGCAAAT ********** ExtractIlluminaBarcodes -BASECALLS_DIR /tmp/eib.3548948540762354946.tmp -LANE 1 -READ_STRUCTURE 25T8B25T -METRICS_FILE /tmp/eib.4186183814005981536.metrics -BARCODE CAACTCTC -BARCODE CAACTCTG -BARCODE ACAGGTAT -BARCODE GACCGTTG -BARCODE ATTATCAA -BARCODE TGCTGCTG -BARCODE AACAATGG -BARCODE TGTAATCA -BARCODE GCCGTCGA -BARCODE GTCCACAG -BARCODE TTGTCTAT -BARCODE GTGGAGAC -BARCODE TTGCAAAT Test: Test method testPairedEndWithBarcodeOnFirstEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testPairedEndWithBarcodeOnFirstEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testPairedEndWithBarcodeOnFirstEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testPairedEndWithBarcodeOnFirstEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:32.555 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:32.555 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedEndWithBarcodeOnFirstEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:32.555 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:32.555 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedEndWithBarcodeOnFirstEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:32.555 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:32.555 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedEndWithBarcodeOnFirstEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:32.555 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:32.555 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedEndWithBarcodeOnFirstEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:32 GMT+14:00 2024] ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib.3548948540762354946.tmp LANE=1 READ_STRUCTURE=25T8B25T BARCODE=[CAACTCTC, CAACTCTG, ACAGGTAT, GACCGTTG, ATTATCAA, TGCTGCTG, AACAATGG, TGTAATCA, GCCGTCGA, GTCCACAG, TTGTCTAT, GTGGAGAC, TTGCAAAT] METRICS_FILE=/tmp/eib.4186183814005981536.metrics MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 DISTANCE_MODE=HAMMING VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:32 GMT+14:00 2024] ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib.3548948540762354946.tmp LANE=1 READ_STRUCTURE=25T8B25T BARCODE=[CAACTCTC, CAACTCTG, ACAGGTAT, GACCGTTG, ATTATCAA, TGCTGCTG, AACAATGG, TGTAATCA, GCCGTCGA, GTCCACAG, TTGTCTAT, GTGGAGAC, TTGCAAAT] METRICS_FILE=/tmp/eib.4186183814005981536.metrics MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 DISTANCE_MODE=HAMMING VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedEndWithBarcodeOnFirstEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedEndWithBarcodeOnFirstEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Processing with 1 PerTileBarcodeExtractor(s). INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Processing with 1 PerTileBarcodeExtractor(s). Test: Test method testPairedEndWithBarcodeOnFirstEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Extracting barcodes for tile 1101 INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Extracting barcodes for tile 1101 Test: Test method testPairedEndWithBarcodeOnFirstEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Extracting barcodes for tile 1201 INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Extracting barcodes for tile 1201 Test: Test method testPairedEndWithBarcodeOnFirstEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Extracting barcodes for tile 2101 INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Extracting barcodes for tile 2101 Test: Test method testPairedEndWithBarcodeOnFirstEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Processed 3 tiles. INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Processed 3 tiles. Test: Test method testPairedEndWithBarcodeOnFirstEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:32 GMT+14:00 2024] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:32 GMT+14:00 2024] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes. Test: Test method testPairedEndWithBarcodeOnFirstEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testPairedEndWithBarcodeOnSecondEnd(picard.illumina.ExtractIlluminaBarcodesTest) Test: Test method testPairedEndWithBarcodeOnSecondEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Gradle suite > Gradle test > picard.illumina.ExtractIlluminaBarcodesTest.testPairedEndWithBarcodeOnSecondEnd STANDARD_ERROR INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Test: Test method testPairedEndWithBarcodeOnSecondEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testPairedEndWithBarcodeOnSecondEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedEndWithBarcodeOnSecondEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testPairedEndWithBarcodeOnSecondEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedEndWithBarcodeOnSecondEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedEndWithBarcodeOnSecondEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testPairedEndWithBarcodeOnSecondEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedEndWithBarcodeOnSecondEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testPairedEndWithBarcodeOnSecondEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ExtractIlluminaBarcodes -BASECALLS_DIR /tmp/eib.3548948540762354946.tmp -LANE 1 -READ_STRUCTURE 25T25T8B -METRICS_FILE /tmp/eib.13465808029022174798.metrics -BARCODE CAACTCTC -BARCODE CAACTCTG -BARCODE ACAGGTAT -BARCODE GACCGTTG -BARCODE ATTATCAA -BARCODE TGCTGCTG -BARCODE AACAATGG -BARCODE TGTAATCA -BARCODE GCCGTCGA -BARCODE GTCCACAG -BARCODE TTGTCTAT -BARCODE GTGGAGAC -BARCODE TTGCAAAT ********** ExtractIlluminaBarcodes -BASECALLS_DIR /tmp/eib.3548948540762354946.tmp -LANE 1 -READ_STRUCTURE 25T25T8B -METRICS_FILE /tmp/eib.13465808029022174798.metrics -BARCODE CAACTCTC -BARCODE CAACTCTG -BARCODE ACAGGTAT -BARCODE GACCGTTG -BARCODE ATTATCAA -BARCODE TGCTGCTG -BARCODE AACAATGG -BARCODE TGTAATCA -BARCODE GCCGTCGA -BARCODE GTCCACAG -BARCODE TTGTCTAT -BARCODE GTGGAGAC -BARCODE TTGCAAAT Test: Test method testPairedEndWithBarcodeOnSecondEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testPairedEndWithBarcodeOnSecondEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testPairedEndWithBarcodeOnSecondEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testPairedEndWithBarcodeOnSecondEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:32.688 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:32.688 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedEndWithBarcodeOnSecondEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:32.688 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:32.688 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedEndWithBarcodeOnSecondEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:32.688 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:32.688 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedEndWithBarcodeOnSecondEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:32.688 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:32.688 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedEndWithBarcodeOnSecondEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:32 GMT+14:00 2024] ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib.3548948540762354946.tmp LANE=1 READ_STRUCTURE=25T25T8B BARCODE=[CAACTCTC, CAACTCTG, ACAGGTAT, GACCGTTG, ATTATCAA, TGCTGCTG, AACAATGG, TGTAATCA, GCCGTCGA, GTCCACAG, TTGTCTAT, GTGGAGAC, TTGCAAAT] METRICS_FILE=/tmp/eib.13465808029022174798.metrics MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 DISTANCE_MODE=HAMMING VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:32 GMT+14:00 2024] ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib.3548948540762354946.tmp LANE=1 READ_STRUCTURE=25T25T8B BARCODE=[CAACTCTC, CAACTCTG, ACAGGTAT, GACCGTTG, ATTATCAA, TGCTGCTG, AACAATGG, TGTAATCA, GCCGTCGA, GTCCACAG, TTGTCTAT, GTGGAGAC, TTGCAAAT] METRICS_FILE=/tmp/eib.13465808029022174798.metrics MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 DISTANCE_MODE=HAMMING VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedEndWithBarcodeOnSecondEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedEndWithBarcodeOnSecondEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Processing with 1 PerTileBarcodeExtractor(s). INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Processing with 1 PerTileBarcodeExtractor(s). Test: Test method testPairedEndWithBarcodeOnSecondEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Extracting barcodes for tile 1101 INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Extracting barcodes for tile 1101 Test: Test method testPairedEndWithBarcodeOnSecondEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Extracting barcodes for tile 1201 INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Extracting barcodes for tile 1201 Test: Test method testPairedEndWithBarcodeOnSecondEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Extracting barcodes for tile 2101 INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Extracting barcodes for tile 2101 Test: Test method testPairedEndWithBarcodeOnSecondEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Processed 3 tiles. INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Processed 3 tiles. Test: Test method testPairedEndWithBarcodeOnSecondEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:32 GMT+14:00 2024] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:32 GMT+14:00 2024] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes. Test: Test method testPairedEndWithBarcodeOnSecondEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testQualityBarcodes[0](16, 0, 1, 0, Barcode has good quality, 1 match)(picard.illumina.ExtractIlluminaBarcodesTest) Test: Test method testQualityBarcodes[0](16, 0, 1, 0, Barcode has good quality, 1 match)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Gradle suite > Gradle test > picard.illumina.ExtractIlluminaBarcodesTest.testQualityBarcodes[0](16, 0, 1, 0, Barcode has good quality, 1 match) STANDARD_ERROR INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Test: Test method testQualityBarcodes[0](16, 0, 1, 0, Barcode has good quality, 1 match)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testQualityBarcodes[0](16, 0, 1, 0, Barcode has good quality, 1 match)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testQualityBarcodes[0](16, 0, 1, 0, Barcode has good quality, 1 match)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testQualityBarcodes[0](16, 0, 1, 0, Barcode has good quality, 1 match)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testQualityBarcodes[0](16, 0, 1, 0, Barcode has good quality, 1 match)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testQualityBarcodes[0](16, 0, 1, 0, Barcode has good quality, 1 match)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testQualityBarcodes[0](16, 0, 1, 0, Barcode has good quality, 1 match)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testQualityBarcodes[0](16, 0, 1, 0, Barcode has good quality, 1 match)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testQualityBarcodes[0](16, 0, 1, 0, Barcode has good quality, 1 match)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ExtractIlluminaBarcodes -BASECALLS_DIR /tmp/eib_qual7042019879597607003.tmp -LANE 1 -READ_STRUCTURE 25T8B25T -METRICS_FILE /tmp/qual.4533226317122471711.metrics -MINIMUM_BASE_QUALITY 16 -MAX_MISMATCHES 0 -BARCODE CAATAGTC ********** ExtractIlluminaBarcodes -BASECALLS_DIR /tmp/eib_qual7042019879597607003.tmp -LANE 1 -READ_STRUCTURE 25T8B25T -METRICS_FILE /tmp/qual.4533226317122471711.metrics -MINIMUM_BASE_QUALITY 16 -MAX_MISMATCHES 0 -BARCODE CAATAGTC Test: Test method testQualityBarcodes[0](16, 0, 1, 0, Barcode has good quality, 1 match)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testQualityBarcodes[0](16, 0, 1, 0, Barcode has good quality, 1 match)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testQualityBarcodes[0](16, 0, 1, 0, Barcode has good quality, 1 match)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testQualityBarcodes[0](16, 0, 1, 0, Barcode has good quality, 1 match)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:32.835 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:32.835 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testQualityBarcodes[0](16, 0, 1, 0, Barcode has good quality, 1 match)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:32.836 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:32.836 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testQualityBarcodes[0](16, 0, 1, 0, Barcode has good quality, 1 match)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:32.836 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:32.836 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testQualityBarcodes[0](16, 0, 1, 0, Barcode has good quality, 1 match)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:32.836 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:32.836 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testQualityBarcodes[0](16, 0, 1, 0, Barcode has good quality, 1 match)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:32 GMT+14:00 2024] ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib_qual7042019879597607003.tmp LANE=1 READ_STRUCTURE=25T8B25T BARCODE=[CAATAGTC] METRICS_FILE=/tmp/qual.4533226317122471711.metrics MAX_MISMATCHES=0 MINIMUM_BASE_QUALITY=16 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 DISTANCE_MODE=HAMMING VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:32 GMT+14:00 2024] ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib_qual7042019879597607003.tmp LANE=1 READ_STRUCTURE=25T8B25T BARCODE=[CAATAGTC] METRICS_FILE=/tmp/qual.4533226317122471711.metrics MAX_MISMATCHES=0 MINIMUM_BASE_QUALITY=16 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 DISTANCE_MODE=HAMMING VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testQualityBarcodes[0](16, 0, 1, 0, Barcode has good quality, 1 match)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testQualityBarcodes[0](16, 0, 1, 0, Barcode has good quality, 1 match)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Processing with 1 PerTileBarcodeExtractor(s). INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Processing with 1 PerTileBarcodeExtractor(s). Test: Test method testQualityBarcodes[0](16, 0, 1, 0, Barcode has good quality, 1 match)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Extracting barcodes for tile 1101 INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Extracting barcodes for tile 1101 Test: Test method testQualityBarcodes[0](16, 0, 1, 0, Barcode has good quality, 1 match)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Processed 1 tiles. INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Processed 1 tiles. Test: Test method testQualityBarcodes[0](16, 0, 1, 0, Barcode has good quality, 1 match)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:32 GMT+14:00 2024] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:32 GMT+14:00 2024] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes. Test: Test method testQualityBarcodes[0](16, 0, 1, 0, Barcode has good quality, 1 match)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testQualityBarcodes[1](25, 0, 0, 0, Barcode has quality failures, no matches)(picard.illumina.ExtractIlluminaBarcodesTest) Test: Test method testQualityBarcodes[1](25, 0, 0, 0, Barcode has quality failures, no matches)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Gradle suite > Gradle test > picard.illumina.ExtractIlluminaBarcodesTest.testQualityBarcodes[1](25, 0, 0, 0, Barcode has quality failures, no matches) STANDARD_ERROR INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Test: Test method testQualityBarcodes[1](25, 0, 0, 0, Barcode has quality failures, no matches)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testQualityBarcodes[1](25, 0, 0, 0, Barcode has quality failures, no matches)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testQualityBarcodes[1](25, 0, 0, 0, Barcode has quality failures, no matches)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testQualityBarcodes[1](25, 0, 0, 0, Barcode has quality failures, no matches)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testQualityBarcodes[1](25, 0, 0, 0, Barcode has quality failures, no matches)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testQualityBarcodes[1](25, 0, 0, 0, Barcode has quality failures, no matches)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testQualityBarcodes[1](25, 0, 0, 0, Barcode has quality failures, no matches)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testQualityBarcodes[1](25, 0, 0, 0, Barcode has quality failures, no matches)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testQualityBarcodes[1](25, 0, 0, 0, Barcode has quality failures, no matches)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ExtractIlluminaBarcodes -BASECALLS_DIR /tmp/eib_qual7042019879597607003.tmp -LANE 1 -READ_STRUCTURE 25T8B25T -METRICS_FILE /tmp/qual.18121298823990902353.metrics -MINIMUM_BASE_QUALITY 25 -MAX_MISMATCHES 0 -BARCODE CAATAGTC ********** ExtractIlluminaBarcodes -BASECALLS_DIR /tmp/eib_qual7042019879597607003.tmp -LANE 1 -READ_STRUCTURE 25T8B25T -METRICS_FILE /tmp/qual.18121298823990902353.metrics -MINIMUM_BASE_QUALITY 25 -MAX_MISMATCHES 0 -BARCODE CAATAGTC Test: Test method testQualityBarcodes[1](25, 0, 0, 0, Barcode has quality failures, no matches)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testQualityBarcodes[1](25, 0, 0, 0, Barcode has quality failures, no matches)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testQualityBarcodes[1](25, 0, 0, 0, Barcode has quality failures, no matches)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testQualityBarcodes[1](25, 0, 0, 0, Barcode has quality failures, no matches)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:32.950 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:32.950 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testQualityBarcodes[1](25, 0, 0, 0, Barcode has quality failures, no matches)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:32.950 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:32.950 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testQualityBarcodes[1](25, 0, 0, 0, Barcode has quality failures, no matches)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:32.951 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:32.951 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testQualityBarcodes[1](25, 0, 0, 0, Barcode has quality failures, no matches)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:32.951 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:32.951 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testQualityBarcodes[1](25, 0, 0, 0, Barcode has quality failures, no matches)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:32 GMT+14:00 2024] ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib_qual7042019879597607003.tmp LANE=1 READ_STRUCTURE=25T8B25T BARCODE=[CAATAGTC] METRICS_FILE=/tmp/qual.18121298823990902353.metrics MAX_MISMATCHES=0 MINIMUM_BASE_QUALITY=25 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 DISTANCE_MODE=HAMMING VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:32 GMT+14:00 2024] ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib_qual7042019879597607003.tmp LANE=1 READ_STRUCTURE=25T8B25T BARCODE=[CAATAGTC] METRICS_FILE=/tmp/qual.18121298823990902353.metrics MAX_MISMATCHES=0 MINIMUM_BASE_QUALITY=25 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 DISTANCE_MODE=HAMMING VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testQualityBarcodes[1](25, 0, 0, 0, Barcode has quality failures, no matches)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testQualityBarcodes[1](25, 0, 0, 0, Barcode has quality failures, no matches)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Processing with 1 PerTileBarcodeExtractor(s). INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Processing with 1 PerTileBarcodeExtractor(s). Test: Test method testQualityBarcodes[1](25, 0, 0, 0, Barcode has quality failures, no matches)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Extracting barcodes for tile 1101 INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Extracting barcodes for tile 1101 Test: Test method testQualityBarcodes[1](25, 0, 0, 0, Barcode has quality failures, no matches)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Processed 1 tiles. INFO 2024-07-02 11:57:32 ExtractIlluminaBarcodes Processed 1 tiles. Test: Test method testQualityBarcodes[1](25, 0, 0, 0, Barcode has quality failures, no matches)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:32 GMT+14:00 2024] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:32 GMT+14:00 2024] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes. Test: Test method testQualityBarcodes[1](25, 0, 0, 0, Barcode has quality failures, no matches)(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSingleEndWithBarcodeAtEnd(picard.illumina.ExtractIlluminaBarcodesTest) Test: Test method testSingleEndWithBarcodeAtEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Gradle suite > Gradle test > picard.illumina.ExtractIlluminaBarcodesTest.testSingleEndWithBarcodeAtEnd STANDARD_ERROR INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Test: Test method testSingleEndWithBarcodeAtEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testSingleEndWithBarcodeAtEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleEndWithBarcodeAtEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testSingleEndWithBarcodeAtEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleEndWithBarcodeAtEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleEndWithBarcodeAtEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testSingleEndWithBarcodeAtEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleEndWithBarcodeAtEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testSingleEndWithBarcodeAtEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ExtractIlluminaBarcodes -BASECALLS_DIR /tmp/eib.3548948540762354946.tmp -LANE 1 -READ_STRUCTURE 25T8B -METRICS_FILE /tmp/eib.3282814782828065118.metrics -BARCODE CAACTCTC -BARCODE CAACTCTG -BARCODE ACAGGTAT -BARCODE GACCGTTG -BARCODE ATTATCAA -BARCODE TGCTGCTG -BARCODE AACAATGG -BARCODE TGTAATCA -BARCODE GCCGTCGA -BARCODE GTCCACAG -BARCODE TTGTCTAT -BARCODE GTGGAGAC -BARCODE TTGCAAAT ********** ExtractIlluminaBarcodes -BASECALLS_DIR /tmp/eib.3548948540762354946.tmp -LANE 1 -READ_STRUCTURE 25T8B -METRICS_FILE /tmp/eib.3282814782828065118.metrics -BARCODE CAACTCTC -BARCODE CAACTCTG -BARCODE ACAGGTAT -BARCODE GACCGTTG -BARCODE ATTATCAA -BARCODE TGCTGCTG -BARCODE AACAATGG -BARCODE TGTAATCA -BARCODE GCCGTCGA -BARCODE GTCCACAG -BARCODE TTGTCTAT -BARCODE GTGGAGAC -BARCODE TTGCAAAT Test: Test method testSingleEndWithBarcodeAtEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testSingleEndWithBarcodeAtEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testSingleEndWithBarcodeAtEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testSingleEndWithBarcodeAtEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:33.083 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:33.083 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleEndWithBarcodeAtEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:33.084 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:33.084 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleEndWithBarcodeAtEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:33.084 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:33.084 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleEndWithBarcodeAtEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:33.084 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:33.084 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleEndWithBarcodeAtEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:33 GMT+14:00 2024] ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib.3548948540762354946.tmp LANE=1 READ_STRUCTURE=25T8B BARCODE=[CAACTCTC, CAACTCTG, ACAGGTAT, GACCGTTG, ATTATCAA, TGCTGCTG, AACAATGG, TGTAATCA, GCCGTCGA, GTCCACAG, TTGTCTAT, GTGGAGAC, TTGCAAAT] METRICS_FILE=/tmp/eib.3282814782828065118.metrics MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 DISTANCE_MODE=HAMMING VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:33 GMT+14:00 2024] ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib.3548948540762354946.tmp LANE=1 READ_STRUCTURE=25T8B BARCODE=[CAACTCTC, CAACTCTG, ACAGGTAT, GACCGTTG, ATTATCAA, TGCTGCTG, AACAATGG, TGTAATCA, GCCGTCGA, GTCCACAG, TTGTCTAT, GTGGAGAC, TTGCAAAT] METRICS_FILE=/tmp/eib.3282814782828065118.metrics MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 DISTANCE_MODE=HAMMING VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleEndWithBarcodeAtEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleEndWithBarcodeAtEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Processing with 1 PerTileBarcodeExtractor(s). INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Processing with 1 PerTileBarcodeExtractor(s). Test: Test method testSingleEndWithBarcodeAtEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Extracting barcodes for tile 1101 INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Extracting barcodes for tile 1101 Test: Test method testSingleEndWithBarcodeAtEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Extracting barcodes for tile 1201 INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Extracting barcodes for tile 1201 Test: Test method testSingleEndWithBarcodeAtEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Extracting barcodes for tile 2101 INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Extracting barcodes for tile 2101 Test: Test method testSingleEndWithBarcodeAtEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Processed 3 tiles. INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Processed 3 tiles. Test: Test method testSingleEndWithBarcodeAtEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:33 GMT+14:00 2024] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:33 GMT+14:00 2024] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes. Test: Test method testSingleEndWithBarcodeAtEnd(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSingleEndWithBarcodeAtEndAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) Test: Test method testSingleEndWithBarcodeAtEndAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Gradle suite > Gradle test > picard.illumina.ExtractIlluminaBarcodesTest.testSingleEndWithBarcodeAtEndAndMolecularIndicies STANDARD_ERROR INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Test: Test method testSingleEndWithBarcodeAtEndAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testSingleEndWithBarcodeAtEndAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleEndWithBarcodeAtEndAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testSingleEndWithBarcodeAtEndAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleEndWithBarcodeAtEndAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleEndWithBarcodeAtEndAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testSingleEndWithBarcodeAtEndAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleEndWithBarcodeAtEndAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testSingleEndWithBarcodeAtEndAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ExtractIlluminaBarcodes -BASECALLS_DIR /tmp/eib.3548948540762354946.tmp -LANE 1 -READ_STRUCTURE 4M21T8B -METRICS_FILE /tmp/eib.9781815089614704040.metrics -BARCODE CAACTCTC -BARCODE CAACTCTG -BARCODE ACAGGTAT -BARCODE GACCGTTG -BARCODE ATTATCAA -BARCODE TGCTGCTG -BARCODE AACAATGG -BARCODE TGTAATCA -BARCODE GCCGTCGA -BARCODE GTCCACAG -BARCODE TTGTCTAT -BARCODE GTGGAGAC -BARCODE TTGCAAAT ********** ExtractIlluminaBarcodes -BASECALLS_DIR /tmp/eib.3548948540762354946.tmp -LANE 1 -READ_STRUCTURE 4M21T8B -METRICS_FILE /tmp/eib.9781815089614704040.metrics -BARCODE CAACTCTC -BARCODE CAACTCTG -BARCODE ACAGGTAT -BARCODE GACCGTTG -BARCODE ATTATCAA -BARCODE TGCTGCTG -BARCODE AACAATGG -BARCODE TGTAATCA -BARCODE GCCGTCGA -BARCODE GTCCACAG -BARCODE TTGTCTAT -BARCODE GTGGAGAC -BARCODE TTGCAAAT Test: Test method testSingleEndWithBarcodeAtEndAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testSingleEndWithBarcodeAtEndAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testSingleEndWithBarcodeAtEndAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testSingleEndWithBarcodeAtEndAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:33.198 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:33.198 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleEndWithBarcodeAtEndAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:33.198 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:33.198 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleEndWithBarcodeAtEndAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:33.198 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:33.198 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleEndWithBarcodeAtEndAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:33.198 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:33.198 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleEndWithBarcodeAtEndAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:33 GMT+14:00 2024] ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib.3548948540762354946.tmp LANE=1 READ_STRUCTURE=4M21T8B BARCODE=[CAACTCTC, CAACTCTG, ACAGGTAT, GACCGTTG, ATTATCAA, TGCTGCTG, AACAATGG, TGTAATCA, GCCGTCGA, GTCCACAG, TTGTCTAT, GTGGAGAC, TTGCAAAT] METRICS_FILE=/tmp/eib.9781815089614704040.metrics MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 DISTANCE_MODE=HAMMING VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:33 GMT+14:00 2024] ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib.3548948540762354946.tmp LANE=1 READ_STRUCTURE=4M21T8B BARCODE=[CAACTCTC, CAACTCTG, ACAGGTAT, GACCGTTG, ATTATCAA, TGCTGCTG, AACAATGG, TGTAATCA, GCCGTCGA, GTCCACAG, TTGTCTAT, GTGGAGAC, TTGCAAAT] METRICS_FILE=/tmp/eib.9781815089614704040.metrics MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 DISTANCE_MODE=HAMMING VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleEndWithBarcodeAtEndAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleEndWithBarcodeAtEndAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Processing with 1 PerTileBarcodeExtractor(s). INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Processing with 1 PerTileBarcodeExtractor(s). Test: Test method testSingleEndWithBarcodeAtEndAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Extracting barcodes for tile 1101 INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Extracting barcodes for tile 1101 Test: Test method testSingleEndWithBarcodeAtEndAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Extracting barcodes for tile 1201 INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Extracting barcodes for tile 1201 Test: Test method testSingleEndWithBarcodeAtEndAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Extracting barcodes for tile 2101 INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Extracting barcodes for tile 2101 Test: Test method testSingleEndWithBarcodeAtEndAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Processed 3 tiles. INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Processed 3 tiles. Test: Test method testSingleEndWithBarcodeAtEndAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:33 GMT+14:00 2024] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:33 GMT+14:00 2024] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes. Test: Test method testSingleEndWithBarcodeAtEndAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSingleEndWithBarcodeAtStart(picard.illumina.ExtractIlluminaBarcodesTest) Test: Test method testSingleEndWithBarcodeAtStart(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Gradle suite > Gradle test > picard.illumina.ExtractIlluminaBarcodesTest.testSingleEndWithBarcodeAtStart STANDARD_ERROR INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Test: Test method testSingleEndWithBarcodeAtStart(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testSingleEndWithBarcodeAtStart(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleEndWithBarcodeAtStart(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testSingleEndWithBarcodeAtStart(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleEndWithBarcodeAtStart(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleEndWithBarcodeAtStart(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testSingleEndWithBarcodeAtStart(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleEndWithBarcodeAtStart(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testSingleEndWithBarcodeAtStart(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ExtractIlluminaBarcodes -BASECALLS_DIR /tmp/eib.3548948540762354946.tmp -LANE 1 -READ_STRUCTURE 8B25T -METRICS_FILE /tmp/eib.13481595502208139815.metrics -BARCODE CAACTCTC -BARCODE CAACTCTG -BARCODE ACAGGTAT -BARCODE GACCGTTG -BARCODE ATTATCAA -BARCODE TGCTGCTG -BARCODE AACAATGG -BARCODE TGTAATCA -BARCODE GCCGTCGA -BARCODE GTCCACAG -BARCODE TTGTCTAT -BARCODE GTGGAGAC -BARCODE TTGCAAAT ********** ExtractIlluminaBarcodes -BASECALLS_DIR /tmp/eib.3548948540762354946.tmp -LANE 1 -READ_STRUCTURE 8B25T -METRICS_FILE /tmp/eib.13481595502208139815.metrics -BARCODE CAACTCTC -BARCODE CAACTCTG -BARCODE ACAGGTAT -BARCODE GACCGTTG -BARCODE ATTATCAA -BARCODE TGCTGCTG -BARCODE AACAATGG -BARCODE TGTAATCA -BARCODE GCCGTCGA -BARCODE GTCCACAG -BARCODE TTGTCTAT -BARCODE GTGGAGAC -BARCODE TTGCAAAT Test: Test method testSingleEndWithBarcodeAtStart(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testSingleEndWithBarcodeAtStart(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testSingleEndWithBarcodeAtStart(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testSingleEndWithBarcodeAtStart(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:33.350 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:33.350 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleEndWithBarcodeAtStart(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:33.350 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:33.350 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleEndWithBarcodeAtStart(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:33.350 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:33.350 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleEndWithBarcodeAtStart(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:33.350 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:33.350 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleEndWithBarcodeAtStart(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:33 GMT+14:00 2024] ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib.3548948540762354946.tmp LANE=1 READ_STRUCTURE=8B25T BARCODE=[CAACTCTC, CAACTCTG, ACAGGTAT, GACCGTTG, ATTATCAA, TGCTGCTG, AACAATGG, TGTAATCA, GCCGTCGA, GTCCACAG, TTGTCTAT, GTGGAGAC, TTGCAAAT] METRICS_FILE=/tmp/eib.13481595502208139815.metrics MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 DISTANCE_MODE=HAMMING VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:33 GMT+14:00 2024] ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib.3548948540762354946.tmp LANE=1 READ_STRUCTURE=8B25T BARCODE=[CAACTCTC, CAACTCTG, ACAGGTAT, GACCGTTG, ATTATCAA, TGCTGCTG, AACAATGG, TGTAATCA, GCCGTCGA, GTCCACAG, TTGTCTAT, GTGGAGAC, TTGCAAAT] METRICS_FILE=/tmp/eib.13481595502208139815.metrics MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 DISTANCE_MODE=HAMMING VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleEndWithBarcodeAtStart(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleEndWithBarcodeAtStart(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Processing with 1 PerTileBarcodeExtractor(s). INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Processing with 1 PerTileBarcodeExtractor(s). Test: Test method testSingleEndWithBarcodeAtStart(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Extracting barcodes for tile 1101 INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Extracting barcodes for tile 1101 Test: Test method testSingleEndWithBarcodeAtStart(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Extracting barcodes for tile 1201 INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Extracting barcodes for tile 1201 Test: Test method testSingleEndWithBarcodeAtStart(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Extracting barcodes for tile 2101 INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Extracting barcodes for tile 2101 Test: Test method testSingleEndWithBarcodeAtStart(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Processed 3 tiles. INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Processed 3 tiles. Test: Test method testSingleEndWithBarcodeAtStart(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:33 GMT+14:00 2024] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:33 GMT+14:00 2024] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes. Test: Test method testSingleEndWithBarcodeAtStart(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSingleEndWithBarcodeAtStartAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) Test: Test method testSingleEndWithBarcodeAtStartAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Gradle suite > Gradle test > picard.illumina.ExtractIlluminaBarcodesTest.testSingleEndWithBarcodeAtStartAndMolecularIndicies STANDARD_ERROR INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Test: Test method testSingleEndWithBarcodeAtStartAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testSingleEndWithBarcodeAtStartAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleEndWithBarcodeAtStartAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testSingleEndWithBarcodeAtStartAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleEndWithBarcodeAtStartAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleEndWithBarcodeAtStartAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testSingleEndWithBarcodeAtStartAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleEndWithBarcodeAtStartAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testSingleEndWithBarcodeAtStartAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ExtractIlluminaBarcodes -BASECALLS_DIR /tmp/eib.3548948540762354946.tmp -LANE 1 -READ_STRUCTURE 8B4M21T -METRICS_FILE /tmp/eib.14975661922005857207.metrics -BARCODE CAACTCTC -BARCODE CAACTCTG -BARCODE ACAGGTAT -BARCODE GACCGTTG -BARCODE ATTATCAA -BARCODE TGCTGCTG -BARCODE AACAATGG -BARCODE TGTAATCA -BARCODE GCCGTCGA -BARCODE GTCCACAG -BARCODE TTGTCTAT -BARCODE GTGGAGAC -BARCODE TTGCAAAT ********** ExtractIlluminaBarcodes -BASECALLS_DIR /tmp/eib.3548948540762354946.tmp -LANE 1 -READ_STRUCTURE 8B4M21T -METRICS_FILE /tmp/eib.14975661922005857207.metrics -BARCODE CAACTCTC -BARCODE CAACTCTG -BARCODE ACAGGTAT -BARCODE GACCGTTG -BARCODE ATTATCAA -BARCODE TGCTGCTG -BARCODE AACAATGG -BARCODE TGTAATCA -BARCODE GCCGTCGA -BARCODE GTCCACAG -BARCODE TTGTCTAT -BARCODE GTGGAGAC -BARCODE TTGCAAAT Test: Test method testSingleEndWithBarcodeAtStartAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: ********** ********** Test: Test method testSingleEndWithBarcodeAtStartAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testSingleEndWithBarcodeAtStartAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Test: Test method testSingleEndWithBarcodeAtStartAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:33.490 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:33.490 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleEndWithBarcodeAtStartAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:33.490 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:33.490 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleEndWithBarcodeAtStartAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:33.490 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:33.490 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleEndWithBarcodeAtStartAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: 11:57:33.490 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:33.490 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleEndWithBarcodeAtStartAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:33 GMT+14:00 2024] ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib.3548948540762354946.tmp LANE=1 READ_STRUCTURE=8B4M21T BARCODE=[CAACTCTC, CAACTCTG, ACAGGTAT, GACCGTTG, ATTATCAA, TGCTGCTG, AACAATGG, TGTAATCA, GCCGTCGA, GTCCACAG, TTGTCTAT, GTGGAGAC, TTGCAAAT] METRICS_FILE=/tmp/eib.14975661922005857207.metrics MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 DISTANCE_MODE=HAMMING VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:33 GMT+14:00 2024] ExtractIlluminaBarcodes BASECALLS_DIR=/tmp/eib.3548948540762354946.tmp LANE=1 READ_STRUCTURE=8B4M21T BARCODE=[CAACTCTC, CAACTCTG, ACAGGTAT, GACCGTTG, ATTATCAA, TGCTGCTG, AACAATGG, TGTAATCA, GCCGTCGA, GTCCACAG, TTGTCTAT, GTGGAGAC, TTGCAAAT] METRICS_FILE=/tmp/eib.14975661922005857207.metrics MAX_MISMATCHES=1 MIN_MISMATCH_DELTA=1 MAX_NO_CALLS=2 MINIMUM_BASE_QUALITY=0 MINIMUM_QUALITY=2 COMPRESS_OUTPUTS=false NUM_PROCESSORS=1 DISTANCE_MODE=HAMMING VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleEndWithBarcodeAtStartAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleEndWithBarcodeAtStartAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Processing with 1 PerTileBarcodeExtractor(s). INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Processing with 1 PerTileBarcodeExtractor(s). Test: Test method testSingleEndWithBarcodeAtStartAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Extracting barcodes for tile 1101 INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Extracting barcodes for tile 1101 Test: Test method testSingleEndWithBarcodeAtStartAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Extracting barcodes for tile 1201 INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Extracting barcodes for tile 1201 Test: Test method testSingleEndWithBarcodeAtStartAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Extracting barcodes for tile 2101 INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Extracting barcodes for tile 2101 Test: Test method testSingleEndWithBarcodeAtStartAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Processed 3 tiles. INFO 2024-07-02 11:57:33 ExtractIlluminaBarcodes Processed 3 tiles. Test: Test method testSingleEndWithBarcodeAtStartAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: [Tue Jul 02 11:57:33 GMT+14:00 2024] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:33 GMT+14:00 2024] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes. Test: Test method testSingleEndWithBarcodeAtStartAndMolecularIndicies(picard.illumina.ExtractIlluminaBarcodesTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testAddInfoForCapping(picard.analysis.FastWgsMetricsCollectorTest) Running Test: Test method testAddInfoForOverlap(picard.analysis.FastWgsMetricsCollectorTest) Running Test: Test method testAddInfoForQuality(picard.analysis.FastWgsMetricsCollectorTest) Running Test: Test method testAddInfoWithoutOverlap(picard.analysis.FastWgsMetricsCollectorTest) Running Test: Test method testForBaseQualityHetSens(picard.analysis.FastWgsMetricsCollectorTest) Running Test: Test method testForCollectorWithoutData(picard.analysis.FastWgsMetricsCollectorTest) Running Test: Test method testForComplicatedCigar(picard.analysis.FastWgsMetricsCollectorTest) Running Test: Test method testForComplicatedCigarNonFast(picard.analysis.FastWgsMetricsCollectorTest) Running Test: Test method testForExcludedForQualityHistogramArray(picard.analysis.FastWgsMetricsCollectorTest) Running Test: Test method testForHistogramArray(picard.analysis.FastWgsMetricsCollectorTest) Running Test: Test method testForSimpleCigar(picard.analysis.FastWgsMetricsCollectorTest) Running Test: Test method testForSimpleCigarNonFast(picard.analysis.FastWgsMetricsCollectorTest) Running Test: Test method readPairNameBad[0](, )(picard.sam.FastqToSamTest) Running Test: Test method readPairNameBad[1](aa/1, bb/2)(picard.sam.FastqToSamTest) Running Test: Test method readPairNameBad[2](aa, bb)(picard.sam.FastqToSamTest) Running Test: Test method readPairNameBad[3](aa/1, aa)(picard.sam.FastqToSamTest) Running Test: Test method readPairNameBad[4](aa, aa/2)(picard.sam.FastqToSamTest) Running Test: Test method readPairNameBad[5](aa/1, aa/1)(picard.sam.FastqToSamTest) Running Test: Test method readPairNameBad[6](aa/2, aa/2)(picard.sam.FastqToSamTest) Running Test: Test method readPairNameOk[0](aa/1, aa/2)(picard.sam.FastqToSamTest) Running Test: Test method readPairNameOk[1](aa, aa)(picard.sam.FastqToSamTest) Running Test: Test method readPairNameOk[2](aa/bb, aa/bb)(picard.sam.FastqToSamTest) Running Test: Test method readPairNameOk[3](aa/bb/, aa/bb/)(picard.sam.FastqToSamTest) Running Test: Test method readPairNameOk[4](aa/bb/1, aa/bb/2)(picard.sam.FastqToSamTest) Running Test: Test method readPairNameOk[5](aa/bb/cc/dd/ee/ff/1, aa/bb/cc/dd/ee/ff/2)(picard.sam.FastqToSamTest) Running Test: Test method readPairNameOk[6](////1, ////2)(picard.sam.FastqToSamTest) Running Test: Test method readPairNameOk[7](/, /)(picard.sam.FastqToSamTest) Running Test: Test method readPairNameOk[8](////, ////)(picard.sam.FastqToSamTest) Running Test: Test method readPairNameOk[9](/aa, /aa)(picard.sam.FastqToSamTest) Running Test: Test method readPairNameOk[10](aa/, aa/)(picard.sam.FastqToSamTest) Running Test: Test method readPairNameOk[11](ab/c, ab/c)(picard.sam.FastqToSamTest) Running Test: Test method testBadFile[0](bad-format/bad-qual-header.txt)(picard.sam.FastqToSamTest) Test: Test method testBadFile[0](bad-format/bad-qual-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:33 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testBadFile[0](bad-format/bad-qual-header.txt) STANDARD_ERROR INFO 2024-07-02 11:57:33 FastqToSam Test: Test method testBadFile[0](bad-format/bad-qual-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testBadFile[0](bad-format/bad-qual-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadFile[0](bad-format/bad-qual-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testBadFile[0](bad-format/bad-qual-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadFile[0](bad-format/bad-qual-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadFile[0](bad-format/bad-qual-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testBadFile[0](bad-format/bad-qual-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadFile[0](bad-format/bad-qual-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testBadFile[0](bad-format/bad-qual-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/bad-qual-header.txt -OUTPUT /tmp/bad-qual-header.txt2320613465851710725.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/bad-qual-header.txt -OUTPUT /tmp/bad-qual-header.txt2320613465851710725.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 Test: Test method testBadFile[0](bad-format/bad-qual-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testBadFile[0](bad-format/bad-qual-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testBadFile[0](bad-format/bad-qual-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testBadFile[0](bad-format/bad-qual-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:33.806 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:33.806 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadFile[0](bad-format/bad-qual-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:33.806 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:33.806 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadFile[0](bad-format/bad-qual-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:33.806 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:33.806 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadFile[0](bad-format/bad-qual-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:33.806 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:33.806 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadFile[0](bad-format/bad-qual-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:33 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/bad-qual-header.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/bad-qual-header.txt2320613465851710725.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:33 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/bad-qual-header.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/bad-qual-header.txt2320613465851710725.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBadFile[0](bad-format/bad-qual-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBadFile[0](bad-format/bad-qual-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:33 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:33 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testBadFile[0](bad-format/bad-qual-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testBadFile[0](bad-format/bad-qual-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testBadFile[1](bad-format/bad-seq-header.txt)(picard.sam.FastqToSamTest) Test: Test method testBadFile[1](bad-format/bad-seq-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:33 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testBadFile[1](bad-format/bad-seq-header.txt) STANDARD_ERROR INFO 2024-07-02 11:57:33 FastqToSam Test: Test method testBadFile[1](bad-format/bad-seq-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testBadFile[1](bad-format/bad-seq-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadFile[1](bad-format/bad-seq-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testBadFile[1](bad-format/bad-seq-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadFile[1](bad-format/bad-seq-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadFile[1](bad-format/bad-seq-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testBadFile[1](bad-format/bad-seq-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadFile[1](bad-format/bad-seq-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testBadFile[1](bad-format/bad-seq-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/bad-seq-header.txt -OUTPUT /tmp/bad-seq-header.txt15828372272503391673.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/bad-seq-header.txt -OUTPUT /tmp/bad-seq-header.txt15828372272503391673.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 Test: Test method testBadFile[1](bad-format/bad-seq-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testBadFile[1](bad-format/bad-seq-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testBadFile[1](bad-format/bad-seq-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testBadFile[1](bad-format/bad-seq-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:33.924 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:33.924 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadFile[1](bad-format/bad-seq-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:33.924 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:33.924 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadFile[1](bad-format/bad-seq-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:33.924 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:33.924 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadFile[1](bad-format/bad-seq-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:33.924 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:33.924 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadFile[1](bad-format/bad-seq-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:33 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/bad-seq-header.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/bad-seq-header.txt15828372272503391673.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:33 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/bad-seq-header.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/bad-seq-header.txt15828372272503391673.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBadFile[1](bad-format/bad-seq-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBadFile[1](bad-format/bad-seq-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:33 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:33 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testBadFile[1](bad-format/bad-seq-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testBadFile[1](bad-format/bad-seq-header.txt)(picard.sam.FastqToSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testBadFile[2](bad-format/extra-line.txt)(picard.sam.FastqToSamTest) Test: Test method testBadFile[2](bad-format/extra-line.txt)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:33 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testBadFile[2](bad-format/extra-line.txt) STANDARD_ERROR INFO 2024-07-02 11:57:33 FastqToSam Test: Test method testBadFile[2](bad-format/extra-line.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testBadFile[2](bad-format/extra-line.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadFile[2](bad-format/extra-line.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testBadFile[2](bad-format/extra-line.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadFile[2](bad-format/extra-line.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadFile[2](bad-format/extra-line.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testBadFile[2](bad-format/extra-line.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadFile[2](bad-format/extra-line.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testBadFile[2](bad-format/extra-line.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/extra-line.txt -OUTPUT /tmp/extra-line.txt18232767593572312869.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/extra-line.txt -OUTPUT /tmp/extra-line.txt18232767593572312869.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 Test: Test method testBadFile[2](bad-format/extra-line.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testBadFile[2](bad-format/extra-line.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testBadFile[2](bad-format/extra-line.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testBadFile[2](bad-format/extra-line.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:33.975 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:33.975 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadFile[2](bad-format/extra-line.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:33.975 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:33.975 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadFile[2](bad-format/extra-line.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:33.975 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:33.975 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadFile[2](bad-format/extra-line.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:33.975 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:33.975 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadFile[2](bad-format/extra-line.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:33 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/extra-line.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/extra-line.txt18232767593572312869.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:33 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/extra-line.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/extra-line.txt18232767593572312869.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBadFile[2](bad-format/extra-line.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBadFile[2](bad-format/extra-line.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:33 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:33 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testBadFile[2](bad-format/extra-line.txt)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testBadFile[2](bad-format/extra-line.txt)(picard.sam.FastqToSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testBadFile[3](bad-format/too-many-quals.txt)(picard.sam.FastqToSamTest) Test: Test method testBadFile[3](bad-format/too-many-quals.txt)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:34 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testBadFile[3](bad-format/too-many-quals.txt) STANDARD_ERROR INFO 2024-07-02 11:57:34 FastqToSam Test: Test method testBadFile[3](bad-format/too-many-quals.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testBadFile[3](bad-format/too-many-quals.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadFile[3](bad-format/too-many-quals.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testBadFile[3](bad-format/too-many-quals.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadFile[3](bad-format/too-many-quals.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadFile[3](bad-format/too-many-quals.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testBadFile[3](bad-format/too-many-quals.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadFile[3](bad-format/too-many-quals.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testBadFile[3](bad-format/too-many-quals.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/too-many-quals.txt -OUTPUT /tmp/too-many-quals.txt11777856610350339470.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/too-many-quals.txt -OUTPUT /tmp/too-many-quals.txt11777856610350339470.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 Test: Test method testBadFile[3](bad-format/too-many-quals.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testBadFile[3](bad-format/too-many-quals.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testBadFile[3](bad-format/too-many-quals.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testBadFile[3](bad-format/too-many-quals.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.037 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:34.037 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadFile[3](bad-format/too-many-quals.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.038 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:34.038 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadFile[3](bad-format/too-many-quals.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.038 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:34.038 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadFile[3](bad-format/too-many-quals.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.038 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:34.038 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadFile[3](bad-format/too-many-quals.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:34 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/too-many-quals.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/too-many-quals.txt11777856610350339470.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:34 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/too-many-quals.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/too-many-quals.txt11777856610350339470.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBadFile[3](bad-format/too-many-quals.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBadFile[3](bad-format/too-many-quals.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:34 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:34 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testBadFile[3](bad-format/too-many-quals.txt)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testBadFile[3](bad-format/too-many-quals.txt)(picard.sam.FastqToSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testBadFile[4](bad-format/1lines.txt)(picard.sam.FastqToSamTest) Test: Test method testBadFile[4](bad-format/1lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:34 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testBadFile[4](bad-format/1lines.txt) STANDARD_ERROR INFO 2024-07-02 11:57:34 FastqToSam Test: Test method testBadFile[4](bad-format/1lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testBadFile[4](bad-format/1lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadFile[4](bad-format/1lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testBadFile[4](bad-format/1lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadFile[4](bad-format/1lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadFile[4](bad-format/1lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testBadFile[4](bad-format/1lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadFile[4](bad-format/1lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testBadFile[4](bad-format/1lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/1lines.txt -OUTPUT /tmp/1lines.txt9606223160626507598.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/1lines.txt -OUTPUT /tmp/1lines.txt9606223160626507598.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 Test: Test method testBadFile[4](bad-format/1lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testBadFile[4](bad-format/1lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testBadFile[4](bad-format/1lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testBadFile[4](bad-format/1lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.093 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:34.093 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadFile[4](bad-format/1lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.093 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:34.093 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadFile[4](bad-format/1lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.094 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:34.094 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadFile[4](bad-format/1lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.094 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:34.094 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadFile[4](bad-format/1lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:34 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/1lines.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/1lines.txt9606223160626507598.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:34 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/1lines.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/1lines.txt9606223160626507598.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBadFile[4](bad-format/1lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBadFile[4](bad-format/1lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:34 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:34 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testBadFile[4](bad-format/1lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testBadFile[4](bad-format/1lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testBadFile[5](bad-format/2lines.txt)(picard.sam.FastqToSamTest) Test: Test method testBadFile[5](bad-format/2lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:34 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testBadFile[5](bad-format/2lines.txt) STANDARD_ERROR INFO 2024-07-02 11:57:34 FastqToSam Test: Test method testBadFile[5](bad-format/2lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testBadFile[5](bad-format/2lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadFile[5](bad-format/2lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testBadFile[5](bad-format/2lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadFile[5](bad-format/2lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadFile[5](bad-format/2lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testBadFile[5](bad-format/2lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadFile[5](bad-format/2lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testBadFile[5](bad-format/2lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/2lines.txt -OUTPUT /tmp/2lines.txt3247756797999362672.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/2lines.txt -OUTPUT /tmp/2lines.txt3247756797999362672.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 Test: Test method testBadFile[5](bad-format/2lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testBadFile[5](bad-format/2lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testBadFile[5](bad-format/2lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testBadFile[5](bad-format/2lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.150 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:34.150 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadFile[5](bad-format/2lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.150 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:34.150 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadFile[5](bad-format/2lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.150 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:34.150 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadFile[5](bad-format/2lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.150 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:34.150 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadFile[5](bad-format/2lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:34 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/2lines.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/2lines.txt3247756797999362672.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:34 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/2lines.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/2lines.txt3247756797999362672.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBadFile[5](bad-format/2lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBadFile[5](bad-format/2lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:34 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:34 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testBadFile[5](bad-format/2lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testBadFile[5](bad-format/2lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testBadFile[6](bad-format/3lines.txt)(picard.sam.FastqToSamTest) Test: Test method testBadFile[6](bad-format/3lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:34 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testBadFile[6](bad-format/3lines.txt) STANDARD_ERROR INFO 2024-07-02 11:57:34 FastqToSam Test: Test method testBadFile[6](bad-format/3lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testBadFile[6](bad-format/3lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadFile[6](bad-format/3lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testBadFile[6](bad-format/3lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadFile[6](bad-format/3lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadFile[6](bad-format/3lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testBadFile[6](bad-format/3lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadFile[6](bad-format/3lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testBadFile[6](bad-format/3lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/3lines.txt -OUTPUT /tmp/3lines.txt473355921956537255.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/3lines.txt -OUTPUT /tmp/3lines.txt473355921956537255.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 Test: Test method testBadFile[6](bad-format/3lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testBadFile[6](bad-format/3lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testBadFile[6](bad-format/3lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testBadFile[6](bad-format/3lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.208 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:34.208 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadFile[6](bad-format/3lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.208 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:34.208 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadFile[6](bad-format/3lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.208 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:34.208 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadFile[6](bad-format/3lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.208 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:34.208 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadFile[6](bad-format/3lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:34 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/3lines.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/3lines.txt473355921956537255.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:34 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-format/3lines.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/3lines.txt473355921956537255.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBadFile[6](bad-format/3lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBadFile[6](bad-format/3lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:34 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:34 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testBadFile[6](bad-format/3lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testBadFile[6](bad-format/3lines.txt)(picard.sam.FastqToSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testFastqVersionBad[0](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Illumina)(picard.sam.FastqToSamTest) Test: Test method testFastqVersionBad[0](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:34 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testFastqVersionBad[0](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Illumina) STANDARD_ERROR INFO 2024-07-02 11:57:34 FastqToSam Test: Test method testFastqVersionBad[0](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionBad[0](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFastqVersionBad[0](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionBad[0](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFastqVersionBad[0](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFastqVersionBad[0](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionBad[0](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFastqVersionBad[0](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionBad[0](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-sanger/sanger_full_range_as_sanger-63.fastq -OUTPUT /tmp/sanger_full_range_as_sanger-63.fastq1140154924900582530.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-sanger/sanger_full_range_as_sanger-63.fastq -OUTPUT /tmp/sanger_full_range_as_sanger-63.fastq1140154924900582530.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 Test: Test method testFastqVersionBad[0](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionBad[0](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionBad[0](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionBad[0](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.266 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:34.266 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFastqVersionBad[0](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.266 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:34.266 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFastqVersionBad[0](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.266 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:34.266 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFastqVersionBad[0](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.266 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:34.266 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFastqVersionBad[0](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:34 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-sanger/sanger_full_range_as_sanger-63.fastq QUALITY_FORMAT=Illumina OUTPUT=/tmp/sanger_full_range_as_sanger-63.fastq1140154924900582530.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:34 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-sanger/sanger_full_range_as_sanger-63.fastq QUALITY_FORMAT=Illumina OUTPUT=/tmp/sanger_full_range_as_sanger-63.fastq1140154924900582530.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFastqVersionBad[0](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFastqVersionBad[0](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:34 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:34 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testFastqVersionBad[0](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testFastqVersionBad[0](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testFastqVersionBad[1](fastq-solexa/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) Test: Test method testFastqVersionBad[1](fastq-solexa/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:34 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testFastqVersionBad[1](fastq-solexa/s_1_sequence.txt, Illumina) STANDARD_ERROR INFO 2024-07-02 11:57:34 FastqToSam Test: Test method testFastqVersionBad[1](fastq-solexa/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionBad[1](fastq-solexa/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFastqVersionBad[1](fastq-solexa/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionBad[1](fastq-solexa/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFastqVersionBad[1](fastq-solexa/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFastqVersionBad[1](fastq-solexa/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionBad[1](fastq-solexa/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFastqVersionBad[1](fastq-solexa/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionBad[1](fastq-solexa/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-solexa/s_1_sequence.txt -OUTPUT /tmp/s_1_sequence.txt10475246719580506957.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-solexa/s_1_sequence.txt -OUTPUT /tmp/s_1_sequence.txt10475246719580506957.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 Test: Test method testFastqVersionBad[1](fastq-solexa/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionBad[1](fastq-solexa/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionBad[1](fastq-solexa/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionBad[1](fastq-solexa/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.321 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:34.321 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFastqVersionBad[1](fastq-solexa/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.321 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:34.321 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFastqVersionBad[1](fastq-solexa/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.322 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:34.322 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFastqVersionBad[1](fastq-solexa/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.322 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:34.322 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFastqVersionBad[1](fastq-solexa/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:34 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-solexa/s_1_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_sequence.txt10475246719580506957.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:34 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-solexa/s_1_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_sequence.txt10475246719580506957.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFastqVersionBad[1](fastq-solexa/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFastqVersionBad[1](fastq-solexa/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:34 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:34 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testFastqVersionBad[1](fastq-solexa/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testFastqVersionBad[1](fastq-solexa/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testFastqVersionOk[0](fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq, Standard)(picard.sam.FastqToSamTest) Test: Test method testFastqVersionOk[0](fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:34 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testFastqVersionOk[0](fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq, Standard) STANDARD_ERROR INFO 2024-07-02 11:57:34 FastqToSam Test: Test method testFastqVersionOk[0](fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionOk[0](fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFastqVersionOk[0](fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[0](fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFastqVersionOk[0](fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFastqVersionOk[0](fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[0](fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFastqVersionOk[0](fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[0](fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq -OUTPUT /tmp/5k-v1-Rhodobacter_LW1.sam.fastq11926087059381840814.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq -OUTPUT /tmp/5k-v1-Rhodobacter_LW1.sam.fastq11926087059381840814.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 Test: Test method testFastqVersionOk[0](fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[0](fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionOk[0](fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionOk[0](fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.509 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:34.509 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFastqVersionOk[0](fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.509 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:34.509 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFastqVersionOk[0](fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.509 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:34.509 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFastqVersionOk[0](fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.509 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:34.509 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFastqVersionOk[0](fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:34 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq QUALITY_FORMAT=Standard OUTPUT=/tmp/5k-v1-Rhodobacter_LW1.sam.fastq11926087059381840814.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:34 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq QUALITY_FORMAT=Standard OUTPUT=/tmp/5k-v1-Rhodobacter_LW1.sam.fastq11926087059381840814.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFastqVersionOk[0](fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFastqVersionOk[0](fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:34 FastqToSam Auto-detected quality format as: Standard. INFO 2024-07-02 11:57:34 FastqToSam Auto-detected quality format as: Standard. Test: Test method testFastqVersionOk[0](fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:34 FastqToSam Processed 5000 fastq reads INFO 2024-07-02 11:57:34 FastqToSam Processed 5000 fastq reads Test: Test method testFastqVersionOk[0](fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:34 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:57:34 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.01 minutes. Test: Test method testFastqVersionOk[0](fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testFastqVersionOk[1](fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq, Standard)(picard.sam.FastqToSamTest) Test: Test method testFastqVersionOk[1](fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:34 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testFastqVersionOk[1](fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq, Standard) STANDARD_ERROR INFO 2024-07-02 11:57:34 FastqToSam Test: Test method testFastqVersionOk[1](fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionOk[1](fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFastqVersionOk[1](fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[1](fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFastqVersionOk[1](fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFastqVersionOk[1](fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[1](fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFastqVersionOk[1](fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[1](fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq -OUTPUT /tmp/5k-30BB2AAXX.3.aligned.sam.fastq1033043663781028969.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq -OUTPUT /tmp/5k-30BB2AAXX.3.aligned.sam.fastq1033043663781028969.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 Test: Test method testFastqVersionOk[1](fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[1](fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionOk[1](fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionOk[1](fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.957 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:34.957 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFastqVersionOk[1](fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.957 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:34.957 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFastqVersionOk[1](fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.957 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:34.957 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFastqVersionOk[1](fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:34.957 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:34.957 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFastqVersionOk[1](fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:34 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq QUALITY_FORMAT=Standard OUTPUT=/tmp/5k-30BB2AAXX.3.aligned.sam.fastq1033043663781028969.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:34 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq QUALITY_FORMAT=Standard OUTPUT=/tmp/5k-30BB2AAXX.3.aligned.sam.fastq1033043663781028969.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFastqVersionOk[1](fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFastqVersionOk[1](fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:35 FastqToSam Auto-detected quality format as: Standard. INFO 2024-07-02 11:57:35 FastqToSam Auto-detected quality format as: Standard. Test: Test method testFastqVersionOk[1](fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:35 FastqToSam Processed 4952 fastq reads INFO 2024-07-02 11:57:35 FastqToSam Processed 4952 fastq reads Test: Test method testFastqVersionOk[1](fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:35 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:35 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testFastqVersionOk[1](fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testFastqVersionOk[2](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Standard)(picard.sam.FastqToSamTest) Test: Test method testFastqVersionOk[2](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:35 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testFastqVersionOk[2](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Standard) STANDARD_ERROR INFO 2024-07-02 11:57:35 FastqToSam Test: Test method testFastqVersionOk[2](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionOk[2](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFastqVersionOk[2](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[2](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFastqVersionOk[2](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFastqVersionOk[2](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[2](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFastqVersionOk[2](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[2](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-sanger/sanger_full_range_as_sanger-63.fastq -OUTPUT /tmp/sanger_full_range_as_sanger-63.fastq9109121468075428528.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-sanger/sanger_full_range_as_sanger-63.fastq -OUTPUT /tmp/sanger_full_range_as_sanger-63.fastq9109121468075428528.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 Test: Test method testFastqVersionOk[2](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[2](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionOk[2](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionOk[2](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.243 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:35.243 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFastqVersionOk[2](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.243 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:35.243 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFastqVersionOk[2](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.243 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:35.243 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFastqVersionOk[2](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.243 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:35.243 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFastqVersionOk[2](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:35 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-sanger/sanger_full_range_as_sanger-63.fastq QUALITY_FORMAT=Standard OUTPUT=/tmp/sanger_full_range_as_sanger-63.fastq9109121468075428528.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:35 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-sanger/sanger_full_range_as_sanger-63.fastq QUALITY_FORMAT=Standard OUTPUT=/tmp/sanger_full_range_as_sanger-63.fastq9109121468075428528.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFastqVersionOk[2](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFastqVersionOk[2](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:35 FastqToSam Auto-detected quality format as: Standard. INFO 2024-07-02 11:57:35 FastqToSam Auto-detected quality format as: Standard. Test: Test method testFastqVersionOk[2](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:35 FastqToSam Processed 1 fastq reads INFO 2024-07-02 11:57:35 FastqToSam Processed 1 fastq reads Test: Test method testFastqVersionOk[2](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:35 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:35 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testFastqVersionOk[2](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testFastqVersionOk[3](fastq-solexa/s_1_sequence.txt, Solexa)(picard.sam.FastqToSamTest) Test: Test method testFastqVersionOk[3](fastq-solexa/s_1_sequence.txt, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:35 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testFastqVersionOk[3](fastq-solexa/s_1_sequence.txt, Solexa) STANDARD_ERROR INFO 2024-07-02 11:57:35 FastqToSam Test: Test method testFastqVersionOk[3](fastq-solexa/s_1_sequence.txt, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionOk[3](fastq-solexa/s_1_sequence.txt, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFastqVersionOk[3](fastq-solexa/s_1_sequence.txt, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[3](fastq-solexa/s_1_sequence.txt, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFastqVersionOk[3](fastq-solexa/s_1_sequence.txt, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFastqVersionOk[3](fastq-solexa/s_1_sequence.txt, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[3](fastq-solexa/s_1_sequence.txt, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFastqVersionOk[3](fastq-solexa/s_1_sequence.txt, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[3](fastq-solexa/s_1_sequence.txt, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-solexa/s_1_sequence.txt -OUTPUT /tmp/s_1_sequence.txt2641692560998321158.sam -QUALITY_FORMAT Solexa -READ_GROUP_NAME rg -SAMPLE_NAME s1 ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-solexa/s_1_sequence.txt -OUTPUT /tmp/s_1_sequence.txt2641692560998321158.sam -QUALITY_FORMAT Solexa -READ_GROUP_NAME rg -SAMPLE_NAME s1 Test: Test method testFastqVersionOk[3](fastq-solexa/s_1_sequence.txt, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[3](fastq-solexa/s_1_sequence.txt, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionOk[3](fastq-solexa/s_1_sequence.txt, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionOk[3](fastq-solexa/s_1_sequence.txt, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.326 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:35.326 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFastqVersionOk[3](fastq-solexa/s_1_sequence.txt, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.326 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:35.326 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFastqVersionOk[3](fastq-solexa/s_1_sequence.txt, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.326 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:35.326 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFastqVersionOk[3](fastq-solexa/s_1_sequence.txt, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.326 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:35.326 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFastqVersionOk[3](fastq-solexa/s_1_sequence.txt, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:35 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-solexa/s_1_sequence.txt QUALITY_FORMAT=Solexa OUTPUT=/tmp/s_1_sequence.txt2641692560998321158.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:35 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-solexa/s_1_sequence.txt QUALITY_FORMAT=Solexa OUTPUT=/tmp/s_1_sequence.txt2641692560998321158.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFastqVersionOk[3](fastq-solexa/s_1_sequence.txt, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFastqVersionOk[3](fastq-solexa/s_1_sequence.txt, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:35 FastqToSam Auto-detected quality format as: Solexa. INFO 2024-07-02 11:57:35 FastqToSam Auto-detected quality format as: Solexa. Test: Test method testFastqVersionOk[3](fastq-solexa/s_1_sequence.txt, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:35 FastqToSam Processed 25 fastq reads INFO 2024-07-02 11:57:35 FastqToSam Processed 25 fastq reads Test: Test method testFastqVersionOk[3](fastq-solexa/s_1_sequence.txt, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:35 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:35 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testFastqVersionOk[3](fastq-solexa/s_1_sequence.txt, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testFastqVersionOk[4](fastq-solexa/solexa_full_range_as_solexa.fastq, Solexa)(picard.sam.FastqToSamTest) Test: Test method testFastqVersionOk[4](fastq-solexa/solexa_full_range_as_solexa.fastq, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:35 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testFastqVersionOk[4](fastq-solexa/solexa_full_range_as_solexa.fastq, Solexa) STANDARD_ERROR INFO 2024-07-02 11:57:35 FastqToSam Test: Test method testFastqVersionOk[4](fastq-solexa/solexa_full_range_as_solexa.fastq, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionOk[4](fastq-solexa/solexa_full_range_as_solexa.fastq, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFastqVersionOk[4](fastq-solexa/solexa_full_range_as_solexa.fastq, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[4](fastq-solexa/solexa_full_range_as_solexa.fastq, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFastqVersionOk[4](fastq-solexa/solexa_full_range_as_solexa.fastq, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFastqVersionOk[4](fastq-solexa/solexa_full_range_as_solexa.fastq, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[4](fastq-solexa/solexa_full_range_as_solexa.fastq, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFastqVersionOk[4](fastq-solexa/solexa_full_range_as_solexa.fastq, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[4](fastq-solexa/solexa_full_range_as_solexa.fastq, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-solexa/solexa_full_range_as_solexa.fastq -OUTPUT /tmp/solexa_full_range_as_solexa.fastq16157064841565439647.sam -QUALITY_FORMAT Solexa -READ_GROUP_NAME rg -SAMPLE_NAME s1 ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-solexa/solexa_full_range_as_solexa.fastq -OUTPUT /tmp/solexa_full_range_as_solexa.fastq16157064841565439647.sam -QUALITY_FORMAT Solexa -READ_GROUP_NAME rg -SAMPLE_NAME s1 Test: Test method testFastqVersionOk[4](fastq-solexa/solexa_full_range_as_solexa.fastq, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[4](fastq-solexa/solexa_full_range_as_solexa.fastq, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionOk[4](fastq-solexa/solexa_full_range_as_solexa.fastq, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionOk[4](fastq-solexa/solexa_full_range_as_solexa.fastq, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.423 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:35.423 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFastqVersionOk[4](fastq-solexa/solexa_full_range_as_solexa.fastq, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.423 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:35.423 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFastqVersionOk[4](fastq-solexa/solexa_full_range_as_solexa.fastq, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.423 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:35.423 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFastqVersionOk[4](fastq-solexa/solexa_full_range_as_solexa.fastq, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.423 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:35.423 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFastqVersionOk[4](fastq-solexa/solexa_full_range_as_solexa.fastq, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:35 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-solexa/solexa_full_range_as_solexa.fastq QUALITY_FORMAT=Solexa OUTPUT=/tmp/solexa_full_range_as_solexa.fastq16157064841565439647.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:35 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-solexa/solexa_full_range_as_solexa.fastq QUALITY_FORMAT=Solexa OUTPUT=/tmp/solexa_full_range_as_solexa.fastq16157064841565439647.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFastqVersionOk[4](fastq-solexa/solexa_full_range_as_solexa.fastq, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFastqVersionOk[4](fastq-solexa/solexa_full_range_as_solexa.fastq, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:35 FastqToSam Auto-detected quality format as: Solexa. INFO 2024-07-02 11:57:35 FastqToSam Auto-detected quality format as: Solexa. Test: Test method testFastqVersionOk[4](fastq-solexa/solexa_full_range_as_solexa.fastq, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:35 FastqToSam Processed 2 fastq reads INFO 2024-07-02 11:57:35 FastqToSam Processed 2 fastq reads Test: Test method testFastqVersionOk[4](fastq-solexa/solexa_full_range_as_solexa.fastq, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:35 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:35 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testFastqVersionOk[4](fastq-solexa/solexa_full_range_as_solexa.fastq, Solexa)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testFastqVersionOk[5](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) Test: Test method testFastqVersionOk[5](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:35 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testFastqVersionOk[5](fastq-illumina/s_1_2_sequence.txt, Illumina) STANDARD_ERROR INFO 2024-07-02 11:57:35 FastqToSam Test: Test method testFastqVersionOk[5](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionOk[5](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFastqVersionOk[5](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[5](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFastqVersionOk[5](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFastqVersionOk[5](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[5](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFastqVersionOk[5](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[5](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_2_sequence.txt -OUTPUT /tmp/s_1_2_sequence.txt16746545741185438426.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_2_sequence.txt -OUTPUT /tmp/s_1_2_sequence.txt16746545741185438426.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 Test: Test method testFastqVersionOk[5](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[5](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionOk[5](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionOk[5](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.504 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:35.504 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFastqVersionOk[5](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:35.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFastqVersionOk[5](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.513 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:35.513 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFastqVersionOk[5](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.513 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:35.513 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFastqVersionOk[5](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:35 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_2_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_2_sequence.txt16746545741185438426.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:35 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_2_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_2_sequence.txt16746545741185438426.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFastqVersionOk[5](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFastqVersionOk[5](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: WARNING 2024-07-02 11:57:35 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. WARNING 2024-07-02 11:57:35 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. Test: Test method testFastqVersionOk[5](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:35 FastqToSam Auto-detected quality format as: Illumina. INFO 2024-07-02 11:57:35 FastqToSam Auto-detected quality format as: Illumina. Test: Test method testFastqVersionOk[5](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:35 FastqToSam Processed 10 fastq reads INFO 2024-07-02 11:57:35 FastqToSam Processed 10 fastq reads Test: Test method testFastqVersionOk[5](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:35 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:35 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testFastqVersionOk[5](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testFastqVersionOk[6](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) Test: Test method testFastqVersionOk[6](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:35 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testFastqVersionOk[6](fastq-illumina/s_1_2_sequence.txt, Illumina) STANDARD_ERROR INFO 2024-07-02 11:57:35 FastqToSam Test: Test method testFastqVersionOk[6](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionOk[6](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFastqVersionOk[6](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[6](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFastqVersionOk[6](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFastqVersionOk[6](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[6](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFastqVersionOk[6](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[6](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_2_sequence.txt -OUTPUT /tmp/s_1_2_sequence.txt4854917498572263725.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_2_sequence.txt -OUTPUT /tmp/s_1_2_sequence.txt4854917498572263725.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 Test: Test method testFastqVersionOk[6](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[6](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionOk[6](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionOk[6](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.601 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:35.601 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFastqVersionOk[6](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.601 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:35.601 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFastqVersionOk[6](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.601 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:35.601 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFastqVersionOk[6](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.601 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:35.601 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFastqVersionOk[6](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:35 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_2_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_2_sequence.txt4854917498572263725.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:35 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_2_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_2_sequence.txt4854917498572263725.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFastqVersionOk[6](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFastqVersionOk[6](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: WARNING 2024-07-02 11:57:35 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. WARNING 2024-07-02 11:57:35 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. Test: Test method testFastqVersionOk[6](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:35 FastqToSam Auto-detected quality format as: Illumina. INFO 2024-07-02 11:57:35 FastqToSam Auto-detected quality format as: Illumina. Test: Test method testFastqVersionOk[6](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:35 FastqToSam Processed 10 fastq reads INFO 2024-07-02 11:57:35 FastqToSam Processed 10 fastq reads Test: Test method testFastqVersionOk[6](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:35 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:35 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testFastqVersionOk[6](fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testFastqVersionOk[7](fastq-illumina/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) Test: Test method testFastqVersionOk[7](fastq-illumina/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:35 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testFastqVersionOk[7](fastq-illumina/s_1_sequence.txt, Illumina) STANDARD_ERROR INFO 2024-07-02 11:57:35 FastqToSam Test: Test method testFastqVersionOk[7](fastq-illumina/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionOk[7](fastq-illumina/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFastqVersionOk[7](fastq-illumina/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[7](fastq-illumina/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFastqVersionOk[7](fastq-illumina/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFastqVersionOk[7](fastq-illumina/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[7](fastq-illumina/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFastqVersionOk[7](fastq-illumina/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[7](fastq-illumina/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_sequence.txt -OUTPUT /tmp/s_1_sequence.txt17694886364503982985.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_sequence.txt -OUTPUT /tmp/s_1_sequence.txt17694886364503982985.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 Test: Test method testFastqVersionOk[7](fastq-illumina/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testFastqVersionOk[7](fastq-illumina/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionOk[7](fastq-illumina/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testFastqVersionOk[7](fastq-illumina/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.676 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:35.676 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFastqVersionOk[7](fastq-illumina/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.677 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:35.677 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFastqVersionOk[7](fastq-illumina/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.681 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:35.681 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFastqVersionOk[7](fastq-illumina/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.681 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:35.681 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFastqVersionOk[7](fastq-illumina/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:35 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_sequence.txt17694886364503982985.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:35 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_sequence.txt17694886364503982985.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFastqVersionOk[7](fastq-illumina/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFastqVersionOk[7](fastq-illumina/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: WARNING 2024-07-02 11:57:35 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. WARNING 2024-07-02 11:57:35 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. Test: Test method testFastqVersionOk[7](fastq-illumina/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:35 FastqToSam Auto-detected quality format as: Illumina. INFO 2024-07-02 11:57:35 FastqToSam Auto-detected quality format as: Illumina. Test: Test method testFastqVersionOk[7](fastq-illumina/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:35 FastqToSam Processed 10 fastq reads INFO 2024-07-02 11:57:35 FastqToSam Processed 10 fastq reads Test: Test method testFastqVersionOk[7](fastq-illumina/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:35 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:35 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testFastqVersionOk[7](fastq-illumina/s_1_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testPairedBad[0](ok-paired/pair1.txt, bad-paired/pair2-one-more-record.txt)(picard.sam.FastqToSamTest) Test: Test method testPairedBad[0](ok-paired/pair1.txt, bad-paired/pair2-one-more-record.txt)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:35 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testPairedBad[0](ok-paired/pair1.txt, bad-paired/pair2-one-more-record.txt) STANDARD_ERROR INFO 2024-07-02 11:57:35 FastqToSam Test: Test method testPairedBad[0](ok-paired/pair1.txt, bad-paired/pair2-one-more-record.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPairedBad[0](ok-paired/pair1.txt, bad-paired/pair2-one-more-record.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedBad[0](ok-paired/pair1.txt, bad-paired/pair2-one-more-record.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedBad[0](ok-paired/pair1.txt, bad-paired/pair2-one-more-record.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedBad[0](ok-paired/pair1.txt, bad-paired/pair2-one-more-record.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedBad[0](ok-paired/pair1.txt, bad-paired/pair2-one-more-record.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedBad[0](ok-paired/pair1.txt, bad-paired/pair2-one-more-record.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedBad[0](ok-paired/pair1.txt, bad-paired/pair2-one-more-record.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedBad[0](ok-paired/pair1.txt, bad-paired/pair2-one-more-record.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair1.txt -OUTPUT /tmp/pair1.txt10158693789613509187.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 -FASTQ2 /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair2-one-more-record.txt ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair1.txt -OUTPUT /tmp/pair1.txt10158693789613509187.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 -FASTQ2 /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair2-one-more-record.txt Test: Test method testPairedBad[0](ok-paired/pair1.txt, bad-paired/pair2-one-more-record.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedBad[0](ok-paired/pair1.txt, bad-paired/pair2-one-more-record.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPairedBad[0](ok-paired/pair1.txt, bad-paired/pair2-one-more-record.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPairedBad[0](ok-paired/pair1.txt, bad-paired/pair2-one-more-record.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.756 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:35.756 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedBad[0](ok-paired/pair1.txt, bad-paired/pair2-one-more-record.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.756 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:35.756 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedBad[0](ok-paired/pair1.txt, bad-paired/pair2-one-more-record.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.769 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:35.769 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedBad[0](ok-paired/pair1.txt, bad-paired/pair2-one-more-record.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.769 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:35.769 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedBad[0](ok-paired/pair1.txt, bad-paired/pair2-one-more-record.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:35 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair1.txt FASTQ2=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair2-one-more-record.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1.txt10158693789613509187.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:35 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair1.txt FASTQ2=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair2-one-more-record.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1.txt10158693789613509187.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedBad[0](ok-paired/pair1.txt, bad-paired/pair2-one-more-record.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedBad[0](ok-paired/pair1.txt, bad-paired/pair2-one-more-record.txt)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:35 FastqToSam Auto-detected quality format as: Standard. INFO 2024-07-02 11:57:35 FastqToSam Auto-detected quality format as: Standard. Test: Test method testPairedBad[0](ok-paired/pair1.txt, bad-paired/pair2-one-more-record.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:35 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:35 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testPairedBad[0](ok-paired/pair1.txt, bad-paired/pair2-one-more-record.txt)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testPairedBad[0](ok-paired/pair1.txt, bad-paired/pair2-one-more-record.txt)(picard.sam.FastqToSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testPairedBad[1](bad-paired/pair1-one-more-record.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) Test: Test method testPairedBad[1](bad-paired/pair1-one-more-record.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:35 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testPairedBad[1](bad-paired/pair1-one-more-record.txt, ok-paired/pair2.txt) STANDARD_ERROR INFO 2024-07-02 11:57:35 FastqToSam Test: Test method testPairedBad[1](bad-paired/pair1-one-more-record.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPairedBad[1](bad-paired/pair1-one-more-record.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedBad[1](bad-paired/pair1-one-more-record.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedBad[1](bad-paired/pair1-one-more-record.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedBad[1](bad-paired/pair1-one-more-record.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedBad[1](bad-paired/pair1-one-more-record.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedBad[1](bad-paired/pair1-one-more-record.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedBad[1](bad-paired/pair1-one-more-record.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedBad[1](bad-paired/pair1-one-more-record.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair1-one-more-record.txt -OUTPUT /tmp/pair1-one-more-record.txt8408580296473364818.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 -FASTQ2 /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair1-one-more-record.txt -OUTPUT /tmp/pair1-one-more-record.txt8408580296473364818.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 -FASTQ2 /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt Test: Test method testPairedBad[1](bad-paired/pair1-one-more-record.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedBad[1](bad-paired/pair1-one-more-record.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPairedBad[1](bad-paired/pair1-one-more-record.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPairedBad[1](bad-paired/pair1-one-more-record.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.861 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:35.861 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedBad[1](bad-paired/pair1-one-more-record.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.861 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:35.861 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedBad[1](bad-paired/pair1-one-more-record.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.861 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:35.861 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedBad[1](bad-paired/pair1-one-more-record.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.862 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:35.862 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedBad[1](bad-paired/pair1-one-more-record.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:35 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair1-one-more-record.txt FASTQ2=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1-one-more-record.txt8408580296473364818.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:35 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair1-one-more-record.txt FASTQ2=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1-one-more-record.txt8408580296473364818.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedBad[1](bad-paired/pair1-one-more-record.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedBad[1](bad-paired/pair1-one-more-record.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:35 FastqToSam Auto-detected quality format as: Standard. INFO 2024-07-02 11:57:35 FastqToSam Auto-detected quality format as: Standard. Test: Test method testPairedBad[1](bad-paired/pair1-one-more-record.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:35 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:35 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testPairedBad[1](bad-paired/pair1-one-more-record.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testPairedBad[1](bad-paired/pair1-one-more-record.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testPairedBad[2](ok-paired/pair1.txt, bad-paired/pair2-badnum.txt)(picard.sam.FastqToSamTest) Test: Test method testPairedBad[2](ok-paired/pair1.txt, bad-paired/pair2-badnum.txt)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:35 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testPairedBad[2](ok-paired/pair1.txt, bad-paired/pair2-badnum.txt) STANDARD_ERROR INFO 2024-07-02 11:57:35 FastqToSam Test: Test method testPairedBad[2](ok-paired/pair1.txt, bad-paired/pair2-badnum.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPairedBad[2](ok-paired/pair1.txt, bad-paired/pair2-badnum.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedBad[2](ok-paired/pair1.txt, bad-paired/pair2-badnum.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedBad[2](ok-paired/pair1.txt, bad-paired/pair2-badnum.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedBad[2](ok-paired/pair1.txt, bad-paired/pair2-badnum.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedBad[2](ok-paired/pair1.txt, bad-paired/pair2-badnum.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedBad[2](ok-paired/pair1.txt, bad-paired/pair2-badnum.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedBad[2](ok-paired/pair1.txt, bad-paired/pair2-badnum.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedBad[2](ok-paired/pair1.txt, bad-paired/pair2-badnum.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair1.txt -OUTPUT /tmp/pair1.txt16531685146366443114.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 -FASTQ2 /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair2-badnum.txt ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair1.txt -OUTPUT /tmp/pair1.txt16531685146366443114.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 -FASTQ2 /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair2-badnum.txt Test: Test method testPairedBad[2](ok-paired/pair1.txt, bad-paired/pair2-badnum.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedBad[2](ok-paired/pair1.txt, bad-paired/pair2-badnum.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPairedBad[2](ok-paired/pair1.txt, bad-paired/pair2-badnum.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPairedBad[2](ok-paired/pair1.txt, bad-paired/pair2-badnum.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.954 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:35.954 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedBad[2](ok-paired/pair1.txt, bad-paired/pair2-badnum.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.954 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:35.954 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedBad[2](ok-paired/pair1.txt, bad-paired/pair2-badnum.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.954 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:35.954 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedBad[2](ok-paired/pair1.txt, bad-paired/pair2-badnum.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:35.954 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:35.954 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedBad[2](ok-paired/pair1.txt, bad-paired/pair2-badnum.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:35 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair1.txt FASTQ2=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair2-badnum.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1.txt16531685146366443114.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:35 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair1.txt FASTQ2=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair2-badnum.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1.txt16531685146366443114.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedBad[2](ok-paired/pair1.txt, bad-paired/pair2-badnum.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedBad[2](ok-paired/pair1.txt, bad-paired/pair2-badnum.txt)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:35 FastqToSam Auto-detected quality format as: Standard. INFO 2024-07-02 11:57:35 FastqToSam Auto-detected quality format as: Standard. Test: Test method testPairedBad[2](ok-paired/pair1.txt, bad-paired/pair2-badnum.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:35 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:35 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testPairedBad[2](ok-paired/pair1.txt, bad-paired/pair2-badnum.txt)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testPairedBad[2](ok-paired/pair1.txt, bad-paired/pair2-badnum.txt)(picard.sam.FastqToSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testPairedBad[3](bad-paired/pair1-badnum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) Test: Test method testPairedBad[3](bad-paired/pair1-badnum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:36 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testPairedBad[3](bad-paired/pair1-badnum.txt, ok-paired/pair2.txt) STANDARD_ERROR INFO 2024-07-02 11:57:36 FastqToSam Test: Test method testPairedBad[3](bad-paired/pair1-badnum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPairedBad[3](bad-paired/pair1-badnum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedBad[3](bad-paired/pair1-badnum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedBad[3](bad-paired/pair1-badnum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedBad[3](bad-paired/pair1-badnum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedBad[3](bad-paired/pair1-badnum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedBad[3](bad-paired/pair1-badnum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedBad[3](bad-paired/pair1-badnum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedBad[3](bad-paired/pair1-badnum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair1-badnum.txt -OUTPUT /tmp/pair1-badnum.txt6048660391567687981.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 -FASTQ2 /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair1-badnum.txt -OUTPUT /tmp/pair1-badnum.txt6048660391567687981.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 -FASTQ2 /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt Test: Test method testPairedBad[3](bad-paired/pair1-badnum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedBad[3](bad-paired/pair1-badnum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPairedBad[3](bad-paired/pair1-badnum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPairedBad[3](bad-paired/pair1-badnum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.039 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:36.039 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedBad[3](bad-paired/pair1-badnum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.039 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:36.039 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedBad[3](bad-paired/pair1-badnum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.040 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:36.040 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedBad[3](bad-paired/pair1-badnum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.040 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:36.040 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedBad[3](bad-paired/pair1-badnum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair1-badnum.txt FASTQ2=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1-badnum.txt6048660391567687981.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:36 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair1-badnum.txt FASTQ2=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1-badnum.txt6048660391567687981.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedBad[3](bad-paired/pair1-badnum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedBad[3](bad-paired/pair1-badnum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:36 FastqToSam Auto-detected quality format as: Standard. INFO 2024-07-02 11:57:36 FastqToSam Auto-detected quality format as: Standard. Test: Test method testPairedBad[3](bad-paired/pair1-badnum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:36 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testPairedBad[3](bad-paired/pair1-badnum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testPairedBad[3](bad-paired/pair1-badnum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testPairedBad[4](bad-paired/pair1-nonum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) Test: Test method testPairedBad[4](bad-paired/pair1-nonum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:36 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testPairedBad[4](bad-paired/pair1-nonum.txt, ok-paired/pair2.txt) STANDARD_ERROR INFO 2024-07-02 11:57:36 FastqToSam Test: Test method testPairedBad[4](bad-paired/pair1-nonum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPairedBad[4](bad-paired/pair1-nonum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedBad[4](bad-paired/pair1-nonum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedBad[4](bad-paired/pair1-nonum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedBad[4](bad-paired/pair1-nonum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedBad[4](bad-paired/pair1-nonum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedBad[4](bad-paired/pair1-nonum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedBad[4](bad-paired/pair1-nonum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedBad[4](bad-paired/pair1-nonum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair1-nonum.txt -OUTPUT /tmp/pair1-nonum.txt11507168138870699346.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 -FASTQ2 /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair1-nonum.txt -OUTPUT /tmp/pair1-nonum.txt11507168138870699346.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 -FASTQ2 /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt Test: Test method testPairedBad[4](bad-paired/pair1-nonum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedBad[4](bad-paired/pair1-nonum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPairedBad[4](bad-paired/pair1-nonum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPairedBad[4](bad-paired/pair1-nonum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.132 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:36.132 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedBad[4](bad-paired/pair1-nonum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.132 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:36.132 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedBad[4](bad-paired/pair1-nonum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.132 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:36.132 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedBad[4](bad-paired/pair1-nonum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.132 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:36.132 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedBad[4](bad-paired/pair1-nonum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair1-nonum.txt FASTQ2=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1-nonum.txt11507168138870699346.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:36 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair1-nonum.txt FASTQ2=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1-nonum.txt11507168138870699346.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedBad[4](bad-paired/pair1-nonum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedBad[4](bad-paired/pair1-nonum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:36 FastqToSam Auto-detected quality format as: Standard. INFO 2024-07-02 11:57:36 FastqToSam Auto-detected quality format as: Standard. Test: Test method testPairedBad[4](bad-paired/pair1-nonum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:36 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testPairedBad[4](bad-paired/pair1-nonum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testPairedBad[4](bad-paired/pair1-nonum.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testPairedBad[5](bad-paired/pair1-onetoken.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) Test: Test method testPairedBad[5](bad-paired/pair1-onetoken.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:36 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testPairedBad[5](bad-paired/pair1-onetoken.txt, ok-paired/pair2.txt) STANDARD_ERROR INFO 2024-07-02 11:57:36 FastqToSam Test: Test method testPairedBad[5](bad-paired/pair1-onetoken.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPairedBad[5](bad-paired/pair1-onetoken.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedBad[5](bad-paired/pair1-onetoken.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedBad[5](bad-paired/pair1-onetoken.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedBad[5](bad-paired/pair1-onetoken.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedBad[5](bad-paired/pair1-onetoken.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedBad[5](bad-paired/pair1-onetoken.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedBad[5](bad-paired/pair1-onetoken.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedBad[5](bad-paired/pair1-onetoken.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair1-onetoken.txt -OUTPUT /tmp/pair1-onetoken.txt1875292938850019823.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 -FASTQ2 /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair1-onetoken.txt -OUTPUT /tmp/pair1-onetoken.txt1875292938850019823.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 -FASTQ2 /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt Test: Test method testPairedBad[5](bad-paired/pair1-onetoken.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedBad[5](bad-paired/pair1-onetoken.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPairedBad[5](bad-paired/pair1-onetoken.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPairedBad[5](bad-paired/pair1-onetoken.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.302 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:36.302 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedBad[5](bad-paired/pair1-onetoken.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.302 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:36.302 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedBad[5](bad-paired/pair1-onetoken.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.302 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:36.302 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedBad[5](bad-paired/pair1-onetoken.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.302 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:36.302 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedBad[5](bad-paired/pair1-onetoken.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair1-onetoken.txt FASTQ2=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1-onetoken.txt1875292938850019823.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:36 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/bad-paired/pair1-onetoken.txt FASTQ2=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1-onetoken.txt1875292938850019823.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedBad[5](bad-paired/pair1-onetoken.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedBad[5](bad-paired/pair1-onetoken.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:36 FastqToSam Auto-detected quality format as: Standard. INFO 2024-07-02 11:57:36 FastqToSam Auto-detected quality format as: Standard. Test: Test method testPairedBad[5](bad-paired/pair1-onetoken.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:36 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testPairedBad[5](bad-paired/pair1-onetoken.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testPairedBad[5](bad-paired/pair1-onetoken.txt, ok-paired/pair2.txt)(picard.sam.FastqToSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testPairedOk[0](ok-paired/pair1.txt, ok-paired/pair2.txt, Standard)(picard.sam.FastqToSamTest) Test: Test method testPairedOk[0](ok-paired/pair1.txt, ok-paired/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:36 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testPairedOk[0](ok-paired/pair1.txt, ok-paired/pair2.txt, Standard) STANDARD_ERROR INFO 2024-07-02 11:57:36 FastqToSam Test: Test method testPairedOk[0](ok-paired/pair1.txt, ok-paired/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPairedOk[0](ok-paired/pair1.txt, ok-paired/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedOk[0](ok-paired/pair1.txt, ok-paired/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedOk[0](ok-paired/pair1.txt, ok-paired/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedOk[0](ok-paired/pair1.txt, ok-paired/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedOk[0](ok-paired/pair1.txt, ok-paired/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedOk[0](ok-paired/pair1.txt, ok-paired/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedOk[0](ok-paired/pair1.txt, ok-paired/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedOk[0](ok-paired/pair1.txt, ok-paired/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair1.txt -OUTPUT /tmp/pair1.txt13992613843424973865.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 -FASTQ2 /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair1.txt -OUTPUT /tmp/pair1.txt13992613843424973865.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 -FASTQ2 /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt Test: Test method testPairedOk[0](ok-paired/pair1.txt, ok-paired/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedOk[0](ok-paired/pair1.txt, ok-paired/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPairedOk[0](ok-paired/pair1.txt, ok-paired/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPairedOk[0](ok-paired/pair1.txt, ok-paired/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.415 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:36.415 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedOk[0](ok-paired/pair1.txt, ok-paired/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.415 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:36.415 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedOk[0](ok-paired/pair1.txt, ok-paired/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.415 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:36.415 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedOk[0](ok-paired/pair1.txt, ok-paired/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.415 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:36.415 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedOk[0](ok-paired/pair1.txt, ok-paired/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair1.txt FASTQ2=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1.txt13992613843424973865.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:36 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair1.txt FASTQ2=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1.txt13992613843424973865.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedOk[0](ok-paired/pair1.txt, ok-paired/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedOk[0](ok-paired/pair1.txt, ok-paired/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:36 FastqToSam Auto-detected quality format as: Standard. INFO 2024-07-02 11:57:36 FastqToSam Auto-detected quality format as: Standard. Test: Test method testPairedOk[0](ok-paired/pair1.txt, ok-paired/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:36 FastqToSam Processed 5 fastq reads INFO 2024-07-02 11:57:36 FastqToSam Processed 5 fastq reads Test: Test method testPairedOk[0](ok-paired/pair1.txt, ok-paired/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:36 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testPairedOk[0](ok-paired/pair1.txt, ok-paired/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testPairedOk[1](fastq-illumina/s_1_1_sequence.txt, fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) Test: Test method testPairedOk[1](fastq-illumina/s_1_1_sequence.txt, fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:36 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testPairedOk[1](fastq-illumina/s_1_1_sequence.txt, fastq-illumina/s_1_2_sequence.txt, Illumina) STANDARD_ERROR INFO 2024-07-02 11:57:36 FastqToSam Test: Test method testPairedOk[1](fastq-illumina/s_1_1_sequence.txt, fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPairedOk[1](fastq-illumina/s_1_1_sequence.txt, fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedOk[1](fastq-illumina/s_1_1_sequence.txt, fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedOk[1](fastq-illumina/s_1_1_sequence.txt, fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedOk[1](fastq-illumina/s_1_1_sequence.txt, fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedOk[1](fastq-illumina/s_1_1_sequence.txt, fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedOk[1](fastq-illumina/s_1_1_sequence.txt, fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedOk[1](fastq-illumina/s_1_1_sequence.txt, fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedOk[1](fastq-illumina/s_1_1_sequence.txt, fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_1_sequence.txt -OUTPUT /tmp/s_1_1_sequence.txt2009007497379432516.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 -FASTQ2 /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_2_sequence.txt ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_1_sequence.txt -OUTPUT /tmp/s_1_1_sequence.txt2009007497379432516.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 -FASTQ2 /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_2_sequence.txt Test: Test method testPairedOk[1](fastq-illumina/s_1_1_sequence.txt, fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPairedOk[1](fastq-illumina/s_1_1_sequence.txt, fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPairedOk[1](fastq-illumina/s_1_1_sequence.txt, fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPairedOk[1](fastq-illumina/s_1_1_sequence.txt, fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.545 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:36.545 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedOk[1](fastq-illumina/s_1_1_sequence.txt, fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.545 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:36.545 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedOk[1](fastq-illumina/s_1_1_sequence.txt, fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.545 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:36.545 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedOk[1](fastq-illumina/s_1_1_sequence.txt, fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.545 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:36.545 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedOk[1](fastq-illumina/s_1_1_sequence.txt, fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_1_sequence.txt FASTQ2=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_2_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_1_sequence.txt2009007497379432516.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:36 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_1_sequence.txt FASTQ2=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_2_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_1_sequence.txt2009007497379432516.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedOk[1](fastq-illumina/s_1_1_sequence.txt, fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedOk[1](fastq-illumina/s_1_1_sequence.txt, fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: WARNING 2024-07-02 11:57:36 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. WARNING 2024-07-02 11:57:36 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. Test: Test method testPairedOk[1](fastq-illumina/s_1_1_sequence.txt, fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:36 FastqToSam Auto-detected quality format as: Illumina. INFO 2024-07-02 11:57:36 FastqToSam Auto-detected quality format as: Illumina. Test: Test method testPairedOk[1](fastq-illumina/s_1_1_sequence.txt, fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:36 FastqToSam Processed 10 fastq reads INFO 2024-07-02 11:57:36 FastqToSam Processed 10 fastq reads Test: Test method testPairedOk[1](fastq-illumina/s_1_1_sequence.txt, fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:36 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testPairedOk[1](fastq-illumina/s_1_1_sequence.txt, fastq-illumina/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testPermissiveFail[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) Test: Test method testPermissiveFail[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:36 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testPermissiveFail[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard) STANDARD_ERROR INFO 2024-07-02 11:57:36 FastqToSam Test: Test method testPermissiveFail[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveFail[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPermissiveFail[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveFail[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPermissiveFail[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPermissiveFail[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveFail[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPermissiveFail[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveFail[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair1.txt -OUTPUT /tmp/pair1.txt13569458265268017555.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 -FASTQ2 /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair2.txt ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair1.txt -OUTPUT /tmp/pair1.txt13569458265268017555.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 -FASTQ2 /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair2.txt Test: Test method testPermissiveFail[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveFail[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveFail[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveFail[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.610 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:36.610 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPermissiveFail[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.610 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:36.610 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPermissiveFail[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.610 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:36.610 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPermissiveFail[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.610 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:36.610 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPermissiveFail[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair1.txt FASTQ2=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1.txt13569458265268017555.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:36 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair1.txt FASTQ2=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1.txt13569458265268017555.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPermissiveFail[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPermissiveFail[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:36 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testPermissiveFail[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testPermissiveFail[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testPermissiveFail[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) Test: Test method testPermissiveFail[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:36 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testPermissiveFail[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina) STANDARD_ERROR INFO 2024-07-02 11:57:36 FastqToSam Test: Test method testPermissiveFail[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveFail[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPermissiveFail[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveFail[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPermissiveFail[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPermissiveFail[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveFail[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPermissiveFail[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveFail[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt -OUTPUT /tmp/s_1_1_sequence.txt3349735834633198108.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 -FASTQ2 /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt -OUTPUT /tmp/s_1_1_sequence.txt3349735834633198108.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 -FASTQ2 /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt Test: Test method testPermissiveFail[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveFail[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveFail[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveFail[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.662 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:36.662 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPermissiveFail[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.662 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:36.662 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPermissiveFail[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.662 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:36.662 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPermissiveFail[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.662 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:36.662 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPermissiveFail[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt FASTQ2=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_1_sequence.txt3349735834633198108.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:36 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt FASTQ2=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_1_sequence.txt3349735834633198108.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPermissiveFail[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPermissiveFail[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:36 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testPermissiveFail[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testPermissiveFail[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testPermissiveFail[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) Test: Test method testPermissiveFail[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:36 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testPermissiveFail[2](permissive-format/pair1.txt, null, Standard) STANDARD_ERROR INFO 2024-07-02 11:57:36 FastqToSam Test: Test method testPermissiveFail[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveFail[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPermissiveFail[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveFail[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPermissiveFail[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPermissiveFail[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveFail[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPermissiveFail[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveFail[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair1.txt -OUTPUT /tmp/pair1.txt7678818852745897061.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair1.txt -OUTPUT /tmp/pair1.txt7678818852745897061.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 Test: Test method testPermissiveFail[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveFail[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveFail[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveFail[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.718 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:36.718 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPermissiveFail[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.718 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:36.718 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPermissiveFail[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.718 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:36.718 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPermissiveFail[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.718 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:36.718 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPermissiveFail[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair1.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1.txt7678818852745897061.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:36 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair1.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1.txt7678818852745897061.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPermissiveFail[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPermissiveFail[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:36 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testPermissiveFail[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testPermissiveFail[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testPermissiveFail[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) Test: Test method testPermissiveFail[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:36 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testPermissiveFail[3](permissive-format/pair2.txt, null, Standard) STANDARD_ERROR INFO 2024-07-02 11:57:36 FastqToSam Test: Test method testPermissiveFail[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveFail[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPermissiveFail[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveFail[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPermissiveFail[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPermissiveFail[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveFail[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPermissiveFail[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveFail[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair2.txt -OUTPUT /tmp/pair2.txt7128642088772282489.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair2.txt -OUTPUT /tmp/pair2.txt7128642088772282489.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 Test: Test method testPermissiveFail[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveFail[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveFail[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveFail[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.760 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:36.760 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPermissiveFail[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.760 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:36.760 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPermissiveFail[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.760 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:36.760 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPermissiveFail[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.760 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:36.760 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPermissiveFail[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair2.txt7128642088772282489.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:36 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair2.txt7128642088772282489.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPermissiveFail[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPermissiveFail[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:36 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testPermissiveFail[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testPermissiveFail[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testPermissiveFail[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) Test: Test method testPermissiveFail[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:36 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testPermissiveFail[4](permissive-format/s_1_1_sequence.txt, null, Illumina) STANDARD_ERROR INFO 2024-07-02 11:57:36 FastqToSam Test: Test method testPermissiveFail[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveFail[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPermissiveFail[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveFail[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPermissiveFail[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPermissiveFail[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveFail[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPermissiveFail[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveFail[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt -OUTPUT /tmp/s_1_1_sequence.txt12022264193249595517.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt -OUTPUT /tmp/s_1_1_sequence.txt12022264193249595517.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 Test: Test method testPermissiveFail[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveFail[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveFail[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveFail[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.819 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:36.819 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPermissiveFail[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.819 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:36.819 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPermissiveFail[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.820 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:36.820 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPermissiveFail[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.820 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:36.820 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPermissiveFail[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_1_sequence.txt12022264193249595517.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:36 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_1_sequence.txt12022264193249595517.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPermissiveFail[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPermissiveFail[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:36 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testPermissiveFail[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testPermissiveFail[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testPermissiveFail[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) Test: Test method testPermissiveFail[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:36 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testPermissiveFail[5](permissive-format/s_1_2_sequence.txt, null, Illumina) STANDARD_ERROR INFO 2024-07-02 11:57:36 FastqToSam Test: Test method testPermissiveFail[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveFail[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPermissiveFail[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveFail[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPermissiveFail[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPermissiveFail[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveFail[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPermissiveFail[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveFail[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt -OUTPUT /tmp/s_1_2_sequence.txt11815867868623338193.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt -OUTPUT /tmp/s_1_2_sequence.txt11815867868623338193.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 Test: Test method testPermissiveFail[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveFail[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveFail[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveFail[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.873 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:36.873 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPermissiveFail[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.873 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:36.873 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPermissiveFail[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.873 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:36.873 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPermissiveFail[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.873 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:36.873 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPermissiveFail[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_2_sequence.txt11815867868623338193.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:36 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_2_sequence.txt11815867868623338193.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPermissiveFail[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPermissiveFail[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:36 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testPermissiveFail[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testPermissiveFail[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testPermissiveFail[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) Test: Test method testPermissiveFail[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:36 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testPermissiveFail[6](permissive-format/s_1_sequence.txt, null, Illumina) STANDARD_ERROR INFO 2024-07-02 11:57:36 FastqToSam Test: Test method testPermissiveFail[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveFail[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPermissiveFail[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveFail[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPermissiveFail[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPermissiveFail[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveFail[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPermissiveFail[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveFail[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_sequence.txt -OUTPUT /tmp/s_1_sequence.txt5885582576438414741.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_sequence.txt -OUTPUT /tmp/s_1_sequence.txt5885582576438414741.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 Test: Test method testPermissiveFail[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveFail[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveFail[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveFail[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.920 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:36.920 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPermissiveFail[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.920 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:36.920 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPermissiveFail[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.920 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:36.920 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPermissiveFail[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.920 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:36.920 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPermissiveFail[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_sequence.txt5885582576438414741.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:36 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_sequence.txt5885582576438414741.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPermissiveFail[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPermissiveFail[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:36 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testPermissiveFail[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testPermissiveFail[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testPermissiveOk[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) Test: Test method testPermissiveOk[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:36 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testPermissiveOk[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard) STANDARD_ERROR INFO 2024-07-02 11:57:36 FastqToSam Test: Test method testPermissiveOk[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveOk[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPermissiveOk[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveOk[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPermissiveOk[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPermissiveOk[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveOk[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPermissiveOk[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveOk[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair1.txt -OUTPUT /tmp/pair1.txt3658330951428996922.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 -FASTQ2 /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair2.txt -ALLOW_AND_IGNORE_EMPTY_LINES true ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair1.txt -OUTPUT /tmp/pair1.txt3658330951428996922.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 -FASTQ2 /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair2.txt -ALLOW_AND_IGNORE_EMPTY_LINES true Test: Test method testPermissiveOk[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveOk[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveOk[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveOk[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.982 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:36.982 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPermissiveOk[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.982 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:36.982 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPermissiveOk[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.982 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:36.982 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPermissiveOk[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:36.982 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:36.982 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPermissiveOk[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair1.txt FASTQ2=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1.txt3658330951428996922.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:36 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair1.txt FASTQ2=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1.txt3658330951428996922.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPermissiveOk[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPermissiveOk[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:36 FastqToSam Auto-detected quality format as: Standard. INFO 2024-07-02 11:57:36 FastqToSam Auto-detected quality format as: Standard. Test: Test method testPermissiveOk[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:36 FastqToSam Processed 5 fastq reads INFO 2024-07-02 11:57:36 FastqToSam Processed 5 fastq reads Test: Test method testPermissiveOk[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:36 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:36 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testPermissiveOk[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testPermissiveOk[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) Test: Test method testPermissiveOk[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testPermissiveOk[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina) STANDARD_ERROR INFO 2024-07-02 11:57:37 FastqToSam Test: Test method testPermissiveOk[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveOk[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPermissiveOk[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveOk[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPermissiveOk[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPermissiveOk[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveOk[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPermissiveOk[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveOk[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt -OUTPUT /tmp/s_1_1_sequence.txt4883994014403566898.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 -FASTQ2 /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt -ALLOW_AND_IGNORE_EMPTY_LINES true ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt -OUTPUT /tmp/s_1_1_sequence.txt4883994014403566898.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 -FASTQ2 /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt -ALLOW_AND_IGNORE_EMPTY_LINES true Test: Test method testPermissiveOk[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveOk[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveOk[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveOk[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.038 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:37.038 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPermissiveOk[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.038 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:37.038 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPermissiveOk[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.038 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:37.038 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPermissiveOk[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.038 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:37.038 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPermissiveOk[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt FASTQ2=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_1_sequence.txt4883994014403566898.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:37 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt FASTQ2=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_1_sequence.txt4883994014403566898.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPermissiveOk[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPermissiveOk[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: WARNING 2024-07-02 11:57:37 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. WARNING 2024-07-02 11:57:37 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. Test: Test method testPermissiveOk[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Auto-detected quality format as: Illumina. INFO 2024-07-02 11:57:37 FastqToSam Auto-detected quality format as: Illumina. Test: Test method testPermissiveOk[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Processed 10 fastq reads INFO 2024-07-02 11:57:37 FastqToSam Processed 10 fastq reads Test: Test method testPermissiveOk[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:37 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testPermissiveOk[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testPermissiveOk[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) Test: Test method testPermissiveOk[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testPermissiveOk[2](permissive-format/pair1.txt, null, Standard) STANDARD_ERROR INFO 2024-07-02 11:57:37 FastqToSam Test: Test method testPermissiveOk[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveOk[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPermissiveOk[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveOk[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPermissiveOk[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPermissiveOk[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveOk[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPermissiveOk[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveOk[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair1.txt -OUTPUT /tmp/pair1.txt14819240352073034977.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 -ALLOW_AND_IGNORE_EMPTY_LINES true ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair1.txt -OUTPUT /tmp/pair1.txt14819240352073034977.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 -ALLOW_AND_IGNORE_EMPTY_LINES true Test: Test method testPermissiveOk[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveOk[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveOk[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveOk[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.095 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:37.095 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPermissiveOk[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.095 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:37.095 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPermissiveOk[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.095 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:37.095 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPermissiveOk[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.095 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:37.095 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPermissiveOk[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair1.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1.txt14819240352073034977.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:37 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair1.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1.txt14819240352073034977.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPermissiveOk[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPermissiveOk[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Auto-detected quality format as: Standard. INFO 2024-07-02 11:57:37 FastqToSam Auto-detected quality format as: Standard. Test: Test method testPermissiveOk[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Processed 5 fastq reads INFO 2024-07-02 11:57:37 FastqToSam Processed 5 fastq reads Test: Test method testPermissiveOk[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:37 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testPermissiveOk[2](permissive-format/pair1.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testPermissiveOk[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) Test: Test method testPermissiveOk[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testPermissiveOk[3](permissive-format/pair2.txt, null, Standard) STANDARD_ERROR INFO 2024-07-02 11:57:37 FastqToSam Test: Test method testPermissiveOk[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveOk[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPermissiveOk[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveOk[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPermissiveOk[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPermissiveOk[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveOk[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPermissiveOk[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveOk[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair2.txt -OUTPUT /tmp/pair2.txt14972735810444156555.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 -ALLOW_AND_IGNORE_EMPTY_LINES true ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair2.txt -OUTPUT /tmp/pair2.txt14972735810444156555.sam -QUALITY_FORMAT Standard -READ_GROUP_NAME rg -SAMPLE_NAME s1 -ALLOW_AND_IGNORE_EMPTY_LINES true Test: Test method testPermissiveOk[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveOk[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveOk[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveOk[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.150 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:37.150 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPermissiveOk[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.150 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:37.150 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPermissiveOk[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.150 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:37.150 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPermissiveOk[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.150 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:37.150 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPermissiveOk[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair2.txt14972735810444156555.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:37 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair2.txt14972735810444156555.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPermissiveOk[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPermissiveOk[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Auto-detected quality format as: Standard. INFO 2024-07-02 11:57:37 FastqToSam Auto-detected quality format as: Standard. Test: Test method testPermissiveOk[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Processed 5 fastq reads INFO 2024-07-02 11:57:37 FastqToSam Processed 5 fastq reads Test: Test method testPermissiveOk[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:37 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testPermissiveOk[3](permissive-format/pair2.txt, null, Standard)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testPermissiveOk[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) Test: Test method testPermissiveOk[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testPermissiveOk[4](permissive-format/s_1_1_sequence.txt, null, Illumina) STANDARD_ERROR INFO 2024-07-02 11:57:37 FastqToSam Test: Test method testPermissiveOk[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveOk[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPermissiveOk[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveOk[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPermissiveOk[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPermissiveOk[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveOk[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPermissiveOk[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveOk[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt -OUTPUT /tmp/s_1_1_sequence.txt8281777259314446271.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 -ALLOW_AND_IGNORE_EMPTY_LINES true ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt -OUTPUT /tmp/s_1_1_sequence.txt8281777259314446271.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 -ALLOW_AND_IGNORE_EMPTY_LINES true Test: Test method testPermissiveOk[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveOk[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveOk[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveOk[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.205 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:37.205 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPermissiveOk[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.205 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:37.205 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPermissiveOk[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.205 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:37.205 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPermissiveOk[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.205 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:37.205 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPermissiveOk[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_1_sequence.txt8281777259314446271.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:37 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_1_sequence.txt8281777259314446271.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPermissiveOk[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPermissiveOk[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: WARNING 2024-07-02 11:57:37 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. WARNING 2024-07-02 11:57:37 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. Test: Test method testPermissiveOk[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Auto-detected quality format as: Illumina. INFO 2024-07-02 11:57:37 FastqToSam Auto-detected quality format as: Illumina. Test: Test method testPermissiveOk[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Processed 10 fastq reads INFO 2024-07-02 11:57:37 FastqToSam Processed 10 fastq reads Test: Test method testPermissiveOk[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:37 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testPermissiveOk[4](permissive-format/s_1_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testPermissiveOk[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) Test: Test method testPermissiveOk[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testPermissiveOk[5](permissive-format/s_1_2_sequence.txt, null, Illumina) STANDARD_ERROR INFO 2024-07-02 11:57:37 FastqToSam Test: Test method testPermissiveOk[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveOk[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPermissiveOk[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveOk[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPermissiveOk[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPermissiveOk[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveOk[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPermissiveOk[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveOk[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt -OUTPUT /tmp/s_1_2_sequence.txt9623157293425758266.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 -ALLOW_AND_IGNORE_EMPTY_LINES true ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt -OUTPUT /tmp/s_1_2_sequence.txt9623157293425758266.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 -ALLOW_AND_IGNORE_EMPTY_LINES true Test: Test method testPermissiveOk[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveOk[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveOk[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveOk[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:37.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPermissiveOk[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:37.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPermissiveOk[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:37.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPermissiveOk[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:37.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPermissiveOk[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_2_sequence.txt9623157293425758266.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:37 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_2_sequence.txt9623157293425758266.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPermissiveOk[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPermissiveOk[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: WARNING 2024-07-02 11:57:37 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. WARNING 2024-07-02 11:57:37 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. Test: Test method testPermissiveOk[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Auto-detected quality format as: Illumina. INFO 2024-07-02 11:57:37 FastqToSam Auto-detected quality format as: Illumina. Test: Test method testPermissiveOk[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Processed 10 fastq reads INFO 2024-07-02 11:57:37 FastqToSam Processed 10 fastq reads Test: Test method testPermissiveOk[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:37 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testPermissiveOk[5](permissive-format/s_1_2_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testPermissiveOk[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) Test: Test method testPermissiveOk[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testPermissiveOk[6](permissive-format/s_1_sequence.txt, null, Illumina) STANDARD_ERROR INFO 2024-07-02 11:57:37 FastqToSam Test: Test method testPermissiveOk[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveOk[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPermissiveOk[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveOk[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPermissiveOk[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPermissiveOk[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveOk[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPermissiveOk[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveOk[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_sequence.txt -OUTPUT /tmp/s_1_sequence.txt15157275157132753020.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 -ALLOW_AND_IGNORE_EMPTY_LINES true ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_sequence.txt -OUTPUT /tmp/s_1_sequence.txt15157275157132753020.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 -ALLOW_AND_IGNORE_EMPTY_LINES true Test: Test method testPermissiveOk[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testPermissiveOk[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveOk[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testPermissiveOk[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.528 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:37.528 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPermissiveOk[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.528 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:37.528 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPermissiveOk[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.528 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:37.528 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPermissiveOk[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.528 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:37.528 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPermissiveOk[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_sequence.txt15157275157132753020.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:37 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/permissive-format/s_1_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_sequence.txt15157275157132753020.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPermissiveOk[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPermissiveOk[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: WARNING 2024-07-02 11:57:37 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. WARNING 2024-07-02 11:57:37 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. Test: Test method testPermissiveOk[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Auto-detected quality format as: Illumina. INFO 2024-07-02 11:57:37 FastqToSam Auto-detected quality format as: Illumina. Test: Test method testPermissiveOk[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Processed 10 fastq reads INFO 2024-07-02 11:57:37 FastqToSam Processed 10 fastq reads Test: Test method testPermissiveOk[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:37 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testPermissiveOk[6](permissive-format/s_1_sequence.txt, null, Illumina)(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Gradle suite > Gradle test > picard.sam.FastqToSamTest.testSequentialFiles STANDARD_ERROR INFO 2024-07-02 11:57:37 FastqToSam Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/single_end_R1_001.fastq -OUTPUT /tmp/single_end_R1_001.fastq15650602908877312803.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 -ALLOW_AND_IGNORE_EMPTY_LINES true ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/single_end_R1_001.fastq -OUTPUT /tmp/single_end_R1_001.fastq15650602908877312803.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 -ALLOW_AND_IGNORE_EMPTY_LINES true Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.595 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:37.595 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.595 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:37.595 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.595 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:37.595 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.596 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:37.596 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/single_end_R1_001.fastq QUALITY_FORMAT=Illumina OUTPUT=/tmp/single_end_R1_001.fastq15650602908877312803.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:37 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/single_end_R1_001.fastq QUALITY_FORMAT=Illumina OUTPUT=/tmp/single_end_R1_001.fastq15650602908877312803.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: WARNING 2024-07-02 11:57:37 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. WARNING 2024-07-02 11:57:37 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Auto-detected quality format as: Illumina. INFO 2024-07-02 11:57:37 FastqToSam Auto-detected quality format as: Illumina. Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Processed 1 fastq reads INFO 2024-07-02 11:57:37 FastqToSam Processed 1 fastq reads Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:37 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam INFO 2024-07-02 11:57:37 FastqToSam Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/single_end_R1_001.fastq -OUTPUT /tmp/single_end_R1_001.fastq16478225379335443511.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 -ALLOW_AND_IGNORE_EMPTY_LINES true -USE_SEQUENTIAL_FASTQS true ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/single_end_R1_001.fastq -OUTPUT /tmp/single_end_R1_001.fastq16478225379335443511.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 -ALLOW_AND_IGNORE_EMPTY_LINES true -USE_SEQUENTIAL_FASTQS true Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.657 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:37.657 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.657 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:37.657 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.657 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:37.657 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.657 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:37.657 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/single_end_R1_001.fastq USE_SEQUENTIAL_FASTQS=true QUALITY_FORMAT=Illumina OUTPUT=/tmp/single_end_R1_001.fastq16478225379335443511.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:37 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/single_end_R1_001.fastq USE_SEQUENTIAL_FASTQS=true QUALITY_FORMAT=Illumina OUTPUT=/tmp/single_end_R1_001.fastq16478225379335443511.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: WARNING 2024-07-02 11:57:37 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. WARNING 2024-07-02 11:57:37 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Auto-detected quality format as: Illumina. INFO 2024-07-02 11:57:37 FastqToSam Auto-detected quality format as: Illumina. Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Processed 1 fastq reads INFO 2024-07-02 11:57:37 FastqToSam Processed 1 fastq reads Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Processed 1 fastq reads INFO 2024-07-02 11:57:37 FastqToSam Processed 1 fastq reads Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:37 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam INFO 2024-07-02 11:57:37 FastqToSam Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/paired_end_R1_001.fastq -OUTPUT /tmp/paired_end_R1_001.fastq3493103105132052237.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 -FASTQ2 /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/paired_end_R2_001.fastq -ALLOW_AND_IGNORE_EMPTY_LINES true ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/paired_end_R1_001.fastq -OUTPUT /tmp/paired_end_R1_001.fastq3493103105132052237.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 -FASTQ2 /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/paired_end_R2_001.fastq -ALLOW_AND_IGNORE_EMPTY_LINES true Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.721 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:37.721 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.721 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:37.721 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.722 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:37.722 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.722 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:37.722 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/paired_end_R1_001.fastq FASTQ2=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/paired_end_R2_001.fastq QUALITY_FORMAT=Illumina OUTPUT=/tmp/paired_end_R1_001.fastq3493103105132052237.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:37 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/paired_end_R1_001.fastq FASTQ2=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/paired_end_R2_001.fastq QUALITY_FORMAT=Illumina OUTPUT=/tmp/paired_end_R1_001.fastq3493103105132052237.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: WARNING 2024-07-02 11:57:37 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. WARNING 2024-07-02 11:57:37 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Auto-detected quality format as: Illumina. INFO 2024-07-02 11:57:37 FastqToSam Auto-detected quality format as: Illumina. Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Processed 1 fastq reads INFO 2024-07-02 11:57:37 FastqToSam Processed 1 fastq reads Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:37 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam INFO 2024-07-02 11:57:37 FastqToSam Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/paired_end_R1_001.fastq -OUTPUT /tmp/paired_end_R1_001.fastq9002835195781810292.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 -FASTQ2 /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/paired_end_R2_001.fastq -ALLOW_AND_IGNORE_EMPTY_LINES true -USE_SEQUENTIAL_FASTQS true ********** FastqToSam -FASTQ /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/paired_end_R1_001.fastq -OUTPUT /tmp/paired_end_R1_001.fastq9002835195781810292.sam -QUALITY_FORMAT Illumina -READ_GROUP_NAME rg -SAMPLE_NAME s1 -FASTQ2 /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/paired_end_R2_001.fastq -ALLOW_AND_IGNORE_EMPTY_LINES true -USE_SEQUENTIAL_FASTQS true Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: ********** ********** Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.771 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:37.771 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.771 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:37.771 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.771 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:37.771 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: 11:57:37.771 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:37.771 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/paired_end_R1_001.fastq FASTQ2=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/paired_end_R2_001.fastq USE_SEQUENTIAL_FASTQS=true QUALITY_FORMAT=Illumina OUTPUT=/tmp/paired_end_R1_001.fastq9002835195781810292.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:37 GMT+14:00 2024] FastqToSam FASTQ=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/paired_end_R1_001.fastq FASTQ2=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/fastq2bam/sequential-files/paired_end_R2_001.fastq USE_SEQUENTIAL_FASTQS=true QUALITY_FORMAT=Illumina OUTPUT=/tmp/paired_end_R1_001.fastq9002835195781810292.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: WARNING 2024-07-02 11:57:37 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. WARNING 2024-07-02 11:57:37 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Auto-detected quality format as: Illumina. INFO 2024-07-02 11:57:37 FastqToSam Auto-detected quality format as: Illumina. Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Processed 1 fastq reads INFO 2024-07-02 11:57:37 FastqToSam Processed 1 fastq reads Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: INFO 2024-07-02 11:57:37 FastqToSam Processed 1 fastq reads INFO 2024-07-02 11:57:37 FastqToSam Processed 1 fastq reads Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: [Tue Jul 02 11:57:37 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:37 GMT+14:00 2024] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Test: Test method testSequentialFiles(picard.sam.FastqToSamTest) produced standard out/err: Runtime.totalMemory()=1159725056 Runtime.totalMemory()=1159725056 Running Test: Test method testFifoBuffer(picard.util.FifoBufferTest) Running Test: Test method readFakedFile(picard.illumina.parser.readers.FilterFileReaderTest) Running Test: Test method readInvalidValuesForPicardException[0](pf_failing1.filter)(picard.illumina.parser.readers.FilterFileReaderTest) Running Test: Test method readInvalidValuesForPicardException[1](pf_failing2.filter)(picard.illumina.parser.readers.FilterFileReaderTest) Running Test: Test method readInvalidValuesForPicardException[2](pf_tooLarge.filter)(picard.illumina.parser.readers.FilterFileReaderTest) Running Test: Test method readInvalidValuesForPicardException[3](pf_tooShort.filter)(picard.illumina.parser.readers.FilterFileReaderTest) Running Test: Test method readInvalidValuesForPicardException[4](pf_badOpeningBytes.filter)(picard.illumina.parser.readers.FilterFileReaderTest) Running Test: Test method readInvalidValuesForPicardException[5](pf_badVersionBytes.filter)(picard.illumina.parser.readers.FilterFileReaderTest) Running Test: Test method readInvalidValuesForSAMException[0](pf_nonExistentFile.filter)(picard.illumina.parser.readers.FilterFileReaderTest) Running Test: Test method readPastEnd(picard.illumina.parser.readers.FilterFileReaderTest) Running Test: Test method readValidFile(picard.illumina.parser.readers.FilterFileReaderTest) Running Test: Test method passingParserTest[0]([Ljava.lang.Integer;@6ddc5180)(picard.illumina.parser.FilterParserTest) Running Test: Test method passingParserTest[1]([Ljava.lang.Integer;@4f5c25e0)(picard.illumina.parser.FilterParserTest) Running Test: Test method passingParserTest[2]([Ljava.lang.Integer;@1c005d79)(picard.illumina.parser.FilterParserTest) Running Test: Test method passingParserTest[3]([Ljava.lang.Integer;@11b859b6)(picard.illumina.parser.FilterParserTest) Running Test: Test method passingParserTest[4]([Ljava.lang.Integer;@668d55e7)(picard.illumina.parser.FilterParserTest) Running Test: Test method passingParserTest[5]([Ljava.lang.Integer;@229d1ab1)(picard.illumina.parser.FilterParserTest) Running Test: Test method passingSeekingParserTest[0](0, 2, [Ljava.lang.Integer;@17521e87, [[Ljava.lang.Boolean;@3a823174)(picard.illumina.parser.FilterParserTest) Running Test: Test method passingSeekingParserTest[1](4, 4, [Ljava.lang.Integer;@996cfa7, [[Ljava.lang.Boolean;@eb75e34)(picard.illumina.parser.FilterParserTest) Running Test: Test method passingSeekingParserTest[2](0, 3, [Ljava.lang.Integer;@52027766, [[Ljava.lang.Boolean;@6dd67176)(picard.illumina.parser.FilterParserTest) Running Test: Test method passingSeekingParserTest[3](15, 3, [Ljava.lang.Integer;@52028dda, [[Ljava.lang.Boolean;@137a69bb)(picard.illumina.parser.FilterParserTest) Running Test: Test method verifyDataTest[0]([Ljava.lang.Integer;@32829e2e, [Ljava.lang.Integer;@7428a9f9)(picard.illumina.parser.FilterParserTest) Running Test: Test method verifyDataTest[1]([Ljava.lang.Integer;@369f1a61, [Ljava.lang.Integer;@10ca9172)(picard.illumina.parser.FilterParserTest) Running Test: Test method verifyDataTest[2]([Ljava.lang.Integer;@6c855427, [Ljava.lang.Integer;@228717c4)(picard.illumina.parser.FilterParserTest) Running Test: Test method verifyDataTest[3]([Ljava.lang.Integer;@23f461c9, [Ljava.lang.Integer;@65163dfc)(picard.illumina.parser.FilterParserTest) Running Test: Test method verifyDataTest[4]([Ljava.lang.Integer;@bdc46c7, [Ljava.lang.Integer;@b26845c)(picard.illumina.parser.FilterParserTest) Running Test: Test method verifyDataTest[5]([Ljava.lang.Integer;@915a502, [Ljava.lang.Integer;@60963099)(picard.illumina.parser.FilterParserTest) Running Test: Test method verifyDataTest[6]([Ljava.lang.Integer;@5dacbd36, [Ljava.lang.Integer;@79352e34)(picard.illumina.parser.FilterParserTest) Running Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:55 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE) STANDARD_ERROR INFO 2024-07-02 11:57:55 FilterSamReads Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.10759675114814656489.sam -FILTER includeJavascript -READ_LIST_FILE /tmp/sam3351383206518211884dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.10759675114814656489.sam -FILTER includeJavascript -READ_LIST_FILE /tmp/sam3351383206518211884dummy Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:55.885 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:55.885 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE may only be specified when using FILTER from includeReadList, excludeReadList, FILTER value: includeJavascript, READ_LIST_FILE value: /tmp/sam3351383206518211884dummy READ_LIST_FILE may only be specified when using FILTER from includeReadList, excludeReadList, FILTER value: includeJavascript, READ_LIST_FILE value: /tmp/sam3351383206518211884dummy Test: Test method testBadArgumentCombinations[0](includeJavascript, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE must be specified when using FILTER=includeJavascript, but it was null. JAVASCRIPT_FILE must be specified when using FILTER=includeJavascript, but it was null. Running Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:56 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE) STANDARD_ERROR INFO 2024-07-02 11:57:56 FilterSamReads Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.16809093412896202522.sam -FILTER excludeAligned -READ_LIST_FILE /tmp/sam8653216595046857600dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.16809093412896202522.sam -FILTER excludeAligned -READ_LIST_FILE /tmp/sam8653216595046857600dummy Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:56.058 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:56.058 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[1](excludeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE may only be specified when using FILTER from includeReadList, excludeReadList, FILTER value: excludeAligned, READ_LIST_FILE value: /tmp/sam8653216595046857600dummy READ_LIST_FILE may only be specified when using FILTER from includeReadList, excludeReadList, FILTER value: excludeAligned, READ_LIST_FILE value: /tmp/sam8653216595046857600dummy Running Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:56 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE) STANDARD_ERROR INFO 2024-07-02 11:57:56 FilterSamReads Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.17610111183056820968.sam -FILTER includeAligned -READ_LIST_FILE /tmp/sam7259508580477562283dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.17610111183056820968.sam -FILTER includeAligned -READ_LIST_FILE /tmp/sam7259508580477562283dummy Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:56.200 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:56.200 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[2](includeAligned, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE may only be specified when using FILTER from includeReadList, excludeReadList, FILTER value: includeAligned, READ_LIST_FILE value: /tmp/sam7259508580477562283dummy READ_LIST_FILE may only be specified when using FILTER from includeReadList, excludeReadList, FILTER value: includeAligned, READ_LIST_FILE value: /tmp/sam7259508580477562283dummy Running Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:56 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE) STANDARD_ERROR INFO 2024-07-02 11:57:56 FilterSamReads Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.14540088173594398035.sam -FILTER includePairedIntervals -READ_LIST_FILE /tmp/sam15815954777154544906dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.14540088173594398035.sam -FILTER includePairedIntervals -READ_LIST_FILE /tmp/sam15815954777154544906dummy Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:56.357 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:56.357 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE may only be specified when using FILTER from includeReadList, excludeReadList, FILTER value: includePairedIntervals, READ_LIST_FILE value: /tmp/sam15815954777154544906dummy READ_LIST_FILE may only be specified when using FILTER from includeReadList, excludeReadList, FILTER value: includePairedIntervals, READ_LIST_FILE value: /tmp/sam15815954777154544906dummy Test: Test method testBadArgumentCombinations[3](includePairedIntervals, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST must be specified when using FILTER=includePairedIntervals, but it was null. INTERVAL_LIST must be specified when using FILTER=includePairedIntervals, but it was null. Running Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:56 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE) STANDARD_ERROR INFO 2024-07-02 11:57:56 FilterSamReads Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.1980521632914500430.sam -FILTER includeTagValues -READ_LIST_FILE /tmp/sam16198252698859347772dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.1980521632914500430.sam -FILTER includeTagValues -READ_LIST_FILE /tmp/sam16198252698859347772dummy Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: WARNING 2024-07-02 11:57:56 FilterSamReads Running FilterSamReads with a Tag Filter but no TAG_VALUE argument provided. This will recreate the original input file i.e. not filter anything WARNING 2024-07-02 11:57:56 FilterSamReads Running FilterSamReads with a Tag Filter but no TAG_VALUE argument provided. This will recreate the original input file i.e. not filter anything Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:56.486 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:56.486 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE may only be specified when using FILTER from includeReadList, excludeReadList, FILTER value: includeTagValues, READ_LIST_FILE value: /tmp/sam16198252698859347772dummy READ_LIST_FILE may only be specified when using FILTER from includeReadList, excludeReadList, FILTER value: includeTagValues, READ_LIST_FILE value: /tmp/sam16198252698859347772dummy Test: Test method testBadArgumentCombinations[4](includeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG must be specified when using FILTER=includeTagValues, but it was null. TAG must be specified when using FILTER=includeTagValues, but it was null. Running Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:56 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE) STANDARD_ERROR INFO 2024-07-02 11:57:56 FilterSamReads Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.10737679945539189302.sam -FILTER excludeTagValues -READ_LIST_FILE /tmp/sam6456513076980699269dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.10737679945539189302.sam -FILTER excludeTagValues -READ_LIST_FILE /tmp/sam6456513076980699269dummy Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: WARNING 2024-07-02 11:57:56 FilterSamReads Running FilterSamReads with a Tag Filter but no TAG_VALUE argument provided. This will recreate the original input file i.e. not filter anything WARNING 2024-07-02 11:57:56 FilterSamReads Running FilterSamReads with a Tag Filter but no TAG_VALUE argument provided. This will recreate the original input file i.e. not filter anything Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:56.648 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:56.648 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE may only be specified when using FILTER from includeReadList, excludeReadList, FILTER value: excludeTagValues, READ_LIST_FILE value: /tmp/sam6456513076980699269dummy READ_LIST_FILE may only be specified when using FILTER from includeReadList, excludeReadList, FILTER value: excludeTagValues, READ_LIST_FILE value: /tmp/sam6456513076980699269dummy Test: Test method testBadArgumentCombinations[5](excludeTagValues, READ_LIST_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG must be specified when using FILTER=excludeTagValues, but it was null. TAG must be specified when using FILTER=excludeTagValues, but it was null. Running Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:56 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST) STANDARD_ERROR INFO 2024-07-02 11:57:56 FilterSamReads Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.7092595481073319090.sam -FILTER includeJavascript -INTERVAL_LIST /tmp/sam493076923422535459dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.7092595481073319090.sam -FILTER includeJavascript -INTERVAL_LIST /tmp/sam493076923422535459dummy Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:56.761 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:56.761 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST may only be specified when using FILTER from includePairedIntervals, FILTER value: includeJavascript, INTERVAL_LIST value: /tmp/sam493076923422535459dummy INTERVAL_LIST may only be specified when using FILTER from includePairedIntervals, FILTER value: includeJavascript, INTERVAL_LIST value: /tmp/sam493076923422535459dummy Test: Test method testBadArgumentCombinations[6](includeJavascript, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE must be specified when using FILTER=includeJavascript, but it was null. JAVASCRIPT_FILE must be specified when using FILTER=includeJavascript, but it was null. Running Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:56 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST) STANDARD_ERROR INFO 2024-07-02 11:57:56 FilterSamReads Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.9997253686684969235.sam -FILTER excludeReadList -INTERVAL_LIST /tmp/sam16161919108335847640dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.9997253686684969235.sam -FILTER excludeReadList -INTERVAL_LIST /tmp/sam16161919108335847640dummy Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:56.867 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:56.867 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE must be specified when using FILTER=excludeReadList, but it was null. READ_LIST_FILE must be specified when using FILTER=excludeReadList, but it was null. Test: Test method testBadArgumentCombinations[7](excludeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST may only be specified when using FILTER from includePairedIntervals, FILTER value: excludeReadList, INTERVAL_LIST value: /tmp/sam16161919108335847640dummy INTERVAL_LIST may only be specified when using FILTER from includePairedIntervals, FILTER value: excludeReadList, INTERVAL_LIST value: /tmp/sam16161919108335847640dummy Running Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:57 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST) STANDARD_ERROR INFO 2024-07-02 11:57:57 FilterSamReads Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.6544200945004971862.sam -FILTER includeReadList -INTERVAL_LIST /tmp/sam7726292078302009410dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.6544200945004971862.sam -FILTER includeReadList -INTERVAL_LIST /tmp/sam7726292078302009410dummy Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:57.016 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:57.016 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE must be specified when using FILTER=includeReadList, but it was null. READ_LIST_FILE must be specified when using FILTER=includeReadList, but it was null. Test: Test method testBadArgumentCombinations[8](includeReadList, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST may only be specified when using FILTER from includePairedIntervals, FILTER value: includeReadList, INTERVAL_LIST value: /tmp/sam7726292078302009410dummy INTERVAL_LIST may only be specified when using FILTER from includePairedIntervals, FILTER value: includeReadList, INTERVAL_LIST value: /tmp/sam7726292078302009410dummy Running Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:57 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST) STANDARD_ERROR INFO 2024-07-02 11:57:57 FilterSamReads Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.4751759027248418658.sam -FILTER excludeAligned -INTERVAL_LIST /tmp/sam4346734904406797944dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.4751759027248418658.sam -FILTER excludeAligned -INTERVAL_LIST /tmp/sam4346734904406797944dummy Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:57.119 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:57.119 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[9](excludeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST may only be specified when using FILTER from includePairedIntervals, FILTER value: excludeAligned, INTERVAL_LIST value: /tmp/sam4346734904406797944dummy INTERVAL_LIST may only be specified when using FILTER from includePairedIntervals, FILTER value: excludeAligned, INTERVAL_LIST value: /tmp/sam4346734904406797944dummy Running Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:57 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST) STANDARD_ERROR INFO 2024-07-02 11:57:57 FilterSamReads Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.6827595988303738862.sam -FILTER includeAligned -INTERVAL_LIST /tmp/sam6584914498272853067dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.6827595988303738862.sam -FILTER includeAligned -INTERVAL_LIST /tmp/sam6584914498272853067dummy Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:57.220 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:57.220 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[10](includeAligned, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST may only be specified when using FILTER from includePairedIntervals, FILTER value: includeAligned, INTERVAL_LIST value: /tmp/sam6584914498272853067dummy INTERVAL_LIST may only be specified when using FILTER from includePairedIntervals, FILTER value: includeAligned, INTERVAL_LIST value: /tmp/sam6584914498272853067dummy Running Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:57 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST) STANDARD_ERROR INFO 2024-07-02 11:57:57 FilterSamReads Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.17728793729783248915.sam -FILTER includeTagValues -INTERVAL_LIST /tmp/sam8415170979023728094dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.17728793729783248915.sam -FILTER includeTagValues -INTERVAL_LIST /tmp/sam8415170979023728094dummy Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: WARNING 2024-07-02 11:57:57 FilterSamReads Running FilterSamReads with a Tag Filter but no TAG_VALUE argument provided. This will recreate the original input file i.e. not filter anything WARNING 2024-07-02 11:57:57 FilterSamReads Running FilterSamReads with a Tag Filter but no TAG_VALUE argument provided. This will recreate the original input file i.e. not filter anything Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:57.330 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:57.330 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST may only be specified when using FILTER from includePairedIntervals, FILTER value: includeTagValues, INTERVAL_LIST value: /tmp/sam8415170979023728094dummy INTERVAL_LIST may only be specified when using FILTER from includePairedIntervals, FILTER value: includeTagValues, INTERVAL_LIST value: /tmp/sam8415170979023728094dummy Test: Test method testBadArgumentCombinations[11](includeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG must be specified when using FILTER=includeTagValues, but it was null. TAG must be specified when using FILTER=includeTagValues, but it was null. Running Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:57 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST) STANDARD_ERROR INFO 2024-07-02 11:57:57 FilterSamReads Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.7769755726418506296.sam -FILTER excludeTagValues -INTERVAL_LIST /tmp/sam10324858716163674680dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.7769755726418506296.sam -FILTER excludeTagValues -INTERVAL_LIST /tmp/sam10324858716163674680dummy Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: WARNING 2024-07-02 11:57:57 FilterSamReads Running FilterSamReads with a Tag Filter but no TAG_VALUE argument provided. This will recreate the original input file i.e. not filter anything WARNING 2024-07-02 11:57:57 FilterSamReads Running FilterSamReads with a Tag Filter but no TAG_VALUE argument provided. This will recreate the original input file i.e. not filter anything Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:57.435 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:57.435 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST may only be specified when using FILTER from includePairedIntervals, FILTER value: excludeTagValues, INTERVAL_LIST value: /tmp/sam10324858716163674680dummy INTERVAL_LIST may only be specified when using FILTER from includePairedIntervals, FILTER value: excludeTagValues, INTERVAL_LIST value: /tmp/sam10324858716163674680dummy Test: Test method testBadArgumentCombinations[12](excludeTagValues, INTERVAL_LIST)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG must be specified when using FILTER=excludeTagValues, but it was null. TAG must be specified when using FILTER=excludeTagValues, but it was null. Running Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:57 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE) STANDARD_ERROR INFO 2024-07-02 11:57:57 FilterSamReads Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.699291680665651804.sam -FILTER excludeReadList -JAVASCRIPT_FILE /tmp/sam18241089601436021638dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.699291680665651804.sam -FILTER excludeReadList -JAVASCRIPT_FILE /tmp/sam18241089601436021638dummy Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:57.563 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:57.563 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE must be specified when using FILTER=excludeReadList, but it was null. READ_LIST_FILE must be specified when using FILTER=excludeReadList, but it was null. Test: Test method testBadArgumentCombinations[13](excludeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE may only be specified when using FILTER from includeJavascript, FILTER value: excludeReadList, JAVASCRIPT_FILE value: /tmp/sam18241089601436021638dummy JAVASCRIPT_FILE may only be specified when using FILTER from includeJavascript, FILTER value: excludeReadList, JAVASCRIPT_FILE value: /tmp/sam18241089601436021638dummy Running Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:57 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE) STANDARD_ERROR INFO 2024-07-02 11:57:57 FilterSamReads Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.7387494105994195705.sam -FILTER includeReadList -JAVASCRIPT_FILE /tmp/sam10747234759080387234dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.7387494105994195705.sam -FILTER includeReadList -JAVASCRIPT_FILE /tmp/sam10747234759080387234dummy Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:57.706 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:57.706 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE must be specified when using FILTER=includeReadList, but it was null. READ_LIST_FILE must be specified when using FILTER=includeReadList, but it was null. Test: Test method testBadArgumentCombinations[14](includeReadList, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE may only be specified when using FILTER from includeJavascript, FILTER value: includeReadList, JAVASCRIPT_FILE value: /tmp/sam10747234759080387234dummy JAVASCRIPT_FILE may only be specified when using FILTER from includeJavascript, FILTER value: includeReadList, JAVASCRIPT_FILE value: /tmp/sam10747234759080387234dummy Running Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:57 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE) STANDARD_ERROR INFO 2024-07-02 11:57:57 FilterSamReads Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.8304812717587282413.sam -FILTER excludeAligned -JAVASCRIPT_FILE /tmp/sam15817315495263223046dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.8304812717587282413.sam -FILTER excludeAligned -JAVASCRIPT_FILE /tmp/sam15817315495263223046dummy Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:57.847 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:57.847 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[15](excludeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE may only be specified when using FILTER from includeJavascript, FILTER value: excludeAligned, JAVASCRIPT_FILE value: /tmp/sam15817315495263223046dummy JAVASCRIPT_FILE may only be specified when using FILTER from includeJavascript, FILTER value: excludeAligned, JAVASCRIPT_FILE value: /tmp/sam15817315495263223046dummy Running Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:57 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE) STANDARD_ERROR INFO 2024-07-02 11:57:57 FilterSamReads Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.11651393611542859010.sam -FILTER includeAligned -JAVASCRIPT_FILE /tmp/sam10190756485711173803dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.11651393611542859010.sam -FILTER includeAligned -JAVASCRIPT_FILE /tmp/sam10190756485711173803dummy Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:57.978 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:57.978 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[16](includeAligned, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE may only be specified when using FILTER from includeJavascript, FILTER value: includeAligned, JAVASCRIPT_FILE value: /tmp/sam10190756485711173803dummy JAVASCRIPT_FILE may only be specified when using FILTER from includeJavascript, FILTER value: includeAligned, JAVASCRIPT_FILE value: /tmp/sam10190756485711173803dummy Running Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:58 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE) STANDARD_ERROR INFO 2024-07-02 11:57:58 FilterSamReads Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.17468411570421929791.sam -FILTER includePairedIntervals -JAVASCRIPT_FILE /tmp/sam7810463718098182465dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.17468411570421929791.sam -FILTER includePairedIntervals -JAVASCRIPT_FILE /tmp/sam7810463718098182465dummy Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:58.112 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:58.112 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST must be specified when using FILTER=includePairedIntervals, but it was null. INTERVAL_LIST must be specified when using FILTER=includePairedIntervals, but it was null. Test: Test method testBadArgumentCombinations[17](includePairedIntervals, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE may only be specified when using FILTER from includeJavascript, FILTER value: includePairedIntervals, JAVASCRIPT_FILE value: /tmp/sam7810463718098182465dummy JAVASCRIPT_FILE may only be specified when using FILTER from includeJavascript, FILTER value: includePairedIntervals, JAVASCRIPT_FILE value: /tmp/sam7810463718098182465dummy Running Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:58 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE) STANDARD_ERROR INFO 2024-07-02 11:57:58 FilterSamReads Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.18133786529027534818.sam -FILTER includeTagValues -JAVASCRIPT_FILE /tmp/sam14603930644195111614dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.18133786529027534818.sam -FILTER includeTagValues -JAVASCRIPT_FILE /tmp/sam14603930644195111614dummy Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: WARNING 2024-07-02 11:57:58 FilterSamReads Running FilterSamReads with a Tag Filter but no TAG_VALUE argument provided. This will recreate the original input file i.e. not filter anything WARNING 2024-07-02 11:57:58 FilterSamReads Running FilterSamReads with a Tag Filter but no TAG_VALUE argument provided. This will recreate the original input file i.e. not filter anything Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:58.250 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:58.250 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE may only be specified when using FILTER from includeJavascript, FILTER value: includeTagValues, JAVASCRIPT_FILE value: /tmp/sam14603930644195111614dummy JAVASCRIPT_FILE may only be specified when using FILTER from includeJavascript, FILTER value: includeTagValues, JAVASCRIPT_FILE value: /tmp/sam14603930644195111614dummy Test: Test method testBadArgumentCombinations[18](includeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG must be specified when using FILTER=includeTagValues, but it was null. TAG must be specified when using FILTER=includeTagValues, but it was null. Running Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:58 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE) STANDARD_ERROR INFO 2024-07-02 11:57:58 FilterSamReads Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.3478922378756175914.sam -FILTER excludeTagValues -JAVASCRIPT_FILE /tmp/sam18196033009474581708dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.3478922378756175914.sam -FILTER excludeTagValues -JAVASCRIPT_FILE /tmp/sam18196033009474581708dummy Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: WARNING 2024-07-02 11:57:58 FilterSamReads Running FilterSamReads with a Tag Filter but no TAG_VALUE argument provided. This will recreate the original input file i.e. not filter anything WARNING 2024-07-02 11:57:58 FilterSamReads Running FilterSamReads with a Tag Filter but no TAG_VALUE argument provided. This will recreate the original input file i.e. not filter anything Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:58.376 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:58.376 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE may only be specified when using FILTER from includeJavascript, FILTER value: excludeTagValues, JAVASCRIPT_FILE value: /tmp/sam18196033009474581708dummy JAVASCRIPT_FILE may only be specified when using FILTER from includeJavascript, FILTER value: excludeTagValues, JAVASCRIPT_FILE value: /tmp/sam18196033009474581708dummy Test: Test method testBadArgumentCombinations[19](excludeTagValues, JAVASCRIPT_FILE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG must be specified when using FILTER=excludeTagValues, but it was null. TAG must be specified when using FILTER=excludeTagValues, but it was null. Running Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:58 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[20](excludeReadList, TAG) STANDARD_ERROR INFO 2024-07-02 11:57:58 FilterSamReads Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.12450989123878750330.sam -FILTER excludeReadList -TAG /tmp/sam15909051839077119731dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.12450989123878750330.sam -FILTER excludeReadList -TAG /tmp/sam15909051839077119731dummy Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:58.520 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:58.520 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE must be specified when using FILTER=excludeReadList, but it was null. READ_LIST_FILE must be specified when using FILTER=excludeReadList, but it was null. Test: Test method testBadArgumentCombinations[20](excludeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG may only be specified when using FILTER from includeTagValues, excludeTagValues, FILTER value: excludeReadList, TAG value: /tmp/sam15909051839077119731dummy TAG may only be specified when using FILTER from includeTagValues, excludeTagValues, FILTER value: excludeReadList, TAG value: /tmp/sam15909051839077119731dummy Running Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:58 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[21](includeReadList, TAG) STANDARD_ERROR INFO 2024-07-02 11:57:58 FilterSamReads Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.5275074382037603434.sam -FILTER includeReadList -TAG /tmp/sam11217690139246516732dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.5275074382037603434.sam -FILTER includeReadList -TAG /tmp/sam11217690139246516732dummy Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:58.658 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:58.658 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE must be specified when using FILTER=includeReadList, but it was null. READ_LIST_FILE must be specified when using FILTER=includeReadList, but it was null. Test: Test method testBadArgumentCombinations[21](includeReadList, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG may only be specified when using FILTER from includeTagValues, excludeTagValues, FILTER value: includeReadList, TAG value: /tmp/sam11217690139246516732dummy TAG may only be specified when using FILTER from includeTagValues, excludeTagValues, FILTER value: includeReadList, TAG value: /tmp/sam11217690139246516732dummy Running Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:58 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[22](excludeAligned, TAG) STANDARD_ERROR INFO 2024-07-02 11:57:58 FilterSamReads Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.14406024968985692529.sam -FILTER excludeAligned -TAG /tmp/sam8277768129143868495dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.14406024968985692529.sam -FILTER excludeAligned -TAG /tmp/sam8277768129143868495dummy Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:58.788 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:58.788 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[22](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG may only be specified when using FILTER from includeTagValues, excludeTagValues, FILTER value: excludeAligned, TAG value: /tmp/sam8277768129143868495dummy TAG may only be specified when using FILTER from includeTagValues, excludeTagValues, FILTER value: excludeAligned, TAG value: /tmp/sam8277768129143868495dummy Running Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:58 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[23](includeAligned, TAG) STANDARD_ERROR INFO 2024-07-02 11:57:58 FilterSamReads Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.8038765636215210781.sam -FILTER includeAligned -TAG /tmp/sam6897496173601936034dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.8038765636215210781.sam -FILTER includeAligned -TAG /tmp/sam6897496173601936034dummy Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:58.927 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:58.927 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[23](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG may only be specified when using FILTER from includeTagValues, excludeTagValues, FILTER value: includeAligned, TAG value: /tmp/sam6897496173601936034dummy TAG may only be specified when using FILTER from includeTagValues, excludeTagValues, FILTER value: includeAligned, TAG value: /tmp/sam6897496173601936034dummy Running Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:59 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[24](includePairedIntervals, TAG) STANDARD_ERROR INFO 2024-07-02 11:57:59 FilterSamReads Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.1923589870050504112.sam -FILTER includePairedIntervals -TAG /tmp/sam7885127344251295976dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.1923589870050504112.sam -FILTER includePairedIntervals -TAG /tmp/sam7885127344251295976dummy Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:59.057 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:59.057 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST must be specified when using FILTER=includePairedIntervals, but it was null. INTERVAL_LIST must be specified when using FILTER=includePairedIntervals, but it was null. Test: Test method testBadArgumentCombinations[24](includePairedIntervals, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG may only be specified when using FILTER from includeTagValues, excludeTagValues, FILTER value: includePairedIntervals, TAG value: /tmp/sam7885127344251295976dummy TAG may only be specified when using FILTER from includeTagValues, excludeTagValues, FILTER value: includePairedIntervals, TAG value: /tmp/sam7885127344251295976dummy Running Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:59 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[25](excludeAligned, TAG) STANDARD_ERROR INFO 2024-07-02 11:57:59 FilterSamReads Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.5913875246645326517.sam -FILTER excludeAligned -TAG /tmp/sam14483598171797887656dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.5913875246645326517.sam -FILTER excludeAligned -TAG /tmp/sam14483598171797887656dummy Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:59.269 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:59.269 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[25](excludeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG may only be specified when using FILTER from includeTagValues, excludeTagValues, FILTER value: excludeAligned, TAG value: /tmp/sam14483598171797887656dummy TAG may only be specified when using FILTER from includeTagValues, excludeTagValues, FILTER value: excludeAligned, TAG value: /tmp/sam14483598171797887656dummy Running Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:59 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[26](includeAligned, TAG) STANDARD_ERROR INFO 2024-07-02 11:57:59 FilterSamReads Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.12878919526267952009.sam -FILTER includeAligned -TAG /tmp/sam11612748050983555440dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.12878919526267952009.sam -FILTER includeAligned -TAG /tmp/sam11612748050983555440dummy Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:59.443 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:59.443 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[26](includeAligned, TAG)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG may only be specified when using FILTER from includeTagValues, excludeTagValues, FILTER value: includeAligned, TAG value: /tmp/sam11612748050983555440dummy TAG may only be specified when using FILTER from includeTagValues, excludeTagValues, FILTER value: includeAligned, TAG value: /tmp/sam11612748050983555440dummy Running Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:59 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[27](excludeReadList, TAG_VALUE) STANDARD_ERROR INFO 2024-07-02 11:57:59 FilterSamReads Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.2781637256343766462.sam -FILTER excludeReadList -TAG_VALUE /tmp/sam18050602907650733200dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.2781637256343766462.sam -FILTER excludeReadList -TAG_VALUE /tmp/sam18050602907650733200dummy Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:59.626 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:59.626 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[27](excludeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE must be specified when using FILTER=excludeReadList, but it was null. READ_LIST_FILE must be specified when using FILTER=excludeReadList, but it was null. Running Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:59 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[28](includeReadList, TAG_VALUE) STANDARD_ERROR INFO 2024-07-02 11:57:59 FilterSamReads Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.16746919478349342884.sam -FILTER includeReadList -TAG_VALUE /tmp/sam17771414019009703352dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.16746919478349342884.sam -FILTER includeReadList -TAG_VALUE /tmp/sam17771414019009703352dummy Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:59.754 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:57:59.754 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[28](includeReadList, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE must be specified when using FILTER=includeReadList, but it was null. READ_LIST_FILE must be specified when using FILTER=includeReadList, but it was null. Running Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:59 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[29](excludeAligned, TAG_VALUE) STANDARD_ERROR INFO 2024-07-02 11:57:59 FilterSamReads Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.17275836136140357319.sam -FILTER excludeAligned -TAG_VALUE /tmp/sam16580795649253046279dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.17275836136140357319.sam -FILTER excludeAligned -TAG_VALUE /tmp/sam16580795649253046279dummy Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:59.882 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:59.882 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:59.882 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:59.882 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:59.882 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:59.882 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:59.882 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:59.882 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: [Tue Jul 02 11:57:59 GMT+14:00 2024] FilterSamReads INPUT=testdata/picard/sam/aligned.sam FILTER=excludeAligned TAG_VALUE=[/tmp/sam16580795649253046279dummy] OUTPUT=/tmp/FilterSamReads.output.17275836136140357319.sam WRITE_READS_FILES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:59 GMT+14:00 2024] FilterSamReads INPUT=testdata/picard/sam/aligned.sam FILTER=excludeAligned TAG_VALUE=[/tmp/sam16580795649253046279dummy] OUTPUT=/tmp/FilterSamReads.output.17275836136140357319.sam WRITE_READS_FILES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: [Tue Jul 02 11:57:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ERROR 2024-07-02 11:57:59 FilterSamReads Failed to filter aligned.sam ERROR 2024-07-02 11:57:59 FilterSamReads Failed to filter aligned.sam Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: htsjdk.samtools.SAMException: Second record is not marked as second of pair: both_reads_present_only_first_aligns 1/2 101b aligned to chr7:1-101. htsjdk.samtools.SAMException: Second record is not marked as second of pair: both_reads_present_only_first_aligns 1/2 101b aligned to chr7:1-101. Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at htsjdk.samtools.SamPairUtil.assertMate(SamPairUtil.java:134) at htsjdk.samtools.SamPairUtil.assertMate(SamPairUtil.java:134) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at htsjdk.samtools.filter.FilteringSamIterator.getNextRecord(FilteringSamIterator.java:140) at htsjdk.samtools.filter.FilteringSamIterator.getNextRecord(FilteringSamIterator.java:140) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at htsjdk.samtools.filter.FilteringSamIterator.(FilteringSamIterator.java:70) at htsjdk.samtools.filter.FilteringSamIterator.(FilteringSamIterator.java:70) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at picard.sam.FilterSamReads.doWork(FilterSamReads.java:312) at picard.sam.FilterSamReads.doWork(FilterSamReads.java:312) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at picard.sam.FilterSamReadsTest.testBadArgumentCombinations(FilterSamReadsTest.java:185) at picard.sam.FilterSamReadsTest.testBadArgumentCombinations(FilterSamReadsTest.java:185) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at jdk.internal.reflect.GeneratedMethodAccessor46.invoke(Unknown Source) at jdk.internal.reflect.GeneratedMethodAccessor46.invoke(Unknown Source) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: [Tue Jul 02 11:57:59 GMT+14:00 2024] picard.sam.FilterSamReads done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:59 GMT+14:00 2024] picard.sam.FilterSamReads done. Elapsed time: 0.00 minutes. Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method testBadArgumentCombinations[29](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:57:59 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[30](includeAligned, TAG_VALUE) STANDARD_ERROR INFO 2024-07-02 11:57:59 FilterSamReads Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.6180458401015406193.sam -FILTER includeAligned -TAG_VALUE /tmp/sam15962984507964232950dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.6180458401015406193.sam -FILTER includeAligned -TAG_VALUE /tmp/sam15962984507964232950dummy Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:59.997 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:59.997 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:59.997 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:59.997 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:59.997 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:57:59.997 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:57:59.997 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:57:59.997 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: [Tue Jul 02 11:57:59 GMT+14:00 2024] FilterSamReads INPUT=testdata/picard/sam/aligned.sam FILTER=includeAligned TAG_VALUE=[/tmp/sam15962984507964232950dummy] OUTPUT=/tmp/FilterSamReads.output.6180458401015406193.sam WRITE_READS_FILES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:57:59 GMT+14:00 2024] FilterSamReads INPUT=testdata/picard/sam/aligned.sam FILTER=includeAligned TAG_VALUE=[/tmp/sam15962984507964232950dummy] OUTPUT=/tmp/FilterSamReads.output.6180458401015406193.sam WRITE_READS_FILES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: [Tue Jul 02 11:57:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:57:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ERROR 2024-07-02 11:57:59 FilterSamReads Failed to filter aligned.sam ERROR 2024-07-02 11:57:59 FilterSamReads Failed to filter aligned.sam Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: htsjdk.samtools.SAMException: Second record is not marked as second of pair: both_reads_present_only_first_aligns 1/2 101b aligned to chr7:1-101. htsjdk.samtools.SAMException: Second record is not marked as second of pair: both_reads_present_only_first_aligns 1/2 101b aligned to chr7:1-101. Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at htsjdk.samtools.SamPairUtil.assertMate(SamPairUtil.java:134) at htsjdk.samtools.SamPairUtil.assertMate(SamPairUtil.java:134) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at htsjdk.samtools.filter.FilteringSamIterator.getNextRecord(FilteringSamIterator.java:140) at htsjdk.samtools.filter.FilteringSamIterator.getNextRecord(FilteringSamIterator.java:140) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at htsjdk.samtools.filter.FilteringSamIterator.(FilteringSamIterator.java:70) at htsjdk.samtools.filter.FilteringSamIterator.(FilteringSamIterator.java:70) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at picard.sam.FilterSamReads.doWork(FilterSamReads.java:308) at picard.sam.FilterSamReads.doWork(FilterSamReads.java:308) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at picard.sam.FilterSamReadsTest.testBadArgumentCombinations(FilterSamReadsTest.java:185) at picard.sam.FilterSamReadsTest.testBadArgumentCombinations(FilterSamReadsTest.java:185) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at jdk.internal.reflect.GeneratedMethodAccessor46.invoke(Unknown Source) at jdk.internal.reflect.GeneratedMethodAccessor46.invoke(Unknown Source) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: [Tue Jul 02 11:57:59 GMT+14:00 2024] picard.sam.FilterSamReads done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:57:59 GMT+14:00 2024] picard.sam.FilterSamReads done. Elapsed time: 0.00 minutes. Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method testBadArgumentCombinations[30](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:00 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE) STANDARD_ERROR INFO 2024-07-02 11:58:00 FilterSamReads Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.2967304865475881110.sam -FILTER includePairedIntervals -TAG_VALUE /tmp/sam6907832491877999401dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.2967304865475881110.sam -FILTER includePairedIntervals -TAG_VALUE /tmp/sam6907832491877999401dummy Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:58:00.102 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 11:58:00.102 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: USAGE: FilterSamReads [options] USAGE: FilterSamReads [options] Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#FilterSamReads Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Subsets reads from a SAM or BAM file by applying one of several filters. Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Takes a SAM or BAM file and subsets it by either excluding or only including certain reads such as aligned or unaligned Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or reads, specific reads based on a list of reads names, an interval list, by Tag Values (type Z / String values only), or Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: using a JavaScript script. using a JavaScript script. Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Usage example: Usage example: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by queryname Filter by queryname Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=read_names.txt \ READ_LIST_FILE=read_names.txt \ Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeReadList FILTER=includeReadList Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by interval Filter by interval Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=regions.interval_list \ INTERVAL_LIST=regions.interval_list \ Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals FILTER=includePairedIntervals Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter by Tag Value (type Z / String values only) Filter by Tag Value (type Z / String values only) Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=CR \ TAG=CR \ Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=TTTGTCATCTCGAGTA \ TAG_VALUE=TTTGTCATCTCGAGTA \ Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeTagValues FILTER=includeTagValues Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Filter reads having a soft clip on the beginning of the read larger than 2 bases with a JavaScript script Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: cat < script.js cat < script.js Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: /** reads having a soft clip larger than 2 bases in beginning of read*/ /** reads having a soft clip larger than 2 bases in beginning of read*/ Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: function accept(rec) { function accept(rec) { Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (rec.getReadUnmappedFlag()) return false; if (rec.getReadUnmappedFlag()) return false; Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: var cigar = rec.getCigar(); var cigar = rec.getCigar(); Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: if (cigar == null) return false; if (cigar == null) return false; Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: var ce = cigar.getCigarElement(0); var ce = cigar.getCigarElement(0); Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: return ce.getOperator().name() == "S" && ce.length() > 2; return ce.getOperator().name() == "S" && ce.length() > 2; Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: accept(record); accept(record); Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: EOF EOF Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: java -jar picard.jar FilterSamReads \ java -jar picard.jar FilterSamReads \ Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=output.bam \ O=output.bam \ Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=script.js \ JAVASCRIPT_FILE=script.js \ Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includeJavascript FILTER=includeJavascript Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Version: null Version: null Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Options: Options: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: --help --help Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: tools. tools. Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: I=File The SAM or BAM file that will be filtered. Required. I=File The SAM or BAM file that will be filtered. Required. Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=Filter Which filter to use. Required. Possible values: { FILTER=Filter Which filter to use. Required. Possible values: { Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. includeAligned (Output aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) (Note: first and second of paired reads must both be aligned to be included in OUTPUT.)) Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. excludeAligned (Output Unmapped reads only. INPUT SAM/BAM must be in queryname SortOrder. Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) (Note: first and second of pair must both be aligned to be excluded from OUTPUT.)) Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE includeReadList (Output reads with names contained in READ_LIST_FILE. See READ_LIST_FILE Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail.) for more detail.) Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See excludeReadList (Output reads with names *not* contained in READ_LIST_FILE. See Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE for more detail.) READ_LIST_FILE for more detail.) Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, includeJavascript (Output reads that have been accepted by the JAVASCRIPT_FILE script, Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument that is, reads for which the value of the script is true. See the JAVASCRIPT_FILE argument Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: for more detail. ) for more detail. ) Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and includePairedIntervals (Output reads that overlap with an interval from INTERVAL_LIST (and Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: their mate). INPUT must be coordinate sorted.) their mate). INPUT must be coordinate sorted.) Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is includeTagValues (OUTPUT SAM/BAM will contain reads that have a value of tag TAG that is Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: contained in the values for TAG_VALUES) contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG excludeTagValues (OUTPUT SAM/BAM will contain reads that do not have a value of tag TAG Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: that is contained in the values for TAG_VALUES) that is contained in the values for TAG_VALUES) Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: } } Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: READ_LIST_FILE=File READ_LIST_FILE=File Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM RLF=File File containing reads that will be included in or excluded from the OUTPUT SAM or BAM Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. file, when using FILTER=includeReadList or FILTER=excludeReadList. Default value: null. Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST=File INTERVAL_LIST=File Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: IL=File Interval List File containing intervals that will be included in the OUTPUT when using IL=File Interval List File containing intervals that will be included in the OUTPUT when using Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: FILTER=includePairedIntervals Default value: null. FILTER=includePairedIntervals Default value: null. Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG=String TAG=String Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: T=String The tag to select from input SAM/BAM Default value: null. T=String The tag to select from input SAM/BAM Default value: null. Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: TAG_VALUE=String TAG_VALUE=String Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more TV=String The tag value(s) to filter by Default value: null. This option may be specified 0 or more Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: times. times. Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default SO=SortOrder SortOrder of the OUTPUT file, otherwise use the SortOrder of the INPUT file. Default Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} value: null. Possible values: {unsorted, queryname, coordinate, duplicate, unknown} Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: O=File SAM or BAM file for resulting reads. Required. O=File SAM or BAM file for resulting reads. Required. Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: JAVASCRIPT_FILE=File JAVASCRIPT_FILE=File Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when JS=File Filters the INPUT with a javascript expression using the java javascript-engine, when Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: using FILTER=includeJavascript. The script puts the following variables in the script using FILTER=includeJavascript. The script puts the following variables in the script Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: context: context: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'record' a SamRecord ( 'record' a SamRecord ( Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMRecord.html ) and Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: 'header' a SAMFileHeader ( 'header' a SAMFileHeader ( Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/SAMFileHeader.html ). Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted all the public members of SamRecord and SAMFileHeader are accessible. A record is accepted Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: if the last value of the script evaluates to true. Default value: null. if the last value of the script evaluates to true. Default value: null. Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging WRITE_READS_FILES=Boolean Create .reads file containing names of reads from INPUT and OUTPUT (for debugging Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: purposes.) Default value: false. This option can be set to 'null' to clear the default purposes.) Default value: false. This option can be set to 'null' to clear the default Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[31](includePairedIntervals, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: INTERVAL_LIST must be specified when using FILTER=includePairedIntervals, but it was null. INTERVAL_LIST must be specified when using FILTER=includePairedIntervals, but it was null. Running Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:00 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[32](excludeAligned, TAG_VALUE) STANDARD_ERROR INFO 2024-07-02 11:58:00 FilterSamReads Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.268081071423225566.sam -FILTER excludeAligned -TAG_VALUE /tmp/sam10661597478971205481dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.268081071423225566.sam -FILTER excludeAligned -TAG_VALUE /tmp/sam10661597478971205481dummy Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:58:00.232 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:00.232 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:58:00.232 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:00.232 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:58:00.232 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:00.232 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:58:00.232 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:00.232 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: [Tue Jul 02 11:58:00 GMT+14:00 2024] FilterSamReads INPUT=testdata/picard/sam/aligned.sam FILTER=excludeAligned TAG_VALUE=[/tmp/sam10661597478971205481dummy] OUTPUT=/tmp/FilterSamReads.output.268081071423225566.sam WRITE_READS_FILES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:00 GMT+14:00 2024] FilterSamReads INPUT=testdata/picard/sam/aligned.sam FILTER=excludeAligned TAG_VALUE=[/tmp/sam10661597478971205481dummy] OUTPUT=/tmp/FilterSamReads.output.268081071423225566.sam WRITE_READS_FILES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: [Tue Jul 02 11:58:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ERROR 2024-07-02 11:58:00 FilterSamReads Failed to filter aligned.sam ERROR 2024-07-02 11:58:00 FilterSamReads Failed to filter aligned.sam Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: htsjdk.samtools.SAMException: Second record is not marked as second of pair: both_reads_present_only_first_aligns 1/2 101b aligned to chr7:1-101. htsjdk.samtools.SAMException: Second record is not marked as second of pair: both_reads_present_only_first_aligns 1/2 101b aligned to chr7:1-101. Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at htsjdk.samtools.SamPairUtil.assertMate(SamPairUtil.java:134) at htsjdk.samtools.SamPairUtil.assertMate(SamPairUtil.java:134) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at htsjdk.samtools.filter.FilteringSamIterator.getNextRecord(FilteringSamIterator.java:140) at htsjdk.samtools.filter.FilteringSamIterator.getNextRecord(FilteringSamIterator.java:140) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at htsjdk.samtools.filter.FilteringSamIterator.(FilteringSamIterator.java:70) at htsjdk.samtools.filter.FilteringSamIterator.(FilteringSamIterator.java:70) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at picard.sam.FilterSamReads.doWork(FilterSamReads.java:312) at picard.sam.FilterSamReads.doWork(FilterSamReads.java:312) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at picard.sam.FilterSamReadsTest.testBadArgumentCombinations(FilterSamReadsTest.java:185) at picard.sam.FilterSamReadsTest.testBadArgumentCombinations(FilterSamReadsTest.java:185) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at jdk.internal.reflect.GeneratedMethodAccessor46.invoke(Unknown Source) at jdk.internal.reflect.GeneratedMethodAccessor46.invoke(Unknown Source) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: [Tue Jul 02 11:58:00 GMT+14:00 2024] picard.sam.FilterSamReads done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:00 GMT+14:00 2024] picard.sam.FilterSamReads done. Elapsed time: 0.00 minutes. Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method testBadArgumentCombinations[32](excludeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:00 FilterSamReads Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testBadArgumentCombinations[33](includeAligned, TAG_VALUE) STANDARD_ERROR INFO 2024-07-02 11:58:00 FilterSamReads Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.13215876353502034418.sam -FILTER includeAligned -TAG_VALUE /tmp/sam11394509995604788113dummy ********** FilterSamReads -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/FilterSamReads.output.13215876353502034418.sam -FILTER includeAligned -TAG_VALUE /tmp/sam11394509995604788113dummy Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ********** ********** Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:58:00.328 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:00.328 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:58:00.328 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:00.328 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:58:00.328 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:00.328 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: 11:58:00.328 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:00.328 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: [Tue Jul 02 11:58:00 GMT+14:00 2024] FilterSamReads INPUT=testdata/picard/sam/aligned.sam FILTER=includeAligned TAG_VALUE=[/tmp/sam11394509995604788113dummy] OUTPUT=/tmp/FilterSamReads.output.13215876353502034418.sam WRITE_READS_FILES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:00 GMT+14:00 2024] FilterSamReads INPUT=testdata/picard/sam/aligned.sam FILTER=includeAligned TAG_VALUE=[/tmp/sam11394509995604788113dummy] OUTPUT=/tmp/FilterSamReads.output.13215876353502034418.sam WRITE_READS_FILES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: [Tue Jul 02 11:58:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: ERROR 2024-07-02 11:58:00 FilterSamReads Failed to filter aligned.sam ERROR 2024-07-02 11:58:00 FilterSamReads Failed to filter aligned.sam Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: htsjdk.samtools.SAMException: Second record is not marked as second of pair: both_reads_present_only_first_aligns 1/2 101b aligned to chr7:1-101. htsjdk.samtools.SAMException: Second record is not marked as second of pair: both_reads_present_only_first_aligns 1/2 101b aligned to chr7:1-101. Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at htsjdk.samtools.SamPairUtil.assertMate(SamPairUtil.java:134) at htsjdk.samtools.SamPairUtil.assertMate(SamPairUtil.java:134) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at htsjdk.samtools.filter.FilteringSamIterator.getNextRecord(FilteringSamIterator.java:140) at htsjdk.samtools.filter.FilteringSamIterator.getNextRecord(FilteringSamIterator.java:140) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at htsjdk.samtools.filter.FilteringSamIterator.(FilteringSamIterator.java:70) at htsjdk.samtools.filter.FilteringSamIterator.(FilteringSamIterator.java:70) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at picard.sam.FilterSamReads.doWork(FilterSamReads.java:308) at picard.sam.FilterSamReads.doWork(FilterSamReads.java:308) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at picard.sam.FilterSamReadsTest.testBadArgumentCombinations(FilterSamReadsTest.java:185) at picard.sam.FilterSamReadsTest.testBadArgumentCombinations(FilterSamReadsTest.java:185) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at jdk.internal.reflect.GeneratedMethodAccessor46.invoke(Unknown Source) at jdk.internal.reflect.GeneratedMethodAccessor46.invoke(Unknown Source) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: [Tue Jul 02 11:58:00 GMT+14:00 2024] picard.sam.FilterSamReads done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:00 GMT+14:00 2024] picard.sam.FilterSamReads done. Elapsed time: 0.00 minutes. Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method testBadArgumentCombinations[33](includeAligned, TAG_VALUE)(picard.sam.FilterSamReadsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testDebugOption[0](null, false)(picard.sam.FilterSamReadsTest) Test: Test method testDebugOption[0](null, false)(picard.sam.FilterSamReadsTest) produced standard out/err: Warning: Nashorn engine is planned to be removed from a future JDK release Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testDebugOption[0](null, false) STANDARD_ERROR Warning: Nashorn engine is planned to be removed from a future JDK release Test: Test method testDebugOption[0](null, false)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:02 FilterSamReads Filtering [presorted=true] aligned.sam -> OUTPUT=FilterSamReads.output.9855286934120459550.sam [sortorder=coordinate] INFO 2024-07-02 11:58:02 FilterSamReads Filtering [presorted=true] aligned.sam -> OUTPUT=FilterSamReads.output.9855286934120459550.sam [sortorder=coordinate] Test: Test method testDebugOption[0](null, false)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:02 FilterSamReads 3 SAMRecords written to FilterSamReads.output.9855286934120459550.sam INFO 2024-07-02 11:58:02 FilterSamReads 3 SAMRecords written to FilterSamReads.output.9855286934120459550.sam Running Test: Test method testDebugOption[1](true, true)(picard.sam.FilterSamReadsTest) Test: Test method testDebugOption[1](true, true)(picard.sam.FilterSamReadsTest) produced standard out/err: Warning: Nashorn engine is planned to be removed from a future JDK release Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testDebugOption[1](true, true) STANDARD_ERROR Warning: Nashorn engine is planned to be removed from a future JDK release Test: Test method testDebugOption[1](true, true)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:03 FilterSamReads Filtering [presorted=true] aligned.sam -> OUTPUT=FilterSamReads.output.4422670862881938758.sam [sortorder=coordinate] INFO 2024-07-02 11:58:03 FilterSamReads Filtering [presorted=true] aligned.sam -> OUTPUT=FilterSamReads.output.4422670862881938758.sam [sortorder=coordinate] Test: Test method testDebugOption[1](true, true)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:03 FilterSamReads 3 SAMRecords written to FilterSamReads.output.4422670862881938758.sam INFO 2024-07-02 11:58:03 FilterSamReads 3 SAMRecords written to FilterSamReads.output.4422670862881938758.sam Running Test: Test method testDebugOption[2](false, false)(picard.sam.FilterSamReadsTest) Test: Test method testDebugOption[2](false, false)(picard.sam.FilterSamReadsTest) produced standard out/err: Warning: Nashorn engine is planned to be removed from a future JDK release Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testDebugOption[2](false, false) STANDARD_ERROR Warning: Nashorn engine is planned to be removed from a future JDK release Test: Test method testDebugOption[2](false, false)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:03 FilterSamReads Filtering [presorted=true] aligned.sam -> OUTPUT=FilterSamReads.output.13395777350341695578.sam [sortorder=coordinate] INFO 2024-07-02 11:58:03 FilterSamReads Filtering [presorted=true] aligned.sam -> OUTPUT=FilterSamReads.output.13395777350341695578.sam [sortorder=coordinate] Test: Test method testDebugOption[2](false, false)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:03 FilterSamReads 3 SAMRecords written to FilterSamReads.output.13395777350341695578.sam INFO 2024-07-02 11:58:03 FilterSamReads 3 SAMRecords written to FilterSamReads.output.13395777350341695578.sam Running Test: Test method testJavaScriptFilters[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/FilterSamReads/filterOddStarts.js, 3)(picard.sam.FilterSamReadsTest) Test: Test method testJavaScriptFilters[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/FilterSamReads/filterOddStarts.js, 3)(picard.sam.FilterSamReadsTest) produced standard out/err: Warning: Nashorn engine is planned to be removed from a future JDK release Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testJavaScriptFilters[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/FilterSamReads/filterOddStarts.js, 3) STANDARD_ERROR Warning: Nashorn engine is planned to be removed from a future JDK release Test: Test method testJavaScriptFilters[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/FilterSamReads/filterOddStarts.js, 3)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:03 FilterSamReads Filtering [presorted=true] aligned.sam -> OUTPUT=FilterSamReads.output.6820915077558449481.sam [sortorder=coordinate] INFO 2024-07-02 11:58:03 FilterSamReads Filtering [presorted=true] aligned.sam -> OUTPUT=FilterSamReads.output.6820915077558449481.sam [sortorder=coordinate] Test: Test method testJavaScriptFilters[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/FilterSamReads/filterOddStarts.js, 3)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:03 FilterSamReads 3 SAMRecords written to FilterSamReads.output.6820915077558449481.sam INFO 2024-07-02 11:58:03 FilterSamReads 3 SAMRecords written to FilterSamReads.output.6820915077558449481.sam Running Test: Test method testJavaScriptFilters[1](testdata/picard/sam/aligned.sam, testdata/picard/sam/FilterSamReads/filterReadsWithout5primeSoftClip.js, 0)(picard.sam.FilterSamReadsTest) Test: Test method testJavaScriptFilters[1](testdata/picard/sam/aligned.sam, testdata/picard/sam/FilterSamReads/filterReadsWithout5primeSoftClip.js, 0)(picard.sam.FilterSamReadsTest) produced standard out/err: Warning: Nashorn engine is planned to be removed from a future JDK release Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testJavaScriptFilters[1](testdata/picard/sam/aligned.sam, testdata/picard/sam/FilterSamReads/filterReadsWithout5primeSoftClip.js, 0) STANDARD_ERROR Warning: Nashorn engine is planned to be removed from a future JDK release Test: Test method testJavaScriptFilters[1](testdata/picard/sam/aligned.sam, testdata/picard/sam/FilterSamReads/filterReadsWithout5primeSoftClip.js, 0)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:04 FilterSamReads Filtering [presorted=true] aligned.sam -> OUTPUT=FilterSamReads.output.2583984449079238657.sam [sortorder=coordinate] INFO 2024-07-02 11:58:04 FilterSamReads Filtering [presorted=true] aligned.sam -> OUTPUT=FilterSamReads.output.2583984449079238657.sam [sortorder=coordinate] Test: Test method testJavaScriptFilters[1](testdata/picard/sam/aligned.sam, testdata/picard/sam/FilterSamReads/filterReadsWithout5primeSoftClip.js, 0)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:04 FilterSamReads 0 SAMRecords written to FilterSamReads.output.2583984449079238657.sam INFO 2024-07-02 11:58:04 FilterSamReads 0 SAMRecords written to FilterSamReads.output.2583984449079238657.sam Running Test: Test method testPairedIntervalFilter[0](FilterSamReads/filter1.interval_list, 4)(picard.sam.FilterSamReadsTest) Test: Test method testPairedIntervalFilter[0](FilterSamReads/filter1.interval_list, 4)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:04 FilterSamReads Filtering [presorted=true] testSam8555792295585050672.bam -> OUTPUT=FilterSamReads.output.7414961554600952235.sam [sortorder=coordinate] Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testPairedIntervalFilter[0](FilterSamReads/filter1.interval_list, 4) STANDARD_ERROR INFO 2024-07-02 11:58:04 FilterSamReads Filtering [presorted=true] testSam8555792295585050672.bam -> OUTPUT=FilterSamReads.output.7414961554600952235.sam [sortorder=coordinate] Test: Test method testPairedIntervalFilter[0](FilterSamReads/filter1.interval_list, 4)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:04 FilterSamReads 4 SAMRecords written to FilterSamReads.output.7414961554600952235.sam INFO 2024-07-02 11:58:04 FilterSamReads 4 SAMRecords written to FilterSamReads.output.7414961554600952235.sam Running Test: Test method testPairedIntervalFilter[1](FilterSamReads/filter2.interval_list, 0)(picard.sam.FilterSamReadsTest) Test: Test method testPairedIntervalFilter[1](FilterSamReads/filter2.interval_list, 0)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:04 FilterSamReads Filtering [presorted=true] testSam11075608700217741867.bam -> OUTPUT=FilterSamReads.output.6417790087290160866.sam [sortorder=coordinate] Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testPairedIntervalFilter[1](FilterSamReads/filter2.interval_list, 0) STANDARD_ERROR INFO 2024-07-02 11:58:04 FilterSamReads Filtering [presorted=true] testSam11075608700217741867.bam -> OUTPUT=FilterSamReads.output.6417790087290160866.sam [sortorder=coordinate] Test: Test method testPairedIntervalFilter[1](FilterSamReads/filter2.interval_list, 0)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:04 FilterSamReads 0 SAMRecords written to FilterSamReads.output.6417790087290160866.sam INFO 2024-07-02 11:58:04 FilterSamReads 0 SAMRecords written to FilterSamReads.output.6417790087290160866.sam Running Test: Test method testReadFilters[0](includeReadList, [mapped_pair_chr1, prove_one_of_pair, one_of_pair], 6)(picard.sam.FilterSamReadsTest) Test: Test method testReadFilters[0](includeReadList, [mapped_pair_chr1, prove_one_of_pair, one_of_pair], 6)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:04 FilterSamReads Filtering [presorted=true] testSam10725768268532595846.sam -> OUTPUT=FilterSamReads.output.8526600538483580848.sam [sortorder=coordinate] Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testReadFilters[0](includeReadList, [mapped_pair_chr1, prove_one_of_pair, one_of_pair], 6) STANDARD_ERROR INFO 2024-07-02 11:58:04 FilterSamReads Filtering [presorted=true] testSam10725768268532595846.sam -> OUTPUT=FilterSamReads.output.8526600538483580848.sam [sortorder=coordinate] Test: Test method testReadFilters[0](includeReadList, [mapped_pair_chr1, prove_one_of_pair, one_of_pair], 6)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:04 FilterSamReads 6 SAMRecords written to FilterSamReads.output.8526600538483580848.sam INFO 2024-07-02 11:58:04 FilterSamReads 6 SAMRecords written to FilterSamReads.output.8526600538483580848.sam Running Test: Test method testReadFilters[1](excludeReadList, [mapped_pair_chr1, prove_one_of_pair, one_of_pair], 2)(picard.sam.FilterSamReadsTest) Test: Test method testReadFilters[1](excludeReadList, [mapped_pair_chr1, prove_one_of_pair, one_of_pair], 2)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:04 FilterSamReads Filtering [presorted=true] testSam17398485207566169812.sam -> OUTPUT=FilterSamReads.output.8377588741043413162.sam [sortorder=coordinate] Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testReadFilters[1](excludeReadList, [mapped_pair_chr1, prove_one_of_pair, one_of_pair], 2) STANDARD_ERROR INFO 2024-07-02 11:58:04 FilterSamReads Filtering [presorted=true] testSam17398485207566169812.sam -> OUTPUT=FilterSamReads.output.8377588741043413162.sam [sortorder=coordinate] Test: Test method testReadFilters[1](excludeReadList, [mapped_pair_chr1, prove_one_of_pair, one_of_pair], 2)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:04 FilterSamReads 2 SAMRecords written to FilterSamReads.output.8377588741043413162.sam INFO 2024-07-02 11:58:04 FilterSamReads 2 SAMRecords written to FilterSamReads.output.8377588741043413162.sam Running Test: Test method testTagFilter[0](testdata/picard/sam/aligned.sam, RG, 0, true, 8)(picard.sam.FilterSamReadsTest) Test: Test method testTagFilter[0](testdata/picard/sam/aligned.sam, RG, 0, true, 8)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:04 FilterSamReads Filtering [presorted=true] aligned.sam -> OUTPUT=FilterSamReads.output.3639598308792647717.sam [sortorder=coordinate] Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testTagFilter[0](testdata/picard/sam/aligned.sam, RG, 0, true, 8) STANDARD_ERROR INFO 2024-07-02 11:58:04 FilterSamReads Filtering [presorted=true] aligned.sam -> OUTPUT=FilterSamReads.output.3639598308792647717.sam [sortorder=coordinate] Test: Test method testTagFilter[0](testdata/picard/sam/aligned.sam, RG, 0, true, 8)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:04 FilterSamReads 8 SAMRecords written to FilterSamReads.output.3639598308792647717.sam INFO 2024-07-02 11:58:04 FilterSamReads 8 SAMRecords written to FilterSamReads.output.3639598308792647717.sam Running Test: Test method testTagFilter[1](testdata/picard/sam/aligned.sam, RG, 0, false, 0)(picard.sam.FilterSamReadsTest) Test: Test method testTagFilter[1](testdata/picard/sam/aligned.sam, RG, 0, false, 0)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:04 FilterSamReads Filtering [presorted=true] aligned.sam -> OUTPUT=FilterSamReads.output.4652910345760893548.sam [sortorder=coordinate] Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testTagFilter[1](testdata/picard/sam/aligned.sam, RG, 0, false, 0) STANDARD_ERROR INFO 2024-07-02 11:58:04 FilterSamReads Filtering [presorted=true] aligned.sam -> OUTPUT=FilterSamReads.output.4652910345760893548.sam [sortorder=coordinate] Test: Test method testTagFilter[1](testdata/picard/sam/aligned.sam, RG, 0, false, 0)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:04 FilterSamReads 0 SAMRecords written to FilterSamReads.output.4652910345760893548.sam INFO 2024-07-02 11:58:04 FilterSamReads 0 SAMRecords written to FilterSamReads.output.4652910345760893548.sam Running Test: Test method testTagFilter[2](testdata/picard/sam/aligned.sam, CB, ACG, false, 3)(picard.sam.FilterSamReadsTest) Test: Test method testTagFilter[2](testdata/picard/sam/aligned.sam, CB, ACG, false, 3)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:04 FilterSamReads Filtering [presorted=true] aligned.sam -> OUTPUT=FilterSamReads.output.2094895505141872393.sam [sortorder=coordinate] Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testTagFilter[2](testdata/picard/sam/aligned.sam, CB, ACG, false, 3) STANDARD_ERROR INFO 2024-07-02 11:58:04 FilterSamReads Filtering [presorted=true] aligned.sam -> OUTPUT=FilterSamReads.output.2094895505141872393.sam [sortorder=coordinate] Test: Test method testTagFilter[2](testdata/picard/sam/aligned.sam, CB, ACG, false, 3)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:04 FilterSamReads 3 SAMRecords written to FilterSamReads.output.2094895505141872393.sam INFO 2024-07-02 11:58:04 FilterSamReads 3 SAMRecords written to FilterSamReads.output.2094895505141872393.sam Running Test: Test method testTagFilter[3](testdata/picard/sam/aligned.sam, CB, ACG, true, 5)(picard.sam.FilterSamReadsTest) Test: Test method testTagFilter[3](testdata/picard/sam/aligned.sam, CB, ACG, true, 5)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:04 FilterSamReads Filtering [presorted=true] aligned.sam -> OUTPUT=FilterSamReads.output.5021305116562322727.sam [sortorder=coordinate] Gradle suite > Gradle test > picard.sam.FilterSamReadsTest.testTagFilter[3](testdata/picard/sam/aligned.sam, CB, ACG, true, 5) STANDARD_ERROR INFO 2024-07-02 11:58:04 FilterSamReads Filtering [presorted=true] aligned.sam -> OUTPUT=FilterSamReads.output.5021305116562322727.sam [sortorder=coordinate] Test: Test method testTagFilter[3](testdata/picard/sam/aligned.sam, CB, ACG, true, 5)(picard.sam.FilterSamReadsTest) produced standard out/err: INFO 2024-07-02 11:58:04 FilterSamReads 5 SAMRecords written to FilterSamReads.output.5021305116562322727.sam INFO 2024-07-02 11:58:04 FilterSamReads 5 SAMRecords written to FilterSamReads.output.5021305116562322727.sam Running Test: Test method testFindMedelianViolations(picard.vcf.MendelianViolations.FindMendelianViolationsTest) Test: Test method testFindMedelianViolations(picard.vcf.MendelianViolations.FindMendelianViolationsTest) produced standard out/err: INFO 2024-07-02 11:58:04 FindMendelianViolations Loading and filtering trios. Gradle suite > Gradle test > picard.vcf.MendelianViolations.FindMendelianViolationsTest.testFindMedelianViolations STANDARD_ERROR INFO 2024-07-02 11:58:04 FindMendelianViolations Loading and filtering trios. Test: Test method testFindMedelianViolations(picard.vcf.MendelianViolations.FindMendelianViolationsTest) produced standard out/err: INFO 2024-07-02 11:58:04 FindMendelianViolations Writing family violation VCFs to /tmp/MendelianViolations4471574482326706873temp/ INFO 2024-07-02 11:58:04 FindMendelianViolations Writing family violation VCFs to /tmp/MendelianViolations4471574482326706873temp/ Test: Test method testFindMedelianViolations(picard.vcf.MendelianViolations.FindMendelianViolationsTest) produced standard out/err: INFO 2024-07-02 11:58:04 FindMendelianViolations Writing FAKE violation VCF to /tmp/MendelianViolations4471574482326706873temp/FAKE.vcf INFO 2024-07-02 11:58:04 FindMendelianViolations Writing FAKE violation VCF to /tmp/MendelianViolations4471574482326706873temp/FAKE.vcf Test: Test method testFindMedelianViolations(picard.vcf.MendelianViolations.FindMendelianViolationsTest) produced standard out/err: INFO 2024-07-02 11:58:04 FindMendelianViolations Writing NA12878 violation VCF to /tmp/MendelianViolations4471574482326706873temp/NA12878.vcf INFO 2024-07-02 11:58:04 FindMendelianViolations Writing NA12878 violation VCF to /tmp/MendelianViolations4471574482326706873temp/NA12878.vcf Running Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:05 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.FingerprintCheckerTest.testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false) STANDARD_ERROR INFO 2024-07-02 11:58:05 CrosscheckFingerprints Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** CrosscheckFingerprints -EXPECT_ALL_GROUPS_TO_MATCH true -LOD_THRESHOLD -1 -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam -VALIDATION_STRINGENCY STRICT -CROSSCHECK_BY FILE ********** CrosscheckFingerprints -EXPECT_ALL_GROUPS_TO_MATCH true -LOD_THRESHOLD -1 -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam -VALIDATION_STRINGENCY STRICT -CROSSCHECK_BY FILE Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:05.153 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:58:05.153 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:05.153 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:58:05.153 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:05.154 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:05.154 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:05.154 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:05.154 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:05.154 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:05.154 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:05.154 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:05.154 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:05 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam] HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE EXPECT_ALL_GROUPS_TO_MATCH=true VALIDATION_STRINGENCY=STRICT CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:05 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam] HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE EXPECT_ALL_GROUPS_TO_MATCH=true VALIDATION_STRINGENCY=STRICT CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:05 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:58:05 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:05 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) WARNING 2024-07-02 11:58:05 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:05 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam) WARNING 2024-07-02 11:58:05 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam) Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ERROR 2024-07-02 11:58:05 FingerprintChecker Found read with no readgroup: HK3T5CCXX160204:8:1214:19390:8745 in file: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam ERROR 2024-07-02 11:58:05 FingerprintChecker Found read with no readgroup: HK3T5CCXX160204:8:1214:19390:8745 in file: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:05 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:58:05 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method testCheckFingerprintsFail[0](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:05 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.FingerprintCheckerTest.testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true) STANDARD_ERROR INFO 2024-07-02 11:58:05 CrosscheckFingerprints Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** CrosscheckFingerprints -EXPECT_ALL_GROUPS_TO_MATCH true -LOD_THRESHOLD -1 -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam -VALIDATION_STRINGENCY STRICT -CROSSCHECK_BY FILE ********** CrosscheckFingerprints -EXPECT_ALL_GROUPS_TO_MATCH true -LOD_THRESHOLD -1 -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam -VALIDATION_STRINGENCY STRICT -CROSSCHECK_BY FILE Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:05.727 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:58:05.727 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:05.727 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:58:05.727 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:05.728 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:05.728 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:05.728 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:05.728 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:05.728 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:05.728 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:05.728 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:05.728 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:05 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam] HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE EXPECT_ALL_GROUPS_TO_MATCH=true VALIDATION_STRINGENCY=STRICT CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:05 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam] HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE EXPECT_ALL_GROUPS_TO_MATCH=true VALIDATION_STRINGENCY=STRICT CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:05 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:58:05 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:05 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam) WARNING 2024-07-02 11:58:05 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam) Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:06 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam) WARNING 2024-07-02 11:58:06 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam) Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ERROR 2024-07-02 11:58:06 FingerprintChecker Found read with no readgroup: HK3T5CCXX160204:8:1214:19390:8745 in file: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam ERROR 2024-07-02 11:58:06 FingerprintChecker Found read with no readgroup: HK3T5CCXX160204:8:1214:19390:8745 in file: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:06 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:58:06 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method testCheckFingerprintsFail[1](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:06 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.FingerprintCheckerTest.testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true) STANDARD_ERROR INFO 2024-07-02 11:58:06 CrosscheckFingerprints Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** CrosscheckFingerprints -EXPECT_ALL_GROUPS_TO_MATCH true -LOD_THRESHOLD -1 -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -VALIDATION_STRINGENCY SILENT -CROSSCHECK_BY FILE -OUTPUT /tmp/crosscheck4056977906581056989.crosscheck_metrics ********** CrosscheckFingerprints -EXPECT_ALL_GROUPS_TO_MATCH true -LOD_THRESHOLD -1 -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -VALIDATION_STRINGENCY SILENT -CROSSCHECK_BY FILE -OUTPUT /tmp/crosscheck4056977906581056989.crosscheck_metrics Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:06.079 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:58:06.079 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:06.080 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:58:06.080 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:06.080 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:06.080 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:06.081 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:06.081 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:06.081 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:06.081 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:06.081 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:06.081 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:06 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam] OUTPUT=/tmp/crosscheck4056977906581056989.crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE EXPECT_ALL_GROUPS_TO_MATCH=true VALIDATION_STRINGENCY=SILENT CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:06 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam] OUTPUT=/tmp/crosscheck4056977906581056989.crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE EXPECT_ALL_GROUPS_TO_MATCH=true VALIDATION_STRINGENCY=SILENT CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:06 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:58:06 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:06 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam) WARNING 2024-07-02 11:58:06 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam) Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:06 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) WARNING 2024-07-02 11:58:06 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:06 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:58:06 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:06 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:58:06 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:06 CrosscheckFingerprints All FILEs are related as expected. INFO 2024-07-02 11:58:06 CrosscheckFingerprints All FILEs are related as expected. Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:06 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:58:06 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCheckFingerprintsSam[0](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:06 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.FingerprintCheckerTest.testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true) STANDARD_ERROR INFO 2024-07-02 11:58:06 CrosscheckFingerprints Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** CrosscheckFingerprints -EXPECT_ALL_GROUPS_TO_MATCH true -LOD_THRESHOLD -1 -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam -VALIDATION_STRINGENCY SILENT -CROSSCHECK_BY FILE -OUTPUT /tmp/crosscheck16650004774085563409.crosscheck_metrics ********** CrosscheckFingerprints -EXPECT_ALL_GROUPS_TO_MATCH true -LOD_THRESHOLD -1 -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam -VALIDATION_STRINGENCY SILENT -CROSSCHECK_BY FILE -OUTPUT /tmp/crosscheck16650004774085563409.crosscheck_metrics Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:06.646 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:58:06.646 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:06.646 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:58:06.646 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:06.647 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:06.647 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:06.647 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:06.647 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:06.647 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:06.647 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:06.647 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:06.647 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:06 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam] OUTPUT=/tmp/crosscheck16650004774085563409.crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE EXPECT_ALL_GROUPS_TO_MATCH=true VALIDATION_STRINGENCY=SILENT CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:06 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam] OUTPUT=/tmp/crosscheck16650004774085563409.crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE EXPECT_ALL_GROUPS_TO_MATCH=true VALIDATION_STRINGENCY=SILENT CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:06 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:58:06 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:06 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) WARNING 2024-07-02 11:58:06 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:06 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) WARNING 2024-07-02 11:58:06 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:07 FingerprintChecker Processed files. 51 fingerprints found in map. INFO 2024-07-02 11:58:07 FingerprintChecker Processed files. 51 fingerprints found in map. Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:07 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:58:07 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:07 CrosscheckFingerprints All FILEs are related as expected. INFO 2024-07-02 11:58:07 CrosscheckFingerprints All FILEs are related as expected. Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:07 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:58:07 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCheckFingerprintsSam[1](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:07 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.FingerprintCheckerTest.testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true) STANDARD_ERROR INFO 2024-07-02 11:58:07 CrosscheckFingerprints Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** CrosscheckFingerprints -EXPECT_ALL_GROUPS_TO_MATCH true -LOD_THRESHOLD -1 -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -VALIDATION_STRINGENCY SILENT -CROSSCHECK_BY FILE -OUTPUT /tmp/crosscheck15900354482939560564.crosscheck_metrics ********** CrosscheckFingerprints -EXPECT_ALL_GROUPS_TO_MATCH true -LOD_THRESHOLD -1 -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -VALIDATION_STRINGENCY SILENT -CROSSCHECK_BY FILE -OUTPUT /tmp/crosscheck15900354482939560564.crosscheck_metrics Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:07.222 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:58:07.222 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:07.222 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:58:07.222 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:07.223 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:07.223 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:07.223 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:07.223 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:07.223 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:07.223 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:07.223 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:07.223 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:07 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam] OUTPUT=/tmp/crosscheck15900354482939560564.crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE EXPECT_ALL_GROUPS_TO_MATCH=true VALIDATION_STRINGENCY=SILENT CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:07 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam] OUTPUT=/tmp/crosscheck15900354482939560564.crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE EXPECT_ALL_GROUPS_TO_MATCH=true VALIDATION_STRINGENCY=SILENT CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:07 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:58:07 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:07 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) WARNING 2024-07-02 11:58:07 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:07 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) WARNING 2024-07-02 11:58:07 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:07 FingerprintChecker Processed files. 51 fingerprints found in map. INFO 2024-07-02 11:58:07 FingerprintChecker Processed files. 51 fingerprints found in map. Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:07 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:58:07 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:07 CrosscheckFingerprints 2 FILEs did not relate as expected. WARNING 2024-07-02 11:58:07 CrosscheckFingerprints 2 FILEs did not relate as expected. Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:07 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:58:07 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method testCheckFingerprintsSam[2](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:07 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.FingerprintCheckerTest.testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true) STANDARD_ERROR INFO 2024-07-02 11:58:07 CrosscheckFingerprints Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** CrosscheckFingerprints -EXPECT_ALL_GROUPS_TO_MATCH true -LOD_THRESHOLD -1 -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam -VALIDATION_STRINGENCY SILENT -CROSSCHECK_BY FILE -OUTPUT /tmp/crosscheck246413939605981649.crosscheck_metrics ********** CrosscheckFingerprints -EXPECT_ALL_GROUPS_TO_MATCH true -LOD_THRESHOLD -1 -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam -VALIDATION_STRINGENCY SILENT -CROSSCHECK_BY FILE -OUTPUT /tmp/crosscheck246413939605981649.crosscheck_metrics Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:07.779 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:58:07.779 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:07.779 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:58:07.779 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:07.780 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:07.780 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:07.780 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:07.780 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:07.780 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:07.780 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:07.780 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:07.780 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:07 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam] OUTPUT=/tmp/crosscheck246413939605981649.crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE EXPECT_ALL_GROUPS_TO_MATCH=true VALIDATION_STRINGENCY=SILENT CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:07 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam] OUTPUT=/tmp/crosscheck246413939605981649.crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE EXPECT_ALL_GROUPS_TO_MATCH=true VALIDATION_STRINGENCY=SILENT CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:07 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:58:07 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:07 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam) WARNING 2024-07-02 11:58:07 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam) Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:08 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam) WARNING 2024-07-02 11:58:08 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam) Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:08 FingerprintChecker Processed files. 55 fingerprints found in map. INFO 2024-07-02 11:58:08 FingerprintChecker Processed files. 55 fingerprints found in map. Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:08 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:58:08 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:08 CrosscheckFingerprints All FILEs are related as expected. INFO 2024-07-02 11:58:08 CrosscheckFingerprints All FILEs are related as expected. Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:08 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:58:08 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCheckFingerprintsSam[3](testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:08 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.FingerprintCheckerTest.testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true) STANDARD_ERROR INFO 2024-07-02 11:58:08 CrosscheckFingerprints Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** CrosscheckFingerprints -EXPECT_ALL_GROUPS_TO_MATCH true -LOD_THRESHOLD -1 -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam -VALIDATION_STRINGENCY SILENT -CROSSCHECK_BY FILE -OUTPUT /tmp/crosscheck15534761261444753227.crosscheck_metrics ********** CrosscheckFingerprints -EXPECT_ALL_GROUPS_TO_MATCH true -LOD_THRESHOLD -1 -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam -VALIDATION_STRINGENCY SILENT -CROSSCHECK_BY FILE -OUTPUT /tmp/crosscheck15534761261444753227.crosscheck_metrics Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:08.355 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:58:08.355 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:08.355 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:58:08.355 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:08.356 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:08.356 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:08.356 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:08.356 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:08.356 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:08.356 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:08.356 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:08.356 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:08 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam] OUTPUT=/tmp/crosscheck15534761261444753227.crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE EXPECT_ALL_GROUPS_TO_MATCH=true VALIDATION_STRINGENCY=SILENT CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:08 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam] OUTPUT=/tmp/crosscheck15534761261444753227.crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE EXPECT_ALL_GROUPS_TO_MATCH=true VALIDATION_STRINGENCY=SILENT CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:08 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:58:08 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:08 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) WARNING 2024-07-02 11:58:08 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:08 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam) WARNING 2024-07-02 11:58:08 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam) Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:09 FingerprintChecker Processed files. 53 fingerprints found in map. INFO 2024-07-02 11:58:09 FingerprintChecker Processed files. 53 fingerprints found in map. Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:09 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:58:09 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:09 CrosscheckFingerprints 2 FILEs did not relate as expected. WARNING 2024-07-02 11:58:09 CrosscheckFingerprints 2 FILEs did not relate as expected. Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:09 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:58:09 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method testCheckFingerprintsSam[4](testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:09 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.FingerprintCheckerTest.testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false) STANDARD_ERROR INFO 2024-07-02 11:58:09 CrosscheckFingerprints Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** CrosscheckFingerprints -EXPECT_ALL_GROUPS_TO_MATCH true -LOD_THRESHOLD -1 -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -VALIDATION_STRINGENCY LENIENT -CROSSCHECK_BY FILE -OUTPUT /tmp/crosscheck18108331722487613605.crosscheck_metrics ********** CrosscheckFingerprints -EXPECT_ALL_GROUPS_TO_MATCH true -LOD_THRESHOLD -1 -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -VALIDATION_STRINGENCY LENIENT -CROSSCHECK_BY FILE -OUTPUT /tmp/crosscheck18108331722487613605.crosscheck_metrics Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:09.018 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:58:09.018 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:09.018 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:58:09.018 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:09.019 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:09.019 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:09.019 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:09.019 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:09.019 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:09.019 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:09.019 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:09.019 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:09 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam] OUTPUT=/tmp/crosscheck18108331722487613605.crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE EXPECT_ALL_GROUPS_TO_MATCH=true VALIDATION_STRINGENCY=LENIENT CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:09 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam] OUTPUT=/tmp/crosscheck18108331722487613605.crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE EXPECT_ALL_GROUPS_TO_MATCH=true VALIDATION_STRINGENCY=LENIENT CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:09 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:58:09 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:09 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) WARNING 2024-07-02 11:58:09 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:09 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) WARNING 2024-07-02 11:58:09 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:09 FingerprintChecker Processed files. 26 fingerprints found in map. INFO 2024-07-02 11:58:09 FingerprintChecker Processed files. 26 fingerprints found in map. Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:09 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:58:09 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:09 CrosscheckFingerprints All FILEs are related as expected. INFO 2024-07-02 11:58:09 CrosscheckFingerprints All FILEs are related as expected. Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:09 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:58:09 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCheckFingerprintsSam[5](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:09 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.FingerprintCheckerTest.testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false) STANDARD_ERROR INFO 2024-07-02 11:58:09 CrosscheckFingerprints Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** CrosscheckFingerprints -EXPECT_ALL_GROUPS_TO_MATCH true -LOD_THRESHOLD -1 -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam -VALIDATION_STRINGENCY LENIENT -CROSSCHECK_BY FILE -OUTPUT /tmp/crosscheck12917918667076399015.crosscheck_metrics ********** CrosscheckFingerprints -EXPECT_ALL_GROUPS_TO_MATCH true -LOD_THRESHOLD -1 -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam -VALIDATION_STRINGENCY LENIENT -CROSSCHECK_BY FILE -OUTPUT /tmp/crosscheck12917918667076399015.crosscheck_metrics Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:09.789 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:58:09.789 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:09.789 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:58:09.789 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:09.799 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:09.799 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:09.799 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:09.799 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:09.800 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:09.800 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:09.800 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:09.800 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:09 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam] OUTPUT=/tmp/crosscheck12917918667076399015.crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE EXPECT_ALL_GROUPS_TO_MATCH=true VALIDATION_STRINGENCY=LENIENT CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:09 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam] OUTPUT=/tmp/crosscheck12917918667076399015.crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE EXPECT_ALL_GROUPS_TO_MATCH=true VALIDATION_STRINGENCY=LENIENT CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:09 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:58:09 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:09 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) WARNING 2024-07-02 11:58:09 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:10 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) WARNING 2024-07-02 11:58:10 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:10 FingerprintChecker Processed files. 26 fingerprints found in map. INFO 2024-07-02 11:58:10 FingerprintChecker Processed files. 26 fingerprints found in map. Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:10 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:58:10 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:10 CrosscheckFingerprints All FILEs are related as expected. INFO 2024-07-02 11:58:10 CrosscheckFingerprints All FILEs are related as expected. Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:10 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:58:10 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCheckFingerprintsSam[6](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:10 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.FingerprintCheckerTest.testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false) STANDARD_ERROR INFO 2024-07-02 11:58:10 CrosscheckFingerprints Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** CrosscheckFingerprints -EXPECT_ALL_GROUPS_TO_MATCH true -LOD_THRESHOLD -1 -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -VALIDATION_STRINGENCY LENIENT -CROSSCHECK_BY FILE -OUTPUT /tmp/crosscheck1200757952805885608.crosscheck_metrics ********** CrosscheckFingerprints -EXPECT_ALL_GROUPS_TO_MATCH true -LOD_THRESHOLD -1 -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -VALIDATION_STRINGENCY LENIENT -CROSSCHECK_BY FILE -OUTPUT /tmp/crosscheck1200757952805885608.crosscheck_metrics Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:10.419 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:58:10.419 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:10.419 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:58:10.419 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:10.420 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:10.420 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:10.420 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:10.420 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:10.420 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:10.420 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:10.420 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:10.420 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:10 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam] OUTPUT=/tmp/crosscheck1200757952805885608.crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE EXPECT_ALL_GROUPS_TO_MATCH=true VALIDATION_STRINGENCY=LENIENT CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:10 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam] OUTPUT=/tmp/crosscheck1200757952805885608.crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE EXPECT_ALL_GROUPS_TO_MATCH=true VALIDATION_STRINGENCY=LENIENT CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:10 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:58:10 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:10 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) WARNING 2024-07-02 11:58:10 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:10 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) WARNING 2024-07-02 11:58:10 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:11 FingerprintChecker Processed files. 52 fingerprints found in map. INFO 2024-07-02 11:58:11 FingerprintChecker Processed files. 52 fingerprints found in map. Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:11 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:58:11 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:11 CrosscheckFingerprints 2 FILEs did not relate as expected. WARNING 2024-07-02 11:58:11 CrosscheckFingerprints 2 FILEs did not relate as expected. Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:11 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:58:11 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method testCheckFingerprintsSam[7](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:11 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.FingerprintCheckerTest.testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false) STANDARD_ERROR INFO 2024-07-02 11:58:11 CrosscheckFingerprints Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** CrosscheckFingerprints -EXPECT_ALL_GROUPS_TO_MATCH true -LOD_THRESHOLD -1 -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam -VALIDATION_STRINGENCY LENIENT -CROSSCHECK_BY FILE -OUTPUT /tmp/crosscheck12877209192590514265.crosscheck_metrics ********** CrosscheckFingerprints -EXPECT_ALL_GROUPS_TO_MATCH true -LOD_THRESHOLD -1 -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam -VALIDATION_STRINGENCY LENIENT -CROSSCHECK_BY FILE -OUTPUT /tmp/crosscheck12877209192590514265.crosscheck_metrics Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:11.039 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:58:11.039 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:11.039 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:58:11.039 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:11.040 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:11.040 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:11.040 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:11.040 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:11.040 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:11.040 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:11.040 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:11.040 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:11 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam] OUTPUT=/tmp/crosscheck12877209192590514265.crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE EXPECT_ALL_GROUPS_TO_MATCH=true VALIDATION_STRINGENCY=LENIENT CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:11 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam] OUTPUT=/tmp/crosscheck12877209192590514265.crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE EXPECT_ALL_GROUPS_TO_MATCH=true VALIDATION_STRINGENCY=LENIENT CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:11 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:58:11 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:11 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) WARNING 2024-07-02 11:58:11 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:11 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam) WARNING 2024-07-02 11:58:11 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam) Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:11 FingerprintChecker Found read with no readgroup: HK3T5CCXX160204:8:1214:19390:8745 in file: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam WARNING 2024-07-02 11:58:11 FingerprintChecker Found read with no readgroup: HK3T5CCXX160204:8:1214:19390:8745 in file: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:11 FingerprintChecker further messages from this file will be suppressed WARNING 2024-07-02 11:58:11 FingerprintChecker further messages from this file will be suppressed Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:11 FingerprintChecker Processed files. 54 fingerprints found in map. INFO 2024-07-02 11:58:11 FingerprintChecker Processed files. 54 fingerprints found in map. Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:11 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:58:11 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:11 CrosscheckFingerprints All FILEs are related as expected. INFO 2024-07-02 11:58:11 CrosscheckFingerprints All FILEs are related as expected. Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:11 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:58:11 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCheckFingerprintsSam[8](testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, true, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:11 CrosscheckFingerprints Gradle suite > Gradle test > picard.fingerprint.FingerprintCheckerTest.testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false) STANDARD_ERROR INFO 2024-07-02 11:58:11 CrosscheckFingerprints Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** CrosscheckFingerprints -EXPECT_ALL_GROUPS_TO_MATCH true -LOD_THRESHOLD -1 -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam -VALIDATION_STRINGENCY LENIENT -CROSSCHECK_BY FILE -OUTPUT /tmp/crosscheck1047335646863616092.crosscheck_metrics ********** CrosscheckFingerprints -EXPECT_ALL_GROUPS_TO_MATCH true -LOD_THRESHOLD -1 -H /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam -VALIDATION_STRINGENCY LENIENT -CROSSCHECK_BY FILE -OUTPUT /tmp/crosscheck1047335646863616092.crosscheck_metrics Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: ********** ********** Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:11.473 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced 11:58:11.473 WARN LegacyCommandLineArgumentParser - Minimum allowed value for argument --MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK is not enforced Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:11.474 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY 11:58:11.474 WARN LegacyCommandLineArgumentParser - Hidden annotation is not honored for --TEST_INPUT_READABILITY Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:11.475 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:11.475 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:11.475 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:11.475 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:11.485 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:11.485 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: 11:58:11.485 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:11.485 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:11 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam] OUTPUT=/tmp/crosscheck1047335646863616092.crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE EXPECT_ALL_GROUPS_TO_MATCH=true VALIDATION_STRINGENCY=LENIENT CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:11 GMT+14:00 2024] CrosscheckFingerprints INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam] OUTPUT=/tmp/crosscheck1047335646863616092.crosscheck_metrics HAPLOTYPE_MAP=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/Homo_sapiens_assembly19.haplotype_database.subset.txt LOD_THRESHOLD=-1.0 CROSSCHECK_BY=FILE EXPECT_ALL_GROUPS_TO_MATCH=true VALIDATION_STRINGENCY=LENIENT CROSSCHECK_MODE=CHECK_SAME_SAMPLE NUM_THREADS=1 CALCULATE_TUMOR_AWARE_RESULTS=true ALLOW_DUPLICATE_READS=false GENOTYPING_ERROR_RATE=0.01 OUTPUT_ERRORS_ONLY=false LOSS_OF_HET_RATE=0.5 EXIT_CODE_WHEN_MISMATCH=1 EXIT_CODE_WHEN_NO_VALID_CHECKS=1 MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK=3.0 TEST_INPUT_READABILITY=true VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:11 CrosscheckFingerprints Fingerprinting 2 INPUT files. INFO 2024-07-02 11:58:11 CrosscheckFingerprints Fingerprinting 2 INPUT files. Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:11 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) WARNING 2024-07-02 11:58:11 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:11 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam) WARNING 2024-07-02 11:58:11 FingerprintChecker Operating without an index! We could be here for a while. (/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam) Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:11 FingerprintChecker Found read with no readgroup: HK3T5CCXX160204:8:1214:19390:8745 in file: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam WARNING 2024-07-02 11:58:11 FingerprintChecker Found read with no readgroup: HK3T5CCXX160204:8:1214:19390:8745 in file: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:11 FingerprintChecker further messages from this file will be suppressed WARNING 2024-07-02 11:58:11 FingerprintChecker further messages from this file will be suppressed Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:12 FingerprintChecker Processed files. 54 fingerprints found in map. INFO 2024-07-02 11:58:12 FingerprintChecker Processed files. 54 fingerprints found in map. Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:12 CrosscheckFingerprints Cross-checking all FILE against each other INFO 2024-07-02 11:58:12 CrosscheckFingerprints Cross-checking all FILE against each other Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:12 CrosscheckFingerprints 2 FILEs did not relate as expected. WARNING 2024-07-02 11:58:12 CrosscheckFingerprints 2 FILEs did not relate as expected. Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: [Tue Jul 02 11:58:12 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:58:12 GMT+14:00 2024] picard.fingerprint.CrosscheckFingerprints done. Elapsed time: 0.01 minutes. Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method testCheckFingerprintsSam[9](testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam, testdata/picard/fingerprint/NA12891.over.fingerprints.noRgTag.sam, false, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMatchResults[0](0.025)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testMatchResults[1](0.05)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testMatchResults[2](0.075)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testMatchResults[3](0.1)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testMatchResults[4](0.125)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testMatchResults[5](0.15)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testMatchResults[6](0.175)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testMatchResults[7](0.2)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testMatchResults[8](0.225)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testMatchResults[9](0.25)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testMatchResults[10](0.275)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testMatchResults[11](0.3)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testMatchResults[12](0.325)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testMatchResults[13](0.35)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testMatchResults[14](0.375)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testMatchResults[15](0.4)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testMatchResults[16](0.425)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testMatchResults[17](0.45)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testMatchResults[18](0.475)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testMergeFingerprintIsSafe[0](picard.fingerprint.HaplotypeProbabilitiesFromGenotype@45e8abf7, picard.fingerprint.HaplotypeProbabilitiesFromGenotype@77041d52)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testMergeFingerprintIsSafe[1](picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor@2b40fcef, picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor@23cfc324)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testMergeFingerprintIsSafe[2](picard.fingerprint.HaplotypeProbabilitiesFromSequence@3635207e, picard.fingerprint.HaplotypeProbabilitiesFromSequence@5849e8c5)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testMergeFingerprintIsSafe[3](picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@255adb8d, picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@509eb955)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testMergeHaplotypeProbabilitiesIsSafe[0](picard.fingerprint.HaplotypeProbabilitiesFromGenotype@567b937b, picard.fingerprint.HaplotypeProbabilitiesFromGenotype@3d66a007)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testMergeHaplotypeProbabilitiesIsSafe[1](picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor@67e0de66, picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor@6d0a69aa)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testMergeHaplotypeProbabilitiesIsSafe[2](picard.fingerprint.HaplotypeProbabilitiesFromSequence@4af417c7, picard.fingerprint.HaplotypeProbabilitiesFromSequence@2b06e311)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testMergeHaplotypeProbabilitiesIsSafe[3](picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@540e10e3, picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@3eae7f8a)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testMergeIsSafeFromSequence(picard.fingerprint.FingerprintCheckerTest) Test: Test method testMergeIsSafeFromSequence(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:12 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam) Gradle suite > Gradle test > picard.fingerprint.FingerprintCheckerTest.testMergeIsSafeFromSequence STANDARD_ERROR WARNING 2024-07-02 11:58:12 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam) Test: Test method testMergeIsSafeFromSequence(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:12 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) WARNING 2024-07-02 11:58:12 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r2.sam) Test: Test method testMergeIsSafeFromSequence(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:12 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) WARNING 2024-07-02 11:58:12 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r1.sam) Test: Test method testMergeIsSafeFromSequence(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:13 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) WARNING 2024-07-02 11:58:13 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12892.over.fingerprints.r2.sam) Test: Test method testMergeIsSafeFromSequence(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:13 FingerprintChecker Processed files. 104 fingerprints found in map. INFO 2024-07-02 11:58:13 FingerprintChecker Processed files. 104 fingerprints found in map. Running Test: Test method testMergeIsSafeFromVCF(picard.fingerprint.FingerprintCheckerTest) Test: Test method testMergeIsSafeFromVCF(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:13 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.fp.vcf going to read through it all. Gradle suite > Gradle test > picard.fingerprint.FingerprintCheckerTest.testMergeIsSafeFromVCF STANDARD_ERROR WARNING 2024-07-02 11:58:13 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.fp.vcf going to read through it all. Test: Test method testMergeIsSafeFromVCF(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:13 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.vcf going to read through it all. WARNING 2024-07-02 11:58:13 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12891.vcf going to read through it all. Test: Test method testMergeIsSafeFromVCF(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:13 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12892.fp.vcf going to read through it all. WARNING 2024-07-02 11:58:13 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12892.fp.vcf going to read through it all. Test: Test method testMergeIsSafeFromVCF(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:13 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12892.vcf going to read through it all. WARNING 2024-07-02 11:58:13 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/NA12892.vcf going to read through it all. Test: Test method testMergeIsSafeFromVCF(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:13 FingerprintChecker Processed files. 4 fingerprints found in map. INFO 2024-07-02 11:58:13 FingerprintChecker Processed files. 4 fingerprints found in map. Running Test: Test method testQueryable[0](testdata/picard/fingerprint/NA12891.fp.vcf, false)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testQueryable[1](testdata/picard/fingerprint/NA12891.vcf, false)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testQueryable[2](/tmp/fingerprintcheckertest.tmp.4437399649487446027.vcf, true)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testQueryable[3](/tmp/fingerprintcheckertest.tmp.48392027057191066.vcf.gz, true)(picard.fingerprint.FingerprintCheckerTest) Running Test: Test method testTerminateOnBadFile[0](NA12891.over.fingerprints.r1.sam, true)(picard.fingerprint.FingerprintCheckerTest) Test: Test method testTerminateOnBadFile[0](NA12891.over.fingerprints.r1.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:14 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam) Gradle suite > Gradle test > picard.fingerprint.FingerprintCheckerTest.testTerminateOnBadFile[0](NA12891.over.fingerprints.r1.sam, true) STANDARD_ERROR WARNING 2024-07-02 11:58:14 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/NA12891.over.fingerprints.r1.sam) Test: Test method testTerminateOnBadFile[0](NA12891.over.fingerprints.r1.sam, true)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: INFO 2024-07-02 11:58:14 FingerprintChecker Processed files. 27 fingerprints found in map. INFO 2024-07-02 11:58:14 FingerprintChecker Processed files. 27 fingerprints found in map. Running Test: Test method testTerminateOnBadFile[1](aligned_queryname_sorted.sam, false)(picard.fingerprint.FingerprintCheckerTest) Test: Test method testTerminateOnBadFile[1](aligned_queryname_sorted.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:14 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/aligned_queryname_sorted.sam) Gradle suite > Gradle test > picard.fingerprint.FingerprintCheckerTest.testTerminateOnBadFile[1](aligned_queryname_sorted.sam, false) STANDARD_ERROR WARNING 2024-07-02 11:58:14 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/aligned_queryname_sorted.sam) Running Test: Test method testTerminateOnBadFile[2](aligned_unsorted.sam, false)(picard.fingerprint.FingerprintCheckerTest) Test: Test method testTerminateOnBadFile[2](aligned_unsorted.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:14 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/aligned_unsorted.sam) Gradle suite > Gradle test > picard.fingerprint.FingerprintCheckerTest.testTerminateOnBadFile[2](aligned_unsorted.sam, false) STANDARD_ERROR WARNING 2024-07-02 11:58:14 FingerprintChecker Operating without an index! We could be here for a while. (testdata/picard/fingerprint/aligned_unsorted.sam) Test: Test method testTerminateOnBadFile[2](aligned_unsorted.sam, false)(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:14 AbstractLocusIterator SamLocusIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. WARNING 2024-07-02 11:58:14 AbstractLocusIterator SamLocusIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. Running Test: Test method testWriteFingerprint(picard.fingerprint.FingerprintCheckerTest) Test: Test method testWriteFingerprint(picard.fingerprint.FingerprintCheckerTest) produced standard out/err: WARNING 2024-07-02 11:58:14 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/testSample_small.vcf going to read through it all. Gradle suite > Gradle test > picard.fingerprint.FingerprintCheckerTest.testWriteFingerprint STANDARD_ERROR WARNING 2024-07-02 11:58:14 FingerprintChecker Couldn't find index for file testdata/picard/fingerprint/testSample_small.vcf going to read through it all. Running Test: Test method ignoreMissingMateExceptionTest(picard.sam.FixMateInformationTest) Test: Test method ignoreMissingMateExceptionTest(picard.sam.FixMateInformationTest) produced standard out/err: INFO 2024-07-02 11:58:14 FixMateInformation Gradle suite > Gradle test > picard.sam.FixMateInformationTest.ignoreMissingMateExceptionTest STANDARD_ERROR INFO 2024-07-02 11:58:14 FixMateInformation Test: Test method ignoreMissingMateExceptionTest(picard.sam.FixMateInformationTest) produced standard out/err: Test: Test method ignoreMissingMateExceptionTest(picard.sam.FixMateInformationTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method ignoreMissingMateExceptionTest(picard.sam.FixMateInformationTest) produced standard out/err: ********** ********** Test: Test method ignoreMissingMateExceptionTest(picard.sam.FixMateInformationTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method ignoreMissingMateExceptionTest(picard.sam.FixMateInformationTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method ignoreMissingMateExceptionTest(picard.sam.FixMateInformationTest) produced standard out/err: ********** ********** Test: Test method ignoreMissingMateExceptionTest(picard.sam.FixMateInformationTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method ignoreMissingMateExceptionTest(picard.sam.FixMateInformationTest) produced standard out/err: ********** ********** Test: Test method ignoreMissingMateExceptionTest(picard.sam.FixMateInformationTest) produced standard out/err: ********** FixMateInformation -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/FixMateInformation/missingMate.sam -OUTPUT /tmp/outMissingMateTest15755380804787818735sam -IGNORE_MISSING_MATES false ********** FixMateInformation -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/FixMateInformation/missingMate.sam -OUTPUT /tmp/outMissingMateTest15755380804787818735sam -IGNORE_MISSING_MATES false Test: Test method ignoreMissingMateExceptionTest(picard.sam.FixMateInformationTest) produced standard out/err: ********** ********** Test: Test method ignoreMissingMateExceptionTest(picard.sam.FixMateInformationTest) produced standard out/err: Test: Test method ignoreMissingMateExceptionTest(picard.sam.FixMateInformationTest) produced standard out/err: Test: Test method ignoreMissingMateExceptionTest(picard.sam.FixMateInformationTest) produced standard out/err: 11:58:14.751 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:14.751 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method ignoreMissingMateExceptionTest(picard.sam.FixMateInformationTest) produced standard out/err: 11:58:14.751 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:14.751 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method ignoreMissingMateExceptionTest(picard.sam.FixMateInformationTest) produced standard out/err: 11:58:14.751 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:14.751 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method ignoreMissingMateExceptionTest(picard.sam.FixMateInformationTest) produced standard out/err: 11:58:14.751 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:14.751 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method ignoreMissingMateExceptionTest(picard.sam.FixMateInformationTest) produced standard out/err: [Tue Jul 02 11:58:14 GMT+14:00 2024] FixMateInformation INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/FixMateInformation/missingMate.sam] OUTPUT=/tmp/outMissingMateTest15755380804787818735sam IGNORE_MISSING_MATES=false ASSUME_SORTED=false ADD_MATE_CIGAR=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:14 GMT+14:00 2024] FixMateInformation INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/FixMateInformation/missingMate.sam] OUTPUT=/tmp/outMissingMateTest15755380804787818735sam IGNORE_MISSING_MATES=false ASSUME_SORTED=false ADD_MATE_CIGAR=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method ignoreMissingMateExceptionTest(picard.sam.FixMateInformationTest) produced standard out/err: [Tue Jul 02 11:58:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method ignoreMissingMateExceptionTest(picard.sam.FixMateInformationTest) produced standard out/err: INFO 2024-07-02 11:58:14 FixMateInformation Sorting input into queryname order. INFO 2024-07-02 11:58:14 FixMateInformation Sorting input into queryname order. Test: Test method ignoreMissingMateExceptionTest(picard.sam.FixMateInformationTest) produced standard out/err: INFO 2024-07-02 11:58:14 FixMateInformation Sorting by queryname complete. INFO 2024-07-02 11:58:14 FixMateInformation Sorting by queryname complete. Test: Test method ignoreMissingMateExceptionTest(picard.sam.FixMateInformationTest) produced standard out/err: INFO 2024-07-02 11:58:14 FixMateInformation Output will be sorted by coordinate INFO 2024-07-02 11:58:14 FixMateInformation Output will be sorted by coordinate Test: Test method ignoreMissingMateExceptionTest(picard.sam.FixMateInformationTest) produced standard out/err: INFO 2024-07-02 11:58:14 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/outMissingMateTest15755380804787818735sam INFO 2024-07-02 11:58:14 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/outMissingMateTest15755380804787818735sam Test: Test method ignoreMissingMateExceptionTest(picard.sam.FixMateInformationTest) produced standard out/err: INFO 2024-07-02 11:58:14 FixMateInformation Traversing query name sorted records and fixing up mate pair information. INFO 2024-07-02 11:58:14 FixMateInformation Traversing query name sorted records and fixing up mate pair information. Test: Test method ignoreMissingMateExceptionTest(picard.sam.FixMateInformationTest) produced standard out/err: [Tue Jul 02 11:58:14 GMT+14:00 2024] picard.sam.FixMateInformation done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:14 GMT+14:00 2024] picard.sam.FixMateInformation done. Elapsed time: 0.00 minutes. Test: Test method ignoreMissingMateExceptionTest(picard.sam.FixMateInformationTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method ignoreMissingMateExceptionTest(picard.sam.FixMateInformationTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method ignoreMissingMateTest(picard.sam.FixMateInformationTest) Test: Test method ignoreMissingMateTest(picard.sam.FixMateInformationTest) produced standard out/err: INFO 2024-07-02 11:58:14 FixMateInformation Gradle suite > Gradle test > picard.sam.FixMateInformationTest.ignoreMissingMateTest STANDARD_ERROR INFO 2024-07-02 11:58:14 FixMateInformation Test: Test method ignoreMissingMateTest(picard.sam.FixMateInformationTest) produced standard out/err: Test: Test method ignoreMissingMateTest(picard.sam.FixMateInformationTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method ignoreMissingMateTest(picard.sam.FixMateInformationTest) produced standard out/err: ********** ********** Test: Test method ignoreMissingMateTest(picard.sam.FixMateInformationTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method ignoreMissingMateTest(picard.sam.FixMateInformationTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method ignoreMissingMateTest(picard.sam.FixMateInformationTest) produced standard out/err: ********** ********** Test: Test method ignoreMissingMateTest(picard.sam.FixMateInformationTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method ignoreMissingMateTest(picard.sam.FixMateInformationTest) produced standard out/err: ********** ********** Test: Test method ignoreMissingMateTest(picard.sam.FixMateInformationTest) produced standard out/err: ********** FixMateInformation -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/FixMateInformation/missingMate.sam -OUTPUT /tmp/outMissingMateTest17996138567515437769sam -IGNORE_MISSING_MATES true ********** FixMateInformation -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/FixMateInformation/missingMate.sam -OUTPUT /tmp/outMissingMateTest17996138567515437769sam -IGNORE_MISSING_MATES true Test: Test method ignoreMissingMateTest(picard.sam.FixMateInformationTest) produced standard out/err: ********** ********** Test: Test method ignoreMissingMateTest(picard.sam.FixMateInformationTest) produced standard out/err: Test: Test method ignoreMissingMateTest(picard.sam.FixMateInformationTest) produced standard out/err: Test: Test method ignoreMissingMateTest(picard.sam.FixMateInformationTest) produced standard out/err: 11:58:14.800 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:14.800 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method ignoreMissingMateTest(picard.sam.FixMateInformationTest) produced standard out/err: 11:58:14.800 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:14.800 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method ignoreMissingMateTest(picard.sam.FixMateInformationTest) produced standard out/err: 11:58:14.800 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:14.800 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method ignoreMissingMateTest(picard.sam.FixMateInformationTest) produced standard out/err: 11:58:14.800 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:14.800 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method ignoreMissingMateTest(picard.sam.FixMateInformationTest) produced standard out/err: [Tue Jul 02 11:58:14 GMT+14:00 2024] FixMateInformation INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/FixMateInformation/missingMate.sam] OUTPUT=/tmp/outMissingMateTest17996138567515437769sam IGNORE_MISSING_MATES=true ASSUME_SORTED=false ADD_MATE_CIGAR=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:14 GMT+14:00 2024] FixMateInformation INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/FixMateInformation/missingMate.sam] OUTPUT=/tmp/outMissingMateTest17996138567515437769sam IGNORE_MISSING_MATES=true ASSUME_SORTED=false ADD_MATE_CIGAR=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method ignoreMissingMateTest(picard.sam.FixMateInformationTest) produced standard out/err: [Tue Jul 02 11:58:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method ignoreMissingMateTest(picard.sam.FixMateInformationTest) produced standard out/err: INFO 2024-07-02 11:58:14 FixMateInformation Sorting input into queryname order. INFO 2024-07-02 11:58:14 FixMateInformation Sorting input into queryname order. Test: Test method ignoreMissingMateTest(picard.sam.FixMateInformationTest) produced standard out/err: INFO 2024-07-02 11:58:14 FixMateInformation Sorting by queryname complete. INFO 2024-07-02 11:58:14 FixMateInformation Sorting by queryname complete. Test: Test method ignoreMissingMateTest(picard.sam.FixMateInformationTest) produced standard out/err: INFO 2024-07-02 11:58:14 FixMateInformation Output will be sorted by coordinate INFO 2024-07-02 11:58:14 FixMateInformation Output will be sorted by coordinate Test: Test method ignoreMissingMateTest(picard.sam.FixMateInformationTest) produced standard out/err: INFO 2024-07-02 11:58:14 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/outMissingMateTest17996138567515437769sam INFO 2024-07-02 11:58:14 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/outMissingMateTest17996138567515437769sam Test: Test method ignoreMissingMateTest(picard.sam.FixMateInformationTest) produced standard out/err: INFO 2024-07-02 11:58:14 FixMateInformation Traversing query name sorted records and fixing up mate pair information. INFO 2024-07-02 11:58:14 FixMateInformation Traversing query name sorted records and fixing up mate pair information. Test: Test method ignoreMissingMateTest(picard.sam.FixMateInformationTest) produced standard out/err: INFO 2024-07-02 11:58:14 FixMateInformation Finished processing reads; re-sorting output file. INFO 2024-07-02 11:58:14 FixMateInformation Finished processing reads; re-sorting output file. Test: Test method ignoreMissingMateTest(picard.sam.FixMateInformationTest) produced standard out/err: [Tue Jul 02 11:58:14 GMT+14:00 2024] picard.sam.FixMateInformation done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:14 GMT+14:00 2024] picard.sam.FixMateInformation done. Elapsed time: 0.00 minutes. Test: Test method ignoreMissingMateTest(picard.sam.FixMateInformationTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testFixVcfHeader[0](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, true)(picard.vcf.FixVcfHeaderTest) Test: Test method testFixVcfHeader[0](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:14.841 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.FixVcfHeaderTest.testFixVcfHeader[0](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, true) STANDARD_ERROR 11:58:14.841 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFixVcfHeader[0](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:14.841 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:14.841 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFixVcfHeader[0](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:14.849 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:14.849 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFixVcfHeader[0](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:14.849 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:14.849 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFixVcfHeader[0](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: [Tue Jul 02 11:58:14 GMT+14:00 2024] FixVcfHeader INPUT=testdata/picard/vcf/FixVcfHeaderTest/input.vcf OUTPUT=/tmp/output.15639110215819011302.vcf CHECK_FIRST_N_RECORDS=-1 HEADER=testdata/picard/vcf/FixVcfHeaderTest/header.vcf ENFORCE_SAME_SAMPLES=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:14 GMT+14:00 2024] FixVcfHeader INPUT=testdata/picard/vcf/FixVcfHeaderTest/input.vcf OUTPUT=/tmp/output.15639110215819011302.vcf CHECK_FIRST_N_RECORDS=-1 HEADER=testdata/picard/vcf/FixVcfHeaderTest/header.vcf ENFORCE_SAME_SAMPLES=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFixVcfHeader[0](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: [Tue Jul 02 11:58:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFixVcfHeader[0](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:14 FixVcfHeader FILTER line found in HEADER will be added to OUTPUT: MissingFilter INFO 2024-07-02 11:58:14 FixVcfHeader FILTER line found in HEADER will be added to OUTPUT: MissingFilter Test: Test method testFixVcfHeader[0](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:14 FixVcfHeader INFO line found in HEADER will be added to OUTPUT: PLNCIIonWG INFO 2024-07-02 11:58:14 FixVcfHeader INFO line found in HEADER will be added to OUTPUT: PLNCIIonWG Test: Test method testFixVcfHeader[0](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:14 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: AD INFO 2024-07-02 11:58:14 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: AD Test: Test method testFixVcfHeader[0](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:14 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: FT INFO 2024-07-02 11:58:14 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: FT Test: Test method testFixVcfHeader[0](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:14 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: GQ INFO 2024-07-02 11:58:14 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: GQ Test: Test method testFixVcfHeader[0](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:14 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: GT INFO 2024-07-02 11:58:14 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: GT Test: Test method testFixVcfHeader[0](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:14 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: PL INFO 2024-07-02 11:58:14 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: PL Test: Test method testFixVcfHeader[0](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:14 FixVcfHeader Writing the output VCF. INFO 2024-07-02 11:58:14 FixVcfHeader Writing the output VCF. Test: Test method testFixVcfHeader[0](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: [Tue Jul 02 11:58:14 GMT+14:00 2024] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:14 GMT+14:00 2024] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes. Test: Test method testFixVcfHeader[0](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testFixVcfHeader[1](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, false)(picard.vcf.FixVcfHeaderTest) Test: Test method testFixVcfHeader[1](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:15.004 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.FixVcfHeaderTest.testFixVcfHeader[1](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, false) STANDARD_ERROR 11:58:15.004 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFixVcfHeader[1](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:15.004 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:15.004 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFixVcfHeader[1](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:15.004 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:15.004 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFixVcfHeader[1](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:15.004 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:15.004 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFixVcfHeader[1](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: [Tue Jul 02 11:58:15 GMT+14:00 2024] FixVcfHeader INPUT=testdata/picard/vcf/FixVcfHeaderTest/input.vcf OUTPUT=/tmp/output.16174473619896434086.vcf CHECK_FIRST_N_RECORDS=-1 HEADER=testdata/picard/vcf/FixVcfHeaderTest/header.vcf ENFORCE_SAME_SAMPLES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:15 GMT+14:00 2024] FixVcfHeader INPUT=testdata/picard/vcf/FixVcfHeaderTest/input.vcf OUTPUT=/tmp/output.16174473619896434086.vcf CHECK_FIRST_N_RECORDS=-1 HEADER=testdata/picard/vcf/FixVcfHeaderTest/header.vcf ENFORCE_SAME_SAMPLES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFixVcfHeader[1](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: [Tue Jul 02 11:58:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFixVcfHeader[1](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader FILTER line found in HEADER will be added to OUTPUT: MissingFilter INFO 2024-07-02 11:58:15 FixVcfHeader FILTER line found in HEADER will be added to OUTPUT: MissingFilter Test: Test method testFixVcfHeader[1](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader INFO line found in HEADER will be added to OUTPUT: PLNCIIonWG INFO 2024-07-02 11:58:15 FixVcfHeader INFO line found in HEADER will be added to OUTPUT: PLNCIIonWG Test: Test method testFixVcfHeader[1](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: AD INFO 2024-07-02 11:58:15 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: AD Test: Test method testFixVcfHeader[1](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: FT INFO 2024-07-02 11:58:15 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: FT Test: Test method testFixVcfHeader[1](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: GQ INFO 2024-07-02 11:58:15 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: GQ Test: Test method testFixVcfHeader[1](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: GT INFO 2024-07-02 11:58:15 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: GT Test: Test method testFixVcfHeader[1](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: PL INFO 2024-07-02 11:58:15 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: PL Test: Test method testFixVcfHeader[1](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader Writing the output VCF. INFO 2024-07-02 11:58:15 FixVcfHeader Writing the output VCF. Test: Test method testFixVcfHeader[1](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: [Tue Jul 02 11:58:15 GMT+14:00 2024] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:15 GMT+14:00 2024] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes. Test: Test method testFixVcfHeader[1](-1, testdata/picard/vcf/FixVcfHeaderTest/header.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testFixVcfHeader[2](-1, testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf, false)(picard.vcf.FixVcfHeaderTest) Test: Test method testFixVcfHeader[2](-1, testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:15.171 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.FixVcfHeaderTest.testFixVcfHeader[2](-1, testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf, false) STANDARD_ERROR 11:58:15.171 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFixVcfHeader[2](-1, testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:15.171 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:15.171 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFixVcfHeader[2](-1, testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:15.172 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:15.172 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFixVcfHeader[2](-1, testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:15.172 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:15.172 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFixVcfHeader[2](-1, testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: [Tue Jul 02 11:58:15 GMT+14:00 2024] FixVcfHeader INPUT=testdata/picard/vcf/FixVcfHeaderTest/input.vcf OUTPUT=/tmp/output.3734106377700603766.vcf CHECK_FIRST_N_RECORDS=-1 HEADER=testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf ENFORCE_SAME_SAMPLES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:15 GMT+14:00 2024] FixVcfHeader INPUT=testdata/picard/vcf/FixVcfHeaderTest/input.vcf OUTPUT=/tmp/output.3734106377700603766.vcf CHECK_FIRST_N_RECORDS=-1 HEADER=testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf ENFORCE_SAME_SAMPLES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFixVcfHeader[2](-1, testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: [Tue Jul 02 11:58:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFixVcfHeader[2](-1, testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader FILTER line found in HEADER will be added to OUTPUT: MissingFilter INFO 2024-07-02 11:58:15 FixVcfHeader FILTER line found in HEADER will be added to OUTPUT: MissingFilter Test: Test method testFixVcfHeader[2](-1, testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader INFO line found in HEADER will be added to OUTPUT: PLNCIIonWG INFO 2024-07-02 11:58:15 FixVcfHeader INFO line found in HEADER will be added to OUTPUT: PLNCIIonWG Test: Test method testFixVcfHeader[2](-1, testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: AD INFO 2024-07-02 11:58:15 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: AD Test: Test method testFixVcfHeader[2](-1, testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: FT INFO 2024-07-02 11:58:15 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: FT Test: Test method testFixVcfHeader[2](-1, testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: GQ INFO 2024-07-02 11:58:15 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: GQ Test: Test method testFixVcfHeader[2](-1, testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: GT INFO 2024-07-02 11:58:15 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: GT Test: Test method testFixVcfHeader[2](-1, testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: PL INFO 2024-07-02 11:58:15 FixVcfHeader FORMAT line found in HEADER will be added to OUTPUT: PL Test: Test method testFixVcfHeader[2](-1, testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader Writing the output VCF. INFO 2024-07-02 11:58:15 FixVcfHeader Writing the output VCF. Test: Test method testFixVcfHeader[2](-1, testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: [Tue Jul 02 11:58:15 GMT+14:00 2024] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:15 GMT+14:00 2024] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes. Test: Test method testFixVcfHeader[2](-1, testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf, false)(picard.vcf.FixVcfHeaderTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testFixVcfHeader[3](-1, null, true)(picard.vcf.FixVcfHeaderTest) Test: Test method testFixVcfHeader[3](-1, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:15.328 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.FixVcfHeaderTest.testFixVcfHeader[3](-1, null, true) STANDARD_ERROR 11:58:15.328 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFixVcfHeader[3](-1, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:15.328 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:15.328 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFixVcfHeader[3](-1, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:15.328 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:15.328 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFixVcfHeader[3](-1, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:15.328 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:15.328 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFixVcfHeader[3](-1, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: [Tue Jul 02 11:58:15 GMT+14:00 2024] FixVcfHeader INPUT=testdata/picard/vcf/FixVcfHeaderTest/input.vcf OUTPUT=/tmp/output.7140521060581383531.vcf CHECK_FIRST_N_RECORDS=-1 ENFORCE_SAME_SAMPLES=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:15 GMT+14:00 2024] FixVcfHeader INPUT=testdata/picard/vcf/FixVcfHeaderTest/input.vcf OUTPUT=/tmp/output.7140521060581383531.vcf CHECK_FIRST_N_RECORDS=-1 ENFORCE_SAME_SAMPLES=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFixVcfHeader[3](-1, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: [Tue Jul 02 11:58:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFixVcfHeader[3](-1, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader Reading in records to re-build the header. INFO 2024-07-02 11:58:15 FixVcfHeader Reading in records to re-build the header. Test: Test method testFixVcfHeader[3](-1, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader Will add an INFO line with id: PLNCIIonWG INFO 2024-07-02 11:58:15 FixVcfHeader Will add an INFO line with id: PLNCIIonWG Test: Test method testFixVcfHeader[3](-1, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader Will add an FILTER line with id: MissingFilter INFO 2024-07-02 11:58:15 FixVcfHeader Will add an FILTER line with id: MissingFilter Test: Test method testFixVcfHeader[3](-1, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader VCF header re-built. INFO 2024-07-02 11:58:15 FixVcfHeader VCF header re-built. Test: Test method testFixVcfHeader[3](-1, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader Writing the output VCF. INFO 2024-07-02 11:58:15 FixVcfHeader Writing the output VCF. Test: Test method testFixVcfHeader[3](-1, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: [Tue Jul 02 11:58:15 GMT+14:00 2024] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:15 GMT+14:00 2024] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes. Test: Test method testFixVcfHeader[3](-1, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testFixVcfHeader[4](2, null, true)(picard.vcf.FixVcfHeaderTest) Test: Test method testFixVcfHeader[4](2, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:15.502 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.FixVcfHeaderTest.testFixVcfHeader[4](2, null, true) STANDARD_ERROR 11:58:15.502 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFixVcfHeader[4](2, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:15.502 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:15.502 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFixVcfHeader[4](2, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:15.502 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:15.502 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFixVcfHeader[4](2, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:15.502 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:15.502 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFixVcfHeader[4](2, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: [Tue Jul 02 11:58:15 GMT+14:00 2024] FixVcfHeader INPUT=testdata/picard/vcf/FixVcfHeaderTest/input.vcf OUTPUT=/tmp/output.1655772781933892153.vcf CHECK_FIRST_N_RECORDS=2 ENFORCE_SAME_SAMPLES=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:15 GMT+14:00 2024] FixVcfHeader INPUT=testdata/picard/vcf/FixVcfHeaderTest/input.vcf OUTPUT=/tmp/output.1655772781933892153.vcf CHECK_FIRST_N_RECORDS=2 ENFORCE_SAME_SAMPLES=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFixVcfHeader[4](2, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: [Tue Jul 02 11:58:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFixVcfHeader[4](2, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader Reading in records to re-build the header. INFO 2024-07-02 11:58:15 FixVcfHeader Reading in records to re-build the header. Test: Test method testFixVcfHeader[4](2, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader Will add an INFO line with id: PLNCIIonWG INFO 2024-07-02 11:58:15 FixVcfHeader Will add an INFO line with id: PLNCIIonWG Test: Test method testFixVcfHeader[4](2, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader Will add an FILTER line with id: MissingFilter INFO 2024-07-02 11:58:15 FixVcfHeader Will add an FILTER line with id: MissingFilter Test: Test method testFixVcfHeader[4](2, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader VCF header re-built. INFO 2024-07-02 11:58:15 FixVcfHeader VCF header re-built. Test: Test method testFixVcfHeader[4](2, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader Writing the output VCF. INFO 2024-07-02 11:58:15 FixVcfHeader Writing the output VCF. Test: Test method testFixVcfHeader[4](2, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: [Tue Jul 02 11:58:15 GMT+14:00 2024] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:15 GMT+14:00 2024] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes. Test: Test method testFixVcfHeader[4](2, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testFixVcfHeader[5](2147483647, null, true)(picard.vcf.FixVcfHeaderTest) Test: Test method testFixVcfHeader[5](2147483647, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:15.650 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.FixVcfHeaderTest.testFixVcfHeader[5](2147483647, null, true) STANDARD_ERROR 11:58:15.650 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFixVcfHeader[5](2147483647, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:15.650 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:15.650 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFixVcfHeader[5](2147483647, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:15.650 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:15.650 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFixVcfHeader[5](2147483647, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:15.650 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:15.650 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFixVcfHeader[5](2147483647, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: [Tue Jul 02 11:58:15 GMT+14:00 2024] FixVcfHeader INPUT=testdata/picard/vcf/FixVcfHeaderTest/input.vcf OUTPUT=/tmp/output.5248680588936577067.vcf CHECK_FIRST_N_RECORDS=2147483647 ENFORCE_SAME_SAMPLES=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:15 GMT+14:00 2024] FixVcfHeader INPUT=testdata/picard/vcf/FixVcfHeaderTest/input.vcf OUTPUT=/tmp/output.5248680588936577067.vcf CHECK_FIRST_N_RECORDS=2147483647 ENFORCE_SAME_SAMPLES=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFixVcfHeader[5](2147483647, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: [Tue Jul 02 11:58:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFixVcfHeader[5](2147483647, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader Reading in records to re-build the header. INFO 2024-07-02 11:58:15 FixVcfHeader Reading in records to re-build the header. Test: Test method testFixVcfHeader[5](2147483647, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader Will add an INFO line with id: PLNCIIonWG INFO 2024-07-02 11:58:15 FixVcfHeader Will add an INFO line with id: PLNCIIonWG Test: Test method testFixVcfHeader[5](2147483647, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader Will add an FILTER line with id: MissingFilter INFO 2024-07-02 11:58:15 FixVcfHeader Will add an FILTER line with id: MissingFilter Test: Test method testFixVcfHeader[5](2147483647, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader VCF header re-built. INFO 2024-07-02 11:58:15 FixVcfHeader VCF header re-built. Test: Test method testFixVcfHeader[5](2147483647, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader Writing the output VCF. INFO 2024-07-02 11:58:15 FixVcfHeader Writing the output VCF. Test: Test method testFixVcfHeader[5](2147483647, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: [Tue Jul 02 11:58:15 GMT+14:00 2024] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:15 GMT+14:00 2024] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes. Test: Test method testFixVcfHeader[5](2147483647, null, true)(picard.vcf.FixVcfHeaderTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testMissingFilterNotInFirstNRecords(picard.vcf.FixVcfHeaderTest) Test: Test method testMissingFilterNotInFirstNRecords(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:15.894 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.FixVcfHeaderTest.testMissingFilterNotInFirstNRecords STANDARD_ERROR 11:58:15.894 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingFilterNotInFirstNRecords(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:15.894 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:15.894 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingFilterNotInFirstNRecords(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:15.895 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:15.895 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingFilterNotInFirstNRecords(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:15.895 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:15.895 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingFilterNotInFirstNRecords(picard.vcf.FixVcfHeaderTest) produced standard out/err: [Tue Jul 02 11:58:15 GMT+14:00 2024] FixVcfHeader INPUT=testdata/picard/vcf/FixVcfHeaderTest/input.vcf OUTPUT=/tmp/output.5403934176302815801.vcf CHECK_FIRST_N_RECORDS=1 ENFORCE_SAME_SAMPLES=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:15 GMT+14:00 2024] FixVcfHeader INPUT=testdata/picard/vcf/FixVcfHeaderTest/input.vcf OUTPUT=/tmp/output.5403934176302815801.vcf CHECK_FIRST_N_RECORDS=1 ENFORCE_SAME_SAMPLES=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingFilterNotInFirstNRecords(picard.vcf.FixVcfHeaderTest) produced standard out/err: [Tue Jul 02 11:58:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingFilterNotInFirstNRecords(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader Reading in records to re-build the header. INFO 2024-07-02 11:58:15 FixVcfHeader Reading in records to re-build the header. Test: Test method testMissingFilterNotInFirstNRecords(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader Will add an INFO line with id: PLNCIIonWG INFO 2024-07-02 11:58:15 FixVcfHeader Will add an INFO line with id: PLNCIIonWG Test: Test method testMissingFilterNotInFirstNRecords(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader VCF header re-built. INFO 2024-07-02 11:58:15 FixVcfHeader VCF header re-built. Test: Test method testMissingFilterNotInFirstNRecords(picard.vcf.FixVcfHeaderTest) produced standard out/err: INFO 2024-07-02 11:58:15 FixVcfHeader Writing the output VCF. INFO 2024-07-02 11:58:15 FixVcfHeader Writing the output VCF. Test: Test method testMissingFilterNotInFirstNRecords(picard.vcf.FixVcfHeaderTest) produced standard out/err: [Tue Jul 02 11:58:15 GMT+14:00 2024] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:15 GMT+14:00 2024] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes. Test: Test method testMissingFilterNotInFirstNRecords(picard.vcf.FixVcfHeaderTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method testMissingFilterNotInFirstNRecords(picard.vcf.FixVcfHeaderTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testReplaceHeaderWithDifferentSamplesError(picard.vcf.FixVcfHeaderTest) Test: Test method testReplaceHeaderWithDifferentSamplesError(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:15.970 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.FixVcfHeaderTest.testReplaceHeaderWithDifferentSamplesError STANDARD_ERROR 11:58:15.970 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testReplaceHeaderWithDifferentSamplesError(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:15.970 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:15.970 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testReplaceHeaderWithDifferentSamplesError(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:15.970 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:15.970 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testReplaceHeaderWithDifferentSamplesError(picard.vcf.FixVcfHeaderTest) produced standard out/err: 11:58:15.970 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:15.970 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testReplaceHeaderWithDifferentSamplesError(picard.vcf.FixVcfHeaderTest) produced standard out/err: [Tue Jul 02 11:58:15 GMT+14:00 2024] FixVcfHeader INPUT=testdata/picard/vcf/FixVcfHeaderTest/input.vcf OUTPUT=/tmp/output.3023500347734031854.vcf CHECK_FIRST_N_RECORDS=-1 HEADER=testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf ENFORCE_SAME_SAMPLES=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:15 GMT+14:00 2024] FixVcfHeader INPUT=testdata/picard/vcf/FixVcfHeaderTest/input.vcf OUTPUT=/tmp/output.3023500347734031854.vcf CHECK_FIRST_N_RECORDS=-1 HEADER=testdata/picard/vcf/FixVcfHeaderTest/header_with_extra_sample.vcf ENFORCE_SAME_SAMPLES=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testReplaceHeaderWithDifferentSamplesError(picard.vcf.FixVcfHeaderTest) produced standard out/err: [Tue Jul 02 11:58:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testReplaceHeaderWithDifferentSamplesError(picard.vcf.FixVcfHeaderTest) produced standard out/err: [Tue Jul 02 11:58:15 GMT+14:00 2024] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:15 GMT+14:00 2024] picard.vcf.FixVcfHeader done. Elapsed time: 0.00 minutes. Test: Test method testReplaceHeaderWithDifferentSamplesError(picard.vcf.FixVcfHeaderTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method testReplaceHeaderWithDifferentSamplesError(picard.vcf.FixVcfHeaderTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: INFO 2024-07-02 11:58:16 GatherBamFiles Gradle suite > Gradle test > picard.sam.GatherBamFilesTest.sanityCheckTheGathering STANDARD_ERROR INFO 2024-07-02 11:58:16 GatherBamFiles Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: ********** ********** Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: ********** ********** Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: ********** ********** Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: ********** GatherBamFiles -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indUnknownChrom.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr1.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr2.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr3.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr4.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr5.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr6.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr7.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr8.bam -OUTPUT /tmp/gatherBamFilesTest.samFile.3621274787509453519.bam ********** GatherBamFiles -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indUnknownChrom.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr1.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr2.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr3.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr4.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr5.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr6.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr7.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr8.bam -OUTPUT /tmp/gatherBamFilesTest.samFile.3621274787509453519.bam Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: ********** ********** Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: 11:58:16.094 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:16.094 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: 11:58:16.094 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:16.094 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: 11:58:16.095 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:16.095 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: 11:58:16.095 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:16.095 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: [Tue Jul 02 11:58:16 GMT+14:00 2024] GatherBamFiles INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indUnknownChrom.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr1.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr2.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr3.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr4.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr5.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr6.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr7.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr8.bam] OUTPUT=/tmp/gatherBamFilesTest.samFile.3621274787509453519.bam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:16 GMT+14:00 2024] GatherBamFiles INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indUnknownChrom.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr1.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr2.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr3.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr4.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr5.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr6.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr7.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr8.bam] OUTPUT=/tmp/gatherBamFilesTest.samFile.3621274787509453519.bam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: [Tue Jul 02 11:58:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indUnknownChrom.bam ... INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indUnknownChrom.bam ... Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr1.bam ... INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr1.bam ... Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr2.bam ... INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr2.bam ... Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr3.bam ... INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr3.bam ... Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr4.bam ... INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr4.bam ... Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr5.bam ... INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr5.bam ... Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr6.bam ... INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr6.bam ... Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr7.bam ... INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr7.bam ... Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr8.bam ... INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr8.bam ... Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: [Tue Jul 02 11:58:16 GMT+14:00 2024] picard.sam.GatherBamFiles done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:16 GMT+14:00 2024] picard.sam.GatherBamFiles done. Elapsed time: 0.00 minutes. Test: Test method sanityCheckTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: INFO 2024-07-02 11:58:16 GatherBamFiles Gradle suite > Gradle test > picard.sam.GatherBamFilesTest.testTheGathering STANDARD_ERROR INFO 2024-07-02 11:58:16 GatherBamFiles Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: ********** ********** Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: ********** ********** Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: ********** ********** Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: ********** GatherBamFiles -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indUnknownChrom.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr1.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr2.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr3.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr4.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr5.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr6.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr7.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr8.bam -OUTPUT /tmp/gatherBamFilesTest.samFile.9596990095589036181.bam ********** GatherBamFiles -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indUnknownChrom.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr1.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr2.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr3.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr4.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr5.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr6.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr7.bam -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr8.bam -OUTPUT /tmp/gatherBamFilesTest.samFile.9596990095589036181.bam Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: ********** ********** Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: 11:58:16.217 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:16.217 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: 11:58:16.217 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:16.217 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: 11:58:16.217 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:16.217 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: 11:58:16.217 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:16.217 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: [Tue Jul 02 11:58:16 GMT+14:00 2024] GatherBamFiles INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indUnknownChrom.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr1.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr2.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr3.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr4.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr5.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr6.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr7.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr8.bam] OUTPUT=/tmp/gatherBamFilesTest.samFile.9596990095589036181.bam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:16 GMT+14:00 2024] GatherBamFiles INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indUnknownChrom.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr1.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr2.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr3.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr4.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr5.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr6.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr7.bam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr8.bam] OUTPUT=/tmp/gatherBamFilesTest.samFile.9596990095589036181.bam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: [Tue Jul 02 11:58:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indUnknownChrom.bam ... INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indUnknownChrom.bam ... Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr1.bam ... INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr1.bam ... Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr2.bam ... INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr2.bam ... Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr3.bam ... INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr3.bam ... Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr4.bam ... INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr4.bam ... Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr5.bam ... INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr5.bam ... Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr6.bam ... INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr6.bam ... Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr7.bam ... INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr7.bam ... Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr8.bam ... INFO 2024-07-02 11:58:16 BamFileIoUtils Block copying /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/GatherBamFiles/indchr8.bam ... Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: [Tue Jul 02 11:58:16 GMT+14:00 2024] picard.sam.GatherBamFiles done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:16 GMT+14:00 2024] picard.sam.GatherBamFiles done. Elapsed time: 0.00 minutes. Test: Test method testTheGathering(picard.sam.GatherBamFilesTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method TestGatherFiles[0]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 0, false)(picard.vcf.GatherVcfsTest) Test: Test method TestGatherFiles[0]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:17 GatherVcfs Gradle suite > Gradle test > picard.vcf.GatherVcfsTest.TestGatherFiles[0]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 0, false) STANDARD_ERROR INFO 2024-07-02 11:58:17 GatherVcfs Test: Test method TestGatherFiles[0]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[0]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestGatherFiles[0]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[0]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestGatherFiles[0]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestGatherFiles[0]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[0]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestGatherFiles[0]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[0]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** GatherVcfs -INPUT /tmp/shard1.4051875402219761934.vcf -INPUT /tmp/shard2.17721206679344426320.vcf -INPUT /tmp/shard38267540453251402273.vcf -OUTPUT /tmp/result16903743316823951960.vcf -COMMENT This is a comment -REORDER_INPUT_BY_FIRST_VARIANT false ********** GatherVcfs -INPUT /tmp/shard1.4051875402219761934.vcf -INPUT /tmp/shard2.17721206679344426320.vcf -INPUT /tmp/shard38267540453251402273.vcf -OUTPUT /tmp/result16903743316823951960.vcf -COMMENT This is a comment -REORDER_INPUT_BY_FIRST_VARIANT false Test: Test method TestGatherFiles[0]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[0]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[0]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[0]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:17.173 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:17.173 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestGatherFiles[0]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:17.174 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:17.174 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestGatherFiles[0]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:17.174 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:17.174 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestGatherFiles[0]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:17.174 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:17.174 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestGatherFiles[0]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:17 GMT+14:00 2024] GatherVcfs INPUT=[/tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf, /tmp/shard38267540453251402273.vcf] OUTPUT=/tmp/result16903743316823951960.vcf COMMENT=[This is a comment] REORDER_INPUT_BY_FIRST_VARIANT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:17 GMT+14:00 2024] GatherVcfs INPUT=[/tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf, /tmp/shard38267540453251402273.vcf] OUTPUT=/tmp/result16903743316823951960.vcf COMMENT=[This is a comment] REORDER_INPUT_BY_FIRST_VARIANT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestGatherFiles[0]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestGatherFiles[0]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:17 GatherVcfs Checking inputs. INFO 2024-07-02 11:58:17 GatherVcfs Checking inputs. Test: Test method TestGatherFiles[0]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:17 GatherVcfs Checking file headers and first records to ensure compatibility. INFO 2024-07-02 11:58:17 GatherVcfs Checking file headers and first records to ensure compatibility. Test: Test method TestGatherFiles[0]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:17 GatherVcfs Gathering by conventional means. INFO 2024-07-02 11:58:17 GatherVcfs Gathering by conventional means. Test: Test method TestGatherFiles[0]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:17 GMT+14:00 2024] picard.vcf.GatherVcfs done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:17 GMT+14:00 2024] picard.vcf.GatherVcfs done. Elapsed time: 0.00 minutes. Test: Test method TestGatherFiles[0]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method TestGatherFiles[1]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 0, true)(picard.vcf.GatherVcfsTest) Test: Test method TestGatherFiles[1]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:17 GatherVcfs Gradle suite > Gradle test > picard.vcf.GatherVcfsTest.TestGatherFiles[1]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 0, true) STANDARD_ERROR INFO 2024-07-02 11:58:17 GatherVcfs Test: Test method TestGatherFiles[1]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[1]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestGatherFiles[1]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[1]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestGatherFiles[1]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestGatherFiles[1]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[1]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestGatherFiles[1]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[1]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** GatherVcfs -INPUT /tmp/shard38267540453251402273.vcf -INPUT /tmp/shard1.4051875402219761934.vcf -INPUT /tmp/shard2.17721206679344426320.vcf -OUTPUT /tmp/result7918654030292174234.vcf -COMMENT This is a comment -REORDER_INPUT_BY_FIRST_VARIANT true ********** GatherVcfs -INPUT /tmp/shard38267540453251402273.vcf -INPUT /tmp/shard1.4051875402219761934.vcf -INPUT /tmp/shard2.17721206679344426320.vcf -OUTPUT /tmp/result7918654030292174234.vcf -COMMENT This is a comment -REORDER_INPUT_BY_FIRST_VARIANT true Test: Test method TestGatherFiles[1]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[1]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[1]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[1]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:17.407 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:17.407 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestGatherFiles[1]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:17.407 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:17.407 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestGatherFiles[1]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:17.407 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:17.407 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestGatherFiles[1]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:17.407 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:17.407 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestGatherFiles[1]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:17 GMT+14:00 2024] GatherVcfs INPUT=[/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf] OUTPUT=/tmp/result7918654030292174234.vcf COMMENT=[This is a comment] REORDER_INPUT_BY_FIRST_VARIANT=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:17 GMT+14:00 2024] GatherVcfs INPUT=[/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf] OUTPUT=/tmp/result7918654030292174234.vcf COMMENT=[This is a comment] REORDER_INPUT_BY_FIRST_VARIANT=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestGatherFiles[1]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestGatherFiles[1]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:17 GatherVcfs Checking inputs. INFO 2024-07-02 11:58:17 GatherVcfs Checking inputs. Test: Test method TestGatherFiles[1]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:17 GatherVcfs Checking file headers and first records to ensure compatibility. INFO 2024-07-02 11:58:17 GatherVcfs Checking file headers and first records to ensure compatibility. Test: Test method TestGatherFiles[1]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:17 GatherVcfs Gathering by conventional means. INFO 2024-07-02 11:58:17 GatherVcfs Gathering by conventional means. Test: Test method TestGatherFiles[1]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:17 GMT+14:00 2024] picard.vcf.GatherVcfs done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:17 GMT+14:00 2024] picard.vcf.GatherVcfs done. Elapsed time: 0.00 minutes. Test: Test method TestGatherFiles[1]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method TestGatherFiles[2]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) Test: Test method TestGatherFiles[2]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:17 GatherVcfs Gradle suite > Gradle test > picard.vcf.GatherVcfsTest.TestGatherFiles[2]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 1, false) STANDARD_ERROR INFO 2024-07-02 11:58:17 GatherVcfs Test: Test method TestGatherFiles[2]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[2]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestGatherFiles[2]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[2]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestGatherFiles[2]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestGatherFiles[2]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[2]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestGatherFiles[2]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[2]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** GatherVcfs -INPUT /tmp/shard1.4051875402219761934.vcf -INPUT /tmp/shard2_bad.3295317619542370336.vcf -INPUT /tmp/shard38267540453251402273.vcf -OUTPUT /tmp/result15318350369842109043.vcf -COMMENT This is a comment -REORDER_INPUT_BY_FIRST_VARIANT false ********** GatherVcfs -INPUT /tmp/shard1.4051875402219761934.vcf -INPUT /tmp/shard2_bad.3295317619542370336.vcf -INPUT /tmp/shard38267540453251402273.vcf -OUTPUT /tmp/result15318350369842109043.vcf -COMMENT This is a comment -REORDER_INPUT_BY_FIRST_VARIANT false Test: Test method TestGatherFiles[2]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[2]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[2]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[2]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:17.750 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:17.750 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestGatherFiles[2]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:17.750 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:17.750 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestGatherFiles[2]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:17.750 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:17.750 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestGatherFiles[2]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:17.750 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:17.750 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestGatherFiles[2]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:17 GMT+14:00 2024] GatherVcfs INPUT=[/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf] OUTPUT=/tmp/result15318350369842109043.vcf COMMENT=[This is a comment] REORDER_INPUT_BY_FIRST_VARIANT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:17 GMT+14:00 2024] GatherVcfs INPUT=[/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf] OUTPUT=/tmp/result15318350369842109043.vcf COMMENT=[This is a comment] REORDER_INPUT_BY_FIRST_VARIANT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestGatherFiles[2]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestGatherFiles[2]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:17 GatherVcfs Checking inputs. INFO 2024-07-02 11:58:17 GatherVcfs Checking inputs. Test: Test method TestGatherFiles[2]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:17 GatherVcfs Checking file headers and first records to ensure compatibility. INFO 2024-07-02 11:58:17 GatherVcfs Checking file headers and first records to ensure compatibility. Test: Test method TestGatherFiles[2]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:17 GatherVcfs Gathering by conventional means. INFO 2024-07-02 11:58:17 GatherVcfs Gathering by conventional means. Test: Test method TestGatherFiles[2]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ERROR 2024-07-02 11:58:17 GatherVcfs There was a problem with gathering the INPUT.java.lang.IllegalArgumentException: First variant in file /tmp/shard2_bad.3295317619542370336.vcf is at 22:17283967 but last variant in earlier file /tmp/shard1.4051875402219761934.vcf is at 22:17283967 ERROR 2024-07-02 11:58:17 GatherVcfs There was a problem with gathering the INPUT.java.lang.IllegalArgumentException: First variant in file /tmp/shard2_bad.3295317619542370336.vcf is at 22:17283967 but last variant in earlier file /tmp/shard1.4051875402219761934.vcf is at 22:17283967 Test: Test method TestGatherFiles[2]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:17 GMT+14:00 2024] picard.vcf.GatherVcfs done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:17 GMT+14:00 2024] picard.vcf.GatherVcfs done. Elapsed time: 0.00 minutes. Test: Test method TestGatherFiles[2]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method TestGatherFiles[2]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard2_bad.3295317619542370336.vcf, /tmp/shard38267540453251402273.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method TestGatherFiles[3]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) Test: Test method TestGatherFiles[3]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:17 GatherVcfs Gradle suite > Gradle test > picard.vcf.GatherVcfsTest.TestGatherFiles[3]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false) STANDARD_ERROR INFO 2024-07-02 11:58:17 GatherVcfs Test: Test method TestGatherFiles[3]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[3]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestGatherFiles[3]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[3]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestGatherFiles[3]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestGatherFiles[3]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[3]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestGatherFiles[3]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[3]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** GatherVcfs -INPUT /tmp/shard1.4051875402219761934.vcf -INPUT /tmp/shard38267540453251402273.vcf -INPUT /tmp/shard2.17721206679344426320.vcf -OUTPUT /tmp/result15586009657454256066.vcf -COMMENT This is a comment -REORDER_INPUT_BY_FIRST_VARIANT false ********** GatherVcfs -INPUT /tmp/shard1.4051875402219761934.vcf -INPUT /tmp/shard38267540453251402273.vcf -INPUT /tmp/shard2.17721206679344426320.vcf -OUTPUT /tmp/result15586009657454256066.vcf -COMMENT This is a comment -REORDER_INPUT_BY_FIRST_VARIANT false Test: Test method TestGatherFiles[3]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[3]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[3]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[3]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:17.956 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:17.956 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestGatherFiles[3]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:17.956 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:17.956 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestGatherFiles[3]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:17.956 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:17.956 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestGatherFiles[3]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:17.956 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:17.956 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestGatherFiles[3]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:17 GMT+14:00 2024] GatherVcfs INPUT=[/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf] OUTPUT=/tmp/result15586009657454256066.vcf COMMENT=[This is a comment] REORDER_INPUT_BY_FIRST_VARIANT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:17 GMT+14:00 2024] GatherVcfs INPUT=[/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf] OUTPUT=/tmp/result15586009657454256066.vcf COMMENT=[This is a comment] REORDER_INPUT_BY_FIRST_VARIANT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestGatherFiles[3]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestGatherFiles[3]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:17 GatherVcfs Checking inputs. INFO 2024-07-02 11:58:17 GatherVcfs Checking inputs. Test: Test method TestGatherFiles[3]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:17 GatherVcfs Checking file headers and first records to ensure compatibility. INFO 2024-07-02 11:58:17 GatherVcfs Checking file headers and first records to ensure compatibility. Test: Test method TestGatherFiles[3]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ERROR 2024-07-02 11:58:17 GatherVcfs There was a problem with gathering the INPUT.java.lang.IllegalArgumentException: First record in file /tmp/shard2.17721206679344426320.vcf is not after first record in previous file /tmp/shard38267540453251402273.vcf ERROR 2024-07-02 11:58:17 GatherVcfs There was a problem with gathering the INPUT.java.lang.IllegalArgumentException: First record in file /tmp/shard2.17721206679344426320.vcf is not after first record in previous file /tmp/shard38267540453251402273.vcf Test: Test method TestGatherFiles[3]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:17 GMT+14:00 2024] picard.vcf.GatherVcfs done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:17 GMT+14:00 2024] picard.vcf.GatherVcfs done. Elapsed time: 0.00 minutes. Test: Test method TestGatherFiles[3]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method TestGatherFiles[3]([/tmp/shard1.4051875402219761934.vcf, /tmp/shard38267540453251402273.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method TestGatherFiles[4]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) Test: Test method TestGatherFiles[4]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:18 GatherVcfs Gradle suite > Gradle test > picard.vcf.GatherVcfsTest.TestGatherFiles[4]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false) STANDARD_ERROR INFO 2024-07-02 11:58:18 GatherVcfs Test: Test method TestGatherFiles[4]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[4]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestGatherFiles[4]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[4]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestGatherFiles[4]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestGatherFiles[4]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[4]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestGatherFiles[4]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[4]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** GatherVcfs -INPUT /tmp/shard38267540453251402273.vcf -INPUT /tmp/shard1.4051875402219761934.vcf -INPUT /tmp/shard2.17721206679344426320.vcf -OUTPUT /tmp/result16601840108188278024.vcf -COMMENT This is a comment -REORDER_INPUT_BY_FIRST_VARIANT false ********** GatherVcfs -INPUT /tmp/shard38267540453251402273.vcf -INPUT /tmp/shard1.4051875402219761934.vcf -INPUT /tmp/shard2.17721206679344426320.vcf -OUTPUT /tmp/result16601840108188278024.vcf -COMMENT This is a comment -REORDER_INPUT_BY_FIRST_VARIANT false Test: Test method TestGatherFiles[4]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[4]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[4]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[4]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:18.056 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:18.056 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestGatherFiles[4]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:18.057 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:18.057 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestGatherFiles[4]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:18.065 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:18.065 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestGatherFiles[4]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:18.065 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:18.065 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestGatherFiles[4]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:18 GMT+14:00 2024] GatherVcfs INPUT=[/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf] OUTPUT=/tmp/result16601840108188278024.vcf COMMENT=[This is a comment] REORDER_INPUT_BY_FIRST_VARIANT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:18 GMT+14:00 2024] GatherVcfs INPUT=[/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf] OUTPUT=/tmp/result16601840108188278024.vcf COMMENT=[This is a comment] REORDER_INPUT_BY_FIRST_VARIANT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestGatherFiles[4]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestGatherFiles[4]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:18 GatherVcfs Checking inputs. INFO 2024-07-02 11:58:18 GatherVcfs Checking inputs. Test: Test method TestGatherFiles[4]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:18 GatherVcfs Checking file headers and first records to ensure compatibility. INFO 2024-07-02 11:58:18 GatherVcfs Checking file headers and first records to ensure compatibility. Test: Test method TestGatherFiles[4]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ERROR 2024-07-02 11:58:18 GatherVcfs There was a problem with gathering the INPUT.java.lang.IllegalArgumentException: First record in file /tmp/shard1.4051875402219761934.vcf is not after first record in previous file /tmp/shard38267540453251402273.vcf ERROR 2024-07-02 11:58:18 GatherVcfs There was a problem with gathering the INPUT.java.lang.IllegalArgumentException: First record in file /tmp/shard1.4051875402219761934.vcf is not after first record in previous file /tmp/shard38267540453251402273.vcf Test: Test method TestGatherFiles[4]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:18 GMT+14:00 2024] picard.vcf.GatherVcfs done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:18 GMT+14:00 2024] picard.vcf.GatherVcfs done. Elapsed time: 0.00 minutes. Test: Test method TestGatherFiles[4]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method TestGatherFiles[4]([/tmp/shard38267540453251402273.vcf, /tmp/shard1.4051875402219761934.vcf, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.11353291515522687672.vcf, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method TestGatherFiles[5]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.4804514997273114429.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, false)(picard.vcf.GatherVcfsTest) Test: Test method TestGatherFiles[5]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.4804514997273114429.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:18 GatherVcfs Gradle suite > Gradle test > picard.vcf.GatherVcfsTest.TestGatherFiles[5]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.4804514997273114429.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, false) STANDARD_ERROR INFO 2024-07-02 11:58:18 GatherVcfs Test: Test method TestGatherFiles[5]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.4804514997273114429.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[5]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.4804514997273114429.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestGatherFiles[5]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.4804514997273114429.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[5]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.4804514997273114429.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestGatherFiles[5]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.4804514997273114429.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestGatherFiles[5]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.4804514997273114429.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[5]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.4804514997273114429.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestGatherFiles[5]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.4804514997273114429.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[5]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.4804514997273114429.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** GatherVcfs -INPUT /tmp/shard1.15727567358331003453.vcf.gz -INPUT /tmp/shard2.4804514997273114429.vcf.gz -INPUT /tmp/shard38267540453251402273.vcf -OUTPUT /tmp/result10548482394584999709.vcf.gz -COMMENT This is a comment -REORDER_INPUT_BY_FIRST_VARIANT false ********** GatherVcfs -INPUT /tmp/shard1.15727567358331003453.vcf.gz -INPUT /tmp/shard2.4804514997273114429.vcf.gz -INPUT /tmp/shard38267540453251402273.vcf -OUTPUT /tmp/result10548482394584999709.vcf.gz -COMMENT This is a comment -REORDER_INPUT_BY_FIRST_VARIANT false Test: Test method TestGatherFiles[5]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.4804514997273114429.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[5]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.4804514997273114429.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[5]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.4804514997273114429.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[5]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.4804514997273114429.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:18.166 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:18.166 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestGatherFiles[5]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.4804514997273114429.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:18.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:18.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestGatherFiles[5]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.4804514997273114429.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:18.167 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:18.167 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestGatherFiles[5]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.4804514997273114429.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:18.167 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:18.167 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestGatherFiles[5]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.4804514997273114429.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:18 GMT+14:00 2024] GatherVcfs INPUT=[/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.4804514997273114429.vcf.gz, /tmp/shard38267540453251402273.vcf] OUTPUT=/tmp/result10548482394584999709.vcf.gz COMMENT=[This is a comment] REORDER_INPUT_BY_FIRST_VARIANT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:18 GMT+14:00 2024] GatherVcfs INPUT=[/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.4804514997273114429.vcf.gz, /tmp/shard38267540453251402273.vcf] OUTPUT=/tmp/result10548482394584999709.vcf.gz COMMENT=[This is a comment] REORDER_INPUT_BY_FIRST_VARIANT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestGatherFiles[5]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.4804514997273114429.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestGatherFiles[5]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.4804514997273114429.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:18 GatherVcfs Checking inputs. INFO 2024-07-02 11:58:18 GatherVcfs Checking inputs. Test: Test method TestGatherFiles[5]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.4804514997273114429.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:18 GatherVcfs Checking file headers and first records to ensure compatibility. INFO 2024-07-02 11:58:18 GatherVcfs Checking file headers and first records to ensure compatibility. Test: Test method TestGatherFiles[5]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.4804514997273114429.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:18 GatherVcfs Gathering by conventional means. INFO 2024-07-02 11:58:18 GatherVcfs Gathering by conventional means. Test: Test method TestGatherFiles[5]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.4804514997273114429.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:18 GMT+14:00 2024] picard.vcf.GatherVcfs done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:18 GMT+14:00 2024] picard.vcf.GatherVcfs done. Elapsed time: 0.00 minutes. Test: Test method TestGatherFiles[5]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.4804514997273114429.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method TestGatherFiles[6]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) Test: Test method TestGatherFiles[6]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:18 GatherVcfs Gradle suite > Gradle test > picard.vcf.GatherVcfsTest.TestGatherFiles[6]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false) STANDARD_ERROR INFO 2024-07-02 11:58:18 GatherVcfs Test: Test method TestGatherFiles[6]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[6]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestGatherFiles[6]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[6]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestGatherFiles[6]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestGatherFiles[6]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[6]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestGatherFiles[6]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[6]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** GatherVcfs -INPUT /tmp/shard1.15727567358331003453.vcf.gz -INPUT /tmp/shard2_bad.10995389296001037841.vcf.gz -INPUT /tmp/shard38267540453251402273.vcf -OUTPUT /tmp/result17123811867929580633.vcf.gz -COMMENT This is a comment -REORDER_INPUT_BY_FIRST_VARIANT false ********** GatherVcfs -INPUT /tmp/shard1.15727567358331003453.vcf.gz -INPUT /tmp/shard2_bad.10995389296001037841.vcf.gz -INPUT /tmp/shard38267540453251402273.vcf -OUTPUT /tmp/result17123811867929580633.vcf.gz -COMMENT This is a comment -REORDER_INPUT_BY_FIRST_VARIANT false Test: Test method TestGatherFiles[6]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[6]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[6]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[6]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:18.501 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:18.501 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestGatherFiles[6]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:18.501 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:18.501 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestGatherFiles[6]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:18.502 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:18.502 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestGatherFiles[6]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:18.502 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:18.502 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestGatherFiles[6]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:18 GMT+14:00 2024] GatherVcfs INPUT=[/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf] OUTPUT=/tmp/result17123811867929580633.vcf.gz COMMENT=[This is a comment] REORDER_INPUT_BY_FIRST_VARIANT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:18 GMT+14:00 2024] GatherVcfs INPUT=[/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf] OUTPUT=/tmp/result17123811867929580633.vcf.gz COMMENT=[This is a comment] REORDER_INPUT_BY_FIRST_VARIANT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestGatherFiles[6]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestGatherFiles[6]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:18 GatherVcfs Checking inputs. INFO 2024-07-02 11:58:18 GatherVcfs Checking inputs. Test: Test method TestGatherFiles[6]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:18 GatherVcfs Checking file headers and first records to ensure compatibility. INFO 2024-07-02 11:58:18 GatherVcfs Checking file headers and first records to ensure compatibility. Test: Test method TestGatherFiles[6]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:18 GatherVcfs Gathering by conventional means. INFO 2024-07-02 11:58:18 GatherVcfs Gathering by conventional means. Test: Test method TestGatherFiles[6]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ERROR 2024-07-02 11:58:18 GatherVcfs There was a problem with gathering the INPUT.java.lang.IllegalArgumentException: First variant in file /tmp/shard2_bad.10995389296001037841.vcf.gz is at 22:17283967 but last variant in earlier file /tmp/shard1.15727567358331003453.vcf.gz is at 22:17283967 ERROR 2024-07-02 11:58:18 GatherVcfs There was a problem with gathering the INPUT.java.lang.IllegalArgumentException: First variant in file /tmp/shard2_bad.10995389296001037841.vcf.gz is at 22:17283967 but last variant in earlier file /tmp/shard1.15727567358331003453.vcf.gz is at 22:17283967 Test: Test method TestGatherFiles[6]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:18 GMT+14:00 2024] picard.vcf.GatherVcfs done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:18 GMT+14:00 2024] picard.vcf.GatherVcfs done. Elapsed time: 0.00 minutes. Test: Test method TestGatherFiles[6]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method TestGatherFiles[6]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2_bad.10995389296001037841.vcf.gz, /tmp/shard38267540453251402273.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method TestGatherFiles[7]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) Test: Test method TestGatherFiles[7]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:18 GatherVcfs Gradle suite > Gradle test > picard.vcf.GatherVcfsTest.TestGatherFiles[7]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false) STANDARD_ERROR INFO 2024-07-02 11:58:18 GatherVcfs Test: Test method TestGatherFiles[7]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[7]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestGatherFiles[7]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[7]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestGatherFiles[7]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestGatherFiles[7]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[7]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestGatherFiles[7]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[7]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** GatherVcfs -INPUT /tmp/shard1.15727567358331003453.vcf.gz -INPUT /tmp/shard3.4569477930763005245.vcf.gz -INPUT /tmp/shard2.17721206679344426320.vcf -OUTPUT /tmp/result3645239258315462424.vcf.gz -COMMENT This is a comment -REORDER_INPUT_BY_FIRST_VARIANT false ********** GatherVcfs -INPUT /tmp/shard1.15727567358331003453.vcf.gz -INPUT /tmp/shard3.4569477930763005245.vcf.gz -INPUT /tmp/shard2.17721206679344426320.vcf -OUTPUT /tmp/result3645239258315462424.vcf.gz -COMMENT This is a comment -REORDER_INPUT_BY_FIRST_VARIANT false Test: Test method TestGatherFiles[7]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[7]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[7]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[7]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:18.786 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:18.786 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestGatherFiles[7]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:18.786 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:18.786 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestGatherFiles[7]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:18.786 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:18.786 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestGatherFiles[7]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:18.786 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:18.786 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestGatherFiles[7]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:18 GMT+14:00 2024] GatherVcfs INPUT=[/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf] OUTPUT=/tmp/result3645239258315462424.vcf.gz COMMENT=[This is a comment] REORDER_INPUT_BY_FIRST_VARIANT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:18 GMT+14:00 2024] GatherVcfs INPUT=[/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf] OUTPUT=/tmp/result3645239258315462424.vcf.gz COMMENT=[This is a comment] REORDER_INPUT_BY_FIRST_VARIANT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestGatherFiles[7]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestGatherFiles[7]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:18 GatherVcfs Checking inputs. INFO 2024-07-02 11:58:18 GatherVcfs Checking inputs. Test: Test method TestGatherFiles[7]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:18 GatherVcfs Checking file headers and first records to ensure compatibility. INFO 2024-07-02 11:58:18 GatherVcfs Checking file headers and first records to ensure compatibility. Test: Test method TestGatherFiles[7]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ERROR 2024-07-02 11:58:18 GatherVcfs There was a problem with gathering the INPUT.java.lang.IllegalArgumentException: First record in file /tmp/shard2.17721206679344426320.vcf is not after first record in previous file /tmp/shard3.4569477930763005245.vcf.gz ERROR 2024-07-02 11:58:18 GatherVcfs There was a problem with gathering the INPUT.java.lang.IllegalArgumentException: First record in file /tmp/shard2.17721206679344426320.vcf is not after first record in previous file /tmp/shard3.4569477930763005245.vcf.gz Test: Test method TestGatherFiles[7]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:18 GMT+14:00 2024] picard.vcf.GatherVcfs done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:18 GMT+14:00 2024] picard.vcf.GatherVcfs done. Elapsed time: 0.00 minutes. Test: Test method TestGatherFiles[7]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method TestGatherFiles[7]([/tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method TestGatherFiles[8]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) Test: Test method TestGatherFiles[8]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:18 GatherVcfs Gradle suite > Gradle test > picard.vcf.GatherVcfsTest.TestGatherFiles[8]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false) STANDARD_ERROR INFO 2024-07-02 11:58:18 GatherVcfs Test: Test method TestGatherFiles[8]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[8]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestGatherFiles[8]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[8]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestGatherFiles[8]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestGatherFiles[8]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[8]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestGatherFiles[8]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[8]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** GatherVcfs -INPUT /tmp/shard3.4569477930763005245.vcf.gz -INPUT /tmp/shard1.15727567358331003453.vcf.gz -INPUT /tmp/shard2.17721206679344426320.vcf -OUTPUT /tmp/result3888294328139671685.vcf.gz -COMMENT This is a comment -REORDER_INPUT_BY_FIRST_VARIANT false ********** GatherVcfs -INPUT /tmp/shard3.4569477930763005245.vcf.gz -INPUT /tmp/shard1.15727567358331003453.vcf.gz -INPUT /tmp/shard2.17721206679344426320.vcf -OUTPUT /tmp/result3888294328139671685.vcf.gz -COMMENT This is a comment -REORDER_INPUT_BY_FIRST_VARIANT false Test: Test method TestGatherFiles[8]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[8]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[8]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[8]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:18.923 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:18.923 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestGatherFiles[8]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:18.923 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:18.923 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestGatherFiles[8]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:18.923 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:18.923 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestGatherFiles[8]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:18.923 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:18.923 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestGatherFiles[8]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:18 GMT+14:00 2024] GatherVcfs INPUT=[/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf] OUTPUT=/tmp/result3888294328139671685.vcf.gz COMMENT=[This is a comment] REORDER_INPUT_BY_FIRST_VARIANT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:18 GMT+14:00 2024] GatherVcfs INPUT=[/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf] OUTPUT=/tmp/result3888294328139671685.vcf.gz COMMENT=[This is a comment] REORDER_INPUT_BY_FIRST_VARIANT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestGatherFiles[8]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestGatherFiles[8]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:18 GatherVcfs Checking inputs. INFO 2024-07-02 11:58:18 GatherVcfs Checking inputs. Test: Test method TestGatherFiles[8]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:18 GatherVcfs Checking file headers and first records to ensure compatibility. INFO 2024-07-02 11:58:18 GatherVcfs Checking file headers and first records to ensure compatibility. Test: Test method TestGatherFiles[8]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: ERROR 2024-07-02 11:58:18 GatherVcfs There was a problem with gathering the INPUT.java.lang.IllegalArgumentException: First record in file /tmp/shard1.15727567358331003453.vcf.gz is not after first record in previous file /tmp/shard3.4569477930763005245.vcf.gz ERROR 2024-07-02 11:58:18 GatherVcfs There was a problem with gathering the INPUT.java.lang.IllegalArgumentException: First record in file /tmp/shard1.15727567358331003453.vcf.gz is not after first record in previous file /tmp/shard3.4569477930763005245.vcf.gz Test: Test method TestGatherFiles[8]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:18 GMT+14:00 2024] picard.vcf.GatherVcfs done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:18 GMT+14:00 2024] picard.vcf.GatherVcfs done. Elapsed time: 0.00 minutes. Test: Test method TestGatherFiles[8]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method TestGatherFiles[8]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 1, false)(picard.vcf.GatherVcfsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method TestGatherFiles[9]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, true)(picard.vcf.GatherVcfsTest) Test: Test method TestGatherFiles[9]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:19 GatherVcfs Gradle suite > Gradle test > picard.vcf.GatherVcfsTest.TestGatherFiles[9]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, true) STANDARD_ERROR INFO 2024-07-02 11:58:19 GatherVcfs Test: Test method TestGatherFiles[9]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[9]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestGatherFiles[9]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[9]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestGatherFiles[9]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestGatherFiles[9]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[9]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestGatherFiles[9]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[9]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** GatherVcfs -INPUT /tmp/shard3.4569477930763005245.vcf.gz -INPUT /tmp/shard1.15727567358331003453.vcf.gz -INPUT /tmp/shard2.17721206679344426320.vcf -OUTPUT /tmp/result6305022346270649864.vcf.gz -COMMENT This is a comment -REORDER_INPUT_BY_FIRST_VARIANT true ********** GatherVcfs -INPUT /tmp/shard3.4569477930763005245.vcf.gz -INPUT /tmp/shard1.15727567358331003453.vcf.gz -INPUT /tmp/shard2.17721206679344426320.vcf -OUTPUT /tmp/result6305022346270649864.vcf.gz -COMMENT This is a comment -REORDER_INPUT_BY_FIRST_VARIANT true Test: Test method TestGatherFiles[9]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: ********** ********** Test: Test method TestGatherFiles[9]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[9]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: Test: Test method TestGatherFiles[9]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:19.030 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:19.030 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestGatherFiles[9]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:19.030 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:19.030 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestGatherFiles[9]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:19.031 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:19.031 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestGatherFiles[9]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: 11:58:19.031 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:19.031 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestGatherFiles[9]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:19 GMT+14:00 2024] GatherVcfs INPUT=[/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf] OUTPUT=/tmp/result6305022346270649864.vcf.gz COMMENT=[This is a comment] REORDER_INPUT_BY_FIRST_VARIANT=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:19 GMT+14:00 2024] GatherVcfs INPUT=[/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf] OUTPUT=/tmp/result6305022346270649864.vcf.gz COMMENT=[This is a comment] REORDER_INPUT_BY_FIRST_VARIANT=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestGatherFiles[9]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestGatherFiles[9]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:19 GatherVcfs Checking inputs. INFO 2024-07-02 11:58:19 GatherVcfs Checking inputs. Test: Test method TestGatherFiles[9]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:19 GatherVcfs Checking file headers and first records to ensure compatibility. INFO 2024-07-02 11:58:19 GatherVcfs Checking file headers and first records to ensure compatibility. Test: Test method TestGatherFiles[9]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: INFO 2024-07-02 11:58:19 GatherVcfs Gathering by conventional means. INFO 2024-07-02 11:58:19 GatherVcfs Gathering by conventional means. Test: Test method TestGatherFiles[9]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: [Tue Jul 02 11:58:19 GMT+14:00 2024] picard.vcf.GatherVcfs done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:19 GMT+14:00 2024] picard.vcf.GatherVcfs done. Elapsed time: 0.00 minutes. Test: Test method TestGatherFiles[9]([/tmp/shard3.4569477930763005245.vcf.gz, /tmp/shard1.15727567358331003453.vcf.gz, /tmp/shard2.17721206679344426320.vcf], /tmp/whole.330489316947721516.vcf.gz, 0, true)(picard.vcf.GatherVcfsTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testGA4GHScheme(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) Test: Test method testGA4GHScheme(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: 11:58:19.201 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.GenotypeConcordanceGA4GHSchemeTest.testGA4GHScheme STANDARD_ERROR 11:58:19.201 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGA4GHScheme(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: 11:58:19.201 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:19.201 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGA4GHScheme(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: 11:58:19.201 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:19.201 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGA4GHScheme(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: 11:58:19.201 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:19.201 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGA4GHScheme(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: [Tue Jul 02 11:58:19 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:19 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testGA4GHScheme(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: [Tue Jul 02 11:58:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testGA4GHScheme(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: INFO 2024-07-02 11:58:19 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:19 GenotypeConcordance Starting iteration over variants. Test: Test method testGA4GHScheme(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: INFO 2024-07-02 11:58:19 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 72 INFO 2024-07-02 11:58:19 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 72 Test: Test method testGA4GHScheme(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: [Tue Jul 02 11:58:19 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:19 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. Test: Test method testGA4GHScheme(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testGA4GHSchemeDiffSamples(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) Test: Test method testGA4GHSchemeDiffSamples(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: 11:58:19.369 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.GenotypeConcordanceGA4GHSchemeTest.testGA4GHSchemeDiffSamples STANDARD_ERROR 11:58:19.369 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGA4GHSchemeDiffSamples(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: 11:58:19.369 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:19.369 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGA4GHSchemeDiffSamples(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: 11:58:19.369 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:19.369 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGA4GHSchemeDiffSamples(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: 11:58:19.369 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:19.369 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGA4GHSchemeDiffSamples(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: [Tue Jul 02 11:58:19 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12891 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:19 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12891 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testGA4GHSchemeDiffSamples(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: [Tue Jul 02 11:58:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testGA4GHSchemeDiffSamples(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: INFO 2024-07-02 11:58:19 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:19 GenotypeConcordance Starting iteration over variants. Test: Test method testGA4GHSchemeDiffSamples(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: INFO 2024-07-02 11:58:19 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 32 INFO 2024-07-02 11:58:19 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 32 Test: Test method testGA4GHSchemeDiffSamples(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: [Tue Jul 02 11:58:19 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:19 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. Test: Test method testGA4GHSchemeDiffSamples(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testGA4GHSchemeDiffSamplesWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) Test: Test method testGA4GHSchemeDiffSamplesWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: 11:58:19.499 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.GenotypeConcordanceGA4GHSchemeTest.testGA4GHSchemeDiffSamplesWithIntervals STANDARD_ERROR 11:58:19.499 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGA4GHSchemeDiffSamplesWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: 11:58:19.499 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:19.499 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGA4GHSchemeDiffSamplesWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: 11:58:19.499 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:19.499 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGA4GHSchemeDiffSamplesWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: 11:58:19.499 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:19.499 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGA4GHSchemeDiffSamplesWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: [Tue Jul 02 11:58:19 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12891 INTERVALS=[testdata/picard/vcf/IntervalListChr1Small.interval_list] INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:19 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12891 INTERVALS=[testdata/picard/vcf/IntervalListChr1Small.interval_list] INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testGA4GHSchemeDiffSamplesWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: [Tue Jul 02 11:58:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testGA4GHSchemeDiffSamplesWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: INFO 2024-07-02 11:58:19 GenotypeConcordance Starting to load intervals list(s). INFO 2024-07-02 11:58:19 GenotypeConcordance Starting to load intervals list(s). Test: Test method testGA4GHSchemeDiffSamplesWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: INFO 2024-07-02 11:58:19 GenotypeConcordance Finished loading up intervals list(s). INFO 2024-07-02 11:58:19 GenotypeConcordance Finished loading up intervals list(s). Test: Test method testGA4GHSchemeDiffSamplesWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: INFO 2024-07-02 11:58:19 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:19 GenotypeConcordance Starting iteration over variants. Test: Test method testGA4GHSchemeDiffSamplesWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: INFO 2024-07-02 11:58:19 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 1 INFO 2024-07-02 11:58:19 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 1 Test: Test method testGA4GHSchemeDiffSamplesWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: [Tue Jul 02 11:58:19 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:19 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. Test: Test method testGA4GHSchemeDiffSamplesWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testGA4GHSchemeWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) Test: Test method testGA4GHSchemeWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: 11:58:19.558 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.GenotypeConcordanceGA4GHSchemeTest.testGA4GHSchemeWithIntervals STANDARD_ERROR 11:58:19.558 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGA4GHSchemeWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: 11:58:19.558 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:19.558 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGA4GHSchemeWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: 11:58:19.558 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:19.558 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGA4GHSchemeWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: 11:58:19.558 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:19.558 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGA4GHSchemeWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: [Tue Jul 02 11:58:19 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERVALS=[testdata/picard/vcf/IntervalListChr1Small.interval_list] INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:19 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERVALS=[testdata/picard/vcf/IntervalListChr1Small.interval_list] INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testGA4GHSchemeWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: [Tue Jul 02 11:58:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testGA4GHSchemeWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: INFO 2024-07-02 11:58:19 GenotypeConcordance Starting to load intervals list(s). INFO 2024-07-02 11:58:19 GenotypeConcordance Starting to load intervals list(s). Test: Test method testGA4GHSchemeWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: INFO 2024-07-02 11:58:19 GenotypeConcordance Finished loading up intervals list(s). INFO 2024-07-02 11:58:19 GenotypeConcordance Finished loading up intervals list(s). Test: Test method testGA4GHSchemeWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: INFO 2024-07-02 11:58:19 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:19 GenotypeConcordance Starting iteration over variants. Test: Test method testGA4GHSchemeWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: INFO 2024-07-02 11:58:19 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 2 INFO 2024-07-02 11:58:19 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 2 Test: Test method testGA4GHSchemeWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: [Tue Jul 02 11:58:19 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:19 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. Test: Test method testGA4GHSchemeWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testMissingHomRefSchemeWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeWithMissingTest) Test: Test method testMissingHomRefSchemeWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeWithMissingTest) produced standard out/err: 11:58:19.597 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.GenotypeConcordanceGA4GHSchemeWithMissingTest.testMissingHomRefSchemeWithIntervals STANDARD_ERROR 11:58:19.597 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingHomRefSchemeWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeWithMissingTest) produced standard out/err: 11:58:19.598 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:19.598 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingHomRefSchemeWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeWithMissingTest) produced standard out/err: 11:58:19.598 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:19.598 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingHomRefSchemeWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeWithMissingTest) produced standard out/err: 11:58:19.598 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:19.598 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingHomRefSchemeWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeWithMissingTest) produced standard out/err: [Tue Jul 02 11:58:19 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/NIST.selected.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERVALS=[testdata/picard/vcf/IntervalList1PerChrom.interval_list] INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=true IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:19 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/NIST.selected.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERVALS=[testdata/picard/vcf/IntervalList1PerChrom.interval_list] INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=true IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingHomRefSchemeWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeWithMissingTest) produced standard out/err: [Tue Jul 02 11:58:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingHomRefSchemeWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeWithMissingTest) produced standard out/err: INFO 2024-07-02 11:58:19 GenotypeConcordance Starting to load intervals list(s). INFO 2024-07-02 11:58:19 GenotypeConcordance Starting to load intervals list(s). Test: Test method testMissingHomRefSchemeWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeWithMissingTest) produced standard out/err: INFO 2024-07-02 11:58:19 GenotypeConcordance Finished loading up intervals list(s). INFO 2024-07-02 11:58:19 GenotypeConcordance Finished loading up intervals list(s). Test: Test method testMissingHomRefSchemeWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeWithMissingTest) produced standard out/err: INFO 2024-07-02 11:58:19 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:19 GenotypeConcordance Starting iteration over variants. Test: Test method testMissingHomRefSchemeWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeWithMissingTest) produced standard out/err: INFO 2024-07-02 11:58:19 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 2 INFO 2024-07-02 11:58:19 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 2 Test: Test method testMissingHomRefSchemeWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeWithMissingTest) produced standard out/err: [Tue Jul 02 11:58:19 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:19 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. Test: Test method testMissingHomRefSchemeWithIntervals(picard.vcf.GenotypeConcordanceGA4GHSchemeWithMissingTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testGenotypeConcordance[0](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) Test: Test method testGenotypeConcordance[0](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:19.648 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.GenotypeConcordanceTest.testGenotypeConcordance[0](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff) STANDARD_ERROR 11:58:19.648 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[0](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:19.648 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:19.648 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[0](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:19.648 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:19.648 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[0](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:19.648 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:19.648 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[0](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:19 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=true TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:19 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=true TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testGenotypeConcordance[0](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testGenotypeConcordance[0](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:19 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:19 GenotypeConcordance Starting iteration over variants. Test: Test method testGenotypeConcordance[0](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:20 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 72 INFO 2024-07-02 11:58:20 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 72 Test: Test method testGenotypeConcordance[0](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:20 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:58:20 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.01 minutes. Test: Test method testGenotypeConcordance[0](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method testGenotypeConcordance[0](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:20.315 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:20.315 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[0](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:20.315 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:20.315 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[0](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:20.316 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:20.316 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[0](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:20.316 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:20.316 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[0](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:20 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:20 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testGenotypeConcordance[0](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testGenotypeConcordance[0](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:20 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:20 GenotypeConcordance Starting iteration over variants. Test: Test method testGenotypeConcordance[0](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:20 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 72 INFO 2024-07-02 11:58:20 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 72 Test: Test method testGenotypeConcordance[0](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:20 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:20 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. Test: Test method testGenotypeConcordance[0](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testGenotypeConcordance[1](testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, null, null, false, false, CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) Test: Test method testGenotypeConcordance[1](testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, null, null, false, false, CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:20.489 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.GenotypeConcordanceTest.testGenotypeConcordance[1](testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, null, null, false, false, CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff) STANDARD_ERROR 11:58:20.489 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[1](testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, null, null, false, false, CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:20.489 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:20.489 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[1](testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, null, null, false, false, CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:20.489 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:20.489 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[1](testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, null, null, false, false, CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:20.489 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:20.489 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[1](testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, null, null, false, false, CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:20 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-indels.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-indels.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=true TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:20 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-indels.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-indels.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=true TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testGenotypeConcordance[1](testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, null, null, false, false, CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testGenotypeConcordance[1](testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, null, null, false, false, CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:20 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:20 GenotypeConcordance Starting iteration over variants. Test: Test method testGenotypeConcordance[1](testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, null, null, false, false, CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:20 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 3 INFO 2024-07-02 11:58:20 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 3 Test: Test method testGenotypeConcordance[1](testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, null, null, false, false, CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:20 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:20 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. Test: Test method testGenotypeConcordance[1](testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, null, null, false, false, CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method testGenotypeConcordance[1](testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, null, null, false, false, CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:20.723 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:20.723 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[1](testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, null, null, false, false, CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:20.723 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:20.723 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[1](testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, null, null, false, false, CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:20.723 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:20.723 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[1](testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, null, null, false, false, CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:20.723 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:20.723 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[1](testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, null, null, false, false, CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:20 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-indels.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-indels.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:20 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-indels.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-indels.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testGenotypeConcordance[1](testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, null, null, false, false, CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testGenotypeConcordance[1](testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, null, null, false, false, CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:20 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:20 GenotypeConcordance Starting iteration over variants. Test: Test method testGenotypeConcordance[1](testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, null, null, false, false, CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:20 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 3 INFO 2024-07-02 11:58:20 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 3 Test: Test method testGenotypeConcordance[1](testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, null, null, false, false, CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:20 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:20 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. Test: Test method testGenotypeConcordance[1](testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, testdata/picard/vcf/CEUTrio-indels.vcf, NA12878, null, null, false, false, CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testGenotypeConcordance[2](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) Test: Test method testGenotypeConcordance[2](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:20.787 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.GenotypeConcordanceTest.testGenotypeConcordance[2](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff) STANDARD_ERROR 11:58:20.787 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[2](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:20.787 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:20.787 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[2](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:20.788 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:20.788 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[2](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:20.788 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:20.788 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[2](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:20 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=true TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:20 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=true TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testGenotypeConcordance[2](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testGenotypeConcordance[2](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:20 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:20 GenotypeConcordance Starting iteration over variants. Test: Test method testGenotypeConcordance[2](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:21 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 72 INFO 2024-07-02 11:58:21 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 72 Test: Test method testGenotypeConcordance[2](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:21 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:58:21 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.01 minutes. Test: Test method testGenotypeConcordance[2](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method testGenotypeConcordance[2](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:21.310 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:21.310 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[2](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:21.310 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:21.310 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[2](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:21.310 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:21.310 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[2](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:21.310 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:21.310 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[2](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:21 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:21 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testGenotypeConcordance[2](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testGenotypeConcordance[2](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:21 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:21 GenotypeConcordance Starting iteration over variants. Test: Test method testGenotypeConcordance[2](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:21 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 72 INFO 2024-07-02 11:58:21 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 72 Test: Test method testGenotypeConcordance[2](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:21 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:21 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. Test: Test method testGenotypeConcordance[2](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testGenotypeConcordance[3](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) Test: Test method testGenotypeConcordance[3](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:21.426 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.GenotypeConcordanceTest.testGenotypeConcordance[3](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff) STANDARD_ERROR 11:58:21.426 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[3](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:21.426 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:21.426 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[3](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:21.427 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:21.427 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[3](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:21.427 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:21.427 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[3](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:21 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=true TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:21 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=true TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testGenotypeConcordance[3](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testGenotypeConcordance[3](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:21 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:21 GenotypeConcordance Starting iteration over variants. Test: Test method testGenotypeConcordance[3](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:21 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 72 INFO 2024-07-02 11:58:21 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 72 Test: Test method testGenotypeConcordance[3](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:21 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:58:21 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.01 minutes. Test: Test method testGenotypeConcordance[3](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method testGenotypeConcordance[3](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:21.891 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:21.891 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[3](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:21.891 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:21.891 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[3](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:21.891 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:21.891 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[3](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:21.891 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:21.891 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[3](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:21 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:21 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testGenotypeConcordance[3](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testGenotypeConcordance[3](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:21 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:21 GenotypeConcordance Starting iteration over variants. Test: Test method testGenotypeConcordance[3](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:22 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 72 INFO 2024-07-02 11:58:22 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 72 Test: Test method testGenotypeConcordance[3](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:22 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:22 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. Test: Test method testGenotypeConcordance[3](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testGenotypeConcordance[4](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_del_line.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) Test: Test method testGenotypeConcordance[4](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_del_line.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:22.091 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.GenotypeConcordanceTest.testGenotypeConcordance[4](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_del_line.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff) STANDARD_ERROR 11:58:22.091 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[4](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_del_line.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:22.091 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:22.091 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[4](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_del_line.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:22.091 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:22.091 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[4](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_del_line.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:22.091 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:22.091 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[4](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_del_line.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:22 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps_del_line.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=true TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:22 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps_del_line.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=true TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testGenotypeConcordance[4](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_del_line.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testGenotypeConcordance[4](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_del_line.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:22 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:22 GenotypeConcordance Starting iteration over variants. Test: Test method testGenotypeConcordance[4](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_del_line.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:22 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 72 INFO 2024-07-02 11:58:22 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 72 Test: Test method testGenotypeConcordance[4](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_del_line.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:22 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:58:22 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.01 minutes. Test: Test method testGenotypeConcordance[4](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_del_line.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method testGenotypeConcordance[4](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_del_line.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:22.431 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:22.431 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[4](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_del_line.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:22.431 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:22.431 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[4](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_del_line.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:22.431 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:22.431 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[4](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_del_line.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:22.431 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:22.431 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[4](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_del_line.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:22 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps_del_line.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:22 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps_del_line.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testGenotypeConcordance[4](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_del_line.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testGenotypeConcordance[4](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_del_line.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:22 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:22 GenotypeConcordance Starting iteration over variants. Test: Test method testGenotypeConcordance[4](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_del_line.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:22 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 72 INFO 2024-07-02 11:58:22 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 72 Test: Test method testGenotypeConcordance[4](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_del_line.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:22 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:22 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. Test: Test method testGenotypeConcordance[4](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps_del_line.vcf, NA12878, null, null, false, false, CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testGenotypeConcordance[5](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, true, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows)(picard.vcf.GenotypeConcordanceTest) Test: Test method testGenotypeConcordance[5](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, true, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:22.523 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.GenotypeConcordanceTest.testGenotypeConcordance[5](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, true, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows) STANDARD_ERROR 11:58:22.523 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[5](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, true, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:22.523 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:22.523 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[5](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, true, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:22.524 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:22.524 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[5](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, true, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:22.524 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:22.524 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[5](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, true, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:22 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=true TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=true USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:22 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=true TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=true USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testGenotypeConcordance[5](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, true, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testGenotypeConcordance[5](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, true, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:22 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:22 GenotypeConcordance Starting iteration over variants. Test: Test method testGenotypeConcordance[5](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, true, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:22 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 72 INFO 2024-07-02 11:58:22 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 72 Test: Test method testGenotypeConcordance[5](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, true, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:23 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:58:23 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.01 minutes. Test: Test method testGenotypeConcordance[5](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, true, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method testGenotypeConcordance[5](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, true, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:23.096 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:23.096 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[5](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, true, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:23.096 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:23.096 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[5](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, true, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:23.096 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:23.096 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[5](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, true, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:23.096 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:23.096 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[5](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, true, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:23 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=true USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:23 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=true USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testGenotypeConcordance[5](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, true, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testGenotypeConcordance[5](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, true, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:23 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:23 GenotypeConcordance Starting iteration over variants. Test: Test method testGenotypeConcordance[5](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, true, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:23 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 72 INFO 2024-07-02 11:58:23 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 72 Test: Test method testGenotypeConcordance[5](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, true, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:23 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:23 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. Test: Test method testGenotypeConcordance[5](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, true, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testGenotypeConcordance[6](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, 40, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq)(picard.vcf.GenotypeConcordanceTest) Test: Test method testGenotypeConcordance[6](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, 40, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:23.278 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.GenotypeConcordanceTest.testGenotypeConcordance[6](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, 40, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq) STANDARD_ERROR 11:58:23.278 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[6](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, 40, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:23.279 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:23.279 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[6](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, 40, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:23.279 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:23.279 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[6](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, 40, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:23.279 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:23.279 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[6](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, 40, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:23 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=true TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12891 INTERSECT_INTERVALS=true MIN_GQ=40 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:23 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=true TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12891 INTERSECT_INTERVALS=true MIN_GQ=40 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testGenotypeConcordance[6](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, 40, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testGenotypeConcordance[6](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, 40, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:23 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:23 GenotypeConcordance Starting iteration over variants. Test: Test method testGenotypeConcordance[6](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, 40, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:23 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 32 INFO 2024-07-02 11:58:23 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 32 Test: Test method testGenotypeConcordance[6](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, 40, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:23 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.01 minutes. [Tue Jul 02 11:58:23 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.01 minutes. Test: Test method testGenotypeConcordance[6](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, 40, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method testGenotypeConcordance[6](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, 40, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:23.707 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:23.707 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[6](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, 40, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:23.707 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:23.707 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[6](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, 40, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:23.707 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:23.707 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[6](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, 40, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:23.707 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:23.707 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[6](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, 40, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:23 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12891 INTERSECT_INTERVALS=true MIN_GQ=40 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:23 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12891 INTERSECT_INTERVALS=true MIN_GQ=40 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testGenotypeConcordance[6](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, 40, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testGenotypeConcordance[6](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, 40, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:23 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:23 GenotypeConcordance Starting iteration over variants. Test: Test method testGenotypeConcordance[6](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, 40, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:23 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 32 INFO 2024-07-02 11:58:23 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 32 Test: Test method testGenotypeConcordance[6](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, 40, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:23 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:23 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. Test: Test method testGenotypeConcordance[6](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, 40, null, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testGenotypeConcordance[7](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, null, 40, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp)(picard.vcf.GenotypeConcordanceTest) Test: Test method testGenotypeConcordance[7](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, null, 40, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:23.814 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.GenotypeConcordanceTest.testGenotypeConcordance[7](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, null, 40, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp) STANDARD_ERROR 11:58:23.814 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[7](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, null, 40, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:23.814 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:23.814 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[7](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, null, 40, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:23.814 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:23.814 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[7](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, null, 40, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:23.814 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:23.814 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[7](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, null, 40, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:23 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=true TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12891 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=40 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:23 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=true TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12891 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=40 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testGenotypeConcordance[7](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, null, 40, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testGenotypeConcordance[7](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, null, 40, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:23 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:23 GenotypeConcordance Starting iteration over variants. Test: Test method testGenotypeConcordance[7](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, null, 40, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:23 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 32 INFO 2024-07-02 11:58:23 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 32 Test: Test method testGenotypeConcordance[7](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, null, 40, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:24 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:24 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. Test: Test method testGenotypeConcordance[7](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, null, 40, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method testGenotypeConcordance[7](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, null, 40, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.120 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:24.120 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[7](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, null, 40, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.120 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:24.120 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[7](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, null, 40, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.120 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:24.120 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[7](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, null, 40, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.120 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:24.120 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[7](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, null, 40, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:24 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12891 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=40 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:24 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/CEUTrio-snps.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12891 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=40 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testGenotypeConcordance[7](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, null, 40, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testGenotypeConcordance[7](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, null, 40, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:24 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:24 GenotypeConcordance Starting iteration over variants. Test: Test method testGenotypeConcordance[7](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, null, 40, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:24 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 32 INFO 2024-07-02 11:58:24 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 32 Test: Test method testGenotypeConcordance[7](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, null, 40, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:24 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:24 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. Test: Test method testGenotypeConcordance[7](testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12891, null, 40, false, false, CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testGenotypeConcordance[8](testdata/picard/vcf/NIST.selected.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, true, NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) Test: Test method testGenotypeConcordance[8](testdata/picard/vcf/NIST.selected.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, true, NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.213 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.GenotypeConcordanceTest.testGenotypeConcordance[8](testdata/picard/vcf/NIST.selected.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, true, NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff) STANDARD_ERROR 11:58:24.213 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[8](testdata/picard/vcf/NIST.selected.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, true, NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.213 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:24.213 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[8](testdata/picard/vcf/NIST.selected.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, true, NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.213 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:24.213 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[8](testdata/picard/vcf/NIST.selected.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, true, NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.213 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:24.213 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[8](testdata/picard/vcf/NIST.selected.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, true, NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:24 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/NIST.selected.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=true TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERVALS=[testdata/picard/vcf/IntervalList1PerChrom.interval_list] INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=true IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:24 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/NIST.selected.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=true TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERVALS=[testdata/picard/vcf/IntervalList1PerChrom.interval_list] INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=true IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testGenotypeConcordance[8](testdata/picard/vcf/NIST.selected.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, true, NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testGenotypeConcordance[8](testdata/picard/vcf/NIST.selected.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, true, NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:24 GenotypeConcordance Starting to load intervals list(s). INFO 2024-07-02 11:58:24 GenotypeConcordance Starting to load intervals list(s). Test: Test method testGenotypeConcordance[8](testdata/picard/vcf/NIST.selected.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, true, NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:24 GenotypeConcordance Finished loading up intervals list(s). INFO 2024-07-02 11:58:24 GenotypeConcordance Finished loading up intervals list(s). Test: Test method testGenotypeConcordance[8](testdata/picard/vcf/NIST.selected.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, true, NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:24 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:24 GenotypeConcordance Starting iteration over variants. Test: Test method testGenotypeConcordance[8](testdata/picard/vcf/NIST.selected.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, true, NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:24 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 2 INFO 2024-07-02 11:58:24 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 2 Test: Test method testGenotypeConcordance[8](testdata/picard/vcf/NIST.selected.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, true, NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:24 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:24 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. Test: Test method testGenotypeConcordance[8](testdata/picard/vcf/NIST.selected.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, true, NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method testGenotypeConcordance[8](testdata/picard/vcf/NIST.selected.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, true, NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.390 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:24.390 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[8](testdata/picard/vcf/NIST.selected.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, true, NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.390 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:24.390 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[8](testdata/picard/vcf/NIST.selected.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, true, NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.390 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:24.390 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[8](testdata/picard/vcf/NIST.selected.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, true, NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.390 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:24.390 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[8](testdata/picard/vcf/NIST.selected.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, true, NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:24 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/NIST.selected.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERVALS=[testdata/picard/vcf/IntervalList1PerChrom.interval_list] INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=true IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:24 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/NIST.selected.vcf CALL_VCF=testdata/picard/vcf/CEUTrio-snps.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERVALS=[testdata/picard/vcf/IntervalList1PerChrom.interval_list] INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=true IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testGenotypeConcordance[8](testdata/picard/vcf/NIST.selected.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, true, NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testGenotypeConcordance[8](testdata/picard/vcf/NIST.selected.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, true, NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:24 GenotypeConcordance Starting to load intervals list(s). INFO 2024-07-02 11:58:24 GenotypeConcordance Starting to load intervals list(s). Test: Test method testGenotypeConcordance[8](testdata/picard/vcf/NIST.selected.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, true, NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:24 GenotypeConcordance Finished loading up intervals list(s). INFO 2024-07-02 11:58:24 GenotypeConcordance Finished loading up intervals list(s). Test: Test method testGenotypeConcordance[8](testdata/picard/vcf/NIST.selected.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, true, NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:24 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:24 GenotypeConcordance Starting iteration over variants. Test: Test method testGenotypeConcordance[8](testdata/picard/vcf/NIST.selected.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, true, NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:24 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 2 INFO 2024-07-02 11:58:24 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 2 Test: Test method testGenotypeConcordance[8](testdata/picard/vcf/NIST.selected.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, true, NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:24 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:24 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. Test: Test method testGenotypeConcordance[8](testdata/picard/vcf/NIST.selected.vcf, NA12878, testdata/picard/vcf/CEUTrio-snps.vcf, NA12878, null, null, false, true, NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testGenotypeConcordance[9](testdata/picard/vcf/spanningDeletionTruth.vcf, /dev/stdin, testdata/picard/vcf/spanningDeletionCallset.vcf, CHMI_CHMI3_WGS2, null, null, false, false, spanningDeletionCallset_vs_spanningDeletionTruth)(picard.vcf.GenotypeConcordanceTest) Test: Test method testGenotypeConcordance[9](testdata/picard/vcf/spanningDeletionTruth.vcf, /dev/stdin, testdata/picard/vcf/spanningDeletionCallset.vcf, CHMI_CHMI3_WGS2, null, null, false, false, spanningDeletionCallset_vs_spanningDeletionTruth)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.442 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.GenotypeConcordanceTest.testGenotypeConcordance[9](testdata/picard/vcf/spanningDeletionTruth.vcf, /dev/stdin, testdata/picard/vcf/spanningDeletionCallset.vcf, CHMI_CHMI3_WGS2, null, null, false, false, spanningDeletionCallset_vs_spanningDeletionTruth) STANDARD_ERROR 11:58:24.442 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[9](testdata/picard/vcf/spanningDeletionTruth.vcf, /dev/stdin, testdata/picard/vcf/spanningDeletionCallset.vcf, CHMI_CHMI3_WGS2, null, null, false, false, spanningDeletionCallset_vs_spanningDeletionTruth)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.442 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:24.442 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[9](testdata/picard/vcf/spanningDeletionTruth.vcf, /dev/stdin, testdata/picard/vcf/spanningDeletionCallset.vcf, CHMI_CHMI3_WGS2, null, null, false, false, spanningDeletionCallset_vs_spanningDeletionTruth)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.442 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:24.442 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[9](testdata/picard/vcf/spanningDeletionTruth.vcf, /dev/stdin, testdata/picard/vcf/spanningDeletionCallset.vcf, CHMI_CHMI3_WGS2, null, null, false, false, spanningDeletionCallset_vs_spanningDeletionTruth)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.442 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:24.442 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[9](testdata/picard/vcf/spanningDeletionTruth.vcf, /dev/stdin, testdata/picard/vcf/spanningDeletionCallset.vcf, CHMI_CHMI3_WGS2, null, null, false, false, spanningDeletionCallset_vs_spanningDeletionTruth)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:24 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/spanningDeletionTruth.vcf CALL_VCF=testdata/picard/vcf/spanningDeletionCallset.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=true TRUTH_SAMPLE=/dev/stdin CALL_SAMPLE=CHMI_CHMI3_WGS2 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:24 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/spanningDeletionTruth.vcf CALL_VCF=testdata/picard/vcf/spanningDeletionCallset.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=true TRUTH_SAMPLE=/dev/stdin CALL_SAMPLE=CHMI_CHMI3_WGS2 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testGenotypeConcordance[9](testdata/picard/vcf/spanningDeletionTruth.vcf, /dev/stdin, testdata/picard/vcf/spanningDeletionCallset.vcf, CHMI_CHMI3_WGS2, null, null, false, false, spanningDeletionCallset_vs_spanningDeletionTruth)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testGenotypeConcordance[9](testdata/picard/vcf/spanningDeletionTruth.vcf, /dev/stdin, testdata/picard/vcf/spanningDeletionCallset.vcf, CHMI_CHMI3_WGS2, null, null, false, false, spanningDeletionCallset_vs_spanningDeletionTruth)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:24 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:24 GenotypeConcordance Starting iteration over variants. Test: Test method testGenotypeConcordance[9](testdata/picard/vcf/spanningDeletionTruth.vcf, /dev/stdin, testdata/picard/vcf/spanningDeletionCallset.vcf, CHMI_CHMI3_WGS2, null, null, false, false, spanningDeletionCallset_vs_spanningDeletionTruth)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:24 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: SNP INDEL 1 INFO 2024-07-02 11:58:24 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: SNP INDEL 1 Test: Test method testGenotypeConcordance[9](testdata/picard/vcf/spanningDeletionTruth.vcf, /dev/stdin, testdata/picard/vcf/spanningDeletionCallset.vcf, CHMI_CHMI3_WGS2, null, null, false, false, spanningDeletionCallset_vs_spanningDeletionTruth)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:24 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:24 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. Test: Test method testGenotypeConcordance[9](testdata/picard/vcf/spanningDeletionTruth.vcf, /dev/stdin, testdata/picard/vcf/spanningDeletionCallset.vcf, CHMI_CHMI3_WGS2, null, null, false, false, spanningDeletionCallset_vs_spanningDeletionTruth)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method testGenotypeConcordance[9](testdata/picard/vcf/spanningDeletionTruth.vcf, /dev/stdin, testdata/picard/vcf/spanningDeletionCallset.vcf, CHMI_CHMI3_WGS2, null, null, false, false, spanningDeletionCallset_vs_spanningDeletionTruth)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.500 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:24.500 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[9](testdata/picard/vcf/spanningDeletionTruth.vcf, /dev/stdin, testdata/picard/vcf/spanningDeletionCallset.vcf, CHMI_CHMI3_WGS2, null, null, false, false, spanningDeletionCallset_vs_spanningDeletionTruth)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.500 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:24.500 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[9](testdata/picard/vcf/spanningDeletionTruth.vcf, /dev/stdin, testdata/picard/vcf/spanningDeletionCallset.vcf, CHMI_CHMI3_WGS2, null, null, false, false, spanningDeletionCallset_vs_spanningDeletionTruth)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.500 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:24.500 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testGenotypeConcordance[9](testdata/picard/vcf/spanningDeletionTruth.vcf, /dev/stdin, testdata/picard/vcf/spanningDeletionCallset.vcf, CHMI_CHMI3_WGS2, null, null, false, false, spanningDeletionCallset_vs_spanningDeletionTruth)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.500 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:24.500 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testGenotypeConcordance[9](testdata/picard/vcf/spanningDeletionTruth.vcf, /dev/stdin, testdata/picard/vcf/spanningDeletionCallset.vcf, CHMI_CHMI3_WGS2, null, null, false, false, spanningDeletionCallset_vs_spanningDeletionTruth)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:24 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/spanningDeletionTruth.vcf CALL_VCF=testdata/picard/vcf/spanningDeletionCallset.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=/dev/stdin CALL_SAMPLE=CHMI_CHMI3_WGS2 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:24 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/spanningDeletionTruth.vcf CALL_VCF=testdata/picard/vcf/spanningDeletionCallset.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/actualGtConc OUTPUT_VCF=false TRUTH_SAMPLE=/dev/stdin CALL_SAMPLE=CHMI_CHMI3_WGS2 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testGenotypeConcordance[9](testdata/picard/vcf/spanningDeletionTruth.vcf, /dev/stdin, testdata/picard/vcf/spanningDeletionCallset.vcf, CHMI_CHMI3_WGS2, null, null, false, false, spanningDeletionCallset_vs_spanningDeletionTruth)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testGenotypeConcordance[9](testdata/picard/vcf/spanningDeletionTruth.vcf, /dev/stdin, testdata/picard/vcf/spanningDeletionCallset.vcf, CHMI_CHMI3_WGS2, null, null, false, false, spanningDeletionCallset_vs_spanningDeletionTruth)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:24 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:24 GenotypeConcordance Starting iteration over variants. Test: Test method testGenotypeConcordance[9](testdata/picard/vcf/spanningDeletionTruth.vcf, /dev/stdin, testdata/picard/vcf/spanningDeletionCallset.vcf, CHMI_CHMI3_WGS2, null, null, false, false, spanningDeletionCallset_vs_spanningDeletionTruth)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:24 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: SNP INDEL 1 INFO 2024-07-02 11:58:24 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: SNP INDEL 1 Test: Test method testGenotypeConcordance[9](testdata/picard/vcf/spanningDeletionTruth.vcf, /dev/stdin, testdata/picard/vcf/spanningDeletionCallset.vcf, CHMI_CHMI3_WGS2, null, null, false, false, spanningDeletionCallset_vs_spanningDeletionTruth)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:24 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:24 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. Test: Test method testGenotypeConcordance[9](testdata/picard/vcf/spanningDeletionTruth.vcf, /dev/stdin, testdata/picard/vcf/spanningDeletionCallset.vcf, CHMI_CHMI3_WGS2, null, null, false, false, spanningDeletionCallset_vs_spanningDeletionTruth)(picard.vcf.GenotypeConcordanceTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testGenotypeConcordanceDetermineState[0](A*, A*, HOM_REF, A*, A*, HOM_REF)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[1](A*, A*, HOM_REF, A*, C, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[2](A*, A*, HOM_REF, C, A*, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[3](A*, A*, HOM_REF, A*, G, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[4](A*, A*, HOM_REF, G, A*, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[5](A*, A*, HOM_REF, A*, T, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[6](A*, A*, HOM_REF, T, A*, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[7](A*, A*, HOM_REF, C, G, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[8](A*, A*, HOM_REF, G, C, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[9](A*, A*, HOM_REF, C, T, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[10](A*, A*, HOM_REF, T, C, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[11](A*, A*, HOM_REF, G, T, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[12](A*, A*, HOM_REF, T, G, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[13](A*, A*, HOM_REF, C, C, HOM_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[14](A*, A*, HOM_REF, G, G, HOM_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[15](A*, A*, HOM_REF, T, T, HOM_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[16](A*, C, HET_REF_VAR1, A*, A*, HOM_REF)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[17](C, A*, HET_REF_VAR1, A*, A*, HOM_REF)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[18](A*, G, HET_REF_VAR1, A*, A*, HOM_REF)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[19](G, A*, HET_REF_VAR1, A*, A*, HOM_REF)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[20](A*, T, HET_REF_VAR1, A*, A*, HOM_REF)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[21](T, A*, HET_REF_VAR1, A*, A*, HOM_REF)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[22](A*, C, HET_REF_VAR1, A*, C, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[23](A*, C, HET_REF_VAR1, C, A*, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[24](C, A*, HET_REF_VAR1, A*, C, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[25](C, A*, HET_REF_VAR1, C, A*, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[26](A*, C, HET_REF_VAR1, A*, G, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[27](A*, C, HET_REF_VAR1, G, A*, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[28](C, A*, HET_REF_VAR1, A*, G, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[29](C, A*, HET_REF_VAR1, G, A*, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[30](A*, C, HET_REF_VAR1, A*, T, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[31](A*, C, HET_REF_VAR1, T, A*, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[32](C, A*, HET_REF_VAR1, A*, T, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[33](C, A*, HET_REF_VAR1, T, A*, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[34](A*, G, HET_REF_VAR1, A*, C, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[35](A*, G, HET_REF_VAR1, C, A*, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[36](G, A*, HET_REF_VAR1, A*, C, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[37](G, A*, HET_REF_VAR1, C, A*, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[38](A*, G, HET_REF_VAR1, A*, G, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[39](A*, G, HET_REF_VAR1, G, A*, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[40](G, A*, HET_REF_VAR1, A*, G, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[41](G, A*, HET_REF_VAR1, G, A*, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[42](A*, G, HET_REF_VAR1, A*, T, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[43](A*, G, HET_REF_VAR1, T, A*, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[44](G, A*, HET_REF_VAR1, A*, T, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[45](G, A*, HET_REF_VAR1, T, A*, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[46](A*, T, HET_REF_VAR1, A*, C, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[47](A*, T, HET_REF_VAR1, C, A*, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[48](T, A*, HET_REF_VAR1, A*, C, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[49](T, A*, HET_REF_VAR1, C, A*, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[50](A*, T, HET_REF_VAR1, A*, G, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[51](A*, T, HET_REF_VAR1, G, A*, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[52](T, A*, HET_REF_VAR1, A*, G, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[53](T, A*, HET_REF_VAR1, G, A*, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[54](A*, T, HET_REF_VAR1, A*, T, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[55](A*, T, HET_REF_VAR1, T, A*, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[56](T, A*, HET_REF_VAR1, A*, T, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[57](T, A*, HET_REF_VAR1, T, A*, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[58](A*, C, HET_REF_VAR1, C, G, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[59](A*, C, HET_REF_VAR1, G, C, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[60](C, A*, HET_REF_VAR1, C, G, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[61](C, A*, HET_REF_VAR1, G, C, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[62](A*, C, HET_REF_VAR1, C, T, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[63](A*, C, HET_REF_VAR1, T, C, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[64](C, A*, HET_REF_VAR1, C, T, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[65](C, A*, HET_REF_VAR1, T, C, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[66](A*, C, HET_REF_VAR1, G, T, HET_VAR3_VAR4)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[67](A*, C, HET_REF_VAR1, T, G, HET_VAR3_VAR4)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[68](C, A*, HET_REF_VAR1, G, T, HET_VAR3_VAR4)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[69](C, A*, HET_REF_VAR1, T, G, HET_VAR3_VAR4)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[70](A*, G, HET_REF_VAR1, C, G, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[71](A*, G, HET_REF_VAR1, G, C, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[72](G, A*, HET_REF_VAR1, C, G, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[73](G, A*, HET_REF_VAR1, G, C, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[74](A*, G, HET_REF_VAR1, C, T, HET_VAR3_VAR4)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[75](A*, G, HET_REF_VAR1, T, C, HET_VAR3_VAR4)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[76](G, A*, HET_REF_VAR1, C, T, HET_VAR3_VAR4)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[77](G, A*, HET_REF_VAR1, T, C, HET_VAR3_VAR4)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[78](A*, G, HET_REF_VAR1, G, T, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[79](A*, G, HET_REF_VAR1, T, G, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[80](G, A*, HET_REF_VAR1, G, T, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[81](G, A*, HET_REF_VAR1, T, G, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[82](A*, T, HET_REF_VAR1, C, G, HET_VAR3_VAR4)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[83](A*, T, HET_REF_VAR1, G, C, HET_VAR3_VAR4)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[84](T, A*, HET_REF_VAR1, C, G, HET_VAR3_VAR4)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[85](T, A*, HET_REF_VAR1, G, C, HET_VAR3_VAR4)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[86](A*, T, HET_REF_VAR1, C, T, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[87](A*, T, HET_REF_VAR1, T, C, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[88](T, A*, HET_REF_VAR1, C, T, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[89](T, A*, HET_REF_VAR1, T, C, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[90](A*, T, HET_REF_VAR1, G, T, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[91](A*, T, HET_REF_VAR1, T, G, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[92](T, A*, HET_REF_VAR1, G, T, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[93](T, A*, HET_REF_VAR1, T, G, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[94](A*, C, HET_REF_VAR1, C, C, HOM_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[95](C, A*, HET_REF_VAR1, C, C, HOM_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[96](A*, C, HET_REF_VAR1, G, G, HOM_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[97](C, A*, HET_REF_VAR1, G, G, HOM_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[98](A*, C, HET_REF_VAR1, T, T, HOM_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[99](C, A*, HET_REF_VAR1, T, T, HOM_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[100](A*, G, HET_REF_VAR1, C, C, HOM_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[101](G, A*, HET_REF_VAR1, C, C, HOM_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[102](A*, G, HET_REF_VAR1, G, G, HOM_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[103](G, A*, HET_REF_VAR1, G, G, HOM_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[104](A*, G, HET_REF_VAR1, T, T, HOM_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[105](G, A*, HET_REF_VAR1, T, T, HOM_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[106](A*, T, HET_REF_VAR1, C, C, HOM_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[107](T, A*, HET_REF_VAR1, C, C, HOM_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[108](A*, T, HET_REF_VAR1, G, G, HOM_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[109](T, A*, HET_REF_VAR1, G, G, HOM_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[110](A*, T, HET_REF_VAR1, T, T, HOM_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[111](T, A*, HET_REF_VAR1, T, T, HOM_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[112](C, G, HET_VAR1_VAR2, A*, A*, HOM_REF)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[113](G, C, HET_VAR1_VAR2, A*, A*, HOM_REF)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[114](C, T, HET_VAR1_VAR2, A*, A*, HOM_REF)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[115](T, C, HET_VAR1_VAR2, A*, A*, HOM_REF)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[116](G, T, HET_VAR1_VAR2, A*, A*, HOM_REF)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[117](T, G, HET_VAR1_VAR2, A*, A*, HOM_REF)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[118](C, G, HET_VAR1_VAR2, A*, C, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[119](C, G, HET_VAR1_VAR2, C, A*, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[120](G, C, HET_VAR1_VAR2, A*, C, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[121](G, C, HET_VAR1_VAR2, C, A*, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[122](C, G, HET_VAR1_VAR2, A*, G, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[123](C, G, HET_VAR1_VAR2, G, A*, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[124](G, C, HET_VAR1_VAR2, A*, G, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[125](G, C, HET_VAR1_VAR2, G, A*, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[126](C, G, HET_VAR1_VAR2, A*, T, HET_REF_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[127](C, G, HET_VAR1_VAR2, T, A*, HET_REF_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[128](G, C, HET_VAR1_VAR2, A*, T, HET_REF_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[129](G, C, HET_VAR1_VAR2, T, A*, HET_REF_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[130](C, T, HET_VAR1_VAR2, A*, C, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[131](C, T, HET_VAR1_VAR2, C, A*, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[132](T, C, HET_VAR1_VAR2, A*, C, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[133](T, C, HET_VAR1_VAR2, C, A*, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[134](C, T, HET_VAR1_VAR2, A*, G, HET_REF_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[135](C, T, HET_VAR1_VAR2, G, A*, HET_REF_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[136](T, C, HET_VAR1_VAR2, A*, G, HET_REF_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[137](T, C, HET_VAR1_VAR2, G, A*, HET_REF_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[138](C, T, HET_VAR1_VAR2, A*, T, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[139](C, T, HET_VAR1_VAR2, T, A*, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[140](T, C, HET_VAR1_VAR2, A*, T, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[141](T, C, HET_VAR1_VAR2, T, A*, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[142](G, T, HET_VAR1_VAR2, A*, C, HET_REF_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[143](G, T, HET_VAR1_VAR2, C, A*, HET_REF_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[144](T, G, HET_VAR1_VAR2, A*, C, HET_REF_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[145](T, G, HET_VAR1_VAR2, C, A*, HET_REF_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[146](G, T, HET_VAR1_VAR2, A*, G, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[147](G, T, HET_VAR1_VAR2, G, A*, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[148](T, G, HET_VAR1_VAR2, A*, G, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[149](T, G, HET_VAR1_VAR2, G, A*, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[150](G, T, HET_VAR1_VAR2, A*, T, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[151](G, T, HET_VAR1_VAR2, T, A*, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[152](T, G, HET_VAR1_VAR2, A*, T, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[153](T, G, HET_VAR1_VAR2, T, A*, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[154](C, G, HET_VAR1_VAR2, C, C, HOM_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[155](G, C, HET_VAR1_VAR2, C, C, HOM_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[156](C, G, HET_VAR1_VAR2, G, G, HOM_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[157](G, C, HET_VAR1_VAR2, G, G, HOM_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[158](C, G, HET_VAR1_VAR2, T, T, HOM_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[159](G, C, HET_VAR1_VAR2, T, T, HOM_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[160](C, T, HET_VAR1_VAR2, C, C, HOM_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[161](T, C, HET_VAR1_VAR2, C, C, HOM_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[162](C, T, HET_VAR1_VAR2, G, G, HOM_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[163](T, C, HET_VAR1_VAR2, G, G, HOM_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[164](C, T, HET_VAR1_VAR2, T, T, HOM_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[165](T, C, HET_VAR1_VAR2, T, T, HOM_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[166](G, T, HET_VAR1_VAR2, C, C, HOM_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[167](T, G, HET_VAR1_VAR2, C, C, HOM_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[168](G, T, HET_VAR1_VAR2, G, G, HOM_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[169](T, G, HET_VAR1_VAR2, G, G, HOM_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[170](G, T, HET_VAR1_VAR2, T, T, HOM_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[171](T, G, HET_VAR1_VAR2, T, T, HOM_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[172](C, G, HET_VAR1_VAR2, C, G, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[173](C, G, HET_VAR1_VAR2, G, C, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[174](G, C, HET_VAR1_VAR2, C, G, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[175](G, C, HET_VAR1_VAR2, G, C, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[176](C, G, HET_VAR1_VAR2, C, T, HET_VAR1_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[177](C, G, HET_VAR1_VAR2, T, C, HET_VAR1_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[178](G, C, HET_VAR1_VAR2, C, T, HET_VAR1_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[179](G, C, HET_VAR1_VAR2, T, C, HET_VAR1_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[180](C, G, HET_VAR1_VAR2, G, T, HET_VAR1_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[181](C, G, HET_VAR1_VAR2, T, G, HET_VAR1_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[182](G, C, HET_VAR1_VAR2, G, T, HET_VAR1_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[183](G, C, HET_VAR1_VAR2, T, G, HET_VAR1_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[184](C, T, HET_VAR1_VAR2, C, G, HET_VAR1_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[185](C, T, HET_VAR1_VAR2, G, C, HET_VAR1_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[186](T, C, HET_VAR1_VAR2, C, G, HET_VAR1_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[187](T, C, HET_VAR1_VAR2, G, C, HET_VAR1_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[188](C, T, HET_VAR1_VAR2, C, T, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[189](C, T, HET_VAR1_VAR2, T, C, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[190](T, C, HET_VAR1_VAR2, C, T, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[191](T, C, HET_VAR1_VAR2, T, C, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[192](C, T, HET_VAR1_VAR2, G, T, HET_VAR1_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[193](C, T, HET_VAR1_VAR2, T, G, HET_VAR1_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[194](T, C, HET_VAR1_VAR2, G, T, HET_VAR1_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[195](T, C, HET_VAR1_VAR2, T, G, HET_VAR1_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[196](G, T, HET_VAR1_VAR2, C, G, HET_VAR1_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[197](G, T, HET_VAR1_VAR2, G, C, HET_VAR1_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[198](T, G, HET_VAR1_VAR2, C, G, HET_VAR1_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[199](T, G, HET_VAR1_VAR2, G, C, HET_VAR1_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[200](G, T, HET_VAR1_VAR2, C, T, HET_VAR1_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[201](G, T, HET_VAR1_VAR2, T, C, HET_VAR1_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[202](T, G, HET_VAR1_VAR2, C, T, HET_VAR1_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[203](T, G, HET_VAR1_VAR2, T, C, HET_VAR1_VAR3)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[204](G, T, HET_VAR1_VAR2, G, T, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[205](G, T, HET_VAR1_VAR2, T, G, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[206](T, G, HET_VAR1_VAR2, G, T, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[207](T, G, HET_VAR1_VAR2, T, G, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[208](C, C, HOM_VAR1, A*, A*, HOM_REF)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[209](G, G, HOM_VAR1, A*, A*, HOM_REF)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[210](T, T, HOM_VAR1, A*, A*, HOM_REF)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[211](C, C, HOM_VAR1, A*, C, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[212](C, C, HOM_VAR1, C, A*, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[213](C, C, HOM_VAR1, A*, G, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[214](C, C, HOM_VAR1, G, A*, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[215](C, C, HOM_VAR1, A*, T, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[216](C, C, HOM_VAR1, T, A*, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[217](G, G, HOM_VAR1, A*, C, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[218](G, G, HOM_VAR1, C, A*, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[219](G, G, HOM_VAR1, A*, G, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[220](G, G, HOM_VAR1, G, A*, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[221](G, G, HOM_VAR1, A*, T, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[222](G, G, HOM_VAR1, T, A*, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[223](T, T, HOM_VAR1, A*, C, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[224](T, T, HOM_VAR1, C, A*, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[225](T, T, HOM_VAR1, A*, G, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[226](T, T, HOM_VAR1, G, A*, HET_REF_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[227](T, T, HOM_VAR1, A*, T, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[228](T, T, HOM_VAR1, T, A*, HET_REF_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[229](C, C, HOM_VAR1, C, C, HOM_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[230](C, C, HOM_VAR1, G, G, HOM_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[231](C, C, HOM_VAR1, T, T, HOM_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[232](G, G, HOM_VAR1, C, C, HOM_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[233](G, G, HOM_VAR1, G, G, HOM_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[234](G, G, HOM_VAR1, T, T, HOM_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[235](T, T, HOM_VAR1, C, C, HOM_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[236](T, T, HOM_VAR1, G, G, HOM_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[237](T, T, HOM_VAR1, T, T, HOM_VAR1)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[238](C, C, HOM_VAR1, C, G, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[239](C, C, HOM_VAR1, G, C, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[240](C, C, HOM_VAR1, C, T, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[241](C, C, HOM_VAR1, T, C, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[242](C, C, HOM_VAR1, G, T, HET_VAR3_VAR4)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[243](C, C, HOM_VAR1, T, G, HET_VAR3_VAR4)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[244](G, G, HOM_VAR1, C, G, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[245](G, G, HOM_VAR1, G, C, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[246](G, G, HOM_VAR1, C, T, HET_VAR3_VAR4)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[247](G, G, HOM_VAR1, T, C, HET_VAR3_VAR4)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[248](G, G, HOM_VAR1, G, T, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[249](G, G, HOM_VAR1, T, G, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[250](T, T, HOM_VAR1, C, G, HET_VAR3_VAR4)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[251](T, T, HOM_VAR1, G, C, HET_VAR3_VAR4)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[252](T, T, HOM_VAR1, C, T, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[253](T, T, HOM_VAR1, T, C, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[254](T, T, HOM_VAR1, G, T, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[255](T, T, HOM_VAR1, T, G, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[256](AA, AA, HOM_VAR1, AAAA, AAAAA, HET_VAR3_VAR4)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[257](AA, AA, HOM_VAR1, AAAAA, AAAA, HET_VAR3_VAR4)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[258](AA, AAA, HET_VAR1_VAR2, AAAA, AAAAA, HET_VAR3_VAR4)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[259](AA, AAA, HET_VAR1_VAR2, AAAAA, AAAA, HET_VAR3_VAR4)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[260](AAA, AA, HET_VAR1_VAR2, AAAA, AAAAA, HET_VAR3_VAR4)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[261](AAA, AA, HET_VAR1_VAR2, AAAAA, AAAA, HET_VAR3_VAR4)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[262](C, AA, IS_MIXED, AAAA, AAAAA, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[263](C, AA, IS_MIXED, AAAAA, AAAA, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[264](AA, C, IS_MIXED, AAAA, AAAAA, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[265](AA, C, IS_MIXED, AAAAA, AAAA, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[266](AA, C, IS_MIXED, AAAA, AAAAA, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[267](AA, C, IS_MIXED, AAAAA, AAAA, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[268](C, AA, IS_MIXED, AAAA, AAAAA, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[269](C, AA, IS_MIXED, AAAAA, AAAA, HET_VAR1_VAR2)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[270](AA, AA, HOM_VAR1, C, AAAAA, IS_MIXED)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[271](AA, AA, HOM_VAR1, AAAAA, C, IS_MIXED)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[272](AA, AAA, HET_VAR1_VAR2, AAAA, C, IS_MIXED)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[273](AA, AAA, HET_VAR1_VAR2, C, AAAA, IS_MIXED)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[274](AAA, AA, HET_VAR1_VAR2, AAAA, C, IS_MIXED)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[275](AAA, AA, HET_VAR1_VAR2, C, AAAA, IS_MIXED)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[276](., A*, NO_CALL, A*, A*, HOM_REF)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[277](A*, ., NO_CALL, A*, A*, HOM_REF)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[278](A*, ., NO_CALL, A*, A*, HOM_REF)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[279](., A*, NO_CALL, A*, A*, HOM_REF)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[280](., ., NO_CALL, A*, A*, HOM_REF)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[281](A*, A*, HOM_REF, ., A*, NO_CALL)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[282](A*, A*, HOM_REF, A*, ., NO_CALL)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[283](A*, A*, HOM_REF, A*, ., NO_CALL)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[284](A*, A*, HOM_REF, ., A*, NO_CALL)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineState[285](A*, A*, HOM_REF, ., ., NO_CALL)(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineStateDp(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineStateFilter(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineStateGq(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testGenotypeConcordanceDetermineStateNull(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testIgnoreFilterStatus(picard.vcf.GenotypeConcordanceTest) Test: Test method testIgnoreFilterStatus(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.605 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.GenotypeConcordanceTest.testIgnoreFilterStatus STANDARD_ERROR 11:58:24.605 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIgnoreFilterStatus(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.605 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:24.605 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIgnoreFilterStatus(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.605 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:24.605 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIgnoreFilterStatus(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.605 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:24.605 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIgnoreFilterStatus(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:24 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/NIST_subset_3sites.vcf CALL_VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/vcf_with_filtered_calls.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/dontIgnoreFilterStatus OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:24 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/NIST_subset_3sites.vcf CALL_VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/vcf_with_filtered_calls.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/dontIgnoreFilterStatus OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIgnoreFilterStatus(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIgnoreFilterStatus(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:24 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:24 GenotypeConcordance Starting iteration over variants. Test: Test method testIgnoreFilterStatus(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:24 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:24 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. Test: Test method testIgnoreFilterStatus(picard.vcf.GenotypeConcordanceTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Test: Test method testIgnoreFilterStatus(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.628 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:24.628 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIgnoreFilterStatus(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.628 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:24.628 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIgnoreFilterStatus(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.628 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:24.628 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIgnoreFilterStatus(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.628 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:24.628 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIgnoreFilterStatus(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:24 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/NIST_subset_3sites.vcf CALL_VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/vcf_with_filtered_calls.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/ignoreFilterStatus OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:24 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/NIST_subset_3sites.vcf CALL_VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/vcf_with_filtered_calls.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/ignoreFilterStatus OUTPUT_VCF=false TRUTH_SAMPLE=NA12878 CALL_SAMPLE=NA12878 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIgnoreFilterStatus(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIgnoreFilterStatus(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:24 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:24 GenotypeConcordance Starting iteration over variants. Test: Test method testIgnoreFilterStatus(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:24 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:24 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. Test: Test method testIgnoreFilterStatus(picard.vcf.GenotypeConcordanceTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testNoCallVariants(picard.vcf.GenotypeConcordanceTest) Test: Test method testNoCallVariants(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.650 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.GenotypeConcordanceTest.testNoCallVariants STANDARD_ERROR 11:58:24.650 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoCallVariants(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.650 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:24.650 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoCallVariants(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.650 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:24.650 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoCallVariants(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:24.650 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:24.650 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoCallVariants(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:24 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/mini.vcf CALL_VCF=testdata/picard/vcf/mini.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/TwoNoCalls OUTPUT_VCF=true TRUTH_SAMPLE=NA20801 CALL_SAMPLE=NA19920 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:24 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=testdata/picard/vcf/mini.vcf CALL_VCF=testdata/picard/vcf/mini.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/TwoNoCalls OUTPUT_VCF=true TRUTH_SAMPLE=NA20801 CALL_SAMPLE=NA19920 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testNoCallVariants(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testNoCallVariants(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:24 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:24 GenotypeConcordance Starting iteration over variants. Test: Test method testNoCallVariants(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:25 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 556 INFO 2024-07-02 11:58:25 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 556 Test: Test method testNoCallVariants(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:25 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.02 minutes. [Tue Jul 02 11:58:25 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.02 minutes. Test: Test method testNoCallVariants(picard.vcf.GenotypeConcordanceTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testNormalizeAllelesForIndels(picard.vcf.GenotypeConcordanceTest) Running Test: Test method testNormalizeAllelesForWritingVCF(picard.vcf.GenotypeConcordanceTest) Test: Test method testNormalizeAllelesForWritingVCF(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:25.624 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.GenotypeConcordanceTest.testNormalizeAllelesForWritingVCF STANDARD_ERROR 11:58:25.624 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNormalizeAllelesForWritingVCF(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:25.624 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:25.624 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNormalizeAllelesForWritingVCF(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:25.624 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:25.624 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNormalizeAllelesForWritingVCF(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:25.624 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:25.624 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNormalizeAllelesForWritingVCF(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:25 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/normalize_no_calls_truth.vcf CALL_VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/normalize_no_calls_call.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/MultipleRefAlleles OUTPUT_VCF=true TRUTH_SAMPLE=truth CALL_SAMPLE=truth INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:25 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/normalize_no_calls_truth.vcf CALL_VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/normalize_no_calls_call.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/MultipleRefAlleles OUTPUT_VCF=true TRUTH_SAMPLE=truth CALL_SAMPLE=truth INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testNormalizeAllelesForWritingVCF(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testNormalizeAllelesForWritingVCF(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:25 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:25 GenotypeConcordance Starting iteration over variants. Test: Test method testNormalizeAllelesForWritingVCF(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:25 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: SYMBOLIC SYMBOLIC 1 INFO 2024-07-02 11:58:25 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: SYMBOLIC SYMBOLIC 1 Test: Test method testNormalizeAllelesForWritingVCF(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:25 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 1 INFO 2024-07-02 11:58:25 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: NO_VARIATION NO_VARIATION 1 Test: Test method testNormalizeAllelesForWritingVCF(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:25 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:25 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. Test: Test method testNormalizeAllelesForWritingVCF(picard.vcf.GenotypeConcordanceTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method testSpanningDeletion(picard.vcf.GenotypeConcordanceTest) Test: Test method testSpanningDeletion(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:25.721 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.GenotypeConcordanceTest.testSpanningDeletion STANDARD_ERROR 11:58:25.721 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSpanningDeletion(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:25.721 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:25.721 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSpanningDeletion(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:25.722 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:25.722 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSpanningDeletion(picard.vcf.GenotypeConcordanceTest) produced standard out/err: 11:58:25.722 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:25.722 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSpanningDeletion(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:25 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/spanningDeletionTruth.vcf CALL_VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/spanningDeletionCallset.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/spanningDeletion OUTPUT_VCF=true TRUTH_SAMPLE=/dev/stdin CALL_SAMPLE=CHMI_CHMI3_WGS2 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:25 GMT+14:00 2024] GenotypeConcordance TRUTH_VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/spanningDeletionTruth.vcf CALL_VCF=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/spanningDeletionCallset.vcf OUTPUT=/tmp/GenotypeConcordanceTest14563364324447571122.tmp/spanningDeletion OUTPUT_VCF=true TRUTH_SAMPLE=/dev/stdin CALL_SAMPLE=CHMI_CHMI3_WGS2 INTERSECT_INTERVALS=true MIN_GQ=0 MIN_DP=0 OUTPUT_ALL_ROWS=false USE_VCF_INDEX=false MISSING_SITES_HOM_REF=false IGNORE_FILTER_STATUS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSpanningDeletion(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSpanningDeletion(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:25 GenotypeConcordance Starting iteration over variants. INFO 2024-07-02 11:58:25 GenotypeConcordance Starting iteration over variants. Test: Test method testSpanningDeletion(picard.vcf.GenotypeConcordanceTest) produced standard out/err: INFO 2024-07-02 11:58:25 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: SNP INDEL 1 INFO 2024-07-02 11:58:25 GenotypeConcordance Uncovered truth/call Variant Context Type Counts: SNP INDEL 1 Test: Test method testSpanningDeletion(picard.vcf.GenotypeConcordanceTest) produced standard out/err: [Tue Jul 02 11:58:25 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. [Tue Jul 02 11:58:25 GMT+14:00 2024] picard.vcf.GenotypeConcordance done. Elapsed time: 0.00 minutes. Test: Test method testSpanningDeletion(picard.vcf.GenotypeConcordanceTest) produced standard out/err: Runtime.totalMemory()=1430257664 Runtime.totalMemory()=1430257664 Running Test: Test method pathologicalInputOrderingTest(picard.util.GraphUtilsTest) Running Test: Test method secondTest(picard.util.GraphUtilsTest) Running Test: Test method simpleTest(picard.util.GraphUtilsTest) Running Test: Test method testGetFingerprintSex(picard.arrays.GtcToVcfTest) Running Test: Test method testGetGenotype(picard.arrays.GtcToVcfTest) Running Test: Test method testPolarToEuclidean[0](0.9228464, 0.1, 0.13941205, 0.04408725, 0.7548494, 0.167997, 0.093297675, 0.048428293)(picard.arrays.GtcToVcfTest) Running Test: Test method testPolarToEuclidean[1](0.7268211, 0.1, 0.5568851, 0.02236068, 0.33085135, 0.39596978, 0.047303885, 0.055978503)(picard.arrays.GtcToVcfTest) Running Test: Test method testPolarToEuclidean[2](0.3930402, 0.1, 0.9743582, 0.010385988, 0.0152258575, 0.37781435, 0.007087064, 0.096309155)(picard.arrays.GtcToVcfTest) Running Test: Test method testEquivalenceHapDBandVCF(picard.fingerprint.HaplotypeMapTest) Running Test: Test method testHaplotypeMapReader[0](testdata/picard/fingerprint/haplotypeMap.txt)(picard.fingerprint.HaplotypeMapTest) Running Test: Test method testHaplotypeMapReader[1](testdata/picard/fingerprint/haplotypeMap.vcf)(picard.fingerprint.HaplotypeMapTest) Running Test: Test method testHaplotypeMapWriteToVcf[0](picard.fingerprint.HaplotypeMap@10fc4237)(picard.fingerprint.HaplotypeMapTest) Running Test: Test method testHaplotypeMapWriter[0](picard.fingerprint.HaplotypeMap@5898a386)(picard.fingerprint.HaplotypeMapTest) Running Test: Test method testHaplotypeProbabilitiesFromContaminatorSequenceAddToProbs[0](picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@53c2d67d, test:1, 0, 0)(picard.fingerprint.HaplotypeProbabilitiesTest) Running Test: Test method testHaplotypeProbabilitiesFromContaminatorSequenceAddToProbs[1](picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@6f2347f3, test:1, 0, 1)(picard.fingerprint.HaplotypeProbabilitiesTest) Running Test: Test method testHaplotypeProbabilitiesFromContaminatorSequenceAddToProbs[2](picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@39c975c9, test:1, 0, 76)(picard.fingerprint.HaplotypeProbabilitiesTest) Running Test: Test method testHaplotypeProbabilitiesFromContaminatorSequenceAddToProbs[3](picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@5c337cac, test:1, 3, 76)(picard.fingerprint.HaplotypeProbabilitiesTest) Running Test: Test method testHaplotypeProbabilitiesFromContaminatorSequenceAddToProbs[4](picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@3be6fc68, test:1, 7, 76)(picard.fingerprint.HaplotypeProbabilitiesTest) Running Test: Test method testHaplotypeProbabilitiesFromContaminatorSequenceAddToProbs[5](picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@84441f, test:1, 35, 76)(picard.fingerprint.HaplotypeProbabilitiesTest) Running Test: Test method testHaplotypeProbabilitiesFromContaminatorSequenceAddToProbs[6](picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@5857564d, test:1, 40, 76)(picard.fingerprint.HaplotypeProbabilitiesTest) Running Test: Test method testHaplotypeProbabilitiesFromContaminatorSequenceAddToProbs[7](picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@111d9ab4, test:1, 45, 76)(picard.fingerprint.HaplotypeProbabilitiesTest) Running Test: Test method testHaplotypeProbabilitiesFromContaminatorSequenceAddToProbs[8](picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@504fd64a, test:1, 69, 76)(picard.fingerprint.HaplotypeProbabilitiesTest) Running Test: Test method testHaplotypeProbabilitiesFromContaminatorSequenceAddToProbs[9](picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@42ada57e, test:1, 73, 76)(picard.fingerprint.HaplotypeProbabilitiesTest) Running Test: Test method testHaplotypeProbabilitiesFromContaminatorSequenceAddToProbs[10](picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence@1e9f4805, test:1, 76, 76)(picard.fingerprint.HaplotypeProbabilitiesTest) Running Test: Test method testHaplotypeProbabilitiesFromSequenceAddToProbs[0](picard.fingerprint.HaplotypeProbabilitiesFromSequence@4cd354c9, test:1, [B@1de09a36, 7)(picard.fingerprint.HaplotypeProbabilitiesTest) Running Test: Test method testHaplotypeProbabilitiesFromSequenceAddToProbs[1](picard.fingerprint.HaplotypeProbabilitiesFromSequence@4eca7cba, test:1, [B@18e90cb6, 7)(picard.fingerprint.HaplotypeProbabilitiesTest) Running Test: Test method testHaplotypeProbabilitiesFromSequenceAddToProbs[2](picard.fingerprint.HaplotypeProbabilitiesFromSequence@218da63e, test:1, [B@3c3f2119, 7)(picard.fingerprint.HaplotypeProbabilitiesTest) Running Test: Test method testHaplotypeProbabilitiesFromSequenceAddToProbs[3](picard.fingerprint.HaplotypeProbabilitiesFromSequence@650ed313, test:1, [B@29fe35da, 7)(picard.fingerprint.HaplotypeProbabilitiesTest) Running Test: Test method testHaplotypeProbabilitiesFromSequenceAddToProbs[4](picard.fingerprint.HaplotypeProbabilitiesFromSequence@18af12b6, test:1, [B@b2accfb, 7)(picard.fingerprint.HaplotypeProbabilitiesTest) Running Test: Test method testHaplotypeProbabilitiesFromSequenceAddToProbs[5](picard.fingerprint.HaplotypeProbabilitiesFromSequence@5855d886, test:1, [B@380f5b98, 7)(picard.fingerprint.HaplotypeProbabilitiesTest) Running Test: Test method testHaplotypeProbabilitiesFromSequenceAddToProbs[6](picard.fingerprint.HaplotypeProbabilitiesFromSequence@25b81e04, test:1, [B@535f63dd, 7)(picard.fingerprint.HaplotypeProbabilitiesTest) Running Test: Test method testHaplotypeProbabilitiesFromSequenceAddToProbs[7](picard.fingerprint.HaplotypeProbabilitiesFromSequence@ce7224f, test:1, [B@694a45e9, 7)(picard.fingerprint.HaplotypeProbabilitiesTest) Running Test: Test method testSymmetricLOD[0]([D@2100509e, [D@1440fbab)(picard.fingerprint.HaplotypeProbabilitiesTest) Running Test: Test method testSymmetricLOD[1]([D@72741180, [D@51d33bf0)(picard.fingerprint.HaplotypeProbabilitiesTest) Running Test: Test method testSymmetricLOD[2]([D@1996bee7, [D@4bbc4444)(picard.fingerprint.HaplotypeProbabilitiesTest) Running Test: Test method testpEvidenceGivenPriorFromGLs[0](picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods@29f156ca, [test:1], [false], [[D@5bca495])(picard.fingerprint.HaplotypeProbabilitiesTest) Running Test: Test method testpEvidenceGivenPriorFromGLs[1](picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods@6864dad1, [test:2], [true], [[D@4b009611])(picard.fingerprint.HaplotypeProbabilitiesTest) Running Test: Test method testpEvidenceGivenPriorFromGLs[2](picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods@5d75abcb, [test:1, test:2], [false, false], [[D@138940e6, [D@5c76ec98])(picard.fingerprint.HaplotypeProbabilitiesTest) Running Test: Test method testpEvidenceGivenPriorFromGLs[3](picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods@47e1c56a, [test:2, test:1], [false, false], [[D@1e363300, [D@75cf0e72])(picard.fingerprint.HaplotypeProbabilitiesTest) Running Test: Test method testpEvidenceGivenPriorFromGLs[4](picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods@5b4c997b, [test:1, test:2], [false, false], [[D@744d1f21, [D@797c3344])(picard.fingerprint.HaplotypeProbabilitiesTest) Running Test: Test method testGetLikelihoods[0](0.0, [D@36690b61, [D@2e97e8fb)(picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumorTest) Running Test: Test method testGetLikelihoods[1](0.0, [D@57f2034f, [D@293e28d3)(picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumorTest) Running Test: Test method testGetLikelihoods[2](0.0, [D@2f180b1b, [D@68b78dcc)(picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumorTest) Running Test: Test method testGetLikelihoods[3](0.0, [D@7647fdb1, [D@196870b1)(picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumorTest) Running Test: Test method testGetLikelihoods[4](0.0, [D@47bd0c28, [D@ededb1b)(picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumorTest) Running Test: Test method testGetLikelihoods[5](0.1, [D@33563216, [D@1c25b418)(picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumorTest) Running Test: Test method testGetLikelihoods[6](0.1, [D@7e543c11, [D@7c90774f)(picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumorTest) Running Test: Test method testGetLikelihoods[7](0.1, [D@7452dd03, [D@2b39c32c)(picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumorTest) Running Test: Test method testGetLikelihoods[8](0.1, [D@3dec9126, [D@5f34f95d)(picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumorTest) Running Test: Test method testGetLikelihoods[9](0.1, [D@9b629da, [D@500afc6b)(picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumorTest) Running Test: Test method testGetLikelihoods[10](0.1, [D@19c525c2, [D@210537d9)(picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumorTest) Running Test: Test method testWriteIlluminaAdpcFile(picard.arrays.illumina.IlluminaAdpcFileWriterTest) Running Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 11:58:26 IlluminaBasecallsToFastq Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToFastqTest.testCbclConvert STANDARD_ERROR INFO 2024-07-02 11:58:26 IlluminaBasecallsToFastq Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** IlluminaBasecallsToFastq -BASECALLS_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 151T8B8B151T -MULTIPLEX_PARAMS /tmp/dualBarcode.1146143084136861833.dir/barcode_double.params -MACHINE_NAME machine1 -FLOWCELL_BARCODE abcdeACXX -MAX_READS_IN_RAM_PER_TILE 100 ********** IlluminaBasecallsToFastq -BASECALLS_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 151T8B8B151T -MULTIPLEX_PARAMS /tmp/dualBarcode.1146143084136861833.dir/barcode_double.params -MACHINE_NAME machine1 -FLOWCELL_BARCODE abcdeACXX -MAX_READS_IN_RAM_PER_TILE 100 Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: WARNING 2024-07-02 11:58:26 IlluminaBasecallsToFastq ADAPTERS_TO_CHECK is not used WARNING 2024-07-02 11:58:26 IlluminaBasecallsToFastq ADAPTERS_TO_CHECK is not used Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 11:58:26.086 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:26.086 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 11:58:26.086 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:26.086 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 11:58:26.087 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:26.087 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 11:58:26.087 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:26.087 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: [Tue Jul 02 11:58:26 GMT+14:00 2024] IlluminaBasecallsToFastq BASECALLS_DIR=testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom MACHINE_NAME=machine1 FLOWCELL_BARCODE=abcdeACXX READ_STRUCTURE=151T8B8B151T MULTIPLEX_PARAMS=/tmp/dualBarcode.1146143084136861833.dir/barcode_double.params MAX_READS_IN_RAM_PER_TILE=100 NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false READ_NAME_FORMAT=CASAVA_1_8 COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:26 GMT+14:00 2024] IlluminaBasecallsToFastq BASECALLS_DIR=testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom MACHINE_NAME=machine1 FLOWCELL_BARCODE=abcdeACXX READ_STRUCTURE=151T8B8B151T MULTIPLEX_PARAMS=/tmp/dualBarcode.1146143084136861833.dir/barcode_double.params MAX_READS_IN_RAM_PER_TILE=100 NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false READ_NAME_FORMAT=CASAVA_1_8 COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: [Tue Jul 02 11:58:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 11:58:27 IlluminaBasecallsToFastq READ STRUCTURE IS 151T8B8B151T INFO 2024-07-02 11:58:27 IlluminaBasecallsToFastq READ STRUCTURE IS 151T8B8B151T Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 11:58:27 CbclReader Processing tile 1101 INFO 2024-07-02 11:58:27 CbclReader Processing tile 1101 Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 11:58:27 CbclReader Processing tile 1102 INFO 2024-07-02 11:58:27 CbclReader Processing tile 1102 Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 11:58:28 NewIlluminaBasecallsConverter Finished processing tile 1101 INFO 2024-07-02 11:58:28 NewIlluminaBasecallsConverter Finished processing tile 1101 Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 11:58:28 NewIlluminaBasecallsConverter Finished processing tile 1102 INFO 2024-07-02 11:58:28 NewIlluminaBasecallsConverter Finished processing tile 1102 Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 11:58:32 NewIlluminaBasecallsConverter Writing out tile 1101 INFO 2024-07-02 11:58:32 NewIlluminaBasecallsConverter Writing out tile 1101 Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 11:58:32 NewIlluminaBasecallsConverter Writing out tile 1102 INFO 2024-07-02 11:58:32 NewIlluminaBasecallsConverter Writing out tile 1102 Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: [Tue Jul 02 11:58:34 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.14 minutes. [Tue Jul 02 11:58:34 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.14 minutes. Test: Test method testCbclConvert(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testDeMultiplexed(picard.illumina.IlluminaBasecallsToFastqTest) Test: Test method testDeMultiplexed(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 11:58:35 IlluminaBasecallsToFastq Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToFastqTest.testDeMultiplexed STANDARD_ERROR INFO 2024-07-02 11:58:35 IlluminaBasecallsToFastq Test: Test method testDeMultiplexed(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Test: Test method testDeMultiplexed(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDeMultiplexed(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testDeMultiplexed(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDeMultiplexed(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDeMultiplexed(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testDeMultiplexed(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDeMultiplexed(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testDeMultiplexed(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** IlluminaBasecallsToFastq -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B25T -MULTIPLEX_PARAMS /tmp/multiplexedBarcode.10974897468276085794.dir/mp_barcode.params -MACHINE_NAME machine1 -FLOWCELL_BARCODE abcdeACXX -MAX_READS_IN_RAM_PER_TILE 100 ********** IlluminaBasecallsToFastq -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B25T -MULTIPLEX_PARAMS /tmp/multiplexedBarcode.10974897468276085794.dir/mp_barcode.params -MACHINE_NAME machine1 -FLOWCELL_BARCODE abcdeACXX -MAX_READS_IN_RAM_PER_TILE 100 Test: Test method testDeMultiplexed(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testDeMultiplexed(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Test: Test method testDeMultiplexed(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Test: Test method testDeMultiplexed(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: WARNING 2024-07-02 11:58:35 IlluminaBasecallsToFastq ADAPTERS_TO_CHECK is not used WARNING 2024-07-02 11:58:35 IlluminaBasecallsToFastq ADAPTERS_TO_CHECK is not used Test: Test method testDeMultiplexed(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 11:58:35.111 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:35.111 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDeMultiplexed(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 11:58:35.111 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:35.111 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDeMultiplexed(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 11:58:35.112 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:35.112 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDeMultiplexed(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 11:58:35.112 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:35.112 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDeMultiplexed(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: [Tue Jul 02 11:58:35 GMT+14:00 2024] IlluminaBasecallsToFastq BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom MACHINE_NAME=machine1 FLOWCELL_BARCODE=abcdeACXX READ_STRUCTURE=25T8B25T MULTIPLEX_PARAMS=/tmp/multiplexedBarcode.10974897468276085794.dir/mp_barcode.params MAX_READS_IN_RAM_PER_TILE=100 NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false READ_NAME_FORMAT=CASAVA_1_8 COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:35 GMT+14:00 2024] IlluminaBasecallsToFastq BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom MACHINE_NAME=machine1 FLOWCELL_BARCODE=abcdeACXX READ_STRUCTURE=25T8B25T MULTIPLEX_PARAMS=/tmp/multiplexedBarcode.10974897468276085794.dir/mp_barcode.params MAX_READS_IN_RAM_PER_TILE=100 NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false READ_NAME_FORMAT=CASAVA_1_8 COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDeMultiplexed(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: [Tue Jul 02 11:58:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDeMultiplexed(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 11:58:35 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B25T INFO 2024-07-02 11:58:35 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B25T Test: Test method testDeMultiplexed(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 11:58:58 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 11:58:58 IlluminaBasecallsConverter All work is complete. Test: Test method testDeMultiplexed(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 11:58:58 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 11:58:58 IlluminaBasecallsConverter All work is complete. Test: Test method testDeMultiplexed(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: [Tue Jul 02 11:58:58 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.38 minutes. [Tue Jul 02 11:58:58 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.38 minutes. Test: Test method testDeMultiplexed(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Gradle is still running, please be patient... Running Test: Test method testDeMultiplexedWithIndex(picard.illumina.IlluminaBasecallsToFastqTest) Test: Test method testDeMultiplexedWithIndex(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 11:58:59 IlluminaBasecallsToFastq Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToFastqTest.testDeMultiplexedWithIndex STANDARD_ERROR INFO 2024-07-02 11:58:59 IlluminaBasecallsToFastq Test: Test method testDeMultiplexedWithIndex(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Test: Test method testDeMultiplexedWithIndex(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDeMultiplexedWithIndex(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testDeMultiplexedWithIndex(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDeMultiplexedWithIndex(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDeMultiplexedWithIndex(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testDeMultiplexedWithIndex(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDeMultiplexedWithIndex(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testDeMultiplexedWithIndex(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** IlluminaBasecallsToFastq -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B4M21T -MULTIPLEX_PARAMS /tmp/multiplexedBarcodeWithIndex.7259427861822602442.dir/mp_barcode.params -MACHINE_NAME machine1 -FLOWCELL_BARCODE abcdeACXX -MAX_READS_IN_RAM_PER_TILE 100 ********** IlluminaBasecallsToFastq -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B4M21T -MULTIPLEX_PARAMS /tmp/multiplexedBarcodeWithIndex.7259427861822602442.dir/mp_barcode.params -MACHINE_NAME machine1 -FLOWCELL_BARCODE abcdeACXX -MAX_READS_IN_RAM_PER_TILE 100 Test: Test method testDeMultiplexedWithIndex(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testDeMultiplexedWithIndex(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Test: Test method testDeMultiplexedWithIndex(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Test: Test method testDeMultiplexedWithIndex(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: WARNING 2024-07-02 11:58:59 IlluminaBasecallsToFastq ADAPTERS_TO_CHECK is not used WARNING 2024-07-02 11:58:59 IlluminaBasecallsToFastq ADAPTERS_TO_CHECK is not used Test: Test method testDeMultiplexedWithIndex(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 11:58:59.844 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:59.844 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDeMultiplexedWithIndex(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 11:58:59.844 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:59.844 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDeMultiplexedWithIndex(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 11:58:59.853 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:58:59.853 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDeMultiplexedWithIndex(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 11:58:59.853 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:58:59.853 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDeMultiplexedWithIndex(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: [Tue Jul 02 11:58:59 GMT+14:00 2024] IlluminaBasecallsToFastq BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom MACHINE_NAME=machine1 FLOWCELL_BARCODE=abcdeACXX READ_STRUCTURE=25T8B4M21T MULTIPLEX_PARAMS=/tmp/multiplexedBarcodeWithIndex.7259427861822602442.dir/mp_barcode.params MAX_READS_IN_RAM_PER_TILE=100 NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false READ_NAME_FORMAT=CASAVA_1_8 COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:58:59 GMT+14:00 2024] IlluminaBasecallsToFastq BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom MACHINE_NAME=machine1 FLOWCELL_BARCODE=abcdeACXX READ_STRUCTURE=25T8B4M21T MULTIPLEX_PARAMS=/tmp/multiplexedBarcodeWithIndex.7259427861822602442.dir/mp_barcode.params MAX_READS_IN_RAM_PER_TILE=100 NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false READ_NAME_FORMAT=CASAVA_1_8 COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDeMultiplexedWithIndex(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: [Tue Jul 02 11:58:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:58:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDeMultiplexedWithIndex(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 11:59:00 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B4M21T INFO 2024-07-02 11:59:00 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B4M21T Test: Test method testDeMultiplexedWithIndex(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 11:59:23 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 11:59:23 IlluminaBasecallsConverter All work is complete. Test: Test method testDeMultiplexedWithIndex(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: [Tue Jul 02 11:59:23 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.40 minutes. [Tue Jul 02 11:59:23 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.40 minutes. Test: Test method testDeMultiplexedWithIndex(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testDeMultiplexedWithtwoIndexes(picard.illumina.IlluminaBasecallsToFastqTest) Test: Test method testDeMultiplexedWithtwoIndexes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 11:59:25 IlluminaBasecallsToFastq Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToFastqTest.testDeMultiplexedWithtwoIndexes STANDARD_ERROR INFO 2024-07-02 11:59:25 IlluminaBasecallsToFastq Test: Test method testDeMultiplexedWithtwoIndexes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Test: Test method testDeMultiplexedWithtwoIndexes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDeMultiplexedWithtwoIndexes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testDeMultiplexedWithtwoIndexes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDeMultiplexedWithtwoIndexes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDeMultiplexedWithtwoIndexes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testDeMultiplexedWithtwoIndexes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDeMultiplexedWithtwoIndexes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testDeMultiplexedWithtwoIndexes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** IlluminaBasecallsToFastq -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B4M4M17T -MULTIPLEX_PARAMS /tmp/multiplexedBarcodeWithTwoIndexes.9708670457442413004.dir/mp_barcode.params -MACHINE_NAME machine1 -FLOWCELL_BARCODE abcdeACXX -MAX_READS_IN_RAM_PER_TILE 100 ********** IlluminaBasecallsToFastq -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B4M4M17T -MULTIPLEX_PARAMS /tmp/multiplexedBarcodeWithTwoIndexes.9708670457442413004.dir/mp_barcode.params -MACHINE_NAME machine1 -FLOWCELL_BARCODE abcdeACXX -MAX_READS_IN_RAM_PER_TILE 100 Test: Test method testDeMultiplexedWithtwoIndexes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testDeMultiplexedWithtwoIndexes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Test: Test method testDeMultiplexedWithtwoIndexes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Test: Test method testDeMultiplexedWithtwoIndexes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: WARNING 2024-07-02 11:59:25 IlluminaBasecallsToFastq ADAPTERS_TO_CHECK is not used WARNING 2024-07-02 11:59:25 IlluminaBasecallsToFastq ADAPTERS_TO_CHECK is not used Test: Test method testDeMultiplexedWithtwoIndexes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 11:59:25.835 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:59:25.835 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDeMultiplexedWithtwoIndexes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 11:59:25.835 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:59:25.835 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDeMultiplexedWithtwoIndexes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 11:59:25.835 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:59:25.835 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDeMultiplexedWithtwoIndexes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 11:59:25.835 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:59:25.835 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDeMultiplexedWithtwoIndexes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: [Tue Jul 02 11:59:25 GMT+14:00 2024] IlluminaBasecallsToFastq BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom MACHINE_NAME=machine1 FLOWCELL_BARCODE=abcdeACXX READ_STRUCTURE=25T8B4M4M17T MULTIPLEX_PARAMS=/tmp/multiplexedBarcodeWithTwoIndexes.9708670457442413004.dir/mp_barcode.params MAX_READS_IN_RAM_PER_TILE=100 NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false READ_NAME_FORMAT=CASAVA_1_8 COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:59:25 GMT+14:00 2024] IlluminaBasecallsToFastq BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom MACHINE_NAME=machine1 FLOWCELL_BARCODE=abcdeACXX READ_STRUCTURE=25T8B4M4M17T MULTIPLEX_PARAMS=/tmp/multiplexedBarcodeWithTwoIndexes.9708670457442413004.dir/mp_barcode.params MAX_READS_IN_RAM_PER_TILE=100 NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false READ_NAME_FORMAT=CASAVA_1_8 COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDeMultiplexedWithtwoIndexes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: [Tue Jul 02 11:59:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:59:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDeMultiplexedWithtwoIndexes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 11:59:26 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B4M4M17T INFO 2024-07-02 11:59:26 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B4M4M17T Test: Test method testDeMultiplexedWithtwoIndexes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 11:59:49 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 11:59:49 IlluminaBasecallsConverter All work is complete. Test: Test method testDeMultiplexedWithtwoIndexes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: [Tue Jul 02 11:59:50 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.41 minutes. [Tue Jul 02 11:59:50 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.41 minutes. Test: Test method testDeMultiplexedWithtwoIndexes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testDualBarcodes(picard.illumina.IlluminaBasecallsToFastqTest) Test: Test method testDualBarcodes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 11:59:52 IlluminaBasecallsToFastq Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToFastqTest.testDualBarcodes STANDARD_ERROR INFO 2024-07-02 11:59:52 IlluminaBasecallsToFastq Test: Test method testDualBarcodes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Test: Test method testDualBarcodes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDualBarcodes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testDualBarcodes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDualBarcodes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDualBarcodes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testDualBarcodes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDualBarcodes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testDualBarcodes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** IlluminaBasecallsToFastq -BASECALLS_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B8B25T -MULTIPLEX_PARAMS /tmp/dualBarcode.7182743556260261727.dir/barcode_double.params -MACHINE_NAME machine1 -FLOWCELL_BARCODE abcdeACXX -MAX_READS_IN_RAM_PER_TILE 100 ********** IlluminaBasecallsToFastq -BASECALLS_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B8B25T -MULTIPLEX_PARAMS /tmp/dualBarcode.7182743556260261727.dir/barcode_double.params -MACHINE_NAME machine1 -FLOWCELL_BARCODE abcdeACXX -MAX_READS_IN_RAM_PER_TILE 100 Test: Test method testDualBarcodes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testDualBarcodes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Test: Test method testDualBarcodes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Test: Test method testDualBarcodes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: WARNING 2024-07-02 11:59:52 IlluminaBasecallsToFastq ADAPTERS_TO_CHECK is not used WARNING 2024-07-02 11:59:52 IlluminaBasecallsToFastq ADAPTERS_TO_CHECK is not used Test: Test method testDualBarcodes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 11:59:52.785 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:59:52.785 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDualBarcodes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 11:59:52.785 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:59:52.785 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDualBarcodes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 11:59:52.786 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:59:52.786 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDualBarcodes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 11:59:52.786 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:59:52.786 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDualBarcodes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: [Tue Jul 02 11:59:52 GMT+14:00 2024] IlluminaBasecallsToFastq BASECALLS_DIR=testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom MACHINE_NAME=machine1 FLOWCELL_BARCODE=abcdeACXX READ_STRUCTURE=25T8B8B25T MULTIPLEX_PARAMS=/tmp/dualBarcode.7182743556260261727.dir/barcode_double.params MAX_READS_IN_RAM_PER_TILE=100 NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false READ_NAME_FORMAT=CASAVA_1_8 COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:59:52 GMT+14:00 2024] IlluminaBasecallsToFastq BASECALLS_DIR=testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom MACHINE_NAME=machine1 FLOWCELL_BARCODE=abcdeACXX READ_STRUCTURE=25T8B8B25T MULTIPLEX_PARAMS=/tmp/dualBarcode.7182743556260261727.dir/barcode_double.params MAX_READS_IN_RAM_PER_TILE=100 NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false READ_NAME_FORMAT=CASAVA_1_8 COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDualBarcodes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: [Tue Jul 02 11:59:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:59:52 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDualBarcodes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 11:59:53 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B8B25T INFO 2024-07-02 11:59:53 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B8B25T Test: Test method testDualBarcodes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 11:59:57 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 11:59:57 IlluminaBasecallsConverter All work is complete. Test: Test method testDualBarcodes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: [Tue Jul 02 11:59:57 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.08 minutes. [Tue Jul 02 11:59:57 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.08 minutes. Test: Test method testDualBarcodes(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testHiseqxSingleLocs(picard.illumina.IlluminaBasecallsToFastqTest) Test: Test method testHiseqxSingleLocs(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 11:59:59 IlluminaBasecallsToFastq Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToFastqTest.testHiseqxSingleLocs STANDARD_ERROR INFO 2024-07-02 11:59:59 IlluminaBasecallsToFastq Test: Test method testHiseqxSingleLocs(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Test: Test method testHiseqxSingleLocs(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testHiseqxSingleLocs(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testHiseqxSingleLocs(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testHiseqxSingleLocs(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testHiseqxSingleLocs(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testHiseqxSingleLocs(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testHiseqxSingleLocs(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testHiseqxSingleLocs(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** IlluminaBasecallsToFastq -BASECALLS_DIR testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B8B25T -MULTIPLEX_PARAMS /tmp/hiseqxSingleLocs.15039040179737369476.dir/barcode_double.params -MACHINE_NAME machine1 -FLOWCELL_BARCODE abcdeACXX -MAX_READS_IN_RAM_PER_TILE 100 ********** IlluminaBasecallsToFastq -BASECALLS_DIR testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B8B25T -MULTIPLEX_PARAMS /tmp/hiseqxSingleLocs.15039040179737369476.dir/barcode_double.params -MACHINE_NAME machine1 -FLOWCELL_BARCODE abcdeACXX -MAX_READS_IN_RAM_PER_TILE 100 Test: Test method testHiseqxSingleLocs(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testHiseqxSingleLocs(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Test: Test method testHiseqxSingleLocs(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Test: Test method testHiseqxSingleLocs(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: WARNING 2024-07-02 11:59:59 IlluminaBasecallsToFastq ADAPTERS_TO_CHECK is not used WARNING 2024-07-02 11:59:59 IlluminaBasecallsToFastq ADAPTERS_TO_CHECK is not used Test: Test method testHiseqxSingleLocs(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 11:59:59.376 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:59:59.376 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testHiseqxSingleLocs(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 11:59:59.377 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:59:59.377 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testHiseqxSingleLocs(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 11:59:59.394 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 11:59:59.394 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testHiseqxSingleLocs(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 11:59:59.395 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 11:59:59.395 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testHiseqxSingleLocs(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: [Tue Jul 02 11:59:59 GMT+14:00 2024] IlluminaBasecallsToFastq BASECALLS_DIR=testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom MACHINE_NAME=machine1 FLOWCELL_BARCODE=abcdeACXX READ_STRUCTURE=25T8B8B25T MULTIPLEX_PARAMS=/tmp/hiseqxSingleLocs.15039040179737369476.dir/barcode_double.params MAX_READS_IN_RAM_PER_TILE=100 NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false READ_NAME_FORMAT=CASAVA_1_8 COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 11:59:59 GMT+14:00 2024] IlluminaBasecallsToFastq BASECALLS_DIR=testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom MACHINE_NAME=machine1 FLOWCELL_BARCODE=abcdeACXX READ_STRUCTURE=25T8B8B25T MULTIPLEX_PARAMS=/tmp/hiseqxSingleLocs.15039040179737369476.dir/barcode_double.params MAX_READS_IN_RAM_PER_TILE=100 NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false READ_NAME_FORMAT=CASAVA_1_8 COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testHiseqxSingleLocs(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: [Tue Jul 02 11:59:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 11:59:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testHiseqxSingleLocs(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 11:59:59 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B8B25T INFO 2024-07-02 11:59:59 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B8B25T Test: Test method testHiseqxSingleLocs(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 12:00:07 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:07 IlluminaBasecallsConverter All work is complete. Test: Test method testHiseqxSingleLocs(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: [Tue Jul 02 12:00:07 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.14 minutes. [Tue Jul 02 12:00:07 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.14 minutes. Test: Test method testHiseqxSingleLocs(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMultiplexWithIlluminaReadNameHeaders(picard.illumina.IlluminaBasecallsToFastqTest) Test: Test method testMultiplexWithIlluminaReadNameHeaders(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 12:00:09 IlluminaBasecallsToFastq Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToFastqTest.testMultiplexWithIlluminaReadNameHeaders STANDARD_ERROR INFO 2024-07-02 12:00:09 IlluminaBasecallsToFastq Test: Test method testMultiplexWithIlluminaReadNameHeaders(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Test: Test method testMultiplexWithIlluminaReadNameHeaders(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMultiplexWithIlluminaReadNameHeaders(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testMultiplexWithIlluminaReadNameHeaders(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMultiplexWithIlluminaReadNameHeaders(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMultiplexWithIlluminaReadNameHeaders(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testMultiplexWithIlluminaReadNameHeaders(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMultiplexWithIlluminaReadNameHeaders(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testMultiplexWithIlluminaReadNameHeaders(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** IlluminaBasecallsToFastq -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B25T -OUTPUT_PREFIX /tmp/testMultiplexRH.8467597762702085741.dir/testMultiplexRH -MACHINE_NAME machine1 -FLOWCELL_BARCODE abcdeACXX -READ_NAME_FORMAT ILLUMINA -MAX_READS_IN_RAM_PER_TILE 100 ********** IlluminaBasecallsToFastq -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B25T -OUTPUT_PREFIX /tmp/testMultiplexRH.8467597762702085741.dir/testMultiplexRH -MACHINE_NAME machine1 -FLOWCELL_BARCODE abcdeACXX -READ_NAME_FORMAT ILLUMINA -MAX_READS_IN_RAM_PER_TILE 100 Test: Test method testMultiplexWithIlluminaReadNameHeaders(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testMultiplexWithIlluminaReadNameHeaders(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Test: Test method testMultiplexWithIlluminaReadNameHeaders(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Test: Test method testMultiplexWithIlluminaReadNameHeaders(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: WARNING 2024-07-02 12:00:09 IlluminaBasecallsToFastq ADAPTERS_TO_CHECK is not used WARNING 2024-07-02 12:00:09 IlluminaBasecallsToFastq ADAPTERS_TO_CHECK is not used Test: Test method testMultiplexWithIlluminaReadNameHeaders(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 12:00:09.933 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:09.933 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultiplexWithIlluminaReadNameHeaders(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 12:00:09.933 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:09.933 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultiplexWithIlluminaReadNameHeaders(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 12:00:09.934 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:09.934 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultiplexWithIlluminaReadNameHeaders(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 12:00:09.934 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:09.934 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultiplexWithIlluminaReadNameHeaders(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: [Tue Jul 02 12:00:09 GMT+14:00 2024] IlluminaBasecallsToFastq BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 OUTPUT_PREFIX=/tmp/testMultiplexRH.8467597762702085741.dir/testMultiplexRH RUN_BARCODE=HiMom MACHINE_NAME=machine1 FLOWCELL_BARCODE=abcdeACXX READ_STRUCTURE=25T8B25T MAX_READS_IN_RAM_PER_TILE=100 READ_NAME_FORMAT=ILLUMINA NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:09 GMT+14:00 2024] IlluminaBasecallsToFastq BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 OUTPUT_PREFIX=/tmp/testMultiplexRH.8467597762702085741.dir/testMultiplexRH RUN_BARCODE=HiMom MACHINE_NAME=machine1 FLOWCELL_BARCODE=abcdeACXX READ_STRUCTURE=25T8B25T MAX_READS_IN_RAM_PER_TILE=100 READ_NAME_FORMAT=ILLUMINA NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMultiplexWithIlluminaReadNameHeaders(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: [Tue Jul 02 12:00:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMultiplexWithIlluminaReadNameHeaders(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 12:00:10 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B25T INFO 2024-07-02 12:00:10 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B25T Test: Test method testMultiplexWithIlluminaReadNameHeaders(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 12:00:11 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:11 IlluminaBasecallsConverter All work is complete. Test: Test method testMultiplexWithIlluminaReadNameHeaders(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: [Tue Jul 02 12:00:11 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.03 minutes. [Tue Jul 02 12:00:11 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.03 minutes. Test: Test method testMultiplexWithIlluminaReadNameHeaders(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testNonBarcoded(picard.illumina.IlluminaBasecallsToFastqTest) Test: Test method testNonBarcoded(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 12:00:11 IlluminaBasecallsToFastq Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToFastqTest.testNonBarcoded STANDARD_ERROR INFO 2024-07-02 12:00:11 IlluminaBasecallsToFastq Test: Test method testNonBarcoded(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Test: Test method testNonBarcoded(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testNonBarcoded(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testNonBarcoded(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testNonBarcoded(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testNonBarcoded(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testNonBarcoded(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testNonBarcoded(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testNonBarcoded(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** IlluminaBasecallsToFastq -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -READ_STRUCTURE 25T8B25T -OUTPUT_PREFIX /tmp/nonBarcoded.16740388006474134825 -RUN_BARCODE HiMom -MACHINE_NAME machine1 -FLOWCELL_BARCODE abcdeACXX -MAX_READS_IN_RAM_PER_TILE 100 ********** IlluminaBasecallsToFastq -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -READ_STRUCTURE 25T8B25T -OUTPUT_PREFIX /tmp/nonBarcoded.16740388006474134825 -RUN_BARCODE HiMom -MACHINE_NAME machine1 -FLOWCELL_BARCODE abcdeACXX -MAX_READS_IN_RAM_PER_TILE 100 Test: Test method testNonBarcoded(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: ********** ********** Test: Test method testNonBarcoded(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Test: Test method testNonBarcoded(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Test: Test method testNonBarcoded(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: WARNING 2024-07-02 12:00:11 IlluminaBasecallsToFastq ADAPTERS_TO_CHECK is not used WARNING 2024-07-02 12:00:11 IlluminaBasecallsToFastq ADAPTERS_TO_CHECK is not used Test: Test method testNonBarcoded(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 12:00:11.783 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:11.783 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNonBarcoded(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 12:00:11.783 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:11.783 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNonBarcoded(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 12:00:11.783 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:11.783 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNonBarcoded(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: 12:00:11.783 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:11.783 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNonBarcoded(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: [Tue Jul 02 12:00:11 GMT+14:00 2024] IlluminaBasecallsToFastq BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 OUTPUT_PREFIX=/tmp/nonBarcoded.16740388006474134825 RUN_BARCODE=HiMom MACHINE_NAME=machine1 FLOWCELL_BARCODE=abcdeACXX READ_STRUCTURE=25T8B25T MAX_READS_IN_RAM_PER_TILE=100 NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false READ_NAME_FORMAT=CASAVA_1_8 COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:11 GMT+14:00 2024] IlluminaBasecallsToFastq BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 OUTPUT_PREFIX=/tmp/nonBarcoded.16740388006474134825 RUN_BARCODE=HiMom MACHINE_NAME=machine1 FLOWCELL_BARCODE=abcdeACXX READ_STRUCTURE=25T8B25T MAX_READS_IN_RAM_PER_TILE=100 NUM_PROCESSORS=0 APPLY_EAMSS_FILTER=true FORCE_GC=true MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false READ_NAME_FORMAT=CASAVA_1_8 COMPRESS_OUTPUTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testNonBarcoded(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: [Tue Jul 02 12:00:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:11 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testNonBarcoded(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 12:00:11 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B25T INFO 2024-07-02 12:00:11 IlluminaBasecallsToFastq READ STRUCTURE IS 25T8B25T Test: Test method testNonBarcoded(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: INFO 2024-07-02 12:00:13 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:13 IlluminaBasecallsConverter All work is complete. Test: Test method testNonBarcoded(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: [Tue Jul 02 12:00:13 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.03 minutes. [Tue Jul 02 12:00:13 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToFastq done. Elapsed time: 0.03 minutes. Test: Test method testNonBarcoded(picard.illumina.IlluminaBasecallsToFastqTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBasic[0](1, 125T125T, null, null, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) Test: Test method testBasic[0](1, 125T125T, null, null, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:13 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamAdapterClippingTest.testBasic[0](1, 125T125T, null, null, 32) STANDARD_ERROR INFO 2024-07-02 12:00:13 IlluminaBasecallsToSam Test: Test method testBasic[0](1, 125T125T, null, null, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[0](1, 125T125T, null, null, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBasic[0](1, 125T125T, null, null, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[0](1, 125T125T, null, null, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBasic[0](1, 125T125T, null, null, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBasic[0](1, 125T125T, null, null, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[0](1, 125T125T, null, null, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBasic[0](1, 125T125T, null, null, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[0](1, 125T125T, null, null, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE 305PJAAXX080716 -READ_STRUCTURE 125T125T -OUTPUT /tmp/.1.illuminaBasecallsToSam12358831181621966177.sam -SEQUENCING_CENTER BI -ALIAS myalias ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE 305PJAAXX080716 -READ_STRUCTURE 125T125T -OUTPUT /tmp/.1.illuminaBasecallsToSam12358831181621966177.sam -SEQUENCING_CENTER BI -ALIAS myalias Test: Test method testBasic[0](1, 125T125T, null, null, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[0](1, 125T125T, null, null, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[0](1, 125T125T, null, null, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[0](1, 125T125T, null, null, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:13.633 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:13.633 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBasic[0](1, 125T125T, null, null, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:13.633 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:13.633 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBasic[0](1, 125T125T, null, null, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:13.633 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:13.633 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBasic[0](1, 125T125T, null, null, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:13.633 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:13.633 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBasic[0](1, 125T125T, null, null, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:13 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/.1.illuminaBasecallsToSam12358831181621966177.sam RUN_BARCODE=305PJAAXX080716 SAMPLE_ALIAS=myalias SEQUENCING_CENTER=BI READ_STRUCTURE=125T125T PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:13 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/.1.illuminaBasecallsToSam12358831181621966177.sam RUN_BARCODE=305PJAAXX080716 SAMPLE_ALIAS=myalias SEQUENCING_CENTER=BI READ_STRUCTURE=125T125T PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBasic[0](1, 125T125T, null, null, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBasic[0](1, 125T125T, null, null, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:13 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T INFO 2024-07-02 12:00:13 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T Test: Test method testBasic[0](1, 125T125T, null, null, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:14 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:14 IlluminaBasecallsConverter All work is complete. Test: Test method testBasic[0](1, 125T125T, null, null, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:14 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.02 minutes. [Tue Jul 02 12:00:14 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.02 minutes. Test: Test method testBasic[0](1, 125T125T, null, null, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBasic[1](2, 125T125T, null, null, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) Test: Test method testBasic[1](2, 125T125T, null, null, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:14 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamAdapterClippingTest.testBasic[1](2, 125T125T, null, null, 108) STANDARD_ERROR INFO 2024-07-02 12:00:14 IlluminaBasecallsToSam Test: Test method testBasic[1](2, 125T125T, null, null, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[1](2, 125T125T, null, null, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBasic[1](2, 125T125T, null, null, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[1](2, 125T125T, null, null, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBasic[1](2, 125T125T, null, null, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBasic[1](2, 125T125T, null, null, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[1](2, 125T125T, null, null, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBasic[1](2, 125T125T, null, null, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[1](2, 125T125T, null, null, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls -LANE 2 -RUN_BARCODE 305PJAAXX080716 -READ_STRUCTURE 125T125T -OUTPUT /tmp/.2.illuminaBasecallsToSam10574444783845836823.sam -SEQUENCING_CENTER BI -ALIAS myalias ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls -LANE 2 -RUN_BARCODE 305PJAAXX080716 -READ_STRUCTURE 125T125T -OUTPUT /tmp/.2.illuminaBasecallsToSam10574444783845836823.sam -SEQUENCING_CENTER BI -ALIAS myalias Test: Test method testBasic[1](2, 125T125T, null, null, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[1](2, 125T125T, null, null, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[1](2, 125T125T, null, null, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[1](2, 125T125T, null, null, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:14.811 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:14.811 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBasic[1](2, 125T125T, null, null, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:14.811 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:14.811 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBasic[1](2, 125T125T, null, null, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:14.812 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:14.812 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBasic[1](2, 125T125T, null, null, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:14.812 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:14.812 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBasic[1](2, 125T125T, null, null, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:14 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls LANE=2 OUTPUT=/tmp/.2.illuminaBasecallsToSam10574444783845836823.sam RUN_BARCODE=305PJAAXX080716 SAMPLE_ALIAS=myalias SEQUENCING_CENTER=BI READ_STRUCTURE=125T125T PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:14 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls LANE=2 OUTPUT=/tmp/.2.illuminaBasecallsToSam10574444783845836823.sam RUN_BARCODE=305PJAAXX080716 SAMPLE_ALIAS=myalias SEQUENCING_CENTER=BI READ_STRUCTURE=125T125T PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBasic[1](2, 125T125T, null, null, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBasic[1](2, 125T125T, null, null, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:14 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T INFO 2024-07-02 12:00:14 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T Test: Test method testBasic[1](2, 125T125T, null, null, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:15 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:15 IlluminaBasecallsConverter All work is complete. Test: Test method testBasic[1](2, 125T125T, null, null, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:15 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 12:00:15 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. Test: Test method testBasic[1](2, 125T125T, null, null, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBasic[2](1, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) Test: Test method testBasic[2](1, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:15 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamAdapterClippingTest.testBasic[2](1, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0) STANDARD_ERROR INFO 2024-07-02 12:00:15 IlluminaBasecallsToSam Test: Test method testBasic[2](1, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[2](1, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBasic[2](1, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[2](1, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBasic[2](1, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBasic[2](1, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[2](1, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBasic[2](1, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[2](1, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE 305PJAAXX080716 -READ_STRUCTURE 125T125T -OUTPUT /tmp/.1.illuminaBasecallsToSam9517343728009776754.sam -SEQUENCING_CENTER BI -ALIAS myalias -ADAPTERS_TO_CHECK null -FIVE_PRIME_ADAPTER ACGTACGTACGTACGT -THREE_PRIME_ADAPTER ACGTACGTACGTACGT ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE 305PJAAXX080716 -READ_STRUCTURE 125T125T -OUTPUT /tmp/.1.illuminaBasecallsToSam9517343728009776754.sam -SEQUENCING_CENTER BI -ALIAS myalias -ADAPTERS_TO_CHECK null -FIVE_PRIME_ADAPTER ACGTACGTACGTACGT -THREE_PRIME_ADAPTER ACGTACGTACGTACGT Test: Test method testBasic[2](1, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[2](1, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[2](1, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[2](1, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:15.758 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:15.758 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBasic[2](1, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:15.758 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:15.758 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBasic[2](1, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:15.758 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:15.758 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBasic[2](1, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:15.758 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:15.758 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBasic[2](1, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:15 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/.1.illuminaBasecallsToSam9517343728009776754.sam RUN_BARCODE=305PJAAXX080716 SAMPLE_ALIAS=myalias SEQUENCING_CENTER=BI READ_STRUCTURE=125T125T ADAPTERS_TO_CHECK=[] FIVE_PRIME_ADAPTER=ACGTACGTACGTACGT THREE_PRIME_ADAPTER=ACGTACGTACGTACGT PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:15 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/.1.illuminaBasecallsToSam9517343728009776754.sam RUN_BARCODE=305PJAAXX080716 SAMPLE_ALIAS=myalias SEQUENCING_CENTER=BI READ_STRUCTURE=125T125T ADAPTERS_TO_CHECK=[] FIVE_PRIME_ADAPTER=ACGTACGTACGTACGT THREE_PRIME_ADAPTER=ACGTACGTACGTACGT PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBasic[2](1, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBasic[2](1, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:15 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T INFO 2024-07-02 12:00:15 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T Test: Test method testBasic[2](1, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:16 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:16 IlluminaBasecallsConverter All work is complete. Test: Test method testBasic[2](1, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:16 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 12:00:16 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. Test: Test method testBasic[2](1, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBasic[3](2, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) Test: Test method testBasic[3](2, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:16 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamAdapterClippingTest.testBasic[3](2, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0) STANDARD_ERROR INFO 2024-07-02 12:00:16 IlluminaBasecallsToSam Test: Test method testBasic[3](2, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[3](2, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBasic[3](2, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[3](2, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBasic[3](2, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBasic[3](2, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[3](2, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBasic[3](2, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[3](2, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls -LANE 2 -RUN_BARCODE 305PJAAXX080716 -READ_STRUCTURE 125T125T -OUTPUT /tmp/.2.illuminaBasecallsToSam16188844687278068638.sam -SEQUENCING_CENTER BI -ALIAS myalias -ADAPTERS_TO_CHECK null -FIVE_PRIME_ADAPTER ACGTACGTACGTACGT -THREE_PRIME_ADAPTER ACGTACGTACGTACGT ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls -LANE 2 -RUN_BARCODE 305PJAAXX080716 -READ_STRUCTURE 125T125T -OUTPUT /tmp/.2.illuminaBasecallsToSam16188844687278068638.sam -SEQUENCING_CENTER BI -ALIAS myalias -ADAPTERS_TO_CHECK null -FIVE_PRIME_ADAPTER ACGTACGTACGTACGT -THREE_PRIME_ADAPTER ACGTACGTACGTACGT Test: Test method testBasic[3](2, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[3](2, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[3](2, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[3](2, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:16.704 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:16.704 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBasic[3](2, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:16.704 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:16.704 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBasic[3](2, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:16.704 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:16.704 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBasic[3](2, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:16.704 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:16.704 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBasic[3](2, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:16 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls LANE=2 OUTPUT=/tmp/.2.illuminaBasecallsToSam16188844687278068638.sam RUN_BARCODE=305PJAAXX080716 SAMPLE_ALIAS=myalias SEQUENCING_CENTER=BI READ_STRUCTURE=125T125T ADAPTERS_TO_CHECK=[] FIVE_PRIME_ADAPTER=ACGTACGTACGTACGT THREE_PRIME_ADAPTER=ACGTACGTACGTACGT PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:16 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls LANE=2 OUTPUT=/tmp/.2.illuminaBasecallsToSam16188844687278068638.sam RUN_BARCODE=305PJAAXX080716 SAMPLE_ALIAS=myalias SEQUENCING_CENTER=BI READ_STRUCTURE=125T125T ADAPTERS_TO_CHECK=[] FIVE_PRIME_ADAPTER=ACGTACGTACGTACGT THREE_PRIME_ADAPTER=ACGTACGTACGTACGT PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBasic[3](2, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBasic[3](2, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:16 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T INFO 2024-07-02 12:00:16 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T Test: Test method testBasic[3](2, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:17 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:17 IlluminaBasecallsConverter All work is complete. Test: Test method testBasic[3](2, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:17 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 12:00:17 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. Test: Test method testBasic[3](2, 125T125T, ACGTACGTACGTACGT, ACGTACGTACGTACGT, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBasic[4](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) Test: Test method testBasic[4](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:17 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamAdapterClippingTest.testBasic[4](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0) STANDARD_ERROR INFO 2024-07-02 12:00:17 IlluminaBasecallsToSam Test: Test method testBasic[4](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[4](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBasic[4](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[4](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBasic[4](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBasic[4](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[4](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBasic[4](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[4](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE 305PJAAXX080716 -READ_STRUCTURE 125T125T -OUTPUT /tmp/.1.illuminaBasecallsToSam6914068161724838615.sam -SEQUENCING_CENTER BI -ALIAS myalias -ADAPTERS_TO_CHECK null -FIVE_PRIME_ADAPTER AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG -THREE_PRIME_ADAPTER CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE 305PJAAXX080716 -READ_STRUCTURE 125T125T -OUTPUT /tmp/.1.illuminaBasecallsToSam6914068161724838615.sam -SEQUENCING_CENTER BI -ALIAS myalias -ADAPTERS_TO_CHECK null -FIVE_PRIME_ADAPTER AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG -THREE_PRIME_ADAPTER CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG Test: Test method testBasic[4](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[4](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[4](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[4](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:17.405 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:17.405 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBasic[4](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:17.405 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:17.405 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBasic[4](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:17.405 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:17.405 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBasic[4](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:17.405 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:17.405 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBasic[4](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:17 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/.1.illuminaBasecallsToSam6914068161724838615.sam RUN_BARCODE=305PJAAXX080716 SAMPLE_ALIAS=myalias SEQUENCING_CENTER=BI READ_STRUCTURE=125T125T ADAPTERS_TO_CHECK=[] FIVE_PRIME_ADAPTER=AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG THREE_PRIME_ADAPTER=CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:17 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/.1.illuminaBasecallsToSam6914068161724838615.sam RUN_BARCODE=305PJAAXX080716 SAMPLE_ALIAS=myalias SEQUENCING_CENTER=BI READ_STRUCTURE=125T125T ADAPTERS_TO_CHECK=[] FIVE_PRIME_ADAPTER=AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG THREE_PRIME_ADAPTER=CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBasic[4](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBasic[4](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:17 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T INFO 2024-07-02 12:00:17 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T Test: Test method testBasic[4](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:18 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:18 IlluminaBasecallsConverter All work is complete. Test: Test method testBasic[4](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:18 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 12:00:18 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. Test: Test method testBasic[4](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBasic[5](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) Test: Test method testBasic[5](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:18 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamAdapterClippingTest.testBasic[5](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0) STANDARD_ERROR INFO 2024-07-02 12:00:18 IlluminaBasecallsToSam Test: Test method testBasic[5](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[5](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBasic[5](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[5](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBasic[5](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBasic[5](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[5](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBasic[5](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[5](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls -LANE 2 -RUN_BARCODE 305PJAAXX080716 -READ_STRUCTURE 125T125T -OUTPUT /tmp/.2.illuminaBasecallsToSam11703505990293782351.sam -SEQUENCING_CENTER BI -ALIAS myalias -ADAPTERS_TO_CHECK null -FIVE_PRIME_ADAPTER AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG -THREE_PRIME_ADAPTER CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls -LANE 2 -RUN_BARCODE 305PJAAXX080716 -READ_STRUCTURE 125T125T -OUTPUT /tmp/.2.illuminaBasecallsToSam11703505990293782351.sam -SEQUENCING_CENTER BI -ALIAS myalias -ADAPTERS_TO_CHECK null -FIVE_PRIME_ADAPTER AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG -THREE_PRIME_ADAPTER CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG Test: Test method testBasic[5](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[5](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[5](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[5](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:18.511 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:18.511 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBasic[5](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:18.511 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:18.511 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBasic[5](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:18.512 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:18.512 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBasic[5](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:18.512 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:18.512 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBasic[5](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:18 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls LANE=2 OUTPUT=/tmp/.2.illuminaBasecallsToSam11703505990293782351.sam RUN_BARCODE=305PJAAXX080716 SAMPLE_ALIAS=myalias SEQUENCING_CENTER=BI READ_STRUCTURE=125T125T ADAPTERS_TO_CHECK=[] FIVE_PRIME_ADAPTER=AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG THREE_PRIME_ADAPTER=CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:18 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls LANE=2 OUTPUT=/tmp/.2.illuminaBasecallsToSam11703505990293782351.sam RUN_BARCODE=305PJAAXX080716 SAMPLE_ALIAS=myalias SEQUENCING_CENTER=BI READ_STRUCTURE=125T125T ADAPTERS_TO_CHECK=[] FIVE_PRIME_ADAPTER=AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG THREE_PRIME_ADAPTER=CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBasic[5](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBasic[5](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:18 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T INFO 2024-07-02 12:00:18 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T Test: Test method testBasic[5](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:19 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:19 IlluminaBasecallsConverter All work is complete. Test: Test method testBasic[5](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:19 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.02 minutes. [Tue Jul 02 12:00:19 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.02 minutes. Test: Test method testBasic[5](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, CTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBasic[6](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) Test: Test method testBasic[6](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:19 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamAdapterClippingTest.testBasic[6](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0) STANDARD_ERROR INFO 2024-07-02 12:00:19 IlluminaBasecallsToSam Test: Test method testBasic[6](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[6](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBasic[6](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[6](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBasic[6](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBasic[6](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[6](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBasic[6](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[6](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE 305PJAAXX080716 -READ_STRUCTURE 125T125T -OUTPUT /tmp/.1.illuminaBasecallsToSam3659885863839531370.sam -SEQUENCING_CENTER BI -ALIAS myalias -ADAPTERS_TO_CHECK null -FIVE_PRIME_ADAPTER AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA -THREE_PRIME_ADAPTER AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE 305PJAAXX080716 -READ_STRUCTURE 125T125T -OUTPUT /tmp/.1.illuminaBasecallsToSam3659885863839531370.sam -SEQUENCING_CENTER BI -ALIAS myalias -ADAPTERS_TO_CHECK null -FIVE_PRIME_ADAPTER AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA -THREE_PRIME_ADAPTER AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG Test: Test method testBasic[6](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[6](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[6](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[6](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:19.691 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:19.691 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBasic[6](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:19.691 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:19.691 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBasic[6](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:19.691 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:19.691 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBasic[6](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:19.691 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:19.691 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBasic[6](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:19 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/.1.illuminaBasecallsToSam3659885863839531370.sam RUN_BARCODE=305PJAAXX080716 SAMPLE_ALIAS=myalias SEQUENCING_CENTER=BI READ_STRUCTURE=125T125T ADAPTERS_TO_CHECK=[] FIVE_PRIME_ADAPTER=AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA THREE_PRIME_ADAPTER=AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:19 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/.1.illuminaBasecallsToSam3659885863839531370.sam RUN_BARCODE=305PJAAXX080716 SAMPLE_ALIAS=myalias SEQUENCING_CENTER=BI READ_STRUCTURE=125T125T ADAPTERS_TO_CHECK=[] FIVE_PRIME_ADAPTER=AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA THREE_PRIME_ADAPTER=AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBasic[6](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBasic[6](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:19 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T INFO 2024-07-02 12:00:19 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T Test: Test method testBasic[6](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:20 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:20 IlluminaBasecallsConverter All work is complete. Test: Test method testBasic[6](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:20 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 12:00:20 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. Test: Test method testBasic[6](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBasic[7](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) Test: Test method testBasic[7](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:20 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamAdapterClippingTest.testBasic[7](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0) STANDARD_ERROR INFO 2024-07-02 12:00:20 IlluminaBasecallsToSam Test: Test method testBasic[7](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[7](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBasic[7](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[7](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBasic[7](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBasic[7](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[7](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBasic[7](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[7](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls -LANE 2 -RUN_BARCODE 305PJAAXX080716 -READ_STRUCTURE 125T125T -OUTPUT /tmp/.2.illuminaBasecallsToSam279704272264636735.sam -SEQUENCING_CENTER BI -ALIAS myalias -ADAPTERS_TO_CHECK null -FIVE_PRIME_ADAPTER AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA -THREE_PRIME_ADAPTER AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls -LANE 2 -RUN_BARCODE 305PJAAXX080716 -READ_STRUCTURE 125T125T -OUTPUT /tmp/.2.illuminaBasecallsToSam279704272264636735.sam -SEQUENCING_CENTER BI -ALIAS myalias -ADAPTERS_TO_CHECK null -FIVE_PRIME_ADAPTER AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA -THREE_PRIME_ADAPTER AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG Test: Test method testBasic[7](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[7](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[7](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[7](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:20.840 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:20.840 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBasic[7](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:20.840 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:20.840 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBasic[7](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:20.840 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:20.840 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBasic[7](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:20.840 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:20.840 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBasic[7](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:20 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls LANE=2 OUTPUT=/tmp/.2.illuminaBasecallsToSam279704272264636735.sam RUN_BARCODE=305PJAAXX080716 SAMPLE_ALIAS=myalias SEQUENCING_CENTER=BI READ_STRUCTURE=125T125T ADAPTERS_TO_CHECK=[] FIVE_PRIME_ADAPTER=AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA THREE_PRIME_ADAPTER=AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:20 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls LANE=2 OUTPUT=/tmp/.2.illuminaBasecallsToSam279704272264636735.sam RUN_BARCODE=305PJAAXX080716 SAMPLE_ALIAS=myalias SEQUENCING_CENTER=BI READ_STRUCTURE=125T125T ADAPTERS_TO_CHECK=[] FIVE_PRIME_ADAPTER=AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA THREE_PRIME_ADAPTER=AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBasic[7](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBasic[7](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:20 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T INFO 2024-07-02 12:00:20 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T Test: Test method testBasic[7](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:21 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:21 IlluminaBasecallsConverter All work is complete. Test: Test method testBasic[7](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:21 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 12:00:21 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. Test: Test method testBasic[7](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA, AGACCAAGTCTCTGCTACCGTANNNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 0)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBasic[8](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) Test: Test method testBasic[8](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:21 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamAdapterClippingTest.testBasic[8](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32) STANDARD_ERROR INFO 2024-07-02 12:00:21 IlluminaBasecallsToSam Test: Test method testBasic[8](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[8](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBasic[8](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[8](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBasic[8](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBasic[8](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[8](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBasic[8](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[8](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE 305PJAAXX080716 -READ_STRUCTURE 125T125T -OUTPUT /tmp/.1.illuminaBasecallsToSam11185623883772128325.sam -SEQUENCING_CENTER BI -ALIAS myalias -ADAPTERS_TO_CHECK null -FIVE_PRIME_ADAPTER AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT -THREE_PRIME_ADAPTER AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE 305PJAAXX080716 -READ_STRUCTURE 125T125T -OUTPUT /tmp/.1.illuminaBasecallsToSam11185623883772128325.sam -SEQUENCING_CENTER BI -ALIAS myalias -ADAPTERS_TO_CHECK null -FIVE_PRIME_ADAPTER AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT -THREE_PRIME_ADAPTER AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG Test: Test method testBasic[8](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[8](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[8](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[8](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:21.752 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:21.752 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBasic[8](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:21.752 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:21.752 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBasic[8](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:21.752 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:21.752 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBasic[8](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:21.752 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:21.752 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBasic[8](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:21 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/.1.illuminaBasecallsToSam11185623883772128325.sam RUN_BARCODE=305PJAAXX080716 SAMPLE_ALIAS=myalias SEQUENCING_CENTER=BI READ_STRUCTURE=125T125T ADAPTERS_TO_CHECK=[] FIVE_PRIME_ADAPTER=AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT THREE_PRIME_ADAPTER=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:21 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/.1.illuminaBasecallsToSam11185623883772128325.sam RUN_BARCODE=305PJAAXX080716 SAMPLE_ALIAS=myalias SEQUENCING_CENTER=BI READ_STRUCTURE=125T125T ADAPTERS_TO_CHECK=[] FIVE_PRIME_ADAPTER=AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT THREE_PRIME_ADAPTER=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBasic[8](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBasic[8](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:21 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T INFO 2024-07-02 12:00:21 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T Test: Test method testBasic[8](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:22 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:22 IlluminaBasecallsConverter All work is complete. Test: Test method testBasic[8](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:22 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 12:00:22 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. Test: Test method testBasic[8](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBasic[9](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) Test: Test method testBasic[9](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:22 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamAdapterClippingTest.testBasic[9](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108) STANDARD_ERROR INFO 2024-07-02 12:00:22 IlluminaBasecallsToSam Test: Test method testBasic[9](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[9](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBasic[9](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[9](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBasic[9](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBasic[9](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[9](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBasic[9](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[9](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls -LANE 2 -RUN_BARCODE 305PJAAXX080716 -READ_STRUCTURE 125T125T -OUTPUT /tmp/.2.illuminaBasecallsToSam15622166228947209721.sam -SEQUENCING_CENTER BI -ALIAS myalias -ADAPTERS_TO_CHECK null -FIVE_PRIME_ADAPTER AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT -THREE_PRIME_ADAPTER AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls -LANE 2 -RUN_BARCODE 305PJAAXX080716 -READ_STRUCTURE 125T125T -OUTPUT /tmp/.2.illuminaBasecallsToSam15622166228947209721.sam -SEQUENCING_CENTER BI -ALIAS myalias -ADAPTERS_TO_CHECK null -FIVE_PRIME_ADAPTER AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT -THREE_PRIME_ADAPTER AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG Test: Test method testBasic[9](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[9](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[9](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[9](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:22.594 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:22.594 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBasic[9](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:22.594 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:22.594 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBasic[9](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:22.594 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:22.594 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBasic[9](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:22.594 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:22.594 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBasic[9](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:22 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls LANE=2 OUTPUT=/tmp/.2.illuminaBasecallsToSam15622166228947209721.sam RUN_BARCODE=305PJAAXX080716 SAMPLE_ALIAS=myalias SEQUENCING_CENTER=BI READ_STRUCTURE=125T125T ADAPTERS_TO_CHECK=[] FIVE_PRIME_ADAPTER=AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT THREE_PRIME_ADAPTER=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:22 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls LANE=2 OUTPUT=/tmp/.2.illuminaBasecallsToSam15622166228947209721.sam RUN_BARCODE=305PJAAXX080716 SAMPLE_ALIAS=myalias SEQUENCING_CENTER=BI READ_STRUCTURE=125T125T ADAPTERS_TO_CHECK=[] FIVE_PRIME_ADAPTER=AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT THREE_PRIME_ADAPTER=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBasic[9](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBasic[9](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:22 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T INFO 2024-07-02 12:00:22 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T Test: Test method testBasic[9](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:23 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:23 IlluminaBasecallsConverter All work is complete. Test: Test method testBasic[9](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:23 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 12:00:23 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. Test: Test method testBasic[9](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBasic[10](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) Test: Test method testBasic[10](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:23 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamAdapterClippingTest.testBasic[10](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32) STANDARD_ERROR INFO 2024-07-02 12:00:23 IlluminaBasecallsToSam Test: Test method testBasic[10](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[10](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBasic[10](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[10](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBasic[10](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBasic[10](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[10](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBasic[10](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[10](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE 305PJAAXX080716 -READ_STRUCTURE 125T125T -OUTPUT /tmp/.1.illuminaBasecallsToSam3009077484111483218.sam -SEQUENCING_CENTER BI -ALIAS myalias -ADAPTERS_TO_CHECK null -FIVE_PRIME_ADAPTER AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT -THREE_PRIME_ADAPTER AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE 305PJAAXX080716 -READ_STRUCTURE 125T125T -OUTPUT /tmp/.1.illuminaBasecallsToSam3009077484111483218.sam -SEQUENCING_CENTER BI -ALIAS myalias -ADAPTERS_TO_CHECK null -FIVE_PRIME_ADAPTER AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT -THREE_PRIME_ADAPTER AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG Test: Test method testBasic[10](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[10](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[10](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[10](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:23.475 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:23.475 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBasic[10](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:23.475 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:23.475 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBasic[10](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:23.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:23.476 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBasic[10](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:23.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:23.476 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBasic[10](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:23 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/.1.illuminaBasecallsToSam3009077484111483218.sam RUN_BARCODE=305PJAAXX080716 SAMPLE_ALIAS=myalias SEQUENCING_CENTER=BI READ_STRUCTURE=125T125T ADAPTERS_TO_CHECK=[] FIVE_PRIME_ADAPTER=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT THREE_PRIME_ADAPTER=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:23 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/.1.illuminaBasecallsToSam3009077484111483218.sam RUN_BARCODE=305PJAAXX080716 SAMPLE_ALIAS=myalias SEQUENCING_CENTER=BI READ_STRUCTURE=125T125T ADAPTERS_TO_CHECK=[] FIVE_PRIME_ADAPTER=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT THREE_PRIME_ADAPTER=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBasic[10](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBasic[10](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:23 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T INFO 2024-07-02 12:00:23 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T Test: Test method testBasic[10](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:24 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:24 IlluminaBasecallsConverter All work is complete. Test: Test method testBasic[10](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:24 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 12:00:24 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. Test: Test method testBasic[10](1, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 32)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testBasic[11](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) Test: Test method testBasic[11](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:24 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamAdapterClippingTest.testBasic[11](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108) STANDARD_ERROR INFO 2024-07-02 12:00:24 IlluminaBasecallsToSam Test: Test method testBasic[11](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[11](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBasic[11](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[11](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBasic[11](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBasic[11](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[11](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBasic[11](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[11](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls -LANE 2 -RUN_BARCODE 305PJAAXX080716 -READ_STRUCTURE 125T125T -OUTPUT /tmp/.2.illuminaBasecallsToSam9741413606483993729.sam -SEQUENCING_CENTER BI -ALIAS myalias -ADAPTERS_TO_CHECK null -FIVE_PRIME_ADAPTER AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT -THREE_PRIME_ADAPTER AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls -LANE 2 -RUN_BARCODE 305PJAAXX080716 -READ_STRUCTURE 125T125T -OUTPUT /tmp/.2.illuminaBasecallsToSam9741413606483993729.sam -SEQUENCING_CENTER BI -ALIAS myalias -ADAPTERS_TO_CHECK null -FIVE_PRIME_ADAPTER AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT -THREE_PRIME_ADAPTER AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG Test: Test method testBasic[11](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: ********** ********** Test: Test method testBasic[11](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[11](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Test: Test method testBasic[11](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:24.306 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:24.306 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBasic[11](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:24.306 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:24.306 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBasic[11](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:24.306 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:24.306 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBasic[11](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: 12:00:24.306 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:24.306 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBasic[11](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:24 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls LANE=2 OUTPUT=/tmp/.2.illuminaBasecallsToSam9741413606483993729.sam RUN_BARCODE=305PJAAXX080716 SAMPLE_ALIAS=myalias SEQUENCING_CENTER=BI READ_STRUCTURE=125T125T ADAPTERS_TO_CHECK=[] FIVE_PRIME_ADAPTER=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT THREE_PRIME_ADAPTER=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:24 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/125T125T/Data/Intensities/BaseCalls LANE=2 OUTPUT=/tmp/.2.illuminaBasecallsToSam9741413606483993729.sam RUN_BARCODE=305PJAAXX080716 SAMPLE_ALIAS=myalias SEQUENCING_CENTER=BI READ_STRUCTURE=125T125T ADAPTERS_TO_CHECK=[] FIVE_PRIME_ADAPTER=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT THREE_PRIME_ADAPTER=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBasic[11](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBasic[11](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:24 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T INFO 2024-07-02 12:00:24 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 125T125T Test: Test method testBasic[11](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: INFO 2024-07-02 12:00:25 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:25 IlluminaBasecallsConverter All work is complete. Test: Test method testBasic[11](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: [Tue Jul 02 12:00:25 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 12:00:25 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. Test: Test method testBasic[11](2, 125T125T, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, 108)(picard.illumina.IlluminaBasecallsToSamAdapterClippingTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testCorruptDataReturnCode(picard.illumina.IlluminaBasecallsToSamTest) Running Test: Test method testMolecularBarcodes[0](25S8S25T, null, null, nonBarcoded.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) Test: Test method testMolecularBarcodes[0](25S8S25T, null, null, nonBarcoded.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:25 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testMolecularBarcodes[0](25S8S25T, null, null, nonBarcoded.sam, 0) STANDARD_ERROR INFO 2024-07-02 12:00:25 IlluminaBasecallsToSam Test: Test method testMolecularBarcodes[0](25S8S25T, null, null, nonBarcoded.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[0](25S8S25T, null, null, nonBarcoded.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMolecularBarcodes[0](25S8S25T, null, null, nonBarcoded.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[0](25S8S25T, null, null, nonBarcoded.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMolecularBarcodes[0](25S8S25T, null, null, nonBarcoded.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMolecularBarcodes[0](25S8S25T, null, null, nonBarcoded.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[0](25S8S25T, null, null, nonBarcoded.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMolecularBarcodes[0](25S8S25T, null, null, nonBarcoded.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[0](25S8S25T, null, null, nonBarcoded.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -READ_STRUCTURE 25S8S25T -OUTPUT /tmp/molecularBarcodeTest.17482159918037443017.sam -RUN_BARCODE HiMom -SAMPLE_ALIAS HiDad -SEQUENCING_CENTER BI -LIBRARY_NAME Hello, World ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -READ_STRUCTURE 25S8S25T -OUTPUT /tmp/molecularBarcodeTest.17482159918037443017.sam -RUN_BARCODE HiMom -SAMPLE_ALIAS HiDad -SEQUENCING_CENTER BI -LIBRARY_NAME Hello, World Test: Test method testMolecularBarcodes[0](25S8S25T, null, null, nonBarcoded.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[0](25S8S25T, null, null, nonBarcoded.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[0](25S8S25T, null, null, nonBarcoded.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[0](25S8S25T, null, null, nonBarcoded.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:25.247 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:25.247 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMolecularBarcodes[0](25S8S25T, null, null, nonBarcoded.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:25.247 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:25.247 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMolecularBarcodes[0](25S8S25T, null, null, nonBarcoded.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:25.248 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:25.248 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMolecularBarcodes[0](25S8S25T, null, null, nonBarcoded.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:25.248 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:25.248 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMolecularBarcodes[0](25S8S25T, null, null, nonBarcoded.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:25 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/molecularBarcodeTest.17482159918037443017.sam RUN_BARCODE=HiMom SAMPLE_ALIAS=HiDad LIBRARY_NAME=Hello, World SEQUENCING_CENTER=BI READ_STRUCTURE=25S8S25T PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:25 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/molecularBarcodeTest.17482159918037443017.sam RUN_BARCODE=HiMom SAMPLE_ALIAS=HiDad LIBRARY_NAME=Hello, World SEQUENCING_CENTER=BI READ_STRUCTURE=25S8S25T PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMolecularBarcodes[0](25S8S25T, null, null, nonBarcoded.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMolecularBarcodes[0](25S8S25T, null, null, nonBarcoded.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:25 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8S25T INFO 2024-07-02 12:00:25 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8S25T Test: Test method testMolecularBarcodes[0](25S8S25T, null, null, nonBarcoded.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:25 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:25 IlluminaBasecallsConverter All work is complete. Test: Test method testMolecularBarcodes[0](25S8S25T, null, null, nonBarcoded.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:25 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:00:25 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. Test: Test method testMolecularBarcodes[0](25S8S25T, null, null, nonBarcoded.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testMolecularBarcodes[0](25S8S25T, null, null, nonBarcoded.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testMolecularBarcodes[0](25S8S25T, null, null, nonBarcoded.sam, 0) STANDARD_OUT No errors found Running Test: Test method testMolecularBarcodes[1](25S8M25T, null, null, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) Test: Test method testMolecularBarcodes[1](25S8M25T, null, null, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:25 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testMolecularBarcodes[1](25S8M25T, null, null, nonBarcodedWithMolecularIndex8M.sam, 0) STANDARD_ERROR INFO 2024-07-02 12:00:25 IlluminaBasecallsToSam Test: Test method testMolecularBarcodes[1](25S8M25T, null, null, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[1](25S8M25T, null, null, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMolecularBarcodes[1](25S8M25T, null, null, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[1](25S8M25T, null, null, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMolecularBarcodes[1](25S8M25T, null, null, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMolecularBarcodes[1](25S8M25T, null, null, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[1](25S8M25T, null, null, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMolecularBarcodes[1](25S8M25T, null, null, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[1](25S8M25T, null, null, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -READ_STRUCTURE 25S8M25T -OUTPUT /tmp/molecularBarcodeTest.17830178716144662396.sam -RUN_BARCODE HiMom -SAMPLE_ALIAS HiDad -SEQUENCING_CENTER BI -LIBRARY_NAME Hello, World ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -READ_STRUCTURE 25S8M25T -OUTPUT /tmp/molecularBarcodeTest.17830178716144662396.sam -RUN_BARCODE HiMom -SAMPLE_ALIAS HiDad -SEQUENCING_CENTER BI -LIBRARY_NAME Hello, World Test: Test method testMolecularBarcodes[1](25S8M25T, null, null, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[1](25S8M25T, null, null, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[1](25S8M25T, null, null, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[1](25S8M25T, null, null, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:25.486 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:25.486 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMolecularBarcodes[1](25S8M25T, null, null, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:25.486 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:25.486 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMolecularBarcodes[1](25S8M25T, null, null, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:25.487 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:25.487 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMolecularBarcodes[1](25S8M25T, null, null, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:25.487 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:25.487 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMolecularBarcodes[1](25S8M25T, null, null, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:25 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/molecularBarcodeTest.17830178716144662396.sam RUN_BARCODE=HiMom SAMPLE_ALIAS=HiDad LIBRARY_NAME=Hello, World SEQUENCING_CENTER=BI READ_STRUCTURE=25S8M25T PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:25 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/molecularBarcodeTest.17830178716144662396.sam RUN_BARCODE=HiMom SAMPLE_ALIAS=HiDad LIBRARY_NAME=Hello, World SEQUENCING_CENTER=BI READ_STRUCTURE=25S8M25T PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMolecularBarcodes[1](25S8M25T, null, null, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMolecularBarcodes[1](25S8M25T, null, null, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:25 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8M25T INFO 2024-07-02 12:00:25 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8M25T Test: Test method testMolecularBarcodes[1](25S8M25T, null, null, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:25 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:25 IlluminaBasecallsConverter All work is complete. Test: Test method testMolecularBarcodes[1](25S8M25T, null, null, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:25 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:00:25 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. Test: Test method testMolecularBarcodes[1](25S8M25T, null, null, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testMolecularBarcodes[1](25S8M25T, null, null, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testMolecularBarcodes[1](25S8M25T, null, null, nonBarcodedWithMolecularIndex8M.sam, 0) STANDARD_OUT No errors found Running Test: Test method testMolecularBarcodes[2](25S8M25T, null, [Ljava.lang.String;@c68fc03, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) Test: Test method testMolecularBarcodes[2](25S8M25T, null, [Ljava.lang.String;@c68fc03, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:25 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testMolecularBarcodes[2](25S8M25T, null, [Ljava.lang.String;@c68fc03, nonBarcodedWithMolecularIndex8M.sam, 0) STANDARD_ERROR INFO 2024-07-02 12:00:25 IlluminaBasecallsToSam Test: Test method testMolecularBarcodes[2](25S8M25T, null, [Ljava.lang.String;@c68fc03, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[2](25S8M25T, null, [Ljava.lang.String;@c68fc03, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMolecularBarcodes[2](25S8M25T, null, [Ljava.lang.String;@c68fc03, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[2](25S8M25T, null, [Ljava.lang.String;@c68fc03, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMolecularBarcodes[2](25S8M25T, null, [Ljava.lang.String;@c68fc03, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMolecularBarcodes[2](25S8M25T, null, [Ljava.lang.String;@c68fc03, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[2](25S8M25T, null, [Ljava.lang.String;@c68fc03, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMolecularBarcodes[2](25S8M25T, null, [Ljava.lang.String;@c68fc03, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[2](25S8M25T, null, [Ljava.lang.String;@c68fc03, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -READ_STRUCTURE 25S8M25T -OUTPUT /tmp/molecularBarcodeTest.3277376117899835711.sam -RUN_BARCODE HiMom -SAMPLE_ALIAS HiDad -SEQUENCING_CENTER BI -LIBRARY_NAME Hello, World -TAG_PER_MOLECULAR_INDEX null ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -READ_STRUCTURE 25S8M25T -OUTPUT /tmp/molecularBarcodeTest.3277376117899835711.sam -RUN_BARCODE HiMom -SAMPLE_ALIAS HiDad -SEQUENCING_CENTER BI -LIBRARY_NAME Hello, World -TAG_PER_MOLECULAR_INDEX null Test: Test method testMolecularBarcodes[2](25S8M25T, null, [Ljava.lang.String;@c68fc03, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[2](25S8M25T, null, [Ljava.lang.String;@c68fc03, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[2](25S8M25T, null, [Ljava.lang.String;@c68fc03, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[2](25S8M25T, null, [Ljava.lang.String;@c68fc03, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:25.735 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:25.735 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMolecularBarcodes[2](25S8M25T, null, [Ljava.lang.String;@c68fc03, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:25.735 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:25.735 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMolecularBarcodes[2](25S8M25T, null, [Ljava.lang.String;@c68fc03, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:25.735 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:25.735 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMolecularBarcodes[2](25S8M25T, null, [Ljava.lang.String;@c68fc03, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:25.735 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:25.735 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMolecularBarcodes[2](25S8M25T, null, [Ljava.lang.String;@c68fc03, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:25 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/molecularBarcodeTest.3277376117899835711.sam RUN_BARCODE=HiMom SAMPLE_ALIAS=HiDad LIBRARY_NAME=Hello, World SEQUENCING_CENTER=BI READ_STRUCTURE=25S8M25T TAG_PER_MOLECULAR_INDEX=[] PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:25 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/molecularBarcodeTest.3277376117899835711.sam RUN_BARCODE=HiMom SAMPLE_ALIAS=HiDad LIBRARY_NAME=Hello, World SEQUENCING_CENTER=BI READ_STRUCTURE=25S8M25T TAG_PER_MOLECULAR_INDEX=[] PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMolecularBarcodes[2](25S8M25T, null, [Ljava.lang.String;@c68fc03, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMolecularBarcodes[2](25S8M25T, null, [Ljava.lang.String;@c68fc03, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:25 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8M25T INFO 2024-07-02 12:00:25 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8M25T Test: Test method testMolecularBarcodes[2](25S8M25T, null, [Ljava.lang.String;@c68fc03, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:25 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:25 IlluminaBasecallsConverter All work is complete. Test: Test method testMolecularBarcodes[2](25S8M25T, null, [Ljava.lang.String;@c68fc03, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:25 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:25 IlluminaBasecallsConverter All work is complete. Test: Test method testMolecularBarcodes[2](25S8M25T, null, [Ljava.lang.String;@c68fc03, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:25 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:00:25 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. Test: Test method testMolecularBarcodes[2](25S8M25T, null, [Ljava.lang.String;@c68fc03, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testMolecularBarcodes[2](25S8M25T, null, [Ljava.lang.String;@c68fc03, nonBarcodedWithMolecularIndex8M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testMolecularBarcodes[2](25S8M25T, null, [Ljava.lang.String;@c68fc03, nonBarcodedWithMolecularIndex8M.sam, 0) STANDARD_OUT No errors found Running Test: Test method testMolecularBarcodes[3](25S4M4M25T, null, null, nonBarcodedWithMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) Test: Test method testMolecularBarcodes[3](25S4M4M25T, null, null, nonBarcodedWithMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:25 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testMolecularBarcodes[3](25S4M4M25T, null, null, nonBarcodedWithMolecularIndex4M4M.sam, 0) STANDARD_ERROR INFO 2024-07-02 12:00:25 IlluminaBasecallsToSam Test: Test method testMolecularBarcodes[3](25S4M4M25T, null, null, nonBarcodedWithMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[3](25S4M4M25T, null, null, nonBarcodedWithMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMolecularBarcodes[3](25S4M4M25T, null, null, nonBarcodedWithMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[3](25S4M4M25T, null, null, nonBarcodedWithMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMolecularBarcodes[3](25S4M4M25T, null, null, nonBarcodedWithMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMolecularBarcodes[3](25S4M4M25T, null, null, nonBarcodedWithMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[3](25S4M4M25T, null, null, nonBarcodedWithMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMolecularBarcodes[3](25S4M4M25T, null, null, nonBarcodedWithMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[3](25S4M4M25T, null, null, nonBarcodedWithMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -READ_STRUCTURE 25S4M4M25T -OUTPUT /tmp/molecularBarcodeTest.2781434221548601850.sam -RUN_BARCODE HiMom -SAMPLE_ALIAS HiDad -SEQUENCING_CENTER BI -LIBRARY_NAME Hello, World ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -READ_STRUCTURE 25S4M4M25T -OUTPUT /tmp/molecularBarcodeTest.2781434221548601850.sam -RUN_BARCODE HiMom -SAMPLE_ALIAS HiDad -SEQUENCING_CENTER BI -LIBRARY_NAME Hello, World Test: Test method testMolecularBarcodes[3](25S4M4M25T, null, null, nonBarcodedWithMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[3](25S4M4M25T, null, null, nonBarcodedWithMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[3](25S4M4M25T, null, null, nonBarcodedWithMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[3](25S4M4M25T, null, null, nonBarcodedWithMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:25.959 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:25.959 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMolecularBarcodes[3](25S4M4M25T, null, null, nonBarcodedWithMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:25.960 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:25.960 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMolecularBarcodes[3](25S4M4M25T, null, null, nonBarcodedWithMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:25.960 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:25.960 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMolecularBarcodes[3](25S4M4M25T, null, null, nonBarcodedWithMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:25.960 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:25.960 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMolecularBarcodes[3](25S4M4M25T, null, null, nonBarcodedWithMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:25 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/molecularBarcodeTest.2781434221548601850.sam RUN_BARCODE=HiMom SAMPLE_ALIAS=HiDad LIBRARY_NAME=Hello, World SEQUENCING_CENTER=BI READ_STRUCTURE=25S4M4M25T PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:25 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/molecularBarcodeTest.2781434221548601850.sam RUN_BARCODE=HiMom SAMPLE_ALIAS=HiDad LIBRARY_NAME=Hello, World SEQUENCING_CENTER=BI READ_STRUCTURE=25S4M4M25T PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMolecularBarcodes[3](25S4M4M25T, null, null, nonBarcodedWithMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMolecularBarcodes[3](25S4M4M25T, null, null, nonBarcodedWithMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:26 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S4M4M25T INFO 2024-07-02 12:00:26 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S4M4M25T Test: Test method testMolecularBarcodes[3](25S4M4M25T, null, null, nonBarcodedWithMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:26 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:26 IlluminaBasecallsConverter All work is complete. Test: Test method testMolecularBarcodes[3](25S4M4M25T, null, null, nonBarcodedWithMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:26 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:00:26 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. Test: Test method testMolecularBarcodes[3](25S4M4M25T, null, null, nonBarcodedWithMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testMolecularBarcodes[3](25S4M4M25T, null, null, nonBarcodedWithMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testMolecularBarcodes[3](25S4M4M25T, null, null, nonBarcodedWithMolecularIndex4M4M.sam, 0) STANDARD_OUT No errors found Running Test: Test method testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) Test: Test method testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:26 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0) STANDARD_ERROR INFO 2024-07-02 12:00:26 IlluminaBasecallsToSam Test: Test method testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -READ_STRUCTURE 25S4M4M25T -OUTPUT /tmp/molecularBarcodeTest.17285306577118294401.sam -RUN_BARCODE HiMom -SAMPLE_ALIAS HiDad -SEQUENCING_CENTER BI -LIBRARY_NAME Hello, World -TAG_PER_MOLECULAR_INDEX ZA -TAG_PER_MOLECULAR_INDEX ZB ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -READ_STRUCTURE 25S4M4M25T -OUTPUT /tmp/molecularBarcodeTest.17285306577118294401.sam -RUN_BARCODE HiMom -SAMPLE_ALIAS HiDad -SEQUENCING_CENTER BI -LIBRARY_NAME Hello, World -TAG_PER_MOLECULAR_INDEX ZA -TAG_PER_MOLECULAR_INDEX ZB Test: Test method testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:26.184 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:26.184 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:26.184 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:26.184 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:26.184 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:26.184 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:26.184 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:26.184 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:26 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/molecularBarcodeTest.17285306577118294401.sam RUN_BARCODE=HiMom SAMPLE_ALIAS=HiDad LIBRARY_NAME=Hello, World SEQUENCING_CENTER=BI READ_STRUCTURE=25S4M4M25T TAG_PER_MOLECULAR_INDEX=[ZA, ZB] PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:26 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/molecularBarcodeTest.17285306577118294401.sam RUN_BARCODE=HiMom SAMPLE_ALIAS=HiDad LIBRARY_NAME=Hello, World SEQUENCING_CENTER=BI READ_STRUCTURE=25S4M4M25T TAG_PER_MOLECULAR_INDEX=[ZA, ZB] PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:26 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S4M4M25T INFO 2024-07-02 12:00:26 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S4M4M25T Test: Test method testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:26 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:26 IlluminaBasecallsConverter All work is complete. Test: Test method testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:26 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:00:26 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. Test: Test method testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0) STANDARD_OUT No errors found Test: Test method testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:26 IlluminaBasecallsConverter All work is complete. Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0) STANDARD_ERROR INFO 2024-07-02 12:00:26 IlluminaBasecallsConverter All work is complete. Test: Test method testMolecularBarcodes[4](25S4M4M25T, [Ljava.lang.String;@5249a6ad, null, nonBarcodedWithTagPerMolecularIndex4M4M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:26 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:26 IlluminaBasecallsConverter All work is complete. Running Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:26 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1) STANDARD_ERROR INFO 2024-07-02 12:00:26 IlluminaBasecallsToSam Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -READ_STRUCTURE 25S4M4M25T -OUTPUT /tmp/molecularBarcodeTest.2149989958569558818.sam -RUN_BARCODE HiMom -SAMPLE_ALIAS HiDad -SEQUENCING_CENTER BI -LIBRARY_NAME Hello, World -TAG_PER_MOLECULAR_INDEX ZA -TAG_PER_MOLECULAR_INDEX ZB -TAG_PER_MOLECULAR_INDEX ZC ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -READ_STRUCTURE 25S4M4M25T -OUTPUT /tmp/molecularBarcodeTest.2149989958569558818.sam -RUN_BARCODE HiMom -SAMPLE_ALIAS HiDad -SEQUENCING_CENTER BI -LIBRARY_NAME Hello, World -TAG_PER_MOLECULAR_INDEX ZA -TAG_PER_MOLECULAR_INDEX ZB -TAG_PER_MOLECULAR_INDEX ZC Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:26.359 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 12:00:26.359 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: USAGE: IlluminaBasecallsToSam [options] USAGE: IlluminaBasecallsToSam [options] Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#IlluminaBasecallsToSam Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#IlluminaBasecallsToSam Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Transforms raw Illumina sequencing data into an unmapped SAM or BAM file. Transforms raw Illumina sequencing data into an unmapped SAM or BAM file. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: The IlluminaBaseCallsToSam program collects, demultiplexes, and sorts reads across all of the tiles of a lane via The IlluminaBaseCallsToSam program collects, demultiplexes, and sorts reads across all of the tiles of a lane via Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: barcode to produce an unmapped SAM/BAM file. An unmapped BAM file is often referred to as a uBAM. All barcode, sample, barcode to produce an unmapped SAM/BAM file. An unmapped BAM file is often referred to as a uBAM. All barcode, sample, Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: and library data is provided in the LIBRARY_PARAMS file. Note, this LIBRARY_PARAMS file should be formatted according and library data is provided in the LIBRARY_PARAMS file. Note, this LIBRARY_PARAMS file should be formatted according Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: to the specifications indicated below. The following is an example of a properly formatted LIBRARY_PARAMS file: to the specifications indicated below. The following is an example of a properly formatted LIBRARY_PARAMS file: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: BARCODE_1 OUTPUT SAMPLE_ALIAS LIBRARY_NAME BARCODE_1 OUTPUT SAMPLE_ALIAS LIBRARY_NAME Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: AAAAAAAA SA_AAAAAAAA.bam SA_AAAAAAAA LN_AAAAAAAA AAAAAAAA SA_AAAAAAAA.bam SA_AAAAAAAA LN_AAAAAAAA Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: AAAAGAAG SA_AAAAGAAG.bam SA_AAAAGAAG LN_AAAAGAAG AAAAGAAG SA_AAAAGAAG.bam SA_AAAAGAAG LN_AAAAGAAG Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: AACAATGG SA_AACAATGG.bam SA_AACAATGG LN_AACAATGG AACAATGG SA_AACAATGG.bam SA_AACAATGG LN_AACAATGG Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: N SA_non_indexed.bam SA_non_indexed LN_NNNNNNNN N SA_non_indexed.bam SA_non_indexed LN_NNNNNNNN Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: The BARCODES_DIR file is produced by the ExtractIlluminaBarcodes The BARCODES_DIR file is produced by the ExtractIlluminaBarcodes Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: (http://broadinstitute.github.io/picard/command-line-overview.html#ExtractIlluminaBarcodes) tool for each lane of a flow (http://broadinstitute.github.io/picard/command-line-overview.html#ExtractIlluminaBarcodes) tool for each lane of a flow Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: cell. cell. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Usage example: Usage example: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: java -jar picard.jar IlluminaBasecallsToSam \ java -jar picard.jar IlluminaBasecallsToSam \ Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: BASECALLS_DIR=/BaseCalls/ \ BASECALLS_DIR=/BaseCalls/ \ Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: LANE=001 \ LANE=001 \ Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: READ_STRUCTURE=25T8B25T \ READ_STRUCTURE=25T8B25T \ Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: RUN_BARCODE=run15 \ RUN_BARCODE=run15 \ Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: IGNORE_UNEXPECTED_BARCODES=true \ IGNORE_UNEXPECTED_BARCODES=true \ Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: LIBRARY_PARAMS=library.params LIBRARY_PARAMS=library.params Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Version: null Version: null Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Options: Options: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: --help --help Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: tools. tools. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: BASECALLS_DIR=File BASECALLS_DIR=File Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: B=File The basecalls directory. Required. B=File The basecalls directory. Required. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: BARCODES_DIR=File BARCODES_DIR=File Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: BCD=File The barcodes directory with _barcode.txt files (generated by ExtractIlluminaBarcodes). If BCD=File The barcodes directory with _barcode.txt files (generated by ExtractIlluminaBarcodes). If Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: not set, use BASECALLS_DIR. Default value: null. not set, use BASECALLS_DIR. Default value: null. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: LANE=Integer LANE=Integer Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: L=Integer Lane number. Required. L=Integer Lane number. Required. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: O=File Deprecated (use LIBRARY_PARAMS). The output SAM or BAM file. Format is determined by O=File Deprecated (use LIBRARY_PARAMS). The output SAM or BAM file. Format is determined by Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: extension. Required. Cannot be used in conjuction with option(s) LIBRARY_PARAMS extension. Required. Cannot be used in conjuction with option(s) LIBRARY_PARAMS Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: BARCODE_PARAMS BARCODE_PARAMS Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: RUN_BARCODE=String The barcode of the run. Prefixed to read names. Required. RUN_BARCODE=String The barcode of the run. Prefixed to read names. Required. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: SAMPLE_ALIAS=String SAMPLE_ALIAS=String Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ALIAS=String Deprecated (use LIBRARY_PARAMS). The name of the sequenced sample Required. Cannot be ALIAS=String Deprecated (use LIBRARY_PARAMS). The name of the sequenced sample Required. Cannot be Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: used in conjuction with option(s) LIBRARY_PARAMS BARCODE_PARAMS used in conjuction with option(s) LIBRARY_PARAMS BARCODE_PARAMS Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: READ_GROUP_ID=String READ_GROUP_ID=String Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: RG=String ID used to link RG header record with RG tag in SAM record. If these are unique in SAM RG=String ID used to link RG header record with RG tag in SAM record. If these are unique in SAM Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: files that get merged, merge performance is better. If not specified, READ_GROUP_ID will files that get merged, merge performance is better. If not specified, READ_GROUP_ID will Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: be set to . . Default value: null. be set to . . Default value: null. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: LIBRARY_NAME=String LIBRARY_NAME=String Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: LIB=String Deprecated (use LIBRARY_PARAMS). The name of the sequenced library Default value: null. LIB=String Deprecated (use LIBRARY_PARAMS). The name of the sequenced library Default value: null. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Cannot be used in conjuction with option(s) LIBRARY_PARAMS BARCODE_PARAMS Cannot be used in conjuction with option(s) LIBRARY_PARAMS BARCODE_PARAMS Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: SEQUENCING_CENTER=String The name of the sequencing center that produced the reads. Used to set the @RG->CN header SEQUENCING_CENTER=String The name of the sequencing center that produced the reads. Used to set the @RG->CN header Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: tag. Required. tag. Required. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: RUN_START_DATE=Date The start date of the run. Default value: null. RUN_START_DATE=Date The start date of the run. Default value: null. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: PLATFORM=String The name of the sequencing technology that produced the read. Default value: ILLUMINA. PLATFORM=String The name of the sequencing technology that produced the read. Default value: ILLUMINA. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INCLUDE_BC_IN_RG_TAG=Boolean Whether to include the barcode information in the @RG->BC header tag. Defaults to false INCLUDE_BC_IN_RG_TAG=Boolean Whether to include the barcode information in the @RG->BC header tag. Defaults to false Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: until included in the SAM spec. Default value: false. This option can be set to 'null' to until included in the SAM spec. Default value: false. This option can be set to 'null' to Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: clear the default value. Possible values: {true, false} clear the default value. Possible values: {true, false} Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: READ_STRUCTURE=String READ_STRUCTURE=String Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: RS=String A description of the logical structure of clusters in an Illumina Run, i.e. a description RS=String A description of the logical structure of clusters in an Illumina Run, i.e. a description Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: of the structure IlluminaBasecallsToSam assumes the data to be in. It should consist of of the structure IlluminaBasecallsToSam assumes the data to be in. It should consist of Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: integer/character pairs describing the number of cycles and the type of those cycles (B integer/character pairs describing the number of cycles and the type of those cycles (B Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: for Sample Barcode, M for molecular barcode, T for Template, and S for skip). E.g. If the for Sample Barcode, M for molecular barcode, T for Template, and S for skip). E.g. If the Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: input data consists of 80 base clusters and we provide a read structure of "28T8M8B8S28T" input data consists of 80 base clusters and we provide a read structure of "28T8M8B8S28T" Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: then the sequence may be split up into four reads: then the sequence may be split up into four reads: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: * read one with 28 cycles (bases) of template * read one with 28 cycles (bases) of template Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: * read two with 8 cycles (bases) of molecular barcode (ex. unique molecular barcode) * read two with 8 cycles (bases) of molecular barcode (ex. unique molecular barcode) Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: * read three with 8 cycles (bases) of sample barcode * read three with 8 cycles (bases) of sample barcode Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: * 8 cycles (bases) skipped. * 8 cycles (bases) skipped. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: * read four with 28 cycles (bases) of template * read four with 28 cycles (bases) of template Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: The skipped cycles would NOT be included in an output SAM/BAM file or in read groups The skipped cycles would NOT be included in an output SAM/BAM file or in read groups Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: therein. Required. therein. Required. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: BARCODE_PARAMS=File Deprecated (use LIBRARY_PARAMS). Tab-separated file for creating all output BAMs for BARCODE_PARAMS=File Deprecated (use LIBRARY_PARAMS). Tab-separated file for creating all output BAMs for Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: barcoded run with single IlluminaBasecallsToSam invocation. Columns are BARCODE, OUTPUT, barcoded run with single IlluminaBasecallsToSam invocation. Columns are BARCODE, OUTPUT, Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: SAMPLE_ALIAS, and LIBRARY_NAME. Row with BARCODE=N is used to specify a file for no SAMPLE_ALIAS, and LIBRARY_NAME. Row with BARCODE=N is used to specify a file for no Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: barcode match Required. Cannot be used in conjuction with option(s) LIBRARY_PARAMS barcode match Required. Cannot be used in conjuction with option(s) LIBRARY_PARAMS Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: SAMPLE_ALIAS (ALIAS) OUTPUT (O) LIBRARY_NAME (LIB) SAMPLE_ALIAS (ALIAS) OUTPUT (O) LIBRARY_NAME (LIB) Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: LIBRARY_PARAMS=File Tab-separated file for creating all output BAMs for a lane with single LIBRARY_PARAMS=File Tab-separated file for creating all output BAMs for a lane with single Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: IlluminaBasecallsToSam invocation. The columns are OUTPUT, SAMPLE_ALIAS, and IlluminaBasecallsToSam invocation. The columns are OUTPUT, SAMPLE_ALIAS, and Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: LIBRARY_NAME, BARCODE_1, BARCODE_2 ... BARCODE_X where X = number of barcodes per cluster LIBRARY_NAME, BARCODE_1, BARCODE_2 ... BARCODE_X where X = number of barcodes per cluster Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: (optional). Row with BARCODE_1 set to 'N' is used to specify a file for no barcode match. (optional). Row with BARCODE_1 set to 'N' is used to specify a file for no barcode match. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: You may also provide any 2 letter RG header attributes (excluding PU, CN, PL, and DT) as You may also provide any 2 letter RG header attributes (excluding PU, CN, PL, and DT) as Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: columns in this file and the values for those columns will be inserted into the RG tag for columns in this file and the values for those columns will be inserted into the RG tag for Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: the BAM file created for a given row. Required. Cannot be used in conjuction with the BAM file created for a given row. Required. Cannot be used in conjuction with Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: option(s) SAMPLE_ALIAS (ALIAS) OUTPUT (O) LIBRARY_NAME (LIB) BARCODE_PARAMS option(s) SAMPLE_ALIAS (ALIAS) OUTPUT (O) LIBRARY_NAME (LIB) BARCODE_PARAMS Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ADAPTERS_TO_CHECK=IlluminaAdapterPair ADAPTERS_TO_CHECK=IlluminaAdapterPair Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Which adapters to look for in the read. Default value: [INDEXED, DUAL_INDEXED, Which adapters to look for in the read. Default value: [INDEXED, DUAL_INDEXED, Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: NEXTERA_V2, FLUIDIGM]. This option can be set to 'null' to clear the default value. NEXTERA_V2, FLUIDIGM]. This option can be set to 'null' to clear the default value. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Possible values: {PAIRED_END, INDEXED, SINGLE_END, NEXTERA_V1, NEXTERA_V2, DUAL_INDEXED, Possible values: {PAIRED_END, INDEXED, SINGLE_END, NEXTERA_V1, NEXTERA_V2, DUAL_INDEXED, Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: FLUIDIGM, TRUSEQ_SMALLRNA, ALTERNATIVE_SINGLE_END} This option may be specified 0 or more FLUIDIGM, TRUSEQ_SMALLRNA, ALTERNATIVE_SINGLE_END} This option may be specified 0 or more Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: times. This option can be set to 'null' to clear the default list. times. This option can be set to 'null' to clear the default list. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: FIVE_PRIME_ADAPTER=String For specifying adapters other than standard Illumina Default value: null. FIVE_PRIME_ADAPTER=String For specifying adapters other than standard Illumina Default value: null. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: THREE_PRIME_ADAPTER=String For specifying adapters other than standard Illumina Default value: null. THREE_PRIME_ADAPTER=String For specifying adapters other than standard Illumina Default value: null. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: NUM_PROCESSORS=Integer The number of threads to run in parallel. If NUM_PROCESSORS = 0, number of cores is NUM_PROCESSORS=Integer The number of threads to run in parallel. If NUM_PROCESSORS = 0, number of cores is Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: automatically set to the number of cores available on the machine. If NUM_PROCESSORS < 0, automatically set to the number of cores available on the machine. If NUM_PROCESSORS < 0, Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: then the number of cores used will be the number available on the machine less then the number of cores used will be the number available on the machine less Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: NUM_PROCESSORS. Default value: 0. This option can be set to 'null' to clear the default NUM_PROCESSORS. Default value: 0. This option can be set to 'null' to clear the default Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: value. value. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: FIRST_TILE=Integer If set, this is the first tile to be processed (used for debugging). Note that tiles are FIRST_TILE=Integer If set, this is the first tile to be processed (used for debugging). Note that tiles are Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: not processed in numerical order. Default value: null. Cannot be used in conjuction with not processed in numerical order. Default value: null. Cannot be used in conjuction with Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: option(s) PROCESS_SINGLE_TILE option(s) PROCESS_SINGLE_TILE Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: TILE_LIMIT=Integer If set, process no more than this many tiles (used for debugging). Default value: null. TILE_LIMIT=Integer If set, process no more than this many tiles (used for debugging). Default value: null. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: PROCESS_SINGLE_TILE=Integer If set, process only the tile number given and prepend the tile number to the output file PROCESS_SINGLE_TILE=Integer If set, process only the tile number given and prepend the tile number to the output file Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: name. Default value: null. Cannot be used in conjuction with option(s) FIRST_TILE name. Default value: null. Cannot be used in conjuction with option(s) FIRST_TILE Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: FORCE_GC=Boolean If true, call System.gc() periodically. This is useful in cases in which the -Xmx value FORCE_GC=Boolean If true, call System.gc() periodically. This is useful in cases in which the -Xmx value Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: passed is larger than the available memory. Default value: true. This option can be set passed is larger than the available memory. Default value: true. This option can be set Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: to 'null' to clear the default value. Possible values: {true, false} to 'null' to clear the default value. Possible values: {true, false} Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: APPLY_EAMSS_FILTER=Boolean Apply EAMSS filtering to identify inappropriately quality scored bases towards the ends of APPLY_EAMSS_FILTER=Boolean Apply EAMSS filtering to identify inappropriately quality scored bases towards the ends of Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: reads and convert their quality scores to Q2. Default value: true. This option can be set reads and convert their quality scores to Q2. Default value: true. This option can be set Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: to 'null' to clear the default value. Possible values: {true, false} to 'null' to clear the default value. Possible values: {true, false} Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: MAX_READS_IN_RAM_PER_TILE=Integer MAX_READS_IN_RAM_PER_TILE=Integer Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Configure SortingCollections to store this many records before spilling to disk. For an Configure SortingCollections to store this many records before spilling to disk. For an Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: indexed run, each SortingCollection gets this value/number of indices. Default value: indexed run, each SortingCollection gets this value/number of indices. Default value: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 1200000. This option can be set to 'null' to clear the default value. 1200000. This option can be set to 'null' to clear the default value. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: MINIMUM_QUALITY=Integer The minimum quality (after transforming 0s to 1s) expected from reads. If qualities are MINIMUM_QUALITY=Integer The minimum quality (after transforming 0s to 1s) expected from reads. If qualities are Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: lower than this value, an error is thrown.The default of 2 is what the Illumina's spec lower than this value, an error is thrown.The default of 2 is what the Illumina's spec Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: describes as the minimum, but in practice the value has been observed lower. Default describes as the minimum, but in practice the value has been observed lower. Default Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: value: 2. This option can be set to 'null' to clear the default value. value: 2. This option can be set to 'null' to clear the default value. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INCLUDE_NON_PF_READS=Boolean INCLUDE_NON_PF_READS=Boolean Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: NONPF=Boolean Whether to include non-PF reads Default value: true. This option can be set to 'null' to NONPF=Boolean Whether to include non-PF reads Default value: true. This option can be set to 'null' to Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: clear the default value. Possible values: {true, false} clear the default value. Possible values: {true, false} Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: IGNORE_UNEXPECTED_BARCODES=Boolean IGNORE_UNEXPECTED_BARCODES=Boolean Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: IGNORE_UNEXPECTED=Boolean Whether to ignore reads whose barcodes are not found in LIBRARY_PARAMS. Useful when IGNORE_UNEXPECTED=Boolean Whether to ignore reads whose barcodes are not found in LIBRARY_PARAMS. Useful when Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: outputting BAMs for only a subset of the barcodes in a lane. Default value: false. This outputting BAMs for only a subset of the barcodes in a lane. Default value: false. This Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: option can be set to 'null' to clear the default value. Possible values: {true, false} option can be set to 'null' to clear the default value. Possible values: {true, false} Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: MOLECULAR_INDEX_TAG=String The tag to use to store any molecular indexes. If more than one molecular index is found, MOLECULAR_INDEX_TAG=String The tag to use to store any molecular indexes. If more than one molecular index is found, Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: they will be concatenated and stored here. Default value: RX. This option can be set to they will be concatenated and stored here. Default value: RX. This option can be set to Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 'null' to clear the default value. 'null' to clear the default value. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: MOLECULAR_INDEX_BASE_QUALITY_TAG=String MOLECULAR_INDEX_BASE_QUALITY_TAG=String Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: The tag to use to store any molecular index base qualities. If more than one molecular The tag to use to store any molecular index base qualities. If more than one molecular Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: index is found, their qualities will be concatenated and stored here (.i.e. the number of index is found, their qualities will be concatenated and stored here (.i.e. the number of Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: "M" operators in the READ_STRUCTURE) Default value: QX. This option can be set to 'null' "M" operators in the READ_STRUCTURE) Default value: QX. This option can be set to 'null' Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: to clear the default value. to clear the default value. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: TAG_PER_MOLECULAR_INDEX=StringThe list of tags to store each molecular index. The number of tags should match the TAG_PER_MOLECULAR_INDEX=StringThe list of tags to store each molecular index. The number of tags should match the Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: number of molecular indexes. Default value: null. This option may be specified 0 or more number of molecular indexes. Default value: null. This option may be specified 0 or more Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: times. times. Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: BARCODE_POPULATION_STRATEGY=PopulateBarcode BARCODE_POPULATION_STRATEGY=PopulateBarcode Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: When should the sample barcode (as read by the sequencer) be placed on the reads in the BC When should the sample barcode (as read by the sequencer) be placed on the reads in the BC Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: tag? Default value: ORPHANS_ONLY. This option can be set to 'null' to clear the default tag? Default value: ORPHANS_ONLY. This option can be set to 'null' to clear the default Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: value. Possible values: { value. Possible values: { Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ORPHANS_ONLY (Put barcodes only into the records that were not assigned to any declared ORPHANS_ONLY (Put barcodes only into the records that were not assigned to any declared Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: barcode.) barcode.) Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INEXACT_MATCH (Put barcodes into records for which an exact match with a declared barcode INEXACT_MATCH (Put barcodes into records for which an exact match with a declared barcode Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: was not found.) was not found.) Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ALWAYS (Put barcodes into all the records.) ALWAYS (Put barcodes into all the records.) Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: } } Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INCLUDE_BARCODE_QUALITY=Boolean INCLUDE_BARCODE_QUALITY=Boolean Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Should the barcode quality be included when the sample barcode is included? Default Should the barcode quality be included when the sample barcode is included? Default Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: value: false. This option can be set to 'null' to clear the default value. Possible value: false. This option can be set to 'null' to clear the default value. Possible Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: values: {true, false} values: {true, false} Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[5](25S4M4M25T, [Ljava.lang.String;@76009496, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: The number of tags given in TAG_PER_MOLECULAR_INDEX does not match the number of molecular indexes in READ_STRUCTURE The number of tags given in TAG_PER_MOLECULAR_INDEX does not match the number of molecular indexes in READ_STRUCTURE Running Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:26 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1) STANDARD_ERROR INFO 2024-07-02 12:00:26 IlluminaBasecallsToSam Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -READ_STRUCTURE 25S2M2M2M2M25T -OUTPUT /tmp/molecularBarcodeTest.6013140652498779431.sam -RUN_BARCODE HiMom -SAMPLE_ALIAS HiDad -SEQUENCING_CENTER BI -LIBRARY_NAME Hello, World -TAG_PER_MOLECULAR_INDEX ZA -TAG_PER_MOLECULAR_INDEX ZB -TAG_PER_MOLECULAR_INDEX ZC ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -READ_STRUCTURE 25S2M2M2M2M25T -OUTPUT /tmp/molecularBarcodeTest.6013140652498779431.sam -RUN_BARCODE HiMom -SAMPLE_ALIAS HiDad -SEQUENCING_CENTER BI -LIBRARY_NAME Hello, World -TAG_PER_MOLECULAR_INDEX ZA -TAG_PER_MOLECULAR_INDEX ZB -TAG_PER_MOLECULAR_INDEX ZC Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:26.633 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 12:00:26.633 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: USAGE: IlluminaBasecallsToSam [options] USAGE: IlluminaBasecallsToSam [options] Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#IlluminaBasecallsToSam Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#IlluminaBasecallsToSam Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Transforms raw Illumina sequencing data into an unmapped SAM or BAM file. Transforms raw Illumina sequencing data into an unmapped SAM or BAM file. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: The IlluminaBaseCallsToSam program collects, demultiplexes, and sorts reads across all of the tiles of a lane via The IlluminaBaseCallsToSam program collects, demultiplexes, and sorts reads across all of the tiles of a lane via Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: barcode to produce an unmapped SAM/BAM file. An unmapped BAM file is often referred to as a uBAM. All barcode, sample, barcode to produce an unmapped SAM/BAM file. An unmapped BAM file is often referred to as a uBAM. All barcode, sample, Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: and library data is provided in the LIBRARY_PARAMS file. Note, this LIBRARY_PARAMS file should be formatted according and library data is provided in the LIBRARY_PARAMS file. Note, this LIBRARY_PARAMS file should be formatted according Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: to the specifications indicated below. The following is an example of a properly formatted LIBRARY_PARAMS file: to the specifications indicated below. The following is an example of a properly formatted LIBRARY_PARAMS file: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: BARCODE_1 OUTPUT SAMPLE_ALIAS LIBRARY_NAME BARCODE_1 OUTPUT SAMPLE_ALIAS LIBRARY_NAME Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: AAAAAAAA SA_AAAAAAAA.bam SA_AAAAAAAA LN_AAAAAAAA AAAAAAAA SA_AAAAAAAA.bam SA_AAAAAAAA LN_AAAAAAAA Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: AAAAGAAG SA_AAAAGAAG.bam SA_AAAAGAAG LN_AAAAGAAG AAAAGAAG SA_AAAAGAAG.bam SA_AAAAGAAG LN_AAAAGAAG Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: AACAATGG SA_AACAATGG.bam SA_AACAATGG LN_AACAATGG AACAATGG SA_AACAATGG.bam SA_AACAATGG LN_AACAATGG Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: N SA_non_indexed.bam SA_non_indexed LN_NNNNNNNN N SA_non_indexed.bam SA_non_indexed LN_NNNNNNNN Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: The BARCODES_DIR file is produced by the ExtractIlluminaBarcodes The BARCODES_DIR file is produced by the ExtractIlluminaBarcodes Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: (http://broadinstitute.github.io/picard/command-line-overview.html#ExtractIlluminaBarcodes) tool for each lane of a flow (http://broadinstitute.github.io/picard/command-line-overview.html#ExtractIlluminaBarcodes) tool for each lane of a flow Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: cell. cell. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Usage example: Usage example: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: java -jar picard.jar IlluminaBasecallsToSam \ java -jar picard.jar IlluminaBasecallsToSam \ Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: BASECALLS_DIR=/BaseCalls/ \ BASECALLS_DIR=/BaseCalls/ \ Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: LANE=001 \ LANE=001 \ Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: READ_STRUCTURE=25T8B25T \ READ_STRUCTURE=25T8B25T \ Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: RUN_BARCODE=run15 \ RUN_BARCODE=run15 \ Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: IGNORE_UNEXPECTED_BARCODES=true \ IGNORE_UNEXPECTED_BARCODES=true \ Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: LIBRARY_PARAMS=library.params LIBRARY_PARAMS=library.params Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Version: null Version: null Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Options: Options: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: --help --help Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: tools. tools. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: BASECALLS_DIR=File BASECALLS_DIR=File Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: B=File The basecalls directory. Required. B=File The basecalls directory. Required. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: BARCODES_DIR=File BARCODES_DIR=File Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: BCD=File The barcodes directory with _barcode.txt files (generated by ExtractIlluminaBarcodes). If BCD=File The barcodes directory with _barcode.txt files (generated by ExtractIlluminaBarcodes). If Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: not set, use BASECALLS_DIR. Default value: null. not set, use BASECALLS_DIR. Default value: null. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: LANE=Integer LANE=Integer Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: L=Integer Lane number. Required. L=Integer Lane number. Required. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: O=File Deprecated (use LIBRARY_PARAMS). The output SAM or BAM file. Format is determined by O=File Deprecated (use LIBRARY_PARAMS). The output SAM or BAM file. Format is determined by Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: extension. Required. Cannot be used in conjuction with option(s) LIBRARY_PARAMS extension. Required. Cannot be used in conjuction with option(s) LIBRARY_PARAMS Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: BARCODE_PARAMS BARCODE_PARAMS Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: RUN_BARCODE=String The barcode of the run. Prefixed to read names. Required. RUN_BARCODE=String The barcode of the run. Prefixed to read names. Required. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: SAMPLE_ALIAS=String SAMPLE_ALIAS=String Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ALIAS=String Deprecated (use LIBRARY_PARAMS). The name of the sequenced sample Required. Cannot be ALIAS=String Deprecated (use LIBRARY_PARAMS). The name of the sequenced sample Required. Cannot be Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: used in conjuction with option(s) LIBRARY_PARAMS BARCODE_PARAMS used in conjuction with option(s) LIBRARY_PARAMS BARCODE_PARAMS Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: READ_GROUP_ID=String READ_GROUP_ID=String Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: RG=String ID used to link RG header record with RG tag in SAM record. If these are unique in SAM RG=String ID used to link RG header record with RG tag in SAM record. If these are unique in SAM Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: files that get merged, merge performance is better. If not specified, READ_GROUP_ID will files that get merged, merge performance is better. If not specified, READ_GROUP_ID will Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: be set to . . Default value: null. be set to . . Default value: null. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: LIBRARY_NAME=String LIBRARY_NAME=String Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: LIB=String Deprecated (use LIBRARY_PARAMS). The name of the sequenced library Default value: null. LIB=String Deprecated (use LIBRARY_PARAMS). The name of the sequenced library Default value: null. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Cannot be used in conjuction with option(s) LIBRARY_PARAMS BARCODE_PARAMS Cannot be used in conjuction with option(s) LIBRARY_PARAMS BARCODE_PARAMS Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: SEQUENCING_CENTER=String The name of the sequencing center that produced the reads. Used to set the @RG->CN header SEQUENCING_CENTER=String The name of the sequencing center that produced the reads. Used to set the @RG->CN header Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: tag. Required. tag. Required. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: RUN_START_DATE=Date The start date of the run. Default value: null. RUN_START_DATE=Date The start date of the run. Default value: null. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: PLATFORM=String The name of the sequencing technology that produced the read. Default value: ILLUMINA. PLATFORM=String The name of the sequencing technology that produced the read. Default value: ILLUMINA. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: This option can be set to 'null' to clear the default value. This option can be set to 'null' to clear the default value. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INCLUDE_BC_IN_RG_TAG=Boolean Whether to include the barcode information in the @RG->BC header tag. Defaults to false INCLUDE_BC_IN_RG_TAG=Boolean Whether to include the barcode information in the @RG->BC header tag. Defaults to false Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: until included in the SAM spec. Default value: false. This option can be set to 'null' to until included in the SAM spec. Default value: false. This option can be set to 'null' to Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: clear the default value. Possible values: {true, false} clear the default value. Possible values: {true, false} Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: READ_STRUCTURE=String READ_STRUCTURE=String Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: RS=String A description of the logical structure of clusters in an Illumina Run, i.e. a description RS=String A description of the logical structure of clusters in an Illumina Run, i.e. a description Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: of the structure IlluminaBasecallsToSam assumes the data to be in. It should consist of of the structure IlluminaBasecallsToSam assumes the data to be in. It should consist of Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: integer/character pairs describing the number of cycles and the type of those cycles (B integer/character pairs describing the number of cycles and the type of those cycles (B Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: for Sample Barcode, M for molecular barcode, T for Template, and S for skip). E.g. If the for Sample Barcode, M for molecular barcode, T for Template, and S for skip). E.g. If the Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: input data consists of 80 base clusters and we provide a read structure of "28T8M8B8S28T" input data consists of 80 base clusters and we provide a read structure of "28T8M8B8S28T" Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: then the sequence may be split up into four reads: then the sequence may be split up into four reads: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: * read one with 28 cycles (bases) of template * read one with 28 cycles (bases) of template Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: * read two with 8 cycles (bases) of molecular barcode (ex. unique molecular barcode) * read two with 8 cycles (bases) of molecular barcode (ex. unique molecular barcode) Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: * read three with 8 cycles (bases) of sample barcode * read three with 8 cycles (bases) of sample barcode Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: * 8 cycles (bases) skipped. * 8 cycles (bases) skipped. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: * read four with 28 cycles (bases) of template * read four with 28 cycles (bases) of template Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: The skipped cycles would NOT be included in an output SAM/BAM file or in read groups The skipped cycles would NOT be included in an output SAM/BAM file or in read groups Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: therein. Required. therein. Required. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: BARCODE_PARAMS=File Deprecated (use LIBRARY_PARAMS). Tab-separated file for creating all output BAMs for BARCODE_PARAMS=File Deprecated (use LIBRARY_PARAMS). Tab-separated file for creating all output BAMs for Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: barcoded run with single IlluminaBasecallsToSam invocation. Columns are BARCODE, OUTPUT, barcoded run with single IlluminaBasecallsToSam invocation. Columns are BARCODE, OUTPUT, Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: SAMPLE_ALIAS, and LIBRARY_NAME. Row with BARCODE=N is used to specify a file for no SAMPLE_ALIAS, and LIBRARY_NAME. Row with BARCODE=N is used to specify a file for no Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: barcode match Required. Cannot be used in conjuction with option(s) LIBRARY_PARAMS barcode match Required. Cannot be used in conjuction with option(s) LIBRARY_PARAMS Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: SAMPLE_ALIAS (ALIAS) OUTPUT (O) LIBRARY_NAME (LIB) SAMPLE_ALIAS (ALIAS) OUTPUT (O) LIBRARY_NAME (LIB) Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: LIBRARY_PARAMS=File Tab-separated file for creating all output BAMs for a lane with single LIBRARY_PARAMS=File Tab-separated file for creating all output BAMs for a lane with single Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: IlluminaBasecallsToSam invocation. The columns are OUTPUT, SAMPLE_ALIAS, and IlluminaBasecallsToSam invocation. The columns are OUTPUT, SAMPLE_ALIAS, and Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: LIBRARY_NAME, BARCODE_1, BARCODE_2 ... BARCODE_X where X = number of barcodes per cluster LIBRARY_NAME, BARCODE_1, BARCODE_2 ... BARCODE_X where X = number of barcodes per cluster Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: (optional). Row with BARCODE_1 set to 'N' is used to specify a file for no barcode match. (optional). Row with BARCODE_1 set to 'N' is used to specify a file for no barcode match. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: You may also provide any 2 letter RG header attributes (excluding PU, CN, PL, and DT) as You may also provide any 2 letter RG header attributes (excluding PU, CN, PL, and DT) as Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: columns in this file and the values for those columns will be inserted into the RG tag for columns in this file and the values for those columns will be inserted into the RG tag for Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: the BAM file created for a given row. Required. Cannot be used in conjuction with the BAM file created for a given row. Required. Cannot be used in conjuction with Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: option(s) SAMPLE_ALIAS (ALIAS) OUTPUT (O) LIBRARY_NAME (LIB) BARCODE_PARAMS option(s) SAMPLE_ALIAS (ALIAS) OUTPUT (O) LIBRARY_NAME (LIB) BARCODE_PARAMS Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ADAPTERS_TO_CHECK=IlluminaAdapterPair ADAPTERS_TO_CHECK=IlluminaAdapterPair Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Which adapters to look for in the read. Default value: [INDEXED, DUAL_INDEXED, Which adapters to look for in the read. Default value: [INDEXED, DUAL_INDEXED, Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: NEXTERA_V2, FLUIDIGM]. This option can be set to 'null' to clear the default value. NEXTERA_V2, FLUIDIGM]. This option can be set to 'null' to clear the default value. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Possible values: {PAIRED_END, INDEXED, SINGLE_END, NEXTERA_V1, NEXTERA_V2, DUAL_INDEXED, Possible values: {PAIRED_END, INDEXED, SINGLE_END, NEXTERA_V1, NEXTERA_V2, DUAL_INDEXED, Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: FLUIDIGM, TRUSEQ_SMALLRNA, ALTERNATIVE_SINGLE_END} This option may be specified 0 or more FLUIDIGM, TRUSEQ_SMALLRNA, ALTERNATIVE_SINGLE_END} This option may be specified 0 or more Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: times. This option can be set to 'null' to clear the default list. times. This option can be set to 'null' to clear the default list. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: FIVE_PRIME_ADAPTER=String For specifying adapters other than standard Illumina Default value: null. FIVE_PRIME_ADAPTER=String For specifying adapters other than standard Illumina Default value: null. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: THREE_PRIME_ADAPTER=String For specifying adapters other than standard Illumina Default value: null. THREE_PRIME_ADAPTER=String For specifying adapters other than standard Illumina Default value: null. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: NUM_PROCESSORS=Integer The number of threads to run in parallel. If NUM_PROCESSORS = 0, number of cores is NUM_PROCESSORS=Integer The number of threads to run in parallel. If NUM_PROCESSORS = 0, number of cores is Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: automatically set to the number of cores available on the machine. If NUM_PROCESSORS < 0, automatically set to the number of cores available on the machine. If NUM_PROCESSORS < 0, Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: then the number of cores used will be the number available on the machine less then the number of cores used will be the number available on the machine less Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: NUM_PROCESSORS. Default value: 0. This option can be set to 'null' to clear the default NUM_PROCESSORS. Default value: 0. This option can be set to 'null' to clear the default Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: value. value. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: FIRST_TILE=Integer If set, this is the first tile to be processed (used for debugging). Note that tiles are FIRST_TILE=Integer If set, this is the first tile to be processed (used for debugging). Note that tiles are Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: not processed in numerical order. Default value: null. Cannot be used in conjuction with not processed in numerical order. Default value: null. Cannot be used in conjuction with Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: option(s) PROCESS_SINGLE_TILE option(s) PROCESS_SINGLE_TILE Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: TILE_LIMIT=Integer If set, process no more than this many tiles (used for debugging). Default value: null. TILE_LIMIT=Integer If set, process no more than this many tiles (used for debugging). Default value: null. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: PROCESS_SINGLE_TILE=Integer If set, process only the tile number given and prepend the tile number to the output file PROCESS_SINGLE_TILE=Integer If set, process only the tile number given and prepend the tile number to the output file Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: name. Default value: null. Cannot be used in conjuction with option(s) FIRST_TILE name. Default value: null. Cannot be used in conjuction with option(s) FIRST_TILE Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: FORCE_GC=Boolean If true, call System.gc() periodically. This is useful in cases in which the -Xmx value FORCE_GC=Boolean If true, call System.gc() periodically. This is useful in cases in which the -Xmx value Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: passed is larger than the available memory. Default value: true. This option can be set passed is larger than the available memory. Default value: true. This option can be set Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: to 'null' to clear the default value. Possible values: {true, false} to 'null' to clear the default value. Possible values: {true, false} Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: APPLY_EAMSS_FILTER=Boolean Apply EAMSS filtering to identify inappropriately quality scored bases towards the ends of APPLY_EAMSS_FILTER=Boolean Apply EAMSS filtering to identify inappropriately quality scored bases towards the ends of Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: reads and convert their quality scores to Q2. Default value: true. This option can be set reads and convert their quality scores to Q2. Default value: true. This option can be set Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: to 'null' to clear the default value. Possible values: {true, false} to 'null' to clear the default value. Possible values: {true, false} Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: MAX_READS_IN_RAM_PER_TILE=Integer MAX_READS_IN_RAM_PER_TILE=Integer Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Configure SortingCollections to store this many records before spilling to disk. For an Configure SortingCollections to store this many records before spilling to disk. For an Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: indexed run, each SortingCollection gets this value/number of indices. Default value: indexed run, each SortingCollection gets this value/number of indices. Default value: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 1200000. This option can be set to 'null' to clear the default value. 1200000. This option can be set to 'null' to clear the default value. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: MINIMUM_QUALITY=Integer The minimum quality (after transforming 0s to 1s) expected from reads. If qualities are MINIMUM_QUALITY=Integer The minimum quality (after transforming 0s to 1s) expected from reads. If qualities are Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: lower than this value, an error is thrown.The default of 2 is what the Illumina's spec lower than this value, an error is thrown.The default of 2 is what the Illumina's spec Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: describes as the minimum, but in practice the value has been observed lower. Default describes as the minimum, but in practice the value has been observed lower. Default Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: value: 2. This option can be set to 'null' to clear the default value. value: 2. This option can be set to 'null' to clear the default value. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INCLUDE_NON_PF_READS=Boolean INCLUDE_NON_PF_READS=Boolean Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: NONPF=Boolean Whether to include non-PF reads Default value: true. This option can be set to 'null' to NONPF=Boolean Whether to include non-PF reads Default value: true. This option can be set to 'null' to Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: clear the default value. Possible values: {true, false} clear the default value. Possible values: {true, false} Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: IGNORE_UNEXPECTED_BARCODES=Boolean IGNORE_UNEXPECTED_BARCODES=Boolean Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: IGNORE_UNEXPECTED=Boolean Whether to ignore reads whose barcodes are not found in LIBRARY_PARAMS. Useful when IGNORE_UNEXPECTED=Boolean Whether to ignore reads whose barcodes are not found in LIBRARY_PARAMS. Useful when Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: outputting BAMs for only a subset of the barcodes in a lane. Default value: false. This outputting BAMs for only a subset of the barcodes in a lane. Default value: false. This Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: option can be set to 'null' to clear the default value. Possible values: {true, false} option can be set to 'null' to clear the default value. Possible values: {true, false} Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: MOLECULAR_INDEX_TAG=String The tag to use to store any molecular indexes. If more than one molecular index is found, MOLECULAR_INDEX_TAG=String The tag to use to store any molecular indexes. If more than one molecular index is found, Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: they will be concatenated and stored here. Default value: RX. This option can be set to they will be concatenated and stored here. Default value: RX. This option can be set to Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 'null' to clear the default value. 'null' to clear the default value. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: MOLECULAR_INDEX_BASE_QUALITY_TAG=String MOLECULAR_INDEX_BASE_QUALITY_TAG=String Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: The tag to use to store any molecular index base qualities. If more than one molecular The tag to use to store any molecular index base qualities. If more than one molecular Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: index is found, their qualities will be concatenated and stored here (.i.e. the number of index is found, their qualities will be concatenated and stored here (.i.e. the number of Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: "M" operators in the READ_STRUCTURE) Default value: QX. This option can be set to 'null' "M" operators in the READ_STRUCTURE) Default value: QX. This option can be set to 'null' Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: to clear the default value. to clear the default value. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: TAG_PER_MOLECULAR_INDEX=StringThe list of tags to store each molecular index. The number of tags should match the TAG_PER_MOLECULAR_INDEX=StringThe list of tags to store each molecular index. The number of tags should match the Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: number of molecular indexes. Default value: null. This option may be specified 0 or more number of molecular indexes. Default value: null. This option may be specified 0 or more Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: times. times. Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: BARCODE_POPULATION_STRATEGY=PopulateBarcode BARCODE_POPULATION_STRATEGY=PopulateBarcode Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: When should the sample barcode (as read by the sequencer) be placed on the reads in the BC When should the sample barcode (as read by the sequencer) be placed on the reads in the BC Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: tag? Default value: ORPHANS_ONLY. This option can be set to 'null' to clear the default tag? Default value: ORPHANS_ONLY. This option can be set to 'null' to clear the default Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: value. Possible values: { value. Possible values: { Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ORPHANS_ONLY (Put barcodes only into the records that were not assigned to any declared ORPHANS_ONLY (Put barcodes only into the records that were not assigned to any declared Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: barcode.) barcode.) Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INEXACT_MATCH (Put barcodes into records for which an exact match with a declared barcode INEXACT_MATCH (Put barcodes into records for which an exact match with a declared barcode Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: was not found.) was not found.) Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ALWAYS (Put barcodes into all the records.) ALWAYS (Put barcodes into all the records.) Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: } } Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INCLUDE_BARCODE_QUALITY=Boolean INCLUDE_BARCODE_QUALITY=Boolean Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Should the barcode quality be included when the sample barcode is included? Default Should the barcode quality be included when the sample barcode is included? Default Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: value: false. This option can be set to 'null' to clear the default value. Possible value: false. This option can be set to 'null' to clear the default value. Possible Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: values: {true, false} values: {true, false} Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[6](25S2M2M2M2M25T, [Ljava.lang.String;@748df739, null, null, 1)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: The number of tags given in TAG_PER_MOLECULAR_INDEX does not match the number of molecular indexes in READ_STRUCTURE The number of tags given in TAG_PER_MOLECULAR_INDEX does not match the number of molecular indexes in READ_STRUCTURE Running Test: Test method testMolecularBarcodes[7](25S2M2M2M2M25T, [Ljava.lang.String;@21bda98e, null, nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) Test: Test method testMolecularBarcodes[7](25S2M2M2M2M25T, [Ljava.lang.String;@21bda98e, null, nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:26 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testMolecularBarcodes[7](25S2M2M2M2M25T, [Ljava.lang.String;@21bda98e, null, nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam, 0) STANDARD_ERROR INFO 2024-07-02 12:00:26 IlluminaBasecallsToSam Test: Test method testMolecularBarcodes[7](25S2M2M2M2M25T, [Ljava.lang.String;@21bda98e, null, nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[7](25S2M2M2M2M25T, [Ljava.lang.String;@21bda98e, null, nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMolecularBarcodes[7](25S2M2M2M2M25T, [Ljava.lang.String;@21bda98e, null, nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[7](25S2M2M2M2M25T, [Ljava.lang.String;@21bda98e, null, nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMolecularBarcodes[7](25S2M2M2M2M25T, [Ljava.lang.String;@21bda98e, null, nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMolecularBarcodes[7](25S2M2M2M2M25T, [Ljava.lang.String;@21bda98e, null, nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[7](25S2M2M2M2M25T, [Ljava.lang.String;@21bda98e, null, nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMolecularBarcodes[7](25S2M2M2M2M25T, [Ljava.lang.String;@21bda98e, null, nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[7](25S2M2M2M2M25T, [Ljava.lang.String;@21bda98e, null, nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -READ_STRUCTURE 25S2M2M2M2M25T -OUTPUT /tmp/molecularBarcodeTest.6031016311419273243.sam -RUN_BARCODE HiMom -SAMPLE_ALIAS HiDad -SEQUENCING_CENTER BI -LIBRARY_NAME Hello, World -TAG_PER_MOLECULAR_INDEX ZA -TAG_PER_MOLECULAR_INDEX ZB -TAG_PER_MOLECULAR_INDEX ZC -TAG_PER_MOLECULAR_INDEX ZD ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -READ_STRUCTURE 25S2M2M2M2M25T -OUTPUT /tmp/molecularBarcodeTest.6031016311419273243.sam -RUN_BARCODE HiMom -SAMPLE_ALIAS HiDad -SEQUENCING_CENTER BI -LIBRARY_NAME Hello, World -TAG_PER_MOLECULAR_INDEX ZA -TAG_PER_MOLECULAR_INDEX ZB -TAG_PER_MOLECULAR_INDEX ZC -TAG_PER_MOLECULAR_INDEX ZD Test: Test method testMolecularBarcodes[7](25S2M2M2M2M25T, [Ljava.lang.String;@21bda98e, null, nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[7](25S2M2M2M2M25T, [Ljava.lang.String;@21bda98e, null, nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[7](25S2M2M2M2M25T, [Ljava.lang.String;@21bda98e, null, nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[7](25S2M2M2M2M25T, [Ljava.lang.String;@21bda98e, null, nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:26.902 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:26.902 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMolecularBarcodes[7](25S2M2M2M2M25T, [Ljava.lang.String;@21bda98e, null, nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:26.902 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:26.902 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMolecularBarcodes[7](25S2M2M2M2M25T, [Ljava.lang.String;@21bda98e, null, nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:26.902 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:26.902 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMolecularBarcodes[7](25S2M2M2M2M25T, [Ljava.lang.String;@21bda98e, null, nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:26.902 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:26.902 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMolecularBarcodes[7](25S2M2M2M2M25T, [Ljava.lang.String;@21bda98e, null, nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:26 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/molecularBarcodeTest.6031016311419273243.sam RUN_BARCODE=HiMom SAMPLE_ALIAS=HiDad LIBRARY_NAME=Hello, World SEQUENCING_CENTER=BI READ_STRUCTURE=25S2M2M2M2M25T TAG_PER_MOLECULAR_INDEX=[ZA, ZB, ZC, ZD] PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:26 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/molecularBarcodeTest.6031016311419273243.sam RUN_BARCODE=HiMom SAMPLE_ALIAS=HiDad LIBRARY_NAME=Hello, World SEQUENCING_CENTER=BI READ_STRUCTURE=25S2M2M2M2M25T TAG_PER_MOLECULAR_INDEX=[ZA, ZB, ZC, ZD] PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMolecularBarcodes[7](25S2M2M2M2M25T, [Ljava.lang.String;@21bda98e, null, nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMolecularBarcodes[7](25S2M2M2M2M25T, [Ljava.lang.String;@21bda98e, null, nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:26 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S2M2M2M2M25T INFO 2024-07-02 12:00:26 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S2M2M2M2M25T Test: Test method testMolecularBarcodes[7](25S2M2M2M2M25T, [Ljava.lang.String;@21bda98e, null, nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:27 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:27 IlluminaBasecallsConverter All work is complete. Test: Test method testMolecularBarcodes[7](25S2M2M2M2M25T, [Ljava.lang.String;@21bda98e, null, nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:27 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:00:27 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. Test: Test method testMolecularBarcodes[7](25S2M2M2M2M25T, [Ljava.lang.String;@21bda98e, null, nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testMolecularBarcodes[7](25S2M2M2M2M25T, [Ljava.lang.String;@21bda98e, null, nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testMolecularBarcodes[7](25S2M2M2M2M25T, [Ljava.lang.String;@21bda98e, null, nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam, 0) STANDARD_OUT No errors found Running Test: Test method testMolecularBarcodes[8](25S8S25T, null, [Ljava.lang.String;@50b5fea5, nonBarcodedTileSubset.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) Test: Test method testMolecularBarcodes[8](25S8S25T, null, [Ljava.lang.String;@50b5fea5, nonBarcodedTileSubset.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:27 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testMolecularBarcodes[8](25S8S25T, null, [Ljava.lang.String;@50b5fea5, nonBarcodedTileSubset.sam, 0) STANDARD_ERROR INFO 2024-07-02 12:00:27 IlluminaBasecallsToSam Test: Test method testMolecularBarcodes[8](25S8S25T, null, [Ljava.lang.String;@50b5fea5, nonBarcodedTileSubset.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[8](25S8S25T, null, [Ljava.lang.String;@50b5fea5, nonBarcodedTileSubset.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMolecularBarcodes[8](25S8S25T, null, [Ljava.lang.String;@50b5fea5, nonBarcodedTileSubset.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[8](25S8S25T, null, [Ljava.lang.String;@50b5fea5, nonBarcodedTileSubset.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMolecularBarcodes[8](25S8S25T, null, [Ljava.lang.String;@50b5fea5, nonBarcodedTileSubset.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMolecularBarcodes[8](25S8S25T, null, [Ljava.lang.String;@50b5fea5, nonBarcodedTileSubset.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[8](25S8S25T, null, [Ljava.lang.String;@50b5fea5, nonBarcodedTileSubset.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMolecularBarcodes[8](25S8S25T, null, [Ljava.lang.String;@50b5fea5, nonBarcodedTileSubset.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[8](25S8S25T, null, [Ljava.lang.String;@50b5fea5, nonBarcodedTileSubset.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -READ_STRUCTURE 25S8S25T -OUTPUT /tmp/molecularBarcodeTest.9448639422833603921.sam -RUN_BARCODE HiMom -SAMPLE_ALIAS HiDad -SEQUENCING_CENTER BI -LIBRARY_NAME Hello, World -FIRST_TILE 1201 -TILE_LIMIT 1 ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -READ_STRUCTURE 25S8S25T -OUTPUT /tmp/molecularBarcodeTest.9448639422833603921.sam -RUN_BARCODE HiMom -SAMPLE_ALIAS HiDad -SEQUENCING_CENTER BI -LIBRARY_NAME Hello, World -FIRST_TILE 1201 -TILE_LIMIT 1 Test: Test method testMolecularBarcodes[8](25S8S25T, null, [Ljava.lang.String;@50b5fea5, nonBarcodedTileSubset.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMolecularBarcodes[8](25S8S25T, null, [Ljava.lang.String;@50b5fea5, nonBarcodedTileSubset.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[8](25S8S25T, null, [Ljava.lang.String;@50b5fea5, nonBarcodedTileSubset.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMolecularBarcodes[8](25S8S25T, null, [Ljava.lang.String;@50b5fea5, nonBarcodedTileSubset.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:27.163 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:27.163 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMolecularBarcodes[8](25S8S25T, null, [Ljava.lang.String;@50b5fea5, nonBarcodedTileSubset.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:27.163 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:27.163 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMolecularBarcodes[8](25S8S25T, null, [Ljava.lang.String;@50b5fea5, nonBarcodedTileSubset.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:27.163 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:27.163 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMolecularBarcodes[8](25S8S25T, null, [Ljava.lang.String;@50b5fea5, nonBarcodedTileSubset.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:27.163 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:27.163 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMolecularBarcodes[8](25S8S25T, null, [Ljava.lang.String;@50b5fea5, nonBarcodedTileSubset.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:27 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/molecularBarcodeTest.9448639422833603921.sam RUN_BARCODE=HiMom SAMPLE_ALIAS=HiDad LIBRARY_NAME=Hello, World SEQUENCING_CENTER=BI READ_STRUCTURE=25S8S25T FIRST_TILE=1201 TILE_LIMIT=1 PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:27 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/molecularBarcodeTest.9448639422833603921.sam RUN_BARCODE=HiMom SAMPLE_ALIAS=HiDad LIBRARY_NAME=Hello, World SEQUENCING_CENTER=BI READ_STRUCTURE=25S8S25T FIRST_TILE=1201 TILE_LIMIT=1 PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMolecularBarcodes[8](25S8S25T, null, [Ljava.lang.String;@50b5fea5, nonBarcodedTileSubset.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMolecularBarcodes[8](25S8S25T, null, [Ljava.lang.String;@50b5fea5, nonBarcodedTileSubset.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:27 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8S25T INFO 2024-07-02 12:00:27 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8S25T Test: Test method testMolecularBarcodes[8](25S8S25T, null, [Ljava.lang.String;@50b5fea5, nonBarcodedTileSubset.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:27 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:27 IlluminaBasecallsConverter All work is complete. Test: Test method testMolecularBarcodes[8](25S8S25T, null, [Ljava.lang.String;@50b5fea5, nonBarcodedTileSubset.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:27 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:00:27 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. Test: Test method testMolecularBarcodes[8](25S8S25T, null, [Ljava.lang.String;@50b5fea5, nonBarcodedTileSubset.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testMolecularBarcodes[8](25S8S25T, null, [Ljava.lang.String;@50b5fea5, nonBarcodedTileSubset.sam, 0)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testMolecularBarcodes[8](25S8S25T, null, [Ljava.lang.String;@50b5fea5, nonBarcodedTileSubset.sam, 0) STANDARD_OUT No errors found Running Test: Test method testMultiplexed[0](true, ALWAYS, false, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS)(picard.illumina.IlluminaBasecallsToSamTest) Test: Test method testMultiplexed[0](true, ALWAYS, false, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:27 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testMultiplexed[0](true, ALWAYS, false, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS) STANDARD_ERROR INFO 2024-07-02 12:00:27 IlluminaBasecallsToSam Test: Test method testMultiplexed[0](true, ALWAYS, false, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMultiplexed[0](true, ALWAYS, false, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMultiplexed[0](true, ALWAYS, false, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMultiplexed[0](true, ALWAYS, false, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMultiplexed[0](true, ALWAYS, false, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMultiplexed[0](true, ALWAYS, false, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMultiplexed[0](true, ALWAYS, false, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMultiplexed[0](true, ALWAYS, false, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMultiplexed[0](true, ALWAYS, false, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B25T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/multiplexedBarcode.5842143340729934699/library.params -INCLUDE_BC_IN_RG_TAG true -BARCODE_POPULATION_STRATEGY ALWAYS -INCLUDE_BARCODE_QUALITY false ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B25T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/multiplexedBarcode.5842143340729934699/library.params -INCLUDE_BC_IN_RG_TAG true -BARCODE_POPULATION_STRATEGY ALWAYS -INCLUDE_BARCODE_QUALITY false Test: Test method testMultiplexed[0](true, ALWAYS, false, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMultiplexed[0](true, ALWAYS, false, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMultiplexed[0](true, ALWAYS, false, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMultiplexed[0](true, ALWAYS, false, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:27.379 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:27.379 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultiplexed[0](true, ALWAYS, false, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:27.379 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:27.379 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultiplexed[0](true, ALWAYS, false, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:27.380 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:27.380 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultiplexed[0](true, ALWAYS, false, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:27.380 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:27.380 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultiplexed[0](true, ALWAYS, false, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:27 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=true READ_STRUCTURE=25T8B25T LIBRARY_PARAMS=/tmp/pbuilder2/multiplexedBarcode.5842143340729934699/library.params BARCODE_POPULATION_STRATEGY=ALWAYS INCLUDE_BARCODE_QUALITY=false PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:27 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=true READ_STRUCTURE=25T8B25T LIBRARY_PARAMS=/tmp/pbuilder2/multiplexedBarcode.5842143340729934699/library.params BARCODE_POPULATION_STRATEGY=ALWAYS INCLUDE_BARCODE_QUALITY=false PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMultiplexed[0](true, ALWAYS, false, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMultiplexed[0](true, ALWAYS, false, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:27 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T INFO 2024-07-02 12:00:27 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T Test: Test method testMultiplexed[0](true, ALWAYS, false, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:27 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:27 IlluminaBasecallsConverter All work is complete. Test: Test method testMultiplexed[0](true, ALWAYS, false, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:27 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 12:00:27 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. Test: Test method testMultiplexed[0](true, ALWAYS, false, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMultiplexed[1](false, INEXACT_MATCH, true, testdata/picard/illumina/25T8B25T/sams_with_INEXACT_MATCH_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) Test: Test method testMultiplexed[1](false, INEXACT_MATCH, true, testdata/picard/illumina/25T8B25T/sams_with_INEXACT_MATCH_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:28 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testMultiplexed[1](false, INEXACT_MATCH, true, testdata/picard/illumina/25T8B25T/sams_with_INEXACT_MATCH_QUALITY) STANDARD_ERROR INFO 2024-07-02 12:00:28 IlluminaBasecallsToSam Test: Test method testMultiplexed[1](false, INEXACT_MATCH, true, testdata/picard/illumina/25T8B25T/sams_with_INEXACT_MATCH_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMultiplexed[1](false, INEXACT_MATCH, true, testdata/picard/illumina/25T8B25T/sams_with_INEXACT_MATCH_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMultiplexed[1](false, INEXACT_MATCH, true, testdata/picard/illumina/25T8B25T/sams_with_INEXACT_MATCH_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMultiplexed[1](false, INEXACT_MATCH, true, testdata/picard/illumina/25T8B25T/sams_with_INEXACT_MATCH_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMultiplexed[1](false, INEXACT_MATCH, true, testdata/picard/illumina/25T8B25T/sams_with_INEXACT_MATCH_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMultiplexed[1](false, INEXACT_MATCH, true, testdata/picard/illumina/25T8B25T/sams_with_INEXACT_MATCH_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMultiplexed[1](false, INEXACT_MATCH, true, testdata/picard/illumina/25T8B25T/sams_with_INEXACT_MATCH_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMultiplexed[1](false, INEXACT_MATCH, true, testdata/picard/illumina/25T8B25T/sams_with_INEXACT_MATCH_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMultiplexed[1](false, INEXACT_MATCH, true, testdata/picard/illumina/25T8B25T/sams_with_INEXACT_MATCH_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B25T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/multiplexedBarcode.4200153215699638269/library.params -INCLUDE_BC_IN_RG_TAG false -BARCODE_POPULATION_STRATEGY INEXACT_MATCH -INCLUDE_BARCODE_QUALITY true ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B25T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/multiplexedBarcode.4200153215699638269/library.params -INCLUDE_BC_IN_RG_TAG false -BARCODE_POPULATION_STRATEGY INEXACT_MATCH -INCLUDE_BARCODE_QUALITY true Test: Test method testMultiplexed[1](false, INEXACT_MATCH, true, testdata/picard/illumina/25T8B25T/sams_with_INEXACT_MATCH_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMultiplexed[1](false, INEXACT_MATCH, true, testdata/picard/illumina/25T8B25T/sams_with_INEXACT_MATCH_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMultiplexed[1](false, INEXACT_MATCH, true, testdata/picard/illumina/25T8B25T/sams_with_INEXACT_MATCH_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMultiplexed[1](false, INEXACT_MATCH, true, testdata/picard/illumina/25T8B25T/sams_with_INEXACT_MATCH_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:28.113 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:28.113 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultiplexed[1](false, INEXACT_MATCH, true, testdata/picard/illumina/25T8B25T/sams_with_INEXACT_MATCH_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:28.113 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:28.113 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultiplexed[1](false, INEXACT_MATCH, true, testdata/picard/illumina/25T8B25T/sams_with_INEXACT_MATCH_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:28.113 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:28.113 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultiplexed[1](false, INEXACT_MATCH, true, testdata/picard/illumina/25T8B25T/sams_with_INEXACT_MATCH_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:28.113 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:28.113 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultiplexed[1](false, INEXACT_MATCH, true, testdata/picard/illumina/25T8B25T/sams_with_INEXACT_MATCH_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:28 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=false READ_STRUCTURE=25T8B25T LIBRARY_PARAMS=/tmp/pbuilder2/multiplexedBarcode.4200153215699638269/library.params BARCODE_POPULATION_STRATEGY=INEXACT_MATCH INCLUDE_BARCODE_QUALITY=true PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:28 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=false READ_STRUCTURE=25T8B25T LIBRARY_PARAMS=/tmp/pbuilder2/multiplexedBarcode.4200153215699638269/library.params BARCODE_POPULATION_STRATEGY=INEXACT_MATCH INCLUDE_BARCODE_QUALITY=true PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMultiplexed[1](false, INEXACT_MATCH, true, testdata/picard/illumina/25T8B25T/sams_with_INEXACT_MATCH_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMultiplexed[1](false, INEXACT_MATCH, true, testdata/picard/illumina/25T8B25T/sams_with_INEXACT_MATCH_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:28 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T INFO 2024-07-02 12:00:28 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T Test: Test method testMultiplexed[1](false, INEXACT_MATCH, true, testdata/picard/illumina/25T8B25T/sams_with_INEXACT_MATCH_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:28 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:28 IlluminaBasecallsConverter All work is complete. Test: Test method testMultiplexed[1](false, INEXACT_MATCH, true, testdata/picard/illumina/25T8B25T/sams_with_INEXACT_MATCH_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:28 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:28 IlluminaBasecallsConverter All work is complete. Test: Test method testMultiplexed[1](false, INEXACT_MATCH, true, testdata/picard/illumina/25T8B25T/sams_with_INEXACT_MATCH_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:28 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:00:28 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. Test: Test method testMultiplexed[1](false, INEXACT_MATCH, true, testdata/picard/illumina/25T8B25T/sams_with_INEXACT_MATCH_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testMultiplexed[1](false, INEXACT_MATCH, true, testdata/picard/illumina/25T8B25T/sams_with_INEXACT_MATCH_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:28 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:28 IlluminaBasecallsConverter All work is complete. Running Test: Test method testMultiplexed[2](true, ALWAYS, true, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) Test: Test method testMultiplexed[2](true, ALWAYS, true, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:28 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testMultiplexed[2](true, ALWAYS, true, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS_QUALITY) STANDARD_ERROR INFO 2024-07-02 12:00:28 IlluminaBasecallsToSam Test: Test method testMultiplexed[2](true, ALWAYS, true, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMultiplexed[2](true, ALWAYS, true, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMultiplexed[2](true, ALWAYS, true, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMultiplexed[2](true, ALWAYS, true, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMultiplexed[2](true, ALWAYS, true, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMultiplexed[2](true, ALWAYS, true, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMultiplexed[2](true, ALWAYS, true, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMultiplexed[2](true, ALWAYS, true, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMultiplexed[2](true, ALWAYS, true, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B25T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/multiplexedBarcode.9853060352800082126/library.params -INCLUDE_BC_IN_RG_TAG true -BARCODE_POPULATION_STRATEGY ALWAYS -INCLUDE_BARCODE_QUALITY true ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B25T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/multiplexedBarcode.9853060352800082126/library.params -INCLUDE_BC_IN_RG_TAG true -BARCODE_POPULATION_STRATEGY ALWAYS -INCLUDE_BARCODE_QUALITY true Test: Test method testMultiplexed[2](true, ALWAYS, true, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMultiplexed[2](true, ALWAYS, true, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMultiplexed[2](true, ALWAYS, true, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMultiplexed[2](true, ALWAYS, true, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:28.983 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:28.983 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultiplexed[2](true, ALWAYS, true, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:28.983 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:28.983 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultiplexed[2](true, ALWAYS, true, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:28.983 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:28.983 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultiplexed[2](true, ALWAYS, true, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:28.983 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:28.983 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultiplexed[2](true, ALWAYS, true, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:28 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=true READ_STRUCTURE=25T8B25T LIBRARY_PARAMS=/tmp/pbuilder2/multiplexedBarcode.9853060352800082126/library.params BARCODE_POPULATION_STRATEGY=ALWAYS INCLUDE_BARCODE_QUALITY=true PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:28 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=true READ_STRUCTURE=25T8B25T LIBRARY_PARAMS=/tmp/pbuilder2/multiplexedBarcode.9853060352800082126/library.params BARCODE_POPULATION_STRATEGY=ALWAYS INCLUDE_BARCODE_QUALITY=true PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMultiplexed[2](true, ALWAYS, true, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMultiplexed[2](true, ALWAYS, true, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:29 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T INFO 2024-07-02 12:00:29 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T Test: Test method testMultiplexed[2](true, ALWAYS, true, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:29 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:29 IlluminaBasecallsConverter All work is complete. Test: Test method testMultiplexed[2](true, ALWAYS, true, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:29 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:29 IlluminaBasecallsConverter All work is complete. Test: Test method testMultiplexed[2](true, ALWAYS, true, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:29 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:00:29 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. Test: Test method testMultiplexed[2](true, ALWAYS, true, testdata/picard/illumina/25T8B25T/sams_with_BC_ALWAYS_QUALITY)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testMultiplexed[3](false, ORPHANS_ONLY, false, testdata/picard/illumina/25T8B25T/sams)(picard.illumina.IlluminaBasecallsToSamTest) Test: Test method testMultiplexed[3](false, ORPHANS_ONLY, false, testdata/picard/illumina/25T8B25T/sams)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:30 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testMultiplexed[3](false, ORPHANS_ONLY, false, testdata/picard/illumina/25T8B25T/sams) STANDARD_ERROR INFO 2024-07-02 12:00:30 IlluminaBasecallsToSam Test: Test method testMultiplexed[3](false, ORPHANS_ONLY, false, testdata/picard/illumina/25T8B25T/sams)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMultiplexed[3](false, ORPHANS_ONLY, false, testdata/picard/illumina/25T8B25T/sams)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMultiplexed[3](false, ORPHANS_ONLY, false, testdata/picard/illumina/25T8B25T/sams)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMultiplexed[3](false, ORPHANS_ONLY, false, testdata/picard/illumina/25T8B25T/sams)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMultiplexed[3](false, ORPHANS_ONLY, false, testdata/picard/illumina/25T8B25T/sams)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMultiplexed[3](false, ORPHANS_ONLY, false, testdata/picard/illumina/25T8B25T/sams)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMultiplexed[3](false, ORPHANS_ONLY, false, testdata/picard/illumina/25T8B25T/sams)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMultiplexed[3](false, ORPHANS_ONLY, false, testdata/picard/illumina/25T8B25T/sams)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMultiplexed[3](false, ORPHANS_ONLY, false, testdata/picard/illumina/25T8B25T/sams)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B25T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/multiplexedBarcode.10578027129912815336/library.params -INCLUDE_BC_IN_RG_TAG false -BARCODE_POPULATION_STRATEGY ORPHANS_ONLY -INCLUDE_BARCODE_QUALITY false ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B25T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/multiplexedBarcode.10578027129912815336/library.params -INCLUDE_BC_IN_RG_TAG false -BARCODE_POPULATION_STRATEGY ORPHANS_ONLY -INCLUDE_BARCODE_QUALITY false Test: Test method testMultiplexed[3](false, ORPHANS_ONLY, false, testdata/picard/illumina/25T8B25T/sams)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testMultiplexed[3](false, ORPHANS_ONLY, false, testdata/picard/illumina/25T8B25T/sams)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMultiplexed[3](false, ORPHANS_ONLY, false, testdata/picard/illumina/25T8B25T/sams)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testMultiplexed[3](false, ORPHANS_ONLY, false, testdata/picard/illumina/25T8B25T/sams)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:30.218 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:30.218 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultiplexed[3](false, ORPHANS_ONLY, false, testdata/picard/illumina/25T8B25T/sams)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:30.218 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:30.218 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultiplexed[3](false, ORPHANS_ONLY, false, testdata/picard/illumina/25T8B25T/sams)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:30.218 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:30.218 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultiplexed[3](false, ORPHANS_ONLY, false, testdata/picard/illumina/25T8B25T/sams)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:30.218 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:30.218 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultiplexed[3](false, ORPHANS_ONLY, false, testdata/picard/illumina/25T8B25T/sams)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:30 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=false READ_STRUCTURE=25T8B25T LIBRARY_PARAMS=/tmp/pbuilder2/multiplexedBarcode.10578027129912815336/library.params BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:30 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=false READ_STRUCTURE=25T8B25T LIBRARY_PARAMS=/tmp/pbuilder2/multiplexedBarcode.10578027129912815336/library.params BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMultiplexed[3](false, ORPHANS_ONLY, false, testdata/picard/illumina/25T8B25T/sams)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMultiplexed[3](false, ORPHANS_ONLY, false, testdata/picard/illumina/25T8B25T/sams)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:30 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T INFO 2024-07-02 12:00:30 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T Test: Test method testMultiplexed[3](false, ORPHANS_ONLY, false, testdata/picard/illumina/25T8B25T/sams)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:30 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:30 IlluminaBasecallsConverter All work is complete. Test: Test method testMultiplexed[3](false, ORPHANS_ONLY, false, testdata/picard/illumina/25T8B25T/sams)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:30 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:00:30 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. Test: Test method testMultiplexed[3](false, ORPHANS_ONLY, false, testdata/picard/illumina/25T8B25T/sams)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testNonBarcodedWithCenter(picard.illumina.IlluminaBasecallsToSamTest) Test: Test method testNonBarcodedWithCenter(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:31 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testNonBarcodedWithCenter STANDARD_ERROR INFO 2024-07-02 12:00:31 IlluminaBasecallsToSam Test: Test method testNonBarcodedWithCenter(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testNonBarcodedWithCenter(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testNonBarcodedWithCenter(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testNonBarcodedWithCenter(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testNonBarcodedWithCenter(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testNonBarcodedWithCenter(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testNonBarcodedWithCenter(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testNonBarcodedWithCenter(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testNonBarcodedWithCenter(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -READ_STRUCTURE 25S8S25T -OUTPUT /tmp/nonBarcodedDescriptionNonBI.5192793430024629485.sam -RUN_BARCODE HiMom -SAMPLE_ALIAS HiDad -SEQUENCING_CENTER TEST_CENTER123 -LIBRARY_NAME Hello, World ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -READ_STRUCTURE 25S8S25T -OUTPUT /tmp/nonBarcodedDescriptionNonBI.5192793430024629485.sam -RUN_BARCODE HiMom -SAMPLE_ALIAS HiDad -SEQUENCING_CENTER TEST_CENTER123 -LIBRARY_NAME Hello, World Test: Test method testNonBarcodedWithCenter(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testNonBarcodedWithCenter(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testNonBarcodedWithCenter(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testNonBarcodedWithCenter(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:31.038 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:31.038 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNonBarcodedWithCenter(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:31.038 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:31.038 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNonBarcodedWithCenter(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:31.038 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:31.038 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNonBarcodedWithCenter(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:31.038 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:31.038 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNonBarcodedWithCenter(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:31 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/nonBarcodedDescriptionNonBI.5192793430024629485.sam RUN_BARCODE=HiMom SAMPLE_ALIAS=HiDad LIBRARY_NAME=Hello, World SEQUENCING_CENTER=TEST_CENTER123 READ_STRUCTURE=25S8S25T PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:31 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 OUTPUT=/tmp/nonBarcodedDescriptionNonBI.5192793430024629485.sam RUN_BARCODE=HiMom SAMPLE_ALIAS=HiDad LIBRARY_NAME=Hello, World SEQUENCING_CENTER=TEST_CENTER123 READ_STRUCTURE=25S8S25T PLATFORM=ILLUMINA INCLUDE_BC_IN_RG_TAG=false ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testNonBarcodedWithCenter(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testNonBarcodedWithCenter(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:31 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8S25T INFO 2024-07-02 12:00:31 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25S8S25T Test: Test method testNonBarcodedWithCenter(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:31 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:31 IlluminaBasecallsConverter All work is complete. Test: Test method testNonBarcodedWithCenter(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:31 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:00:31 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. Test: Test method testNonBarcodedWithCenter(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Test: Test method testNonBarcodedWithCenter(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testNonBarcodedWithCenter STANDARD_OUT No errors found Running Test: Test method testTileNumberComparator(picard.illumina.IlluminaBasecallsToSamTest) Running Test: Test method testVariousConfigurations[0](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_DS, null)(picard.illumina.IlluminaBasecallsToSamTest) Test: Test method testVariousConfigurations[0](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_DS, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:31 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testVariousConfigurations[0](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_DS, null) STANDARD_ERROR INFO 2024-07-02 12:00:31 IlluminaBasecallsToSam Test: Test method testVariousConfigurations[0](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_DS, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[0](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_DS, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testVariousConfigurations[0](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_DS, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[0](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_DS, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testVariousConfigurations[0](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_DS, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testVariousConfigurations[0](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_DS, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[0](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_DS, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testVariousConfigurations[0](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_DS, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[0](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_DS, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B25T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/multiplexedBarcode.17201619486228936459/library.params -INCLUDE_BC_IN_RG_TAG false -BARCODE_POPULATION_STRATEGY ORPHANS_ONLY -INCLUDE_BARCODE_QUALITY false ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B25T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/multiplexedBarcode.17201619486228936459/library.params -INCLUDE_BC_IN_RG_TAG false -BARCODE_POPULATION_STRATEGY ORPHANS_ONLY -INCLUDE_BARCODE_QUALITY false Test: Test method testVariousConfigurations[0](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_DS, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[0](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_DS, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[0](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_DS, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[0](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_DS, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:31.279 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:31.279 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVariousConfigurations[0](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_DS, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:31.279 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:31.279 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVariousConfigurations[0](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_DS, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:31.279 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:31.279 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVariousConfigurations[0](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_DS, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:31.279 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:31.279 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVariousConfigurations[0](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_DS, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:31 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=false READ_STRUCTURE=25T8B25T LIBRARY_PARAMS=/tmp/pbuilder2/multiplexedBarcode.17201619486228936459/library.params BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:31 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=false READ_STRUCTURE=25T8B25T LIBRARY_PARAMS=/tmp/pbuilder2/multiplexedBarcode.17201619486228936459/library.params BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testVariousConfigurations[0](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_DS, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testVariousConfigurations[0](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_DS, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:31 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T INFO 2024-07-02 12:00:31 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T Test: Test method testVariousConfigurations[0](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_DS, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:31 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:31 IlluminaBasecallsConverter All work is complete. Test: Test method testVariousConfigurations[0](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_DS, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:31 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:00:31 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. Test: Test method testVariousConfigurations[0](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_DS, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testVariousConfigurations[1](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) Test: Test method testVariousConfigurations[1](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:31 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testVariousConfigurations[1](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null) STANDARD_ERROR INFO 2024-07-02 12:00:31 IlluminaBasecallsToSam Test: Test method testVariousConfigurations[1](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[1](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testVariousConfigurations[1](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[1](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testVariousConfigurations[1](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testVariousConfigurations[1](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[1](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testVariousConfigurations[1](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[1](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B25T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/multiplexedBarcode.16310079964838367908/library.params -INCLUDE_BC_IN_RG_TAG false -BARCODE_POPULATION_STRATEGY ORPHANS_ONLY -INCLUDE_BARCODE_QUALITY false ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B25T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/multiplexedBarcode.16310079964838367908/library.params -INCLUDE_BC_IN_RG_TAG false -BARCODE_POPULATION_STRATEGY ORPHANS_ONLY -INCLUDE_BARCODE_QUALITY false Test: Test method testVariousConfigurations[1](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[1](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[1](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[1](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:31.919 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:31.919 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVariousConfigurations[1](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:31.919 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:31.919 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVariousConfigurations[1](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:31.919 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:31.919 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVariousConfigurations[1](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:31.919 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:31.919 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVariousConfigurations[1](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:31 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=false READ_STRUCTURE=25T8B25T LIBRARY_PARAMS=/tmp/pbuilder2/multiplexedBarcode.16310079964838367908/library.params BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:31 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=false READ_STRUCTURE=25T8B25T LIBRARY_PARAMS=/tmp/pbuilder2/multiplexedBarcode.16310079964838367908/library.params BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testVariousConfigurations[1](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testVariousConfigurations[1](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:32 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T INFO 2024-07-02 12:00:32 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T Test: Test method testVariousConfigurations[1](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:32 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:32 IlluminaBasecallsConverter All work is complete. Test: Test method testVariousConfigurations[1](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:32 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:00:32 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. Test: Test method testVariousConfigurations[1](multiplexedBarcode., library.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testVariousConfigurations[2](multiplexedBarcode., library.params, 1, 25T8B4M21T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M, null)(picard.illumina.IlluminaBasecallsToSamTest) Test: Test method testVariousConfigurations[2](multiplexedBarcode., library.params, 1, 25T8B4M21T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:32 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testVariousConfigurations[2](multiplexedBarcode., library.params, 1, 25T8B4M21T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M, null) STANDARD_ERROR INFO 2024-07-02 12:00:32 IlluminaBasecallsToSam Test: Test method testVariousConfigurations[2](multiplexedBarcode., library.params, 1, 25T8B4M21T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[2](multiplexedBarcode., library.params, 1, 25T8B4M21T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testVariousConfigurations[2](multiplexedBarcode., library.params, 1, 25T8B4M21T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[2](multiplexedBarcode., library.params, 1, 25T8B4M21T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testVariousConfigurations[2](multiplexedBarcode., library.params, 1, 25T8B4M21T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testVariousConfigurations[2](multiplexedBarcode., library.params, 1, 25T8B4M21T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[2](multiplexedBarcode., library.params, 1, 25T8B4M21T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testVariousConfigurations[2](multiplexedBarcode., library.params, 1, 25T8B4M21T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[2](multiplexedBarcode., library.params, 1, 25T8B4M21T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B4M21T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/multiplexedBarcode.8647803791910501446/library.params -INCLUDE_BC_IN_RG_TAG false -BARCODE_POPULATION_STRATEGY ORPHANS_ONLY -INCLUDE_BARCODE_QUALITY false ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B4M21T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/multiplexedBarcode.8647803791910501446/library.params -INCLUDE_BC_IN_RG_TAG false -BARCODE_POPULATION_STRATEGY ORPHANS_ONLY -INCLUDE_BARCODE_QUALITY false Test: Test method testVariousConfigurations[2](multiplexedBarcode., library.params, 1, 25T8B4M21T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[2](multiplexedBarcode., library.params, 1, 25T8B4M21T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[2](multiplexedBarcode., library.params, 1, 25T8B4M21T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[2](multiplexedBarcode., library.params, 1, 25T8B4M21T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:32.560 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:32.560 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVariousConfigurations[2](multiplexedBarcode., library.params, 1, 25T8B4M21T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:32.560 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:32.560 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVariousConfigurations[2](multiplexedBarcode., library.params, 1, 25T8B4M21T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:32.560 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:32.560 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVariousConfigurations[2](multiplexedBarcode., library.params, 1, 25T8B4M21T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:32.560 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:32.560 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVariousConfigurations[2](multiplexedBarcode., library.params, 1, 25T8B4M21T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:32 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=false READ_STRUCTURE=25T8B4M21T LIBRARY_PARAMS=/tmp/pbuilder2/multiplexedBarcode.8647803791910501446/library.params BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:32 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=false READ_STRUCTURE=25T8B4M21T LIBRARY_PARAMS=/tmp/pbuilder2/multiplexedBarcode.8647803791910501446/library.params BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testVariousConfigurations[2](multiplexedBarcode., library.params, 1, 25T8B4M21T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testVariousConfigurations[2](multiplexedBarcode., library.params, 1, 25T8B4M21T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:32 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B4M21T INFO 2024-07-02 12:00:32 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B4M21T Test: Test method testVariousConfigurations[2](multiplexedBarcode., library.params, 1, 25T8B4M21T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:32 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:32 IlluminaBasecallsConverter All work is complete. Test: Test method testVariousConfigurations[2](multiplexedBarcode., library.params, 1, 25T8B4M21T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:32 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:00:32 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. Test: Test method testVariousConfigurations[2](multiplexedBarcode., library.params, 1, 25T8B4M21T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testVariousConfigurations[3](multiplexedBarcode2., library.params, 1, 25T8B4M4M17T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M4M, null)(picard.illumina.IlluminaBasecallsToSamTest) Test: Test method testVariousConfigurations[3](multiplexedBarcode2., library.params, 1, 25T8B4M4M17T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:33 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testVariousConfigurations[3](multiplexedBarcode2., library.params, 1, 25T8B4M4M17T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M4M, null) STANDARD_ERROR INFO 2024-07-02 12:00:33 IlluminaBasecallsToSam Test: Test method testVariousConfigurations[3](multiplexedBarcode2., library.params, 1, 25T8B4M4M17T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[3](multiplexedBarcode2., library.params, 1, 25T8B4M4M17T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testVariousConfigurations[3](multiplexedBarcode2., library.params, 1, 25T8B4M4M17T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[3](multiplexedBarcode2., library.params, 1, 25T8B4M4M17T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testVariousConfigurations[3](multiplexedBarcode2., library.params, 1, 25T8B4M4M17T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testVariousConfigurations[3](multiplexedBarcode2., library.params, 1, 25T8B4M4M17T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[3](multiplexedBarcode2., library.params, 1, 25T8B4M4M17T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testVariousConfigurations[3](multiplexedBarcode2., library.params, 1, 25T8B4M4M17T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[3](multiplexedBarcode2., library.params, 1, 25T8B4M4M17T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B4M4M17T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/multiplexedBarcode2.5920831353908903501/library.params -INCLUDE_BC_IN_RG_TAG false -BARCODE_POPULATION_STRATEGY ORPHANS_ONLY -INCLUDE_BARCODE_QUALITY false ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B4M4M17T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/multiplexedBarcode2.5920831353908903501/library.params -INCLUDE_BC_IN_RG_TAG false -BARCODE_POPULATION_STRATEGY ORPHANS_ONLY -INCLUDE_BARCODE_QUALITY false Test: Test method testVariousConfigurations[3](multiplexedBarcode2., library.params, 1, 25T8B4M4M17T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[3](multiplexedBarcode2., library.params, 1, 25T8B4M4M17T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[3](multiplexedBarcode2., library.params, 1, 25T8B4M4M17T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[3](multiplexedBarcode2., library.params, 1, 25T8B4M4M17T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:33.241 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:33.241 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVariousConfigurations[3](multiplexedBarcode2., library.params, 1, 25T8B4M4M17T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:33.241 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:33.241 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVariousConfigurations[3](multiplexedBarcode2., library.params, 1, 25T8B4M4M17T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:33.241 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:33.241 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVariousConfigurations[3](multiplexedBarcode2., library.params, 1, 25T8B4M4M17T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:33.241 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:33.241 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVariousConfigurations[3](multiplexedBarcode2., library.params, 1, 25T8B4M4M17T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:33 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=false READ_STRUCTURE=25T8B4M4M17T LIBRARY_PARAMS=/tmp/pbuilder2/multiplexedBarcode2.5920831353908903501/library.params BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:33 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=false READ_STRUCTURE=25T8B4M4M17T LIBRARY_PARAMS=/tmp/pbuilder2/multiplexedBarcode2.5920831353908903501/library.params BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testVariousConfigurations[3](multiplexedBarcode2., library.params, 1, 25T8B4M4M17T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testVariousConfigurations[3](multiplexedBarcode2., library.params, 1, 25T8B4M4M17T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:33 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B4M4M17T INFO 2024-07-02 12:00:33 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B4M4M17T Test: Test method testVariousConfigurations[3](multiplexedBarcode2., library.params, 1, 25T8B4M4M17T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:33 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:33 IlluminaBasecallsConverter All work is complete. Test: Test method testVariousConfigurations[3](multiplexedBarcode2., library.params, 1, 25T8B4M4M17T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:33 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:00:33 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. Test: Test method testVariousConfigurations[3](multiplexedBarcode2., library.params, 1, 25T8B4M4M17T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams_with_4M4M, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testVariousConfigurations[4](singleBarcodeAltName., multiplexed_positive_rgtags.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) Test: Test method testVariousConfigurations[4](singleBarcodeAltName., multiplexed_positive_rgtags.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:33 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testVariousConfigurations[4](singleBarcodeAltName., multiplexed_positive_rgtags.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null) STANDARD_ERROR INFO 2024-07-02 12:00:33 IlluminaBasecallsToSam Test: Test method testVariousConfigurations[4](singleBarcodeAltName., multiplexed_positive_rgtags.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[4](singleBarcodeAltName., multiplexed_positive_rgtags.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testVariousConfigurations[4](singleBarcodeAltName., multiplexed_positive_rgtags.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[4](singleBarcodeAltName., multiplexed_positive_rgtags.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testVariousConfigurations[4](singleBarcodeAltName., multiplexed_positive_rgtags.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testVariousConfigurations[4](singleBarcodeAltName., multiplexed_positive_rgtags.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[4](singleBarcodeAltName., multiplexed_positive_rgtags.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testVariousConfigurations[4](singleBarcodeAltName., multiplexed_positive_rgtags.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[4](singleBarcodeAltName., multiplexed_positive_rgtags.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B25T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/singleBarcodeAltName.2092961578790909175/multiplexed_positive_rgtags.params -INCLUDE_BC_IN_RG_TAG false -BARCODE_POPULATION_STRATEGY ORPHANS_ONLY -INCLUDE_BARCODE_QUALITY false ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B25T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/singleBarcodeAltName.2092961578790909175/multiplexed_positive_rgtags.params -INCLUDE_BC_IN_RG_TAG false -BARCODE_POPULATION_STRATEGY ORPHANS_ONLY -INCLUDE_BARCODE_QUALITY false Test: Test method testVariousConfigurations[4](singleBarcodeAltName., multiplexed_positive_rgtags.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[4](singleBarcodeAltName., multiplexed_positive_rgtags.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[4](singleBarcodeAltName., multiplexed_positive_rgtags.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[4](singleBarcodeAltName., multiplexed_positive_rgtags.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:33.812 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:33.812 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVariousConfigurations[4](singleBarcodeAltName., multiplexed_positive_rgtags.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:33.812 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:33.812 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVariousConfigurations[4](singleBarcodeAltName., multiplexed_positive_rgtags.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:33.812 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:33.812 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVariousConfigurations[4](singleBarcodeAltName., multiplexed_positive_rgtags.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:33.812 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:33.812 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVariousConfigurations[4](singleBarcodeAltName., multiplexed_positive_rgtags.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:33 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=false READ_STRUCTURE=25T8B25T LIBRARY_PARAMS=/tmp/pbuilder2/singleBarcodeAltName.2092961578790909175/multiplexed_positive_rgtags.params BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:33 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=false READ_STRUCTURE=25T8B25T LIBRARY_PARAMS=/tmp/pbuilder2/singleBarcodeAltName.2092961578790909175/multiplexed_positive_rgtags.params BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testVariousConfigurations[4](singleBarcodeAltName., multiplexed_positive_rgtags.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testVariousConfigurations[4](singleBarcodeAltName., multiplexed_positive_rgtags.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:33 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T INFO 2024-07-02 12:00:33 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B25T Test: Test method testVariousConfigurations[4](singleBarcodeAltName., multiplexed_positive_rgtags.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:33 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:33 IlluminaBasecallsConverter All work is complete. Test: Test method testVariousConfigurations[4](singleBarcodeAltName., multiplexed_positive_rgtags.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:34 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:00:34 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. Test: Test method testVariousConfigurations[4](singleBarcodeAltName., multiplexed_positive_rgtags.params, 1, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Runtime.totalMemory()=1073741824 Runtime.totalMemory()=1073741824 Running Test: Test method testVariousConfigurations[5](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) Test: Test method testVariousConfigurations[5](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:34 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testVariousConfigurations[5](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, null) STANDARD_ERROR INFO 2024-07-02 12:00:34 IlluminaBasecallsToSam Test: Test method testVariousConfigurations[5](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[5](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testVariousConfigurations[5](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[5](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testVariousConfigurations[5](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testVariousConfigurations[5](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[5](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testVariousConfigurations[5](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[5](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B8B25T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/dualBarcode.18090693515938634130/library_double.params -INCLUDE_BC_IN_RG_TAG false -BARCODE_POPULATION_STRATEGY ORPHANS_ONLY -INCLUDE_BARCODE_QUALITY false ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B8B25T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/dualBarcode.18090693515938634130/library_double.params -INCLUDE_BC_IN_RG_TAG false -BARCODE_POPULATION_STRATEGY ORPHANS_ONLY -INCLUDE_BARCODE_QUALITY false Test: Test method testVariousConfigurations[5](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[5](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[5](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[5](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:34.488 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:34.488 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVariousConfigurations[5](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:34.488 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:34.488 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVariousConfigurations[5](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:34.489 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:34.489 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVariousConfigurations[5](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:34.489 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:34.489 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVariousConfigurations[5](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:34 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=false READ_STRUCTURE=25T8B8B25T LIBRARY_PARAMS=/tmp/pbuilder2/dualBarcode.18090693515938634130/library_double.params BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:34 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=false READ_STRUCTURE=25T8B8B25T LIBRARY_PARAMS=/tmp/pbuilder2/dualBarcode.18090693515938634130/library_double.params BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testVariousConfigurations[5](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testVariousConfigurations[5](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:34 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B8B25T INFO 2024-07-02 12:00:34 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B8B25T Test: Test method testVariousConfigurations[5](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:34 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:34 IlluminaBasecallsConverter All work is complete. Test: Test method testVariousConfigurations[5](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:34 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 12:00:34 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.01 minutes. Test: Test method testVariousConfigurations[5](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:35 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null) STANDARD_ERROR INFO 2024-07-02 12:00:35 IlluminaBasecallsToSam Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 151T8B8B151T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/cbclConvert.13991409937945439955/library_double.params -INCLUDE_BC_IN_RG_TAG false -BARCODE_POPULATION_STRATEGY ORPHANS_ONLY -INCLUDE_BARCODE_QUALITY false ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 151T8B8B151T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/cbclConvert.13991409937945439955/library_double.params -INCLUDE_BC_IN_RG_TAG false -BARCODE_POPULATION_STRATEGY ORPHANS_ONLY -INCLUDE_BARCODE_QUALITY false Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:35.290 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:35.290 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:35.290 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:35.290 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:35.291 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:35.291 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:35.291 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:35.291 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:35 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=false READ_STRUCTURE=151T8B8B151T LIBRARY_PARAMS=/tmp/pbuilder2/cbclConvert.13991409937945439955/library_double.params BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:35 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=false READ_STRUCTURE=151T8B8B151T LIBRARY_PARAMS=/tmp/pbuilder2/cbclConvert.13991409937945439955/library_double.params BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:36 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 151T8B8B151T INFO 2024-07-02 12:00:36 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 151T8B8B151T Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:36 CbclReader Processing tile 1101 INFO 2024-07-02 12:00:36 CbclReader Processing tile 1101 Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:36 CbclReader Processing tile 1102 INFO 2024-07-02 12:00:36 CbclReader Processing tile 1102 Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:36 NewIlluminaBasecallsConverter Finished processing tile 1101 INFO 2024-07-02 12:00:36 NewIlluminaBasecallsConverter Finished processing tile 1101 Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:36 NewIlluminaBasecallsConverter Finished processing tile 1102 INFO 2024-07-02 12:00:36 NewIlluminaBasecallsConverter Finished processing tile 1102 Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:41 NewIlluminaBasecallsConverter Writing out tile 1101 INFO 2024-07-02 12:00:41 NewIlluminaBasecallsConverter Writing out tile 1101 Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:41 NewIlluminaBasecallsConverter Writing out tile 1102 INFO 2024-07-02 12:00:41 NewIlluminaBasecallsConverter Writing out tile 1102 Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:41 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.10 minutes. [Tue Jul 02 12:00:41 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.10 minutes. Test: Test method testVariousConfigurations[6](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testVariousConfigurations[7](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) Test: Test method testVariousConfigurations[7](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:41 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testVariousConfigurations[7](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null) STANDARD_ERROR INFO 2024-07-02 12:00:41 IlluminaBasecallsToSam Test: Test method testVariousConfigurations[7](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[7](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testVariousConfigurations[7](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[7](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testVariousConfigurations[7](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testVariousConfigurations[7](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[7](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testVariousConfigurations[7](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[7](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B8B25T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/hiseqxSingleLocs.16614220605694863500/library_double.params -INCLUDE_BC_IN_RG_TAG false -BARCODE_POPULATION_STRATEGY ORPHANS_ONLY -INCLUDE_BARCODE_QUALITY false ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B8B25T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/hiseqxSingleLocs.16614220605694863500/library_double.params -INCLUDE_BC_IN_RG_TAG false -BARCODE_POPULATION_STRATEGY ORPHANS_ONLY -INCLUDE_BARCODE_QUALITY false Test: Test method testVariousConfigurations[7](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[7](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[7](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[7](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:41.717 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:41.717 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVariousConfigurations[7](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:41.717 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:41.717 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVariousConfigurations[7](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:41.717 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:41.717 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVariousConfigurations[7](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:41.717 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:41.717 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVariousConfigurations[7](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:41 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=false READ_STRUCTURE=25T8B8B25T LIBRARY_PARAMS=/tmp/pbuilder2/hiseqxSingleLocs.16614220605694863500/library_double.params BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:41 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=false READ_STRUCTURE=25T8B8B25T LIBRARY_PARAMS=/tmp/pbuilder2/hiseqxSingleLocs.16614220605694863500/library_double.params BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testVariousConfigurations[7](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testVariousConfigurations[7](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:41 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B8B25T INFO 2024-07-02 12:00:41 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B8B25T Test: Test method testVariousConfigurations[7](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:41 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:41 IlluminaBasecallsConverter All work is complete. Test: Test method testVariousConfigurations[7](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:41 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:41 IlluminaBasecallsConverter All work is complete. Test: Test method testVariousConfigurations[7](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:41 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:00:41 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. Test: Test method testVariousConfigurations[7](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testVariousConfigurations[8](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) Test: Test method testVariousConfigurations[8](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:43 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testVariousConfigurations[8](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null) STANDARD_ERROR INFO 2024-07-02 12:00:43 IlluminaBasecallsToSam Test: Test method testVariousConfigurations[8](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[8](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testVariousConfigurations[8](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[8](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testVariousConfigurations[8](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testVariousConfigurations[8](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[8](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testVariousConfigurations[8](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[8](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B8B25T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/hiseqxSingleLocs.16494396704832164998/library_double.params -INCLUDE_BC_IN_RG_TAG false -BARCODE_POPULATION_STRATEGY ORPHANS_ONLY -INCLUDE_BARCODE_QUALITY false ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B8B25T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/hiseqxSingleLocs.16494396704832164998/library_double.params -INCLUDE_BC_IN_RG_TAG false -BARCODE_POPULATION_STRATEGY ORPHANS_ONLY -INCLUDE_BARCODE_QUALITY false Test: Test method testVariousConfigurations[8](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[8](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[8](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[8](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:43.434 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:43.434 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVariousConfigurations[8](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:43.434 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:43.434 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVariousConfigurations[8](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:43.434 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:43.434 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVariousConfigurations[8](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:43.434 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:43.434 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVariousConfigurations[8](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:43 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=false READ_STRUCTURE=25T8B8B25T LIBRARY_PARAMS=/tmp/pbuilder2/hiseqxSingleLocs.16494396704832164998/library_double.params BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:43 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=false READ_STRUCTURE=25T8B8B25T LIBRARY_PARAMS=/tmp/pbuilder2/hiseqxSingleLocs.16494396704832164998/library_double.params BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testVariousConfigurations[8](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testVariousConfigurations[8](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:43 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B8B25T INFO 2024-07-02 12:00:43 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B8B25T Test: Test method testVariousConfigurations[8](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:43 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:43 IlluminaBasecallsConverter All work is complete. Test: Test method testVariousConfigurations[8](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:43 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:00:43 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. Test: Test method testVariousConfigurations[8](hiseqxSingleLocs., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T_hiseqx/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T_hiseqx/sams, null)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testVariousConfigurations[9](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, 1101)(picard.illumina.IlluminaBasecallsToSamTest) Test: Test method testVariousConfigurations[9](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, 1101)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:43 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testVariousConfigurations[9](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, 1101) STANDARD_ERROR INFO 2024-07-02 12:00:43 IlluminaBasecallsToSam Test: Test method testVariousConfigurations[9](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, 1101)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[9](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, 1101)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testVariousConfigurations[9](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, 1101)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[9](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, 1101)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testVariousConfigurations[9](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, 1101)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testVariousConfigurations[9](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, 1101)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[9](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, 1101)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testVariousConfigurations[9](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, 1101)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[9](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, 1101)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B8B25T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/dualBarcode.4349228534892509390/library_double.params -INCLUDE_BC_IN_RG_TAG false -BARCODE_POPULATION_STRATEGY ORPHANS_ONLY -INCLUDE_BARCODE_QUALITY false -PROCESS_SINGLE_TILE 1101 ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 25T8B8B25T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/dualBarcode.4349228534892509390/library_double.params -INCLUDE_BC_IN_RG_TAG false -BARCODE_POPULATION_STRATEGY ORPHANS_ONLY -INCLUDE_BARCODE_QUALITY false -PROCESS_SINGLE_TILE 1101 Test: Test method testVariousConfigurations[9](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, 1101)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[9](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, 1101)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[9](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, 1101)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[9](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, 1101)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:43.978 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:43.978 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVariousConfigurations[9](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, 1101)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:43.978 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:43.978 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVariousConfigurations[9](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, 1101)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:43.978 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:43.978 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVariousConfigurations[9](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, 1101)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:43.979 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:43.979 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVariousConfigurations[9](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, 1101)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:43 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=false READ_STRUCTURE=25T8B8B25T LIBRARY_PARAMS=/tmp/pbuilder2/dualBarcode.4349228534892509390/library_double.params PROCESS_SINGLE_TILE=1101 BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:43 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=false READ_STRUCTURE=25T8B8B25T LIBRARY_PARAMS=/tmp/pbuilder2/dualBarcode.4349228534892509390/library_double.params PROCESS_SINGLE_TILE=1101 BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testVariousConfigurations[9](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, 1101)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testVariousConfigurations[9](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, 1101)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:44 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B8B25T INFO 2024-07-02 12:00:44 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 25T8B8B25T Test: Test method testVariousConfigurations[9](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, 1101)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:44 IlluminaBasecallsConverter All work is complete. INFO 2024-07-02 12:00:44 IlluminaBasecallsConverter All work is complete. Test: Test method testVariousConfigurations[9](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, 1101)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:44 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:00:44 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.00 minutes. Test: Test method testVariousConfigurations[9](dualBarcode., library_double.params, 2, 25T8B8B25T, testdata/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls, testdata/picard/illumina/25T8B8B25T/sams, 1101)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testVariousConfigurations[10](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, 1102)(picard.illumina.IlluminaBasecallsToSamTest) Test: Test method testVariousConfigurations[10](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, 1102)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:44 IlluminaBasecallsToSam Gradle suite > Gradle test > picard.illumina.IlluminaBasecallsToSamTest.testVariousConfigurations[10](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, 1102) STANDARD_ERROR INFO 2024-07-02 12:00:44 IlluminaBasecallsToSam Test: Test method testVariousConfigurations[10](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, 1102)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[10](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, 1102)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testVariousConfigurations[10](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, 1102)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[10](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, 1102)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testVariousConfigurations[10](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, 1102)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testVariousConfigurations[10](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, 1102)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[10](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, 1102)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testVariousConfigurations[10](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, 1102)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[10](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, 1102)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 151T8B8B151T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/cbclConvert.1844682900961071927/library_double.params -INCLUDE_BC_IN_RG_TAG false -BARCODE_POPULATION_STRATEGY ORPHANS_ONLY -INCLUDE_BARCODE_QUALITY false -PROCESS_SINGLE_TILE 1102 ********** IlluminaBasecallsToSam -BASECALLS_DIR testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls -LANE 1 -RUN_BARCODE HiMom -READ_STRUCTURE 151T8B8B151T -SEQUENCING_CENTER BI -LIBRARY_PARAMS /tmp/pbuilder2/cbclConvert.1844682900961071927/library_double.params -INCLUDE_BC_IN_RG_TAG false -BARCODE_POPULATION_STRATEGY ORPHANS_ONLY -INCLUDE_BARCODE_QUALITY false -PROCESS_SINGLE_TILE 1102 Test: Test method testVariousConfigurations[10](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, 1102)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: ********** ********** Test: Test method testVariousConfigurations[10](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, 1102)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[10](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, 1102)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Test: Test method testVariousConfigurations[10](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, 1102)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:44.640 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:44.640 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVariousConfigurations[10](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, 1102)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:44.640 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:44.640 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVariousConfigurations[10](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, 1102)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:44.640 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:00:44.640 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVariousConfigurations[10](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, 1102)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: 12:00:44.640 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:00:44.640 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVariousConfigurations[10](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, 1102)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:44 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=false READ_STRUCTURE=151T8B8B151T LIBRARY_PARAMS=/tmp/pbuilder2/cbclConvert.1844682900961071927/library_double.params PROCESS_SINGLE_TILE=1102 BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:00:44 GMT+14:00 2024] IlluminaBasecallsToSam BASECALLS_DIR=testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls LANE=1 RUN_BARCODE=HiMom SEQUENCING_CENTER=BI INCLUDE_BC_IN_RG_TAG=false READ_STRUCTURE=151T8B8B151T LIBRARY_PARAMS=/tmp/pbuilder2/cbclConvert.1844682900961071927/library_double.params PROCESS_SINGLE_TILE=1102 BARCODE_POPULATION_STRATEGY=ORPHANS_ONLY INCLUDE_BARCODE_QUALITY=false PLATFORM=ILLUMINA ADAPTERS_TO_CHECK=[INDEXED, DUAL_INDEXED, NEXTERA_V2, FLUIDIGM] NUM_PROCESSORS=0 FORCE_GC=true APPLY_EAMSS_FILTER=true MAX_READS_IN_RAM_PER_TILE=1200000 MINIMUM_QUALITY=2 INCLUDE_NON_PF_READS=true IGNORE_UNEXPECTED_BARCODES=false MOLECULAR_INDEX_TAG=RX MOLECULAR_INDEX_BASE_QUALITY_TAG=QX VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testVariousConfigurations[10](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, 1102)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:00:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testVariousConfigurations[10](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, 1102)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:45 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 151T8B8B151T INFO 2024-07-02 12:00:45 IlluminaBasecallsToSam DONE_READING STRUCTURE IS 151T8B8B151T Test: Test method testVariousConfigurations[10](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, 1102)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:45 CbclReader Processing tile 1102 INFO 2024-07-02 12:00:45 CbclReader Processing tile 1102 Test: Test method testVariousConfigurations[10](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, 1102)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:45 NewIlluminaBasecallsConverter Finished processing tile 1102 INFO 2024-07-02 12:00:45 NewIlluminaBasecallsConverter Finished processing tile 1102 Test: Test method testVariousConfigurations[10](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, 1102)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: INFO 2024-07-02 12:00:50 NewIlluminaBasecallsConverter Writing out tile 1102 INFO 2024-07-02 12:00:50 NewIlluminaBasecallsConverter Writing out tile 1102 Test: Test method testVariousConfigurations[10](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, 1102)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: [Tue Jul 02 12:00:50 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.10 minutes. [Tue Jul 02 12:00:50 GMT+14:00 2024] picard.illumina.IlluminaBasecallsToSam done. Elapsed time: 0.10 minutes. Test: Test method testVariousConfigurations[10](cbclConvert., library_double.params, 2, 151T8B8B151T, testdata/picard/illumina/151T8B8B151T_cbcl/Data/Intensities/BaseCalls, testdata/picard/illumina/151T8B8B151T_cbcl/sams, 1102)(picard.illumina.IlluminaBasecallsToSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method barcodeParsingTest(picard.illumina.parser.IlluminaDataProviderTest) Running Test: Test method testIlluminaDataProviderBclMethod[0](Bustard Parsing Test(25T8B25T) w/Clocs, 1, 180, [1101, 1201, 2101], [Lpicard.illumina.parser.IlluminaDataType;@6068e63a, 25T8B25T, 0, 0, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls)(picard.illumina.parser.IlluminaDataProviderTest) Running Test: Test method testIlluminaDataProviderBclMethod[1](Bustard Parsing Test(25T8S25T) w/Clocs, 1, 180, [1101, 1201, 2101], [Lpicard.illumina.parser.IlluminaDataType;@1cb88d67, 25T8S25T, 0, 0, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls)(picard.illumina.parser.IlluminaDataProviderTest) Running Test: Test method testIlluminaDataProviderBclMethod[2](Bustard Parsing Test(25T8S25T) w/Clocs with ending skip, 1, 180, [1101, 1201, 2101], [Lpicard.illumina.parser.IlluminaDataType;@76279fb8, 25T8B1S, 0, 0, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls)(picard.illumina.parser.IlluminaDataProviderTest) Running Test: Test method testIlluminaDataProviderBclMethod[3](Bustard Parsing Test(25S8S25T) w/Clocs, 1, 180, [1101, 1201, 2101], [Lpicard.illumina.parser.IlluminaDataType;@49ffe2d3, 25S8S25T, 0, 0, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls)(picard.illumina.parser.IlluminaDataProviderTest) Running Test: Test method testIlluminaDataProviderBclMethod[4](Bustard Parsing Test(25T8B25T) w/Clocs And Seeking, 1, 61, [1101, 1201, 2101], [Lpicard.illumina.parser.IlluminaDataType;@5ef3fc48, 25T8B25T, 2101, 4631, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls)(picard.illumina.parser.IlluminaDataProviderTest) Running Test: Test method testIlluminaDataProviderMissingDatas[0](Bad Lane(5), 5, 60, [1101, 1201, 2101], [Lpicard.illumina.parser.IlluminaDataType;@1d1c341d, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls)(picard.illumina.parser.IlluminaDataProviderTest) Running Test: Test method testIlluminaDataProviderMissingDatas[1](Bad Read Structure(25TB25T), 4, 60, [1101, 1201, 2101], [Lpicard.illumina.parser.IlluminaDataType;@595495b8, 25TB25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls)(picard.illumina.parser.IlluminaDataProviderTest) Running Test: Test method testIlluminaDataProviderMissingDatas[2](Bad Read Structure(25T0B25T), 4, 60, [1101, 1201, 2101], [Lpicard.illumina.parser.IlluminaDataType;@595495b8, 25T0B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls)(picard.illumina.parser.IlluminaDataProviderTest) Running Test: Test method testIlluminaDataProviderMissingDatas[3](Bad Read Structure(-225T0B25T), 4, 60, [1101, 1201, 2101], [Lpicard.illumina.parser.IlluminaDataType;@595495b8, -25T0B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls)(picard.illumina.parser.IlluminaDataProviderTest) Running Test: Test method testIlluminaDataProviderMissingDatas[4](Missing Barcodes File, 9, 60, [1101, 1201, 2101], [Lpicard.illumina.parser.IlluminaDataType;@2f00dcfc, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls)(picard.illumina.parser.IlluminaDataProviderTest) Running Test: Test method testIlluminaDataProviderMissingDatas[5](Missing Cycle File, 9, 60, [1101, 1201, 2101], [Lpicard.illumina.parser.IlluminaDataType;@50c6ea85, 25T8B25T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls)(picard.illumina.parser.IlluminaDataProviderTest) Running Test: Test method testIlluminaDataProviderMissingDatas[6](Missing Filter File, 9, 60, [1101, 1201, 2101], [Lpicard.illumina.parser.IlluminaDataType;@82f1b52, 25T8B24T, testdata/picard/illumina/25T8B25T/Data/Intensities/BaseCalls)(picard.illumina.parser.IlluminaDataProviderTest) Running Test: Test method invalidLaneForLTRegex[0](-1000)(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method invalidLaneForLTRegex[1](-10)(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method invalidLaneForLTRegex[2](-1)(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method missingTileTest[0](1, [Bcl, Barcode], [Bcl, Barcode], [BaseCalls/s_1_0007_barcode.txt.gz], .gz)(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method missingTileTest[1](2, [Bcl, Locs, Clocs, Pos, Filter, Barcode, MultiTileFilter, MultiTileLocs, MultiTileBcl], [Bcl, Locs, Clocs, Pos, Filter, Barcode, MultiTileFilter, MultiTileLocs, MultiTileBcl], [BaseCalls/L002/C1.1/s_2_2.bcl, BaseCalls/L002/C2.1/s_2_2.bcl, BaseCalls/L002/C3.1/s_2_2.bcl, BaseCalls/L002/C4.1/s_2_2.bcl, BaseCalls/L002/C5.1/s_2_2.bcl, BaseCalls/L002/C6.1/s_2_2.bcl, BaseCalls/L002/C7.1/s_2_2.bcl, BaseCalls/L002/C8.1/s_2_2.bcl, BaseCalls/L002/C9.1/s_2_2.bcl, BaseCalls/L002/C10.1/s_2_2.bcl, BaseCalls/L002/C11.1/s_2_2.bcl, BaseCalls/L002/C12.1/s_2_2.bcl, BaseCalls/L002/C13.1/s_2_2.bcl, BaseCalls/L002/C14.1/s_2_2.bcl, BaseCalls/L002/C15.1/s_2_2.bcl, BaseCalls/L002/C16.1/s_2_2.bcl, BaseCalls/L002/C17.1/s_2_2.bcl, BaseCalls/L002/C18.1/s_2_2.bcl, BaseCalls/L002/C19.1/s_2_2.bcl, BaseCalls/L002/C20.1/s_2_2.bcl], .gz)(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method missingTileTest[2](3, [Bcl, Locs, Clocs, Pos, Filter, Barcode, MultiTileFilter, MultiTileLocs, MultiTileBcl], [Bcl, Locs, Clocs, Pos, Filter, Barcode, MultiTileFilter, MultiTileLocs, MultiTileBcl], [BaseCalls/L003/C1.1/s_3_2.bcl], .bz2)(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method missingTileTest[3](4, [Bcl, Locs, Clocs, Pos, Filter, Barcode, MultiTileFilter, MultiTileLocs, MultiTileBcl], [Pos, Locs], [s_4_10_pos.txt, L004/s_4_2.locs], null)(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method notMatchingRegexTest[0](0, s_-0_111)(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method notMatchingRegexTest[1](1, s_1_A3)(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method notMatchingRegexTest[2](10, s_-100_1)(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method notMatchingRegexTest[3](20, s_21_1)(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method passNewUtilTest(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method passingVerifyTest(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method perTileFileUtilsTest[0](Locs, null, false, L007)(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method perTileFileUtilsTest[1](Clocs, null, false, L007)(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method perTileFileUtilsTest[2](Pos, .gz, false, null)(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method perTileFileUtilsTest[3](Pos, null, false, null)(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method perTileFileUtilsTest[4](Filter, null, true, BaseCalls/L007)(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method perTileFileUtilsTest[5](Barcode, .bz2, true, BaseCalls)(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method perTilePerCycleFileUtilsMissingCycleTest[0]([Range(10, 15, 6)])(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method perTilePerCycleFileUtilsMissingCycleTest[1]([Range(9, 12, 4), Range(14, 15, 2)])(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method perTilePerCycleFileUtilsTest[0](Bcl, BaseCalls/L007, [I@624a226e, false, false)(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method perTilePerCycleFileUtilsTest[1](Bcl, BaseCalls/L007, [I@131f61f3, true, true)(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method regexTests[0](0, s_0_1111.test)(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method regexTests[1](1, s_1_23.test)(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method regexTests[2](10, s_10_1.test)(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method testHasCbcls[0](1, true, true, true)(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method testHasCbcls[1](1, true, false, false)(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method testHasCbcls[2](1, false, false, false)(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method testHasCbcls[3](-1, false, false, false)(picard.illumina.parser.IlluminaFileUtilTest) Running Test: Test method testCollectIlluminaLaneMetrics[0](A7LE0, 25T8B8B25T, false)(picard.illumina.IlluminaLaneMetricsCollectorTest) Test: Test method testCollectIlluminaLaneMetrics[0](A7LE0, 25T8B8B25T, false)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 1 lane metrics to /tmp/illuminaLaneMetricsCollectorTest4958234469704715689.tmp/test.illumina_lane_metrics ... Gradle suite > Gradle test > picard.illumina.IlluminaLaneMetricsCollectorTest.testCollectIlluminaLaneMetrics[0](A7LE0, 25T8B8B25T, false) STANDARD_ERROR INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 1 lane metrics to /tmp/illuminaLaneMetricsCollectorTest4958234469704715689.tmp/test.illumina_lane_metrics ... Test: Test method testCollectIlluminaLaneMetrics[0](A7LE0, 25T8B8B25T, false)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest4958234469704715689.tmp/test.illumina_phasing_metrics ... INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest4958234469704715689.tmp/test.illumina_phasing_metrics ... Test: Test method testCollectIlluminaLaneMetrics[0](A7LE0, 25T8B8B25T, false)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 1 lane metrics to /tmp/illuminaLaneMetricsCollectorTest9459328585225519166.tmp/test.illumina_lane_metrics ... INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 1 lane metrics to /tmp/illuminaLaneMetricsCollectorTest9459328585225519166.tmp/test.illumina_lane_metrics ... Test: Test method testCollectIlluminaLaneMetrics[0](A7LE0, 25T8B8B25T, false)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest9459328585225519166.tmp/test.illumina_phasing_metrics ... INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest9459328585225519166.tmp/test.illumina_phasing_metrics ... Running Test: Test method testCollectIlluminaLaneMetrics[1](C2MFAACXX, 95T101T, false)(picard.illumina.IlluminaLaneMetricsCollectorTest) Test: Test method testCollectIlluminaLaneMetrics[1](C2MFAACXX, 95T101T, false)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 8 lane metrics to /tmp/illuminaLaneMetricsCollectorTest4050878420830519657.tmp/test.illumina_lane_metrics ... Gradle suite > Gradle test > picard.illumina.IlluminaLaneMetricsCollectorTest.testCollectIlluminaLaneMetrics[1](C2MFAACXX, 95T101T, false) STANDARD_ERROR INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 8 lane metrics to /tmp/illuminaLaneMetricsCollectorTest4050878420830519657.tmp/test.illumina_lane_metrics ... Test: Test method testCollectIlluminaLaneMetrics[1](C2MFAACXX, 95T101T, false)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 16 lane metrics to /tmp/illuminaLaneMetricsCollectorTest4050878420830519657.tmp/test.illumina_phasing_metrics ... INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 16 lane metrics to /tmp/illuminaLaneMetricsCollectorTest4050878420830519657.tmp/test.illumina_phasing_metrics ... Test: Test method testCollectIlluminaLaneMetrics[1](C2MFAACXX, 95T101T, false)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 8 lane metrics to /tmp/illuminaLaneMetricsCollectorTest208042550544579761.tmp/test.illumina_lane_metrics ... INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 8 lane metrics to /tmp/illuminaLaneMetricsCollectorTest208042550544579761.tmp/test.illumina_lane_metrics ... Test: Test method testCollectIlluminaLaneMetrics[1](C2MFAACXX, 95T101T, false)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 16 lane metrics to /tmp/illuminaLaneMetricsCollectorTest208042550544579761.tmp/test.illumina_phasing_metrics ... INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 16 lane metrics to /tmp/illuminaLaneMetricsCollectorTest208042550544579761.tmp/test.illumina_phasing_metrics ... Running Test: Test method testCollectIlluminaLaneMetrics[2](H7BATADXX, 76T8B76T, false)(picard.illumina.IlluminaLaneMetricsCollectorTest) Test: Test method testCollectIlluminaLaneMetrics[2](H7BATADXX, 76T8B76T, false)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest5065944639879593539.tmp/test.illumina_lane_metrics ... Gradle suite > Gradle test > picard.illumina.IlluminaLaneMetricsCollectorTest.testCollectIlluminaLaneMetrics[2](H7BATADXX, 76T8B76T, false) STANDARD_ERROR INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest5065944639879593539.tmp/test.illumina_lane_metrics ... Test: Test method testCollectIlluminaLaneMetrics[2](H7BATADXX, 76T8B76T, false)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 4 lane metrics to /tmp/illuminaLaneMetricsCollectorTest5065944639879593539.tmp/test.illumina_phasing_metrics ... INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 4 lane metrics to /tmp/illuminaLaneMetricsCollectorTest5065944639879593539.tmp/test.illumina_phasing_metrics ... Test: Test method testCollectIlluminaLaneMetrics[2](H7BATADXX, 76T8B76T, false)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest4892970667045857087.tmp/test.illumina_lane_metrics ... INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest4892970667045857087.tmp/test.illumina_lane_metrics ... Test: Test method testCollectIlluminaLaneMetrics[2](H7BATADXX, 76T8B76T, false)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 4 lane metrics to /tmp/illuminaLaneMetricsCollectorTest4892970667045857087.tmp/test.illumina_phasing_metrics ... INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 4 lane metrics to /tmp/illuminaLaneMetricsCollectorTest4892970667045857087.tmp/test.illumina_phasing_metrics ... Running Test: Test method testCollectIlluminaLaneMetrics[3](H7H7RADXX, 101T8B8B101T, false)(picard.illumina.IlluminaLaneMetricsCollectorTest) Test: Test method testCollectIlluminaLaneMetrics[3](H7H7RADXX, 101T8B8B101T, false)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest4282923906182478820.tmp/test.illumina_lane_metrics ... Gradle suite > Gradle test > picard.illumina.IlluminaLaneMetricsCollectorTest.testCollectIlluminaLaneMetrics[3](H7H7RADXX, 101T8B8B101T, false) STANDARD_ERROR INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest4282923906182478820.tmp/test.illumina_lane_metrics ... Test: Test method testCollectIlluminaLaneMetrics[3](H7H7RADXX, 101T8B8B101T, false)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 4 lane metrics to /tmp/illuminaLaneMetricsCollectorTest4282923906182478820.tmp/test.illumina_phasing_metrics ... INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 4 lane metrics to /tmp/illuminaLaneMetricsCollectorTest4282923906182478820.tmp/test.illumina_phasing_metrics ... Test: Test method testCollectIlluminaLaneMetrics[3](H7H7RADXX, 101T8B8B101T, false)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest14876727971623118194.tmp/test.illumina_lane_metrics ... INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest14876727971623118194.tmp/test.illumina_lane_metrics ... Test: Test method testCollectIlluminaLaneMetrics[3](H7H7RADXX, 101T8B8B101T, false)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 4 lane metrics to /tmp/illuminaLaneMetricsCollectorTest14876727971623118194.tmp/test.illumina_phasing_metrics ... INFO 2024-07-02 12:00:55 IlluminaLaneMetricsCollector Writing 4 lane metrics to /tmp/illuminaLaneMetricsCollectorTest14876727971623118194.tmp/test.illumina_phasing_metrics ... Running Test: Test method testCollectIlluminaLaneMetrics[4](A67HY, 8B8B, false)(picard.illumina.IlluminaLaneMetricsCollectorTest) Test: Test method testCollectIlluminaLaneMetrics[4](A67HY, 8B8B, false)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:56 IlluminaLaneMetricsCollector Writing 1 lane metrics to /tmp/illuminaLaneMetricsCollectorTest17415887818944074895.tmp/test.illumina_lane_metrics ... Gradle suite > Gradle test > picard.illumina.IlluminaLaneMetricsCollectorTest.testCollectIlluminaLaneMetrics[4](A67HY, 8B8B, false) STANDARD_ERROR INFO 2024-07-02 12:00:56 IlluminaLaneMetricsCollector Writing 1 lane metrics to /tmp/illuminaLaneMetricsCollectorTest17415887818944074895.tmp/test.illumina_lane_metrics ... Test: Test method testCollectIlluminaLaneMetrics[4](A67HY, 8B8B, false)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:56 IlluminaLaneMetricsCollector Writing 0 lane metrics to /tmp/illuminaLaneMetricsCollectorTest17415887818944074895.tmp/test.illumina_phasing_metrics ... INFO 2024-07-02 12:00:56 IlluminaLaneMetricsCollector Writing 0 lane metrics to /tmp/illuminaLaneMetricsCollectorTest17415887818944074895.tmp/test.illumina_phasing_metrics ... Test: Test method testCollectIlluminaLaneMetrics[4](A67HY, 8B8B, false)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:56 IlluminaLaneMetricsCollector Writing 1 lane metrics to /tmp/illuminaLaneMetricsCollectorTest4706148099183145907.tmp/test.illumina_lane_metrics ... INFO 2024-07-02 12:00:56 IlluminaLaneMetricsCollector Writing 1 lane metrics to /tmp/illuminaLaneMetricsCollectorTest4706148099183145907.tmp/test.illumina_lane_metrics ... Test: Test method testCollectIlluminaLaneMetrics[4](A67HY, 8B8B, false)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:56 IlluminaLaneMetricsCollector Writing 0 lane metrics to /tmp/illuminaLaneMetricsCollectorTest4706148099183145907.tmp/test.illumina_phasing_metrics ... INFO 2024-07-02 12:00:56 IlluminaLaneMetricsCollector Writing 0 lane metrics to /tmp/illuminaLaneMetricsCollectorTest4706148099183145907.tmp/test.illumina_phasing_metrics ... Running Test: Test method testCollectIlluminaLaneMetrics[5](NovaSeq, 151T8B8B151T, true)(picard.illumina.IlluminaLaneMetricsCollectorTest) Test: Test method testCollectIlluminaLaneMetrics[5](NovaSeq, 151T8B8B151T, true)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:57 IlluminaLaneMetricsCollector Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest10726303290189417676.tmp/test.illumina_lane_metrics ... Gradle suite > Gradle test > picard.illumina.IlluminaLaneMetricsCollectorTest.testCollectIlluminaLaneMetrics[5](NovaSeq, 151T8B8B151T, true) STANDARD_ERROR INFO 2024-07-02 12:00:57 IlluminaLaneMetricsCollector Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest10726303290189417676.tmp/test.illumina_lane_metrics ... Test: Test method testCollectIlluminaLaneMetrics[5](NovaSeq, 151T8B8B151T, true)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:57 IlluminaLaneMetricsCollector Writing 4 lane metrics to /tmp/illuminaLaneMetricsCollectorTest10726303290189417676.tmp/test.illumina_phasing_metrics ... INFO 2024-07-02 12:00:57 IlluminaLaneMetricsCollector Writing 4 lane metrics to /tmp/illuminaLaneMetricsCollectorTest10726303290189417676.tmp/test.illumina_phasing_metrics ... Test: Test method testCollectIlluminaLaneMetrics[5](NovaSeq, 151T8B8B151T, true)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:58 IlluminaLaneMetricsCollector Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest9194784174457707413.tmp/test.illumina_lane_metrics ... INFO 2024-07-02 12:00:58 IlluminaLaneMetricsCollector Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest9194784174457707413.tmp/test.illumina_lane_metrics ... Test: Test method testCollectIlluminaLaneMetrics[5](NovaSeq, 151T8B8B151T, true)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:58 IlluminaLaneMetricsCollector Writing 4 lane metrics to /tmp/illuminaLaneMetricsCollectorTest9194784174457707413.tmp/test.illumina_phasing_metrics ... INFO 2024-07-02 12:00:58 IlluminaLaneMetricsCollector Writing 4 lane metrics to /tmp/illuminaLaneMetricsCollectorTest9194784174457707413.tmp/test.illumina_phasing_metrics ... Running Test: Test method testMissingPhasingValuesSilent(picard.illumina.IlluminaLaneMetricsCollectorTest) Test: Test method testMissingPhasingValuesSilent(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:58 IlluminaLaneMetricsCollector Writing 4 lane metrics to /tmp/illuminaLaneMetricsCollectorTest2391036995779323656.tmp/test.illumina_lane_metrics ... Gradle suite > Gradle test > picard.illumina.IlluminaLaneMetricsCollectorTest.testMissingPhasingValuesSilent STANDARD_ERROR INFO 2024-07-02 12:00:58 IlluminaLaneMetricsCollector Writing 4 lane metrics to /tmp/illuminaLaneMetricsCollectorTest2391036995779323656.tmp/test.illumina_lane_metrics ... Test: Test method testMissingPhasingValuesSilent(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:58 IlluminaLaneMetricsCollector Writing 8 lane metrics to /tmp/illuminaLaneMetricsCollectorTest2391036995779323656.tmp/test.illumina_phasing_metrics ... INFO 2024-07-02 12:00:58 IlluminaLaneMetricsCollector Writing 8 lane metrics to /tmp/illuminaLaneMetricsCollectorTest2391036995779323656.tmp/test.illumina_phasing_metrics ... Test: Test method testMissingPhasingValuesSilent(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:58 IlluminaLaneMetricsCollector Writing 4 lane metrics to /tmp/illuminaLaneMetricsCollectorTest6220392069025038542.tmp/test.illumina_lane_metrics ... INFO 2024-07-02 12:00:58 IlluminaLaneMetricsCollector Writing 4 lane metrics to /tmp/illuminaLaneMetricsCollectorTest6220392069025038542.tmp/test.illumina_lane_metrics ... Test: Test method testMissingPhasingValuesSilent(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:58 IlluminaLaneMetricsCollector Writing 8 lane metrics to /tmp/illuminaLaneMetricsCollectorTest6220392069025038542.tmp/test.illumina_phasing_metrics ... INFO 2024-07-02 12:00:58 IlluminaLaneMetricsCollector Writing 8 lane metrics to /tmp/illuminaLaneMetricsCollectorTest6220392069025038542.tmp/test.illumina_phasing_metrics ... Running Test: Test method testMissingPhasingValuesStrict(picard.illumina.IlluminaLaneMetricsCollectorTest) Running Test: Test method testWriteLaneMetrics[0](130321_SL-MAK_0035_FC000000000-A306B)(picard.illumina.IlluminaLaneMetricsCollectorTest) Test: Test method testWriteLaneMetrics[0](130321_SL-MAK_0035_FC000000000-A306B)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:58 IlluminaLaneMetricsCollector Writing 1 lane metrics to /tmp/illuminaLaneMetricsCollectorTest4245914103390806024.tmp/test.illumina_lane_metrics ... Gradle suite > Gradle test > picard.illumina.IlluminaLaneMetricsCollectorTest.testWriteLaneMetrics[0](130321_SL-MAK_0035_FC000000000-A306B) STANDARD_ERROR INFO 2024-07-02 12:00:58 IlluminaLaneMetricsCollector Writing 1 lane metrics to /tmp/illuminaLaneMetricsCollectorTest4245914103390806024.tmp/test.illumina_lane_metrics ... Test: Test method testWriteLaneMetrics[0](130321_SL-MAK_0035_FC000000000-A306B)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:58 IlluminaLaneMetricsCollector Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest4245914103390806024.tmp/test.illumina_phasing_metrics ... INFO 2024-07-02 12:00:58 IlluminaLaneMetricsCollector Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest4245914103390806024.tmp/test.illumina_phasing_metrics ... Test: Test method testWriteLaneMetrics[0](130321_SL-MAK_0035_FC000000000-A306B)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:59 IlluminaLaneMetricsCollector Writing 1 lane metrics to /tmp/illuminaLaneMetricsCollectorTest11976537508386048774.tmp/test.illumina_lane_metrics ... INFO 2024-07-02 12:00:59 IlluminaLaneMetricsCollector Writing 1 lane metrics to /tmp/illuminaLaneMetricsCollectorTest11976537508386048774.tmp/test.illumina_lane_metrics ... Test: Test method testWriteLaneMetrics[0](130321_SL-MAK_0035_FC000000000-A306B)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:59 IlluminaLaneMetricsCollector Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest11976537508386048774.tmp/test.illumina_phasing_metrics ... INFO 2024-07-02 12:00:59 IlluminaLaneMetricsCollector Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest11976537508386048774.tmp/test.illumina_phasing_metrics ... Running Test: Test method testWriteLaneMetrics[1](130318_SL-HBB_0226_BFCC1WYMACXX)(picard.illumina.IlluminaLaneMetricsCollectorTest) Test: Test method testWriteLaneMetrics[1](130318_SL-HBB_0226_BFCC1WYMACXX)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:59 IlluminaLaneMetricsCollector Writing 8 lane metrics to /tmp/illuminaLaneMetricsCollectorTest17821906075586201080.tmp/test.illumina_lane_metrics ... Gradle suite > Gradle test > picard.illumina.IlluminaLaneMetricsCollectorTest.testWriteLaneMetrics[1](130318_SL-HBB_0226_BFCC1WYMACXX) STANDARD_ERROR INFO 2024-07-02 12:00:59 IlluminaLaneMetricsCollector Writing 8 lane metrics to /tmp/illuminaLaneMetricsCollectorTest17821906075586201080.tmp/test.illumina_lane_metrics ... Test: Test method testWriteLaneMetrics[1](130318_SL-HBB_0226_BFCC1WYMACXX)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:59 IlluminaLaneMetricsCollector Writing 16 lane metrics to /tmp/illuminaLaneMetricsCollectorTest17821906075586201080.tmp/test.illumina_phasing_metrics ... INFO 2024-07-02 12:00:59 IlluminaLaneMetricsCollector Writing 16 lane metrics to /tmp/illuminaLaneMetricsCollectorTest17821906075586201080.tmp/test.illumina_phasing_metrics ... Test: Test method testWriteLaneMetrics[1](130318_SL-HBB_0226_BFCC1WYMACXX)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:59 IlluminaLaneMetricsCollector Writing 8 lane metrics to /tmp/illuminaLaneMetricsCollectorTest3950720733456053454.tmp/test.illumina_lane_metrics ... INFO 2024-07-02 12:00:59 IlluminaLaneMetricsCollector Writing 8 lane metrics to /tmp/illuminaLaneMetricsCollectorTest3950720733456053454.tmp/test.illumina_lane_metrics ... Test: Test method testWriteLaneMetrics[1](130318_SL-HBB_0226_BFCC1WYMACXX)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:59 IlluminaLaneMetricsCollector Writing 16 lane metrics to /tmp/illuminaLaneMetricsCollectorTest3950720733456053454.tmp/test.illumina_phasing_metrics ... INFO 2024-07-02 12:00:59 IlluminaLaneMetricsCollector Writing 16 lane metrics to /tmp/illuminaLaneMetricsCollectorTest3950720733456053454.tmp/test.illumina_phasing_metrics ... Running Test: Test method testWriteLaneMetrics[2](130401_SL-HAC_0022_BH07PBADXX)(picard.illumina.IlluminaLaneMetricsCollectorTest) Test: Test method testWriteLaneMetrics[2](130401_SL-HAC_0022_BH07PBADXX)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:59 IlluminaLaneMetricsCollector Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest9758193879867720129.tmp/test.illumina_lane_metrics ... Gradle suite > Gradle test > picard.illumina.IlluminaLaneMetricsCollectorTest.testWriteLaneMetrics[2](130401_SL-HAC_0022_BH07PBADXX) STANDARD_ERROR INFO 2024-07-02 12:00:59 IlluminaLaneMetricsCollector Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest9758193879867720129.tmp/test.illumina_lane_metrics ... Test: Test method testWriteLaneMetrics[2](130401_SL-HAC_0022_BH07PBADXX)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:59 IlluminaLaneMetricsCollector Writing 4 lane metrics to /tmp/illuminaLaneMetricsCollectorTest9758193879867720129.tmp/test.illumina_phasing_metrics ... INFO 2024-07-02 12:00:59 IlluminaLaneMetricsCollector Writing 4 lane metrics to /tmp/illuminaLaneMetricsCollectorTest9758193879867720129.tmp/test.illumina_phasing_metrics ... Test: Test method testWriteLaneMetrics[2](130401_SL-HAC_0022_BH07PBADXX)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:59 IlluminaLaneMetricsCollector Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest7693175731615780237.tmp/test.illumina_lane_metrics ... INFO 2024-07-02 12:00:59 IlluminaLaneMetricsCollector Writing 2 lane metrics to /tmp/illuminaLaneMetricsCollectorTest7693175731615780237.tmp/test.illumina_lane_metrics ... Test: Test method testWriteLaneMetrics[2](130401_SL-HAC_0022_BH07PBADXX)(picard.illumina.IlluminaLaneMetricsCollectorTest) produced standard out/err: INFO 2024-07-02 12:00:59 IlluminaLaneMetricsCollector Writing 4 lane metrics to /tmp/illuminaLaneMetricsCollectorTest7693175731615780237.tmp/test.illumina_phasing_metrics ... INFO 2024-07-02 12:00:59 IlluminaLaneMetricsCollector Writing 4 lane metrics to /tmp/illuminaLaneMetricsCollectorTest7693175731615780237.tmp/test.illumina_phasing_metrics ... Running Test: Test method tesIlluminaManifest(picard.arrays.illumina.IlluminaManifestTest) Running Test: Test method testInvalidIlluminaManifest(picard.arrays.illumina.IlluminaManifestTest) Running Test: Test method performanceTestGetTileFromReadName(picard.util.IlluminaUtilTest) Test: Test method performanceTestGetTileFromReadName(picard.util.IlluminaUtilTest) produced standard out/err: Time taken: 1489ms. Gradle suite > Gradle test > picard.util.IlluminaUtilTest.performanceTestGetTileFromReadName STANDARD_OUT Time taken: 1489ms. Running Test: Test method testFindTileInReadName[0](300WFAAXX:1:119:1024:978#0/1, 119)(picard.util.IlluminaUtilTest) Running Test: Test method testFindTileInReadName[1](300WFAAXX090909:1:1:1024:978#0/1, 1)(picard.util.IlluminaUtilTest) Running Test: Test method testFindTileInReadName[2](FOO, null)(picard.util.IlluminaUtilTest) Running Test: Test method testFindTileInReadName[3](FOO:BAR_splat, null)(picard.util.IlluminaUtilTest) Running Test: Test method testByteArrayToCharArray(picard.arrays.illumina.InfiniumDataFileTest) Running Test: Test method testByteArrayToFloat[0]([B@39bad7f0, 23.0)(picard.arrays.illumina.InfiniumDataFileTest) Running Test: Test method testByteArrayToFloat[1]([B@2fc0280a, 3.14159)(picard.arrays.illumina.InfiniumDataFileTest) Running Test: Test method testByteArrayToFloat[2]([B@73f8a650, 3.4028235E38)(picard.arrays.illumina.InfiniumDataFileTest) Running Test: Test method testByteArrayToFloat[3]([B@567c2432, 1.4E-45)(picard.arrays.illumina.InfiniumDataFileTest) Running Test: Test method testByteArrayToFloat[4]([B@6b22af1a, 0.0)(picard.arrays.illumina.InfiniumDataFileTest) Running Test: Test method testFloatToByteArray[0]([B@32ee9001, 23.0)(picard.arrays.illumina.InfiniumDataFileTest) Running Test: Test method testFloatToByteArray[1]([B@637d4835, 3.14159)(picard.arrays.illumina.InfiniumDataFileTest) Running Test: Test method testFloatToByteArray[2]([B@33e3697, 3.4028235E38)(picard.arrays.illumina.InfiniumDataFileTest) Running Test: Test method testFloatToByteArray[3]([B@5c7368d0, 1.4E-45)(picard.arrays.illumina.InfiniumDataFileTest) Running Test: Test method testFloatToByteArray[4]([B@5dab89b9, 0.0)(picard.arrays.illumina.InfiniumDataFileTest) Running Test: Test method testInfiniumNormalizationManifest(picard.arrays.illumina.InfiniumNormalizationManifestTest) Running Test: Test method testInvalidInfiniumNormalizationManifest(picard.arrays.illumina.InfiniumNormalizationManifestTest) Running Test: Test method testGetNonExistentDateFromVcfOtherHeaderLine(picard.arrays.illumina.InfiniumVcfFieldsTest) Running Test: Test method testGetNonExistentIntegerFromVcfOtherHeaderLine(picard.arrays.illumina.InfiniumVcfFieldsTest) Running Test: Test method testGetNonExistentValueFromVcfOtherHeaderLine(picard.arrays.illumina.InfiniumVcfFieldsTest) Running Test: Test method testGetValueFromVcfOtherHeaderLine(picard.arrays.illumina.InfiniumVcfFieldsTest) Running Test: Test method testGetWronglyFormattedDateFromVcfOtherHeaderLine(picard.arrays.illumina.InfiniumVcfFieldsTest) Running Test: Test method testIntelDeflaterIsAvailable(picard.IntelInflaterDeflaterLoadTest) Test: Test method testIntelDeflaterIsAvailable(picard.IntelInflaterDeflaterLoadTest) produced standard out/err: 12:01:00.953 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.IntelInflaterDeflaterLoadTest.testIntelDeflaterIsAvailable STANDARD_ERROR 12:01:00.953 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIntelDeflaterIsAvailable(picard.IntelInflaterDeflaterLoadTest) produced standard out/err: 12:01:00.961 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:00.961 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Running Test: Test method testIntelInflaterIsAvailable(picard.IntelInflaterDeflaterLoadTest) Test: Test method testIntelInflaterIsAvailable(picard.IntelInflaterDeflaterLoadTest) produced standard out/err: 12:01:00.962 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.IntelInflaterDeflaterLoadTest.testIntelInflaterIsAvailable STANDARD_ERROR 12:01:00.962 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIntelInflaterIsAvailable(picard.IntelInflaterDeflaterLoadTest) produced standard out/err: 12:01:00.962 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:00.962 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Running Test: Test method testScatter[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListScattererTest) Running Test: Test method testScatter[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListScattererTest) Running Test: Test method testScatter[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListScattererTest) Running Test: Test method testScatter[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListScattererTest) Running Test: Test method testScatter[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListScattererTest) Running Test: Test method testScatter[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListScattererTest) Running Test: Test method testScatter[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListScattererTest) Running Test: Test method testScatter[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListScattererTest) Running Test: Test method testScatter[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListScattererTest) Running Test: Test method testScatter[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListScattererTest) Running Test: Test method testScatter[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListScattererTest) Running Test: Test method testScatter[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListScattererTest) Running Test: Test method testScatter[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListScattererTest) Running Test: Test method testScatter[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListScattererTest) Running Test: Test method testScatter[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListScattererTest) Running Test: Test method testScatter[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListScattererTest) Running Test: Test method testScatter[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListScattererTest) Running Test: Test method testScatter[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListScattererTest) Running Test: Test method testConvertToBed(picard.util.IntervalListToBedTest) Test: Test method testConvertToBed(picard.util.IntervalListToBedTest) produced standard out/err: INFO 2024-07-02 12:01:01 IntervalListToBed Gradle suite > Gradle test > picard.util.IntervalListToBedTest.testConvertToBed STANDARD_ERROR INFO 2024-07-02 12:01:01 IntervalListToBed Test: Test method testConvertToBed(picard.util.IntervalListToBedTest) produced standard out/err: Test: Test method testConvertToBed(picard.util.IntervalListToBedTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testConvertToBed(picard.util.IntervalListToBedTest) produced standard out/err: ********** ********** Test: Test method testConvertToBed(picard.util.IntervalListToBedTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testConvertToBed(picard.util.IntervalListToBedTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testConvertToBed(picard.util.IntervalListToBedTest) produced standard out/err: ********** ********** Test: Test method testConvertToBed(picard.util.IntervalListToBedTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testConvertToBed(picard.util.IntervalListToBedTest) produced standard out/err: ********** ********** Test: Test method testConvertToBed(picard.util.IntervalListToBedTest) produced standard out/err: ********** IntervalListToBed -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/interval_list_to_bed_test.interval_list -OUTPUT /tmp/interval_list_to_bed_test_output5683289288297464669.bed -SCORE 333 ********** IntervalListToBed -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/interval_list_to_bed_test.interval_list -OUTPUT /tmp/interval_list_to_bed_test_output5683289288297464669.bed -SCORE 333 Test: Test method testConvertToBed(picard.util.IntervalListToBedTest) produced standard out/err: ********** ********** Test: Test method testConvertToBed(picard.util.IntervalListToBedTest) produced standard out/err: Test: Test method testConvertToBed(picard.util.IntervalListToBedTest) produced standard out/err: Test: Test method testConvertToBed(picard.util.IntervalListToBedTest) produced standard out/err: 12:01:01.457 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:01.457 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testConvertToBed(picard.util.IntervalListToBedTest) produced standard out/err: 12:01:01.457 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:01.457 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testConvertToBed(picard.util.IntervalListToBedTest) produced standard out/err: 12:01:01.457 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:01.457 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testConvertToBed(picard.util.IntervalListToBedTest) produced standard out/err: 12:01:01.457 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:01.457 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testConvertToBed(picard.util.IntervalListToBedTest) produced standard out/err: [Tue Jul 02 12:01:01 GMT+14:00 2024] IntervalListToBed INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/interval_list_to_bed_test.interval_list OUTPUT=/tmp/interval_list_to_bed_test_output5683289288297464669.bed SCORE=333 SORT=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:01 GMT+14:00 2024] IntervalListToBed INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/interval_list_to_bed_test.interval_list OUTPUT=/tmp/interval_list_to_bed_test_output5683289288297464669.bed SCORE=333 SORT=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testConvertToBed(picard.util.IntervalListToBedTest) produced standard out/err: [Tue Jul 02 12:01:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testConvertToBed(picard.util.IntervalListToBedTest) produced standard out/err: [Tue Jul 02 12:01:01 GMT+14:00 2024] picard.util.IntervalListToBed done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:01 GMT+14:00 2024] picard.util.IntervalListToBed done. Elapsed time: 0.00 minutes. Test: Test method testConvertToBed(picard.util.IntervalListToBedTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testConvertUnsortedIntervalToBed(picard.util.IntervalListToBedTest) Test: Test method testConvertUnsortedIntervalToBed(picard.util.IntervalListToBedTest) produced standard out/err: INFO 2024-07-02 12:01:01 IntervalListToBed Gradle suite > Gradle test > picard.util.IntervalListToBedTest.testConvertUnsortedIntervalToBed STANDARD_ERROR INFO 2024-07-02 12:01:01 IntervalListToBed Test: Test method testConvertUnsortedIntervalToBed(picard.util.IntervalListToBedTest) produced standard out/err: Test: Test method testConvertUnsortedIntervalToBed(picard.util.IntervalListToBedTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testConvertUnsortedIntervalToBed(picard.util.IntervalListToBedTest) produced standard out/err: ********** ********** Test: Test method testConvertUnsortedIntervalToBed(picard.util.IntervalListToBedTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testConvertUnsortedIntervalToBed(picard.util.IntervalListToBedTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testConvertUnsortedIntervalToBed(picard.util.IntervalListToBedTest) produced standard out/err: ********** ********** Test: Test method testConvertUnsortedIntervalToBed(picard.util.IntervalListToBedTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testConvertUnsortedIntervalToBed(picard.util.IntervalListToBedTest) produced standard out/err: ********** ********** Test: Test method testConvertUnsortedIntervalToBed(picard.util.IntervalListToBedTest) produced standard out/err: ********** IntervalListToBed -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/unsorted_interval_list_to_bed_test.interval_list -OUTPUT /tmp/interval_list_to_bed_test_output5002493296302736801.bed -SCORE 333 -SORT TRUE ********** IntervalListToBed -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/unsorted_interval_list_to_bed_test.interval_list -OUTPUT /tmp/interval_list_to_bed_test_output5002493296302736801.bed -SCORE 333 -SORT TRUE Test: Test method testConvertUnsortedIntervalToBed(picard.util.IntervalListToBedTest) produced standard out/err: ********** ********** Test: Test method testConvertUnsortedIntervalToBed(picard.util.IntervalListToBedTest) produced standard out/err: Test: Test method testConvertUnsortedIntervalToBed(picard.util.IntervalListToBedTest) produced standard out/err: Test: Test method testConvertUnsortedIntervalToBed(picard.util.IntervalListToBedTest) produced standard out/err: 12:01:01.497 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:01.497 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testConvertUnsortedIntervalToBed(picard.util.IntervalListToBedTest) produced standard out/err: 12:01:01.497 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:01.497 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testConvertUnsortedIntervalToBed(picard.util.IntervalListToBedTest) produced standard out/err: 12:01:01.497 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:01.497 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testConvertUnsortedIntervalToBed(picard.util.IntervalListToBedTest) produced standard out/err: 12:01:01.497 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:01.497 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testConvertUnsortedIntervalToBed(picard.util.IntervalListToBedTest) produced standard out/err: [Tue Jul 02 12:01:01 GMT+14:00 2024] IntervalListToBed INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/unsorted_interval_list_to_bed_test.interval_list OUTPUT=/tmp/interval_list_to_bed_test_output5002493296302736801.bed SCORE=333 SORT=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:01 GMT+14:00 2024] IntervalListToBed INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/unsorted_interval_list_to_bed_test.interval_list OUTPUT=/tmp/interval_list_to_bed_test_output5002493296302736801.bed SCORE=333 SORT=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testConvertUnsortedIntervalToBed(picard.util.IntervalListToBedTest) produced standard out/err: [Tue Jul 02 12:01:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testConvertUnsortedIntervalToBed(picard.util.IntervalListToBedTest) produced standard out/err: [Tue Jul 02 12:01:01 GMT+14:00 2024] picard.util.IntervalListToBed done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:01 GMT+14:00 2024] picard.util.IntervalListToBed done. Elapsed time: 0.00 minutes. Test: Test method testConvertUnsortedIntervalToBed(picard.util.IntervalListToBedTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:01 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testActionsWithDontMergeAbutting[0](CONCAT, 8, 3) STANDARD_ERROR INFO 2024-07-02 12:01:01 IntervalListTools Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT testdata/picard/util/abutting.interval_list -INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT /tmp/IntervalListTools778863738774955156.interval_list ********** IntervalListTools -ACTION CONCAT -INPUT testdata/picard/util/abutting.interval_list -INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT /tmp/IntervalListTools778863738774955156.interval_list Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:01.655 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:01.655 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:01.655 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:01.655 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:01.656 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:01.656 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:01.656 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:01.656 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:01 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list, testdata/picard/util/abutting.interval_list] OUTPUT=/tmp/IntervalListTools778863738774955156.interval_list UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=CONCAT PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:01 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list, testdata/picard/util/abutting.interval_list] OUTPUT=/tmp/IntervalListTools778863738774955156.interval_list UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=CONCAT PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:01 IntervalListTools Produced 3 intervals totalling 8 bases. INFO 2024-07-02 12:01:01 IntervalListTools Produced 3 intervals totalling 8 bases. Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:01 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:01 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:01 IntervalListTools INFO 2024-07-02 12:01:01 IntervalListTools Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT testdata/picard/util/abutting.interval_list -INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT_VALUE BASES -COUNT_OUTPUT /tmp/IntervalListTools11552083906132683520txt ********** IntervalListTools -ACTION CONCAT -INPUT testdata/picard/util/abutting.interval_list -INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT_VALUE BASES -COUNT_OUTPUT /tmp/IntervalListTools11552083906132683520txt Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:01.824 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:01.824 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:01.824 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:01.824 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:01.824 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:01.824 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:01.824 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:01.824 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:01 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list, testdata/picard/util/abutting.interval_list] UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=CONCAT OUTPUT_VALUE=BASES COUNT_OUTPUT=/tmp/IntervalListTools11552083906132683520txt PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:01 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list, testdata/picard/util/abutting.interval_list] UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=CONCAT OUTPUT_VALUE=BASES COUNT_OUTPUT=/tmp/IntervalListTools11552083906132683520txt PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:01 IntervalListTools Produced 3 intervals totalling 8 bases. INFO 2024-07-02 12:01:01 IntervalListTools Produced 3 intervals totalling 8 bases. Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:01 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:01 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:01 IntervalListTools INFO 2024-07-02 12:01:01 IntervalListTools Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT testdata/picard/util/abutting.interval_list -INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT_VALUE INTERVALS -COUNT_OUTPUT /tmp/IntervalListTools82178920835568092txt ********** IntervalListTools -ACTION CONCAT -INPUT testdata/picard/util/abutting.interval_list -INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT_VALUE INTERVALS -COUNT_OUTPUT /tmp/IntervalListTools82178920835568092txt Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:01.976 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:01.976 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:01.976 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:01.976 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:01.976 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:01.976 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:01.976 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:01.976 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:01 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list, testdata/picard/util/abutting.interval_list] UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=CONCAT OUTPUT_VALUE=INTERVALS COUNT_OUTPUT=/tmp/IntervalListTools82178920835568092txt PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:01 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list, testdata/picard/util/abutting.interval_list] UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=CONCAT OUTPUT_VALUE=INTERVALS COUNT_OUTPUT=/tmp/IntervalListTools82178920835568092txt PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:01 IntervalListTools Produced 3 intervals totalling 8 bases. INFO 2024-07-02 12:01:01 IntervalListTools Produced 3 intervals totalling 8 bases. Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:01 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:01 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithDontMergeAbutting[0](CONCAT, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:02 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testActionsWithDontMergeAbutting[1](UNION, 8, 3) STANDARD_ERROR INFO 2024-07-02 12:01:02 IntervalListTools Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION UNION -INPUT testdata/picard/util/abutting.interval_list -INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT /tmp/IntervalListTools18255082994967901444.interval_list ********** IntervalListTools -ACTION UNION -INPUT testdata/picard/util/abutting.interval_list -INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT /tmp/IntervalListTools18255082994967901444.interval_list Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.065 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:02.065 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.065 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:02.065 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.065 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:02.065 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.065 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:02.065 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list, testdata/picard/util/abutting.interval_list] OUTPUT=/tmp/IntervalListTools18255082994967901444.interval_list UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=UNION PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:02 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list, testdata/picard/util/abutting.interval_list] OUTPUT=/tmp/IntervalListTools18255082994967901444.interval_list UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=UNION PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:02 IntervalListTools Produced 3 intervals totalling 8 bases. INFO 2024-07-02 12:01:02 IntervalListTools Produced 3 intervals totalling 8 bases. Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:02 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:02 IntervalListTools INFO 2024-07-02 12:01:02 IntervalListTools Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION UNION -INPUT testdata/picard/util/abutting.interval_list -INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT_VALUE BASES -COUNT_OUTPUT /tmp/IntervalListTools7588547653361392636txt ********** IntervalListTools -ACTION UNION -INPUT testdata/picard/util/abutting.interval_list -INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT_VALUE BASES -COUNT_OUTPUT /tmp/IntervalListTools7588547653361392636txt Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.130 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:02.130 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.130 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:02.130 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.130 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:02.130 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.130 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:02.130 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list, testdata/picard/util/abutting.interval_list] UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=UNION OUTPUT_VALUE=BASES COUNT_OUTPUT=/tmp/IntervalListTools7588547653361392636txt PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:02 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list, testdata/picard/util/abutting.interval_list] UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=UNION OUTPUT_VALUE=BASES COUNT_OUTPUT=/tmp/IntervalListTools7588547653361392636txt PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:02 IntervalListTools Produced 3 intervals totalling 8 bases. INFO 2024-07-02 12:01:02 IntervalListTools Produced 3 intervals totalling 8 bases. Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:02 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:02 IntervalListTools INFO 2024-07-02 12:01:02 IntervalListTools Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION UNION -INPUT testdata/picard/util/abutting.interval_list -INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT_VALUE INTERVALS -COUNT_OUTPUT /tmp/IntervalListTools17796366454277287801txt ********** IntervalListTools -ACTION UNION -INPUT testdata/picard/util/abutting.interval_list -INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT_VALUE INTERVALS -COUNT_OUTPUT /tmp/IntervalListTools17796366454277287801txt Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.202 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:02.202 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.202 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:02.202 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.202 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:02.202 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.202 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:02.202 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list, testdata/picard/util/abutting.interval_list] UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=UNION OUTPUT_VALUE=INTERVALS COUNT_OUTPUT=/tmp/IntervalListTools17796366454277287801txt PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:02 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list, testdata/picard/util/abutting.interval_list] UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=UNION OUTPUT_VALUE=INTERVALS COUNT_OUTPUT=/tmp/IntervalListTools17796366454277287801txt PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:02 IntervalListTools Produced 3 intervals totalling 8 bases. INFO 2024-07-02 12:01:02 IntervalListTools Produced 3 intervals totalling 8 bases. Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:02 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithDontMergeAbutting[1](UNION, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:02 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2) STANDARD_ERROR INFO 2024-07-02 12:01:02 IntervalListTools Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION INTERSECT -INPUT testdata/picard/util/abutting.interval_list -INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT /tmp/IntervalListTools10521171839984738856.interval_list ********** IntervalListTools -ACTION INTERSECT -INPUT testdata/picard/util/abutting.interval_list -INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT /tmp/IntervalListTools10521171839984738856.interval_list Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.272 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:02.272 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.273 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:02.273 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.275 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:02.275 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.275 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:02.275 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list, testdata/picard/util/abutting.interval_list] OUTPUT=/tmp/IntervalListTools10521171839984738856.interval_list UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=INTERSECT PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:02 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list, testdata/picard/util/abutting.interval_list] OUTPUT=/tmp/IntervalListTools10521171839984738856.interval_list UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=INTERSECT PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:02 IntervalListTools Produced 2 intervals totalling 8 bases. INFO 2024-07-02 12:01:02 IntervalListTools Produced 2 intervals totalling 8 bases. Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:02 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:02 IntervalListTools INFO 2024-07-02 12:01:02 IntervalListTools Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION INTERSECT -INPUT testdata/picard/util/abutting.interval_list -INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT_VALUE BASES -COUNT_OUTPUT /tmp/IntervalListTools4349078233747506949txt ********** IntervalListTools -ACTION INTERSECT -INPUT testdata/picard/util/abutting.interval_list -INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT_VALUE BASES -COUNT_OUTPUT /tmp/IntervalListTools4349078233747506949txt Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.469 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:02.469 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.469 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:02.469 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.469 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:02.469 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.469 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:02.469 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list, testdata/picard/util/abutting.interval_list] UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=INTERSECT OUTPUT_VALUE=BASES COUNT_OUTPUT=/tmp/IntervalListTools4349078233747506949txt PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:02 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list, testdata/picard/util/abutting.interval_list] UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=INTERSECT OUTPUT_VALUE=BASES COUNT_OUTPUT=/tmp/IntervalListTools4349078233747506949txt PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:02 IntervalListTools Produced 2 intervals totalling 8 bases. INFO 2024-07-02 12:01:02 IntervalListTools Produced 2 intervals totalling 8 bases. Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:02 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:02 IntervalListTools INFO 2024-07-02 12:01:02 IntervalListTools Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION INTERSECT -INPUT testdata/picard/util/abutting.interval_list -INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT_VALUE INTERVALS -COUNT_OUTPUT /tmp/IntervalListTools7157436029266609071txt ********** IntervalListTools -ACTION INTERSECT -INPUT testdata/picard/util/abutting.interval_list -INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT_VALUE INTERVALS -COUNT_OUTPUT /tmp/IntervalListTools7157436029266609071txt Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.551 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:02.551 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.551 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:02.551 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.552 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:02.552 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.552 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:02.552 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list, testdata/picard/util/abutting.interval_list] UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=INTERSECT OUTPUT_VALUE=INTERVALS COUNT_OUTPUT=/tmp/IntervalListTools7157436029266609071txt PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:02 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list, testdata/picard/util/abutting.interval_list] UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=INTERSECT OUTPUT_VALUE=INTERVALS COUNT_OUTPUT=/tmp/IntervalListTools7157436029266609071txt PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:02 IntervalListTools Produced 2 intervals totalling 8 bases. INFO 2024-07-02 12:01:02 IntervalListTools Produced 2 intervals totalling 8 bases. Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:02 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithDontMergeAbutting[2](INTERSECT, 8, 2)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:02 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0) STANDARD_ERROR INFO 2024-07-02 12:01:02 IntervalListTools Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION SUBTRACT -INPUT testdata/picard/util/abutting.interval_list -SECOND_INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT /tmp/IntervalListTools13195486134176655139.interval_list ********** IntervalListTools -ACTION SUBTRACT -INPUT testdata/picard/util/abutting.interval_list -SECOND_INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT /tmp/IntervalListTools13195486134176655139.interval_list Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.652 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:02.652 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.652 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:02.652 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.652 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:02.652 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.652 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:02.652 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list] OUTPUT=/tmp/IntervalListTools13195486134176655139.interval_list UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=SUBTRACT SECOND_INPUT=[testdata/picard/util/abutting.interval_list] PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:02 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list] OUTPUT=/tmp/IntervalListTools13195486134176655139.interval_list UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=SUBTRACT SECOND_INPUT=[testdata/picard/util/abutting.interval_list] PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:02 IntervalListTools Produced 0 intervals totalling 0 bases. INFO 2024-07-02 12:01:02 IntervalListTools Produced 0 intervals totalling 0 bases. Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:02 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:02 IntervalListTools INFO 2024-07-02 12:01:02 IntervalListTools Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION SUBTRACT -INPUT testdata/picard/util/abutting.interval_list -SECOND_INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT_VALUE BASES -COUNT_OUTPUT /tmp/IntervalListTools5073680670710096559txt ********** IntervalListTools -ACTION SUBTRACT -INPUT testdata/picard/util/abutting.interval_list -SECOND_INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT_VALUE BASES -COUNT_OUTPUT /tmp/IntervalListTools5073680670710096559txt Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.739 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:02.739 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.739 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:02.739 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.740 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:02.740 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.740 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:02.740 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list] UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=SUBTRACT SECOND_INPUT=[testdata/picard/util/abutting.interval_list] OUTPUT_VALUE=BASES COUNT_OUTPUT=/tmp/IntervalListTools5073680670710096559txt PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:02 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list] UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=SUBTRACT SECOND_INPUT=[testdata/picard/util/abutting.interval_list] OUTPUT_VALUE=BASES COUNT_OUTPUT=/tmp/IntervalListTools5073680670710096559txt PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:02 IntervalListTools Produced 0 intervals totalling 0 bases. INFO 2024-07-02 12:01:02 IntervalListTools Produced 0 intervals totalling 0 bases. Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:02 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:02 IntervalListTools INFO 2024-07-02 12:01:02 IntervalListTools Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION SUBTRACT -INPUT testdata/picard/util/abutting.interval_list -SECOND_INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT_VALUE INTERVALS -COUNT_OUTPUT /tmp/IntervalListTools17201245044732504074txt ********** IntervalListTools -ACTION SUBTRACT -INPUT testdata/picard/util/abutting.interval_list -SECOND_INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT_VALUE INTERVALS -COUNT_OUTPUT /tmp/IntervalListTools17201245044732504074txt Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.831 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:02.831 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.831 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:02.831 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.831 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:02.831 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.831 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:02.831 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list] UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=SUBTRACT SECOND_INPUT=[testdata/picard/util/abutting.interval_list] OUTPUT_VALUE=INTERVALS COUNT_OUTPUT=/tmp/IntervalListTools17201245044732504074txt PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:02 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list] UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=SUBTRACT SECOND_INPUT=[testdata/picard/util/abutting.interval_list] OUTPUT_VALUE=INTERVALS COUNT_OUTPUT=/tmp/IntervalListTools17201245044732504074txt PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:02 IntervalListTools Produced 0 intervals totalling 0 bases. INFO 2024-07-02 12:01:02 IntervalListTools Produced 0 intervals totalling 0 bases. Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:02 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithDontMergeAbutting[3](SUBTRACT, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:02 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0) STANDARD_ERROR INFO 2024-07-02 12:01:02 IntervalListTools Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION SYMDIFF -INPUT testdata/picard/util/abutting.interval_list -SECOND_INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT /tmp/IntervalListTools13065982352953524050.interval_list ********** IntervalListTools -ACTION SYMDIFF -INPUT testdata/picard/util/abutting.interval_list -SECOND_INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT /tmp/IntervalListTools13065982352953524050.interval_list Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.915 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:02.915 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.915 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:02.915 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.915 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:02.915 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:02.915 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:02.915 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list] OUTPUT=/tmp/IntervalListTools13065982352953524050.interval_list UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=SYMDIFF SECOND_INPUT=[testdata/picard/util/abutting.interval_list] PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:02 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list] OUTPUT=/tmp/IntervalListTools13065982352953524050.interval_list UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=SYMDIFF SECOND_INPUT=[testdata/picard/util/abutting.interval_list] PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:02 IntervalListTools Produced 0 intervals totalling 0 bases. INFO 2024-07-02 12:01:02 IntervalListTools Produced 0 intervals totalling 0 bases. Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:02 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:02 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:02 IntervalListTools INFO 2024-07-02 12:01:02 IntervalListTools Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION SYMDIFF -INPUT testdata/picard/util/abutting.interval_list -SECOND_INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT_VALUE BASES -COUNT_OUTPUT /tmp/IntervalListTools2001259758081519428txt ********** IntervalListTools -ACTION SYMDIFF -INPUT testdata/picard/util/abutting.interval_list -SECOND_INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT_VALUE BASES -COUNT_OUTPUT /tmp/IntervalListTools2001259758081519428txt Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.001 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:03.001 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.001 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:03.001 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.001 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:03.001 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.001 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:03.001 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:03 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list] UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=SYMDIFF SECOND_INPUT=[testdata/picard/util/abutting.interval_list] OUTPUT_VALUE=BASES COUNT_OUTPUT=/tmp/IntervalListTools2001259758081519428txt PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:03 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list] UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=SYMDIFF SECOND_INPUT=[testdata/picard/util/abutting.interval_list] OUTPUT_VALUE=BASES COUNT_OUTPUT=/tmp/IntervalListTools2001259758081519428txt PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:03 IntervalListTools Produced 0 intervals totalling 0 bases. INFO 2024-07-02 12:01:03 IntervalListTools Produced 0 intervals totalling 0 bases. Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:03 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:03 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:03 IntervalListTools INFO 2024-07-02 12:01:03 IntervalListTools Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION SYMDIFF -INPUT testdata/picard/util/abutting.interval_list -SECOND_INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT_VALUE INTERVALS -COUNT_OUTPUT /tmp/IntervalListTools3355531802382388798txt ********** IntervalListTools -ACTION SYMDIFF -INPUT testdata/picard/util/abutting.interval_list -SECOND_INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT_VALUE INTERVALS -COUNT_OUTPUT /tmp/IntervalListTools3355531802382388798txt Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.068 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:03.068 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.068 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:03.068 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.069 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:03.069 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.075 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:03.075 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:03 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list] UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=SYMDIFF SECOND_INPUT=[testdata/picard/util/abutting.interval_list] OUTPUT_VALUE=INTERVALS COUNT_OUTPUT=/tmp/IntervalListTools3355531802382388798txt PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:03 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list] UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=SYMDIFF SECOND_INPUT=[testdata/picard/util/abutting.interval_list] OUTPUT_VALUE=INTERVALS COUNT_OUTPUT=/tmp/IntervalListTools3355531802382388798txt PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:03 IntervalListTools Produced 0 intervals totalling 0 bases. INFO 2024-07-02 12:01:03 IntervalListTools Produced 0 intervals totalling 0 bases. Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:03 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:03 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithDontMergeAbutting[4](SYMDIFF, 0, 0)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:03 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3) STANDARD_ERROR INFO 2024-07-02 12:01:03 IntervalListTools Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION OVERLAPS -INPUT testdata/picard/util/abutting.interval_list -SECOND_INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT /tmp/IntervalListTools11941233430042033057.interval_list ********** IntervalListTools -ACTION OVERLAPS -INPUT testdata/picard/util/abutting.interval_list -SECOND_INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT /tmp/IntervalListTools11941233430042033057.interval_list Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.166 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:03.166 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:03.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.166 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:03.166 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:03.166 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:03 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list] OUTPUT=/tmp/IntervalListTools11941233430042033057.interval_list UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=OVERLAPS SECOND_INPUT=[testdata/picard/util/abutting.interval_list] PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:03 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list] OUTPUT=/tmp/IntervalListTools11941233430042033057.interval_list UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=OVERLAPS SECOND_INPUT=[testdata/picard/util/abutting.interval_list] PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:03 IntervalListTools Produced 3 intervals totalling 8 bases. INFO 2024-07-02 12:01:03 IntervalListTools Produced 3 intervals totalling 8 bases. Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:03 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:03 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:03 IntervalListTools INFO 2024-07-02 12:01:03 IntervalListTools Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION OVERLAPS -INPUT testdata/picard/util/abutting.interval_list -SECOND_INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT_VALUE BASES -COUNT_OUTPUT /tmp/IntervalListTools8277129472142886995txt ********** IntervalListTools -ACTION OVERLAPS -INPUT testdata/picard/util/abutting.interval_list -SECOND_INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT_VALUE BASES -COUNT_OUTPUT /tmp/IntervalListTools8277129472142886995txt Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.250 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:03.250 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.250 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:03.250 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.250 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:03.250 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.251 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:03.251 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:03 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list] UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=OVERLAPS SECOND_INPUT=[testdata/picard/util/abutting.interval_list] OUTPUT_VALUE=BASES COUNT_OUTPUT=/tmp/IntervalListTools8277129472142886995txt PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:03 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list] UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=OVERLAPS SECOND_INPUT=[testdata/picard/util/abutting.interval_list] OUTPUT_VALUE=BASES COUNT_OUTPUT=/tmp/IntervalListTools8277129472142886995txt PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:03 IntervalListTools Produced 3 intervals totalling 8 bases. INFO 2024-07-02 12:01:03 IntervalListTools Produced 3 intervals totalling 8 bases. Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:03 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:03 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:03 IntervalListTools INFO 2024-07-02 12:01:03 IntervalListTools Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION OVERLAPS -INPUT testdata/picard/util/abutting.interval_list -SECOND_INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT_VALUE INTERVALS -COUNT_OUTPUT /tmp/IntervalListTools4623548227379119055txt ********** IntervalListTools -ACTION OVERLAPS -INPUT testdata/picard/util/abutting.interval_list -SECOND_INPUT testdata/picard/util/abutting.interval_list -UNIQUE true -DONT_MERGE_ABUTTING true -OUTPUT_VALUE INTERVALS -COUNT_OUTPUT /tmp/IntervalListTools4623548227379119055txt Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.330 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:03.330 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.331 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:03.331 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.331 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:03.331 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.331 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:03.331 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:03 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list] UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=OVERLAPS SECOND_INPUT=[testdata/picard/util/abutting.interval_list] OUTPUT_VALUE=INTERVALS COUNT_OUTPUT=/tmp/IntervalListTools4623548227379119055txt PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:03 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list] UNIQUE=true DONT_MERGE_ABUTTING=true ACTION=OVERLAPS SECOND_INPUT=[testdata/picard/util/abutting.interval_list] OUTPUT_VALUE=INTERVALS COUNT_OUTPUT=/tmp/IntervalListTools4623548227379119055txt PADDING=0 SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:03 IntervalListTools Produced 3 intervals totalling 8 bases. INFO 2024-07-02 12:01:03 IntervalListTools Produced 3 intervals totalling 8 bases. Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:03 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:03 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithDontMergeAbutting[5](OVERLAPS, 8, 3)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:03 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testActionsWithInvert[0](CONCAT, 3101976361, 87) STANDARD_ERROR INFO 2024-07-02 12:01:03 IntervalListTools Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT testdata/picard/util/scatterable.interval_list -INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT /tmp/IntervalListTools17446775041748282555.interval_list ********** IntervalListTools -ACTION CONCAT -INPUT testdata/picard/util/scatterable.interval_list -INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT /tmp/IntervalListTools17446775041748282555.interval_list Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.407 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:03.407 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.407 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:03.407 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.407 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:03.407 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.407 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:03.407 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:03 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list, testdata/picard/util/secondInput.interval_list] OUTPUT=/tmp/IntervalListTools17446775041748282555.interval_list ACTION=CONCAT INVERT=true PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:03 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list, testdata/picard/util/secondInput.interval_list] OUTPUT=/tmp/IntervalListTools17446775041748282555.interval_list ACTION=CONCAT INVERT=true PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:03 IntervalListTools Produced 87 intervals totalling 3101976361 bases. INFO 2024-07-02 12:01:03 IntervalListTools Produced 87 intervals totalling 3101976361 bases. Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:03 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:03 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:03 IntervalListTools INFO 2024-07-02 12:01:03 IntervalListTools Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT testdata/picard/util/scatterable.interval_list -INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT_VALUE BASES -COUNT_OUTPUT /tmp/IntervalListTools8926677191626222044txt ********** IntervalListTools -ACTION CONCAT -INPUT testdata/picard/util/scatterable.interval_list -INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT_VALUE BASES -COUNT_OUTPUT /tmp/IntervalListTools8926677191626222044txt Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.553 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:03.553 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.553 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:03.553 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.554 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:03.554 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.554 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:03.554 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:03 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list, testdata/picard/util/secondInput.interval_list] ACTION=CONCAT INVERT=true OUTPUT_VALUE=BASES COUNT_OUTPUT=/tmp/IntervalListTools8926677191626222044txt PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:03 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list, testdata/picard/util/secondInput.interval_list] ACTION=CONCAT INVERT=true OUTPUT_VALUE=BASES COUNT_OUTPUT=/tmp/IntervalListTools8926677191626222044txt PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:03 IntervalListTools Produced 87 intervals totalling 3101976361 bases. INFO 2024-07-02 12:01:03 IntervalListTools Produced 87 intervals totalling 3101976361 bases. Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:03 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:03 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:03 IntervalListTools INFO 2024-07-02 12:01:03 IntervalListTools Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT testdata/picard/util/scatterable.interval_list -INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT_VALUE INTERVALS -COUNT_OUTPUT /tmp/IntervalListTools16719863354344395717txt ********** IntervalListTools -ACTION CONCAT -INPUT testdata/picard/util/scatterable.interval_list -INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT_VALUE INTERVALS -COUNT_OUTPUT /tmp/IntervalListTools16719863354344395717txt Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.801 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:03.801 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.801 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:03.801 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.801 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:03.801 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.801 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:03.801 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:03 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list, testdata/picard/util/secondInput.interval_list] ACTION=CONCAT INVERT=true OUTPUT_VALUE=INTERVALS COUNT_OUTPUT=/tmp/IntervalListTools16719863354344395717txt PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:03 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list, testdata/picard/util/secondInput.interval_list] ACTION=CONCAT INVERT=true OUTPUT_VALUE=INTERVALS COUNT_OUTPUT=/tmp/IntervalListTools16719863354344395717txt PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:03 IntervalListTools Produced 87 intervals totalling 3101976361 bases. INFO 2024-07-02 12:01:03 IntervalListTools Produced 87 intervals totalling 3101976361 bases. Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:03 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:03 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithInvert[0](CONCAT, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:03 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testActionsWithInvert[1](UNION, 3101976361, 87) STANDARD_ERROR INFO 2024-07-02 12:01:03 IntervalListTools Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION UNION -INPUT testdata/picard/util/scatterable.interval_list -INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT /tmp/IntervalListTools11433376906835354803.interval_list ********** IntervalListTools -ACTION UNION -INPUT testdata/picard/util/scatterable.interval_list -INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT /tmp/IntervalListTools11433376906835354803.interval_list Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.971 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:03.971 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.971 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:03.971 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.971 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:03.971 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:03.971 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:03.971 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:03 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list, testdata/picard/util/secondInput.interval_list] OUTPUT=/tmp/IntervalListTools11433376906835354803.interval_list ACTION=UNION INVERT=true PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:03 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list, testdata/picard/util/secondInput.interval_list] OUTPUT=/tmp/IntervalListTools11433376906835354803.interval_list ACTION=UNION INVERT=true PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:04 IntervalListTools Produced 87 intervals totalling 3101976361 bases. INFO 2024-07-02 12:01:04 IntervalListTools Produced 87 intervals totalling 3101976361 bases. Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:04 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:04 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:04 IntervalListTools INFO 2024-07-02 12:01:04 IntervalListTools Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION UNION -INPUT testdata/picard/util/scatterable.interval_list -INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT_VALUE BASES -COUNT_OUTPUT /tmp/IntervalListTools12028987481674266504txt ********** IntervalListTools -ACTION UNION -INPUT testdata/picard/util/scatterable.interval_list -INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT_VALUE BASES -COUNT_OUTPUT /tmp/IntervalListTools12028987481674266504txt Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:04.137 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:04.137 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:04.137 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:04.137 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:04.137 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:04.137 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:04.137 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:04.137 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:04 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list, testdata/picard/util/secondInput.interval_list] ACTION=UNION INVERT=true OUTPUT_VALUE=BASES COUNT_OUTPUT=/tmp/IntervalListTools12028987481674266504txt PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:04 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list, testdata/picard/util/secondInput.interval_list] ACTION=UNION INVERT=true OUTPUT_VALUE=BASES COUNT_OUTPUT=/tmp/IntervalListTools12028987481674266504txt PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:04 IntervalListTools Produced 87 intervals totalling 3101976361 bases. INFO 2024-07-02 12:01:04 IntervalListTools Produced 87 intervals totalling 3101976361 bases. Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:04 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:04 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:04 IntervalListTools INFO 2024-07-02 12:01:04 IntervalListTools Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION UNION -INPUT testdata/picard/util/scatterable.interval_list -INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT_VALUE INTERVALS -COUNT_OUTPUT /tmp/IntervalListTools13124632113186999326txt ********** IntervalListTools -ACTION UNION -INPUT testdata/picard/util/scatterable.interval_list -INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT_VALUE INTERVALS -COUNT_OUTPUT /tmp/IntervalListTools13124632113186999326txt Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:04.263 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:04.263 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:04.263 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:04.263 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:04.264 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:04.264 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:04.264 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:04.264 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:04 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list, testdata/picard/util/secondInput.interval_list] ACTION=UNION INVERT=true OUTPUT_VALUE=INTERVALS COUNT_OUTPUT=/tmp/IntervalListTools13124632113186999326txt PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:04 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list, testdata/picard/util/secondInput.interval_list] ACTION=UNION INVERT=true OUTPUT_VALUE=INTERVALS COUNT_OUTPUT=/tmp/IntervalListTools13124632113186999326txt PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:04 IntervalListTools Produced 87 intervals totalling 3101976361 bases. INFO 2024-07-02 12:01:04 IntervalListTools Produced 87 intervals totalling 3101976361 bases. Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:04 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:04 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithInvert[1](UNION, 3101976361, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:04 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testActionsWithInvert[2](INTERSECT, 3101976422, 87) STANDARD_ERROR INFO 2024-07-02 12:01:04 IntervalListTools Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION INTERSECT -INPUT testdata/picard/util/scatterable.interval_list -INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT /tmp/IntervalListTools4598578364090731899.interval_list ********** IntervalListTools -ACTION INTERSECT -INPUT testdata/picard/util/scatterable.interval_list -INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT /tmp/IntervalListTools4598578364090731899.interval_list Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:04.407 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:04.407 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:04.407 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:04.407 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:04.407 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:04.407 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:04.407 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:04.407 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:04 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list, testdata/picard/util/secondInput.interval_list] OUTPUT=/tmp/IntervalListTools4598578364090731899.interval_list ACTION=INTERSECT INVERT=true PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:04 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list, testdata/picard/util/secondInput.interval_list] OUTPUT=/tmp/IntervalListTools4598578364090731899.interval_list ACTION=INTERSECT INVERT=true PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:04 IntervalListTools Produced 87 intervals totalling 3101976422 bases. INFO 2024-07-02 12:01:04 IntervalListTools Produced 87 intervals totalling 3101976422 bases. Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:04 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:04 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:04 IntervalListTools INFO 2024-07-02 12:01:04 IntervalListTools Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION INTERSECT -INPUT testdata/picard/util/scatterable.interval_list -INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT_VALUE BASES -COUNT_OUTPUT /tmp/IntervalListTools9819485036312589139txt ********** IntervalListTools -ACTION INTERSECT -INPUT testdata/picard/util/scatterable.interval_list -INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT_VALUE BASES -COUNT_OUTPUT /tmp/IntervalListTools9819485036312589139txt Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:04.600 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:04.600 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:04.600 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:04.600 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:04.601 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:04.601 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:04.601 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:04.601 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:04 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list, testdata/picard/util/secondInput.interval_list] ACTION=INTERSECT INVERT=true OUTPUT_VALUE=BASES COUNT_OUTPUT=/tmp/IntervalListTools9819485036312589139txt PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:04 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list, testdata/picard/util/secondInput.interval_list] ACTION=INTERSECT INVERT=true OUTPUT_VALUE=BASES COUNT_OUTPUT=/tmp/IntervalListTools9819485036312589139txt PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:04 IntervalListTools Produced 87 intervals totalling 3101976422 bases. INFO 2024-07-02 12:01:04 IntervalListTools Produced 87 intervals totalling 3101976422 bases. Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:04 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:04 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:04 IntervalListTools INFO 2024-07-02 12:01:04 IntervalListTools Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION INTERSECT -INPUT testdata/picard/util/scatterable.interval_list -INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT_VALUE INTERVALS -COUNT_OUTPUT /tmp/IntervalListTools11293992940082698473txt ********** IntervalListTools -ACTION INTERSECT -INPUT testdata/picard/util/scatterable.interval_list -INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT_VALUE INTERVALS -COUNT_OUTPUT /tmp/IntervalListTools11293992940082698473txt Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:04.766 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:04.766 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:04.766 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:04.766 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:04.767 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:04.767 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:04.767 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:04.767 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:04 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list, testdata/picard/util/secondInput.interval_list] ACTION=INTERSECT INVERT=true OUTPUT_VALUE=INTERVALS COUNT_OUTPUT=/tmp/IntervalListTools11293992940082698473txt PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:04 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list, testdata/picard/util/secondInput.interval_list] ACTION=INTERSECT INVERT=true OUTPUT_VALUE=INTERVALS COUNT_OUTPUT=/tmp/IntervalListTools11293992940082698473txt PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:04 IntervalListTools Produced 87 intervals totalling 3101976422 bases. INFO 2024-07-02 12:01:04 IntervalListTools Produced 87 intervals totalling 3101976422 bases. Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:04 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:04 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithInvert[2](INTERSECT, 3101976422, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:04 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testActionsWithInvert[3](SUBTRACT, 3101976502, 87) STANDARD_ERROR INFO 2024-07-02 12:01:04 IntervalListTools Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION SUBTRACT -INPUT testdata/picard/util/scatterable.interval_list -SECOND_INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT /tmp/IntervalListTools8631627513383226684.interval_list ********** IntervalListTools -ACTION SUBTRACT -INPUT testdata/picard/util/scatterable.interval_list -SECOND_INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT /tmp/IntervalListTools8631627513383226684.interval_list Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:04.868 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:04.868 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:04.869 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:04.869 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:04.877 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:04.877 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:04.878 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:04.878 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:04 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools8631627513383226684.interval_list ACTION=SUBTRACT SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] INVERT=true PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:04 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools8631627513383226684.interval_list ACTION=SUBTRACT SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] INVERT=true PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:04 IntervalListTools Produced 87 intervals totalling 3101976502 bases. INFO 2024-07-02 12:01:04 IntervalListTools Produced 87 intervals totalling 3101976502 bases. Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:04 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:04 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:05 IntervalListTools INFO 2024-07-02 12:01:05 IntervalListTools Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION SUBTRACT -INPUT testdata/picard/util/scatterable.interval_list -SECOND_INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT_VALUE BASES -COUNT_OUTPUT /tmp/IntervalListTools11430167940784014724txt ********** IntervalListTools -ACTION SUBTRACT -INPUT testdata/picard/util/scatterable.interval_list -SECOND_INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT_VALUE BASES -COUNT_OUTPUT /tmp/IntervalListTools11430167940784014724txt Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:05.003 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:05.003 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:05.003 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:05.003 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:05.004 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:05.004 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:05.004 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:05.004 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:05 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] ACTION=SUBTRACT SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] INVERT=true OUTPUT_VALUE=BASES COUNT_OUTPUT=/tmp/IntervalListTools11430167940784014724txt PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:05 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] ACTION=SUBTRACT SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] INVERT=true OUTPUT_VALUE=BASES COUNT_OUTPUT=/tmp/IntervalListTools11430167940784014724txt PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:05 IntervalListTools Produced 87 intervals totalling 3101976502 bases. INFO 2024-07-02 12:01:05 IntervalListTools Produced 87 intervals totalling 3101976502 bases. Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:05 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:05 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:05 IntervalListTools INFO 2024-07-02 12:01:05 IntervalListTools Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION SUBTRACT -INPUT testdata/picard/util/scatterable.interval_list -SECOND_INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT_VALUE INTERVALS -COUNT_OUTPUT /tmp/IntervalListTools15292322713311175527txt ********** IntervalListTools -ACTION SUBTRACT -INPUT testdata/picard/util/scatterable.interval_list -SECOND_INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT_VALUE INTERVALS -COUNT_OUTPUT /tmp/IntervalListTools15292322713311175527txt Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:05.133 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:05.133 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:05.133 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:05.133 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:05.133 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:05.133 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:05.133 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:05.133 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:05 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] ACTION=SUBTRACT SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] INVERT=true OUTPUT_VALUE=INTERVALS COUNT_OUTPUT=/tmp/IntervalListTools15292322713311175527txt PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:05 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] ACTION=SUBTRACT SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] INVERT=true OUTPUT_VALUE=INTERVALS COUNT_OUTPUT=/tmp/IntervalListTools15292322713311175527txt PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:05 IntervalListTools Produced 87 intervals totalling 3101976502 bases. INFO 2024-07-02 12:01:05 IntervalListTools Produced 87 intervals totalling 3101976502 bases. Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:05 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:05 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithInvert[3](SUBTRACT, 3101976502, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:05 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testActionsWithInvert[4](SYMDIFF, 3101976501, 88) STANDARD_ERROR INFO 2024-07-02 12:01:05 IntervalListTools Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION SYMDIFF -INPUT testdata/picard/util/scatterable.interval_list -SECOND_INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT /tmp/IntervalListTools7459046955173645921.interval_list ********** IntervalListTools -ACTION SYMDIFF -INPUT testdata/picard/util/scatterable.interval_list -SECOND_INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT /tmp/IntervalListTools7459046955173645921.interval_list Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:05.286 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:05.286 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:05.286 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:05.286 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:05.286 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:05.286 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:05.286 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:05.286 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:05 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools7459046955173645921.interval_list ACTION=SYMDIFF SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] INVERT=true PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:05 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools7459046955173645921.interval_list ACTION=SYMDIFF SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] INVERT=true PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:05 IntervalListTools Produced 88 intervals totalling 3101976501 bases. INFO 2024-07-02 12:01:05 IntervalListTools Produced 88 intervals totalling 3101976501 bases. Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:05 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:05 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:05 IntervalListTools INFO 2024-07-02 12:01:05 IntervalListTools Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION SYMDIFF -INPUT testdata/picard/util/scatterable.interval_list -SECOND_INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT_VALUE BASES -COUNT_OUTPUT /tmp/IntervalListTools5306705693529423238txt ********** IntervalListTools -ACTION SYMDIFF -INPUT testdata/picard/util/scatterable.interval_list -SECOND_INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT_VALUE BASES -COUNT_OUTPUT /tmp/IntervalListTools5306705693529423238txt Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:05.506 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:05.506 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:05.506 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:05.506 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:05.506 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:05.506 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:05.506 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:05.506 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:05 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] ACTION=SYMDIFF SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] INVERT=true OUTPUT_VALUE=BASES COUNT_OUTPUT=/tmp/IntervalListTools5306705693529423238txt PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:05 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] ACTION=SYMDIFF SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] INVERT=true OUTPUT_VALUE=BASES COUNT_OUTPUT=/tmp/IntervalListTools5306705693529423238txt PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:05 IntervalListTools Produced 88 intervals totalling 3101976501 bases. INFO 2024-07-02 12:01:05 IntervalListTools Produced 88 intervals totalling 3101976501 bases. Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:05 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:05 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:05 IntervalListTools INFO 2024-07-02 12:01:05 IntervalListTools Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION SYMDIFF -INPUT testdata/picard/util/scatterable.interval_list -SECOND_INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT_VALUE INTERVALS -COUNT_OUTPUT /tmp/IntervalListTools16043370341048198026txt ********** IntervalListTools -ACTION SYMDIFF -INPUT testdata/picard/util/scatterable.interval_list -SECOND_INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT_VALUE INTERVALS -COUNT_OUTPUT /tmp/IntervalListTools16043370341048198026txt Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:05.726 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:05.726 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:05.726 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:05.726 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:05.726 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:05.726 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:05.726 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:05.726 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:05 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] ACTION=SYMDIFF SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] INVERT=true OUTPUT_VALUE=INTERVALS COUNT_OUTPUT=/tmp/IntervalListTools16043370341048198026txt PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:05 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] ACTION=SYMDIFF SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] INVERT=true OUTPUT_VALUE=INTERVALS COUNT_OUTPUT=/tmp/IntervalListTools16043370341048198026txt PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:05 IntervalListTools Produced 88 intervals totalling 3101976501 bases. INFO 2024-07-02 12:01:05 IntervalListTools Produced 88 intervals totalling 3101976501 bases. Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:05 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:05 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithInvert[4](SYMDIFF, 3101976501, 88)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:05 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testActionsWithInvert[5](OVERLAPS, 3101976412, 87) STANDARD_ERROR INFO 2024-07-02 12:01:05 IntervalListTools Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION OVERLAPS -INPUT testdata/picard/util/scatterable.interval_list -SECOND_INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT /tmp/IntervalListTools292884416747325705.interval_list ********** IntervalListTools -ACTION OVERLAPS -INPUT testdata/picard/util/scatterable.interval_list -SECOND_INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT /tmp/IntervalListTools292884416747325705.interval_list Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:05.942 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:05.942 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:05.942 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:05.942 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:05.942 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:05.942 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:05.942 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:05.942 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:05 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools292884416747325705.interval_list ACTION=OVERLAPS SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] INVERT=true PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:05 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools292884416747325705.interval_list ACTION=OVERLAPS SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] INVERT=true PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:06 IntervalListTools Produced 87 intervals totalling 3101976412 bases. INFO 2024-07-02 12:01:06 IntervalListTools Produced 87 intervals totalling 3101976412 bases. Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:06 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:06 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:06 IntervalListTools INFO 2024-07-02 12:01:06 IntervalListTools Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION OVERLAPS -INPUT testdata/picard/util/scatterable.interval_list -SECOND_INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT_VALUE BASES -COUNT_OUTPUT /tmp/IntervalListTools11441458040996360134txt ********** IntervalListTools -ACTION OVERLAPS -INPUT testdata/picard/util/scatterable.interval_list -SECOND_INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT_VALUE BASES -COUNT_OUTPUT /tmp/IntervalListTools11441458040996360134txt Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:06.156 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:06.156 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:06.156 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:06.156 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:06.156 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:06.156 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:06.156 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:06.156 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:06 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] ACTION=OVERLAPS SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] INVERT=true OUTPUT_VALUE=BASES COUNT_OUTPUT=/tmp/IntervalListTools11441458040996360134txt PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:06 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] ACTION=OVERLAPS SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] INVERT=true OUTPUT_VALUE=BASES COUNT_OUTPUT=/tmp/IntervalListTools11441458040996360134txt PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:06 IntervalListTools Produced 87 intervals totalling 3101976412 bases. INFO 2024-07-02 12:01:06 IntervalListTools Produced 87 intervals totalling 3101976412 bases. Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:06 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:06 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:06 IntervalListTools INFO 2024-07-02 12:01:06 IntervalListTools Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION OVERLAPS -INPUT testdata/picard/util/scatterable.interval_list -SECOND_INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT_VALUE INTERVALS -COUNT_OUTPUT /tmp/IntervalListTools5367175328973875112txt ********** IntervalListTools -ACTION OVERLAPS -INPUT testdata/picard/util/scatterable.interval_list -SECOND_INPUT testdata/picard/util/secondInput.interval_list -INVERT true -OUTPUT_VALUE INTERVALS -COUNT_OUTPUT /tmp/IntervalListTools5367175328973875112txt Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:06.295 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:06.295 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:06.295 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:06.295 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:06.296 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:06.296 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:06.296 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:06.296 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:06 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] ACTION=OVERLAPS SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] INVERT=true OUTPUT_VALUE=INTERVALS COUNT_OUTPUT=/tmp/IntervalListTools5367175328973875112txt PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:06 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] ACTION=OVERLAPS SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] INVERT=true OUTPUT_VALUE=INTERVALS COUNT_OUTPUT=/tmp/IntervalListTools5367175328973875112txt PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:06 IntervalListTools Produced 87 intervals totalling 3101976412 bases. INFO 2024-07-02 12:01:06 IntervalListTools Produced 87 intervals totalling 3101976412 bases. Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:06 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:06 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testActionsWithInvert[5](OVERLAPS, 3101976412, 87)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testAllActions[0](CONCAT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) Test: Test method testAllActions[0](CONCAT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:06 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testAllActions[0](CONCAT, testdata/picard/util/scatterable.interval_list) STANDARD_ERROR INFO 2024-07-02 12:01:06 IntervalListTools Test: Test method testAllActions[0](CONCAT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[0](CONCAT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testAllActions[0](CONCAT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[0](CONCAT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testAllActions[0](CONCAT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testAllActions[0](CONCAT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[0](CONCAT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testAllActions[0](CONCAT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[0](CONCAT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT testdata/picard/util/scatterable.interval_list -OUTPUT /tmp/IntervalListTools586718047689334879interval_list ********** IntervalListTools -ACTION CONCAT -INPUT testdata/picard/util/scatterable.interval_list -OUTPUT /tmp/IntervalListTools586718047689334879interval_list Test: Test method testAllActions[0](CONCAT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[0](CONCAT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[0](CONCAT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[0](CONCAT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:06.454 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:06.454 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAllActions[0](CONCAT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:06.455 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:06.455 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAllActions[0](CONCAT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:06.455 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:06.455 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAllActions[0](CONCAT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:06.455 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:06.455 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAllActions[0](CONCAT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:06 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools586718047689334879interval_list ACTION=CONCAT PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:06 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools586718047689334879interval_list ACTION=CONCAT PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testAllActions[0](CONCAT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testAllActions[0](CONCAT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:06 IntervalListTools Produced 3 intervals totalling 200 bases. INFO 2024-07-02 12:01:06 IntervalListTools Produced 3 intervals totalling 200 bases. Test: Test method testAllActions[0](CONCAT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:06 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:06 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testAllActions[0](CONCAT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testAllActions[1](UNION, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) Test: Test method testAllActions[1](UNION, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:06 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testAllActions[1](UNION, testdata/picard/util/scatterable.interval_list) STANDARD_ERROR INFO 2024-07-02 12:01:06 IntervalListTools Test: Test method testAllActions[1](UNION, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[1](UNION, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testAllActions[1](UNION, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[1](UNION, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testAllActions[1](UNION, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testAllActions[1](UNION, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[1](UNION, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testAllActions[1](UNION, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[1](UNION, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION UNION -INPUT testdata/picard/util/scatterable.interval_list -OUTPUT /tmp/IntervalListTools7803555857253149491interval_list ********** IntervalListTools -ACTION UNION -INPUT testdata/picard/util/scatterable.interval_list -OUTPUT /tmp/IntervalListTools7803555857253149491interval_list Test: Test method testAllActions[1](UNION, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[1](UNION, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[1](UNION, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[1](UNION, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:06.550 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:06.550 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAllActions[1](UNION, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:06.550 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:06.550 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAllActions[1](UNION, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:06.550 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:06.550 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAllActions[1](UNION, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:06.550 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:06.550 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAllActions[1](UNION, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:06 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools7803555857253149491interval_list ACTION=UNION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:06 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools7803555857253149491interval_list ACTION=UNION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testAllActions[1](UNION, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testAllActions[1](UNION, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:06 IntervalListTools Produced 3 intervals totalling 200 bases. INFO 2024-07-02 12:01:06 IntervalListTools Produced 3 intervals totalling 200 bases. Test: Test method testAllActions[1](UNION, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:06 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:06 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testAllActions[1](UNION, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testAllActions[2](INTERSECT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) Test: Test method testAllActions[2](INTERSECT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:06 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testAllActions[2](INTERSECT, testdata/picard/util/scatterable.interval_list) STANDARD_ERROR INFO 2024-07-02 12:01:06 IntervalListTools Test: Test method testAllActions[2](INTERSECT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[2](INTERSECT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testAllActions[2](INTERSECT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[2](INTERSECT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testAllActions[2](INTERSECT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testAllActions[2](INTERSECT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[2](INTERSECT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testAllActions[2](INTERSECT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[2](INTERSECT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION INTERSECT -INPUT testdata/picard/util/scatterable.interval_list -OUTPUT /tmp/IntervalListTools1409260423752770906interval_list ********** IntervalListTools -ACTION INTERSECT -INPUT testdata/picard/util/scatterable.interval_list -OUTPUT /tmp/IntervalListTools1409260423752770906interval_list Test: Test method testAllActions[2](INTERSECT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[2](INTERSECT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[2](INTERSECT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[2](INTERSECT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:06.639 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:06.639 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAllActions[2](INTERSECT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:06.639 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:06.639 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAllActions[2](INTERSECT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:06.639 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:06.639 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAllActions[2](INTERSECT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:06.639 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:06.639 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAllActions[2](INTERSECT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:06 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools1409260423752770906interval_list ACTION=INTERSECT PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:06 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools1409260423752770906interval_list ACTION=INTERSECT PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testAllActions[2](INTERSECT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testAllActions[2](INTERSECT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:06 IntervalListTools Produced 3 intervals totalling 200 bases. INFO 2024-07-02 12:01:06 IntervalListTools Produced 3 intervals totalling 200 bases. Test: Test method testAllActions[2](INTERSECT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:06 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:06 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testAllActions[2](INTERSECT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testAllActions[3](SUBTRACT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) Test: Test method testAllActions[3](SUBTRACT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:06 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testAllActions[3](SUBTRACT, testdata/picard/util/scatterable.interval_list) STANDARD_ERROR INFO 2024-07-02 12:01:06 IntervalListTools Test: Test method testAllActions[3](SUBTRACT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[3](SUBTRACT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testAllActions[3](SUBTRACT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[3](SUBTRACT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testAllActions[3](SUBTRACT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testAllActions[3](SUBTRACT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[3](SUBTRACT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testAllActions[3](SUBTRACT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[3](SUBTRACT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION SUBTRACT -INPUT testdata/picard/util/scatterable.interval_list -SECOND_INPUT testdata/picard/util/secondInput.interval_list -OUTPUT /tmp/IntervalListTools4529106955085174494interval_list ********** IntervalListTools -ACTION SUBTRACT -INPUT testdata/picard/util/scatterable.interval_list -SECOND_INPUT testdata/picard/util/secondInput.interval_list -OUTPUT /tmp/IntervalListTools4529106955085174494interval_list Test: Test method testAllActions[3](SUBTRACT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[3](SUBTRACT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[3](SUBTRACT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[3](SUBTRACT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:06.724 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:06.724 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAllActions[3](SUBTRACT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:06.724 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:06.724 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAllActions[3](SUBTRACT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:06.724 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:06.724 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAllActions[3](SUBTRACT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:06.724 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:06.724 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAllActions[3](SUBTRACT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:06 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools4529106955085174494interval_list ACTION=SUBTRACT SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:06 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools4529106955085174494interval_list ACTION=SUBTRACT SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testAllActions[3](SUBTRACT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testAllActions[3](SUBTRACT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:06 IntervalListTools Produced 2 intervals totalling 60 bases. INFO 2024-07-02 12:01:06 IntervalListTools Produced 2 intervals totalling 60 bases. Test: Test method testAllActions[3](SUBTRACT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:06 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:06 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testAllActions[3](SUBTRACT, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testAllActions[4](SYMDIFF, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) Test: Test method testAllActions[4](SYMDIFF, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:06 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testAllActions[4](SYMDIFF, testdata/picard/util/scatterable.interval_list) STANDARD_ERROR INFO 2024-07-02 12:01:06 IntervalListTools Test: Test method testAllActions[4](SYMDIFF, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[4](SYMDIFF, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testAllActions[4](SYMDIFF, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[4](SYMDIFF, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testAllActions[4](SYMDIFF, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testAllActions[4](SYMDIFF, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[4](SYMDIFF, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testAllActions[4](SYMDIFF, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[4](SYMDIFF, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION SYMDIFF -INPUT testdata/picard/util/scatterable.interval_list -SECOND_INPUT testdata/picard/util/secondInput.interval_list -OUTPUT /tmp/IntervalListTools17240200817599893964interval_list ********** IntervalListTools -ACTION SYMDIFF -INPUT testdata/picard/util/scatterable.interval_list -SECOND_INPUT testdata/picard/util/secondInput.interval_list -OUTPUT /tmp/IntervalListTools17240200817599893964interval_list Test: Test method testAllActions[4](SYMDIFF, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[4](SYMDIFF, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[4](SYMDIFF, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[4](SYMDIFF, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:06.849 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:06.849 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAllActions[4](SYMDIFF, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:06.849 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:06.849 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAllActions[4](SYMDIFF, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:06.850 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:06.850 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAllActions[4](SYMDIFF, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:06.850 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:06.850 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAllActions[4](SYMDIFF, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:06 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools17240200817599893964interval_list ACTION=SYMDIFF SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:06 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools17240200817599893964interval_list ACTION=SYMDIFF SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testAllActions[4](SYMDIFF, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testAllActions[4](SYMDIFF, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:06 IntervalListTools Produced 3 intervals totalling 61 bases. INFO 2024-07-02 12:01:06 IntervalListTools Produced 3 intervals totalling 61 bases. Test: Test method testAllActions[4](SYMDIFF, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:06 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:06 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testAllActions[4](SYMDIFF, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testAllActions[5](OVERLAPS, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) Test: Test method testAllActions[5](OVERLAPS, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:07 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testAllActions[5](OVERLAPS, testdata/picard/util/scatterable.interval_list) STANDARD_ERROR INFO 2024-07-02 12:01:07 IntervalListTools Test: Test method testAllActions[5](OVERLAPS, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[5](OVERLAPS, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testAllActions[5](OVERLAPS, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[5](OVERLAPS, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testAllActions[5](OVERLAPS, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testAllActions[5](OVERLAPS, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[5](OVERLAPS, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testAllActions[5](OVERLAPS, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[5](OVERLAPS, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION OVERLAPS -INPUT testdata/picard/util/scatterable.interval_list -SECOND_INPUT testdata/picard/util/secondInput.interval_list -OUTPUT /tmp/IntervalListTools9166628063497841693interval_list ********** IntervalListTools -ACTION OVERLAPS -INPUT testdata/picard/util/scatterable.interval_list -SECOND_INPUT testdata/picard/util/secondInput.interval_list -OUTPUT /tmp/IntervalListTools9166628063497841693interval_list Test: Test method testAllActions[5](OVERLAPS, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[5](OVERLAPS, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[5](OVERLAPS, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[5](OVERLAPS, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.018 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:07.018 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAllActions[5](OVERLAPS, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.018 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:07.018 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAllActions[5](OVERLAPS, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.018 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:07.018 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAllActions[5](OVERLAPS, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.018 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:07.018 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAllActions[5](OVERLAPS, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:07 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools9166628063497841693interval_list ACTION=OVERLAPS SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:07 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools9166628063497841693interval_list ACTION=OVERLAPS SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testAllActions[5](OVERLAPS, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testAllActions[5](OVERLAPS, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:07 IntervalListTools Produced 2 intervals totalling 150 bases. INFO 2024-07-02 12:01:07 IntervalListTools Produced 2 intervals totalling 150 bases. Test: Test method testAllActions[5](OVERLAPS, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:07 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:07 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testAllActions[5](OVERLAPS, testdata/picard/util/scatterable.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testAllActions[6](CONCAT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) Test: Test method testAllActions[6](CONCAT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:07 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testAllActions[6](CONCAT, testdata/picard/util/scatterable_stdin) STANDARD_ERROR INFO 2024-07-02 12:01:07 IntervalListTools Test: Test method testAllActions[6](CONCAT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[6](CONCAT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testAllActions[6](CONCAT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[6](CONCAT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testAllActions[6](CONCAT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testAllActions[6](CONCAT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[6](CONCAT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testAllActions[6](CONCAT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[6](CONCAT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT testdata/picard/util/scatterable_stdin -OUTPUT /tmp/IntervalListTools8660093456031715299interval_list ********** IntervalListTools -ACTION CONCAT -INPUT testdata/picard/util/scatterable_stdin -OUTPUT /tmp/IntervalListTools8660093456031715299interval_list Test: Test method testAllActions[6](CONCAT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[6](CONCAT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[6](CONCAT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[6](CONCAT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.223 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:07.223 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAllActions[6](CONCAT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.224 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:07.224 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAllActions[6](CONCAT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.224 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:07.224 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAllActions[6](CONCAT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.224 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:07.224 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAllActions[6](CONCAT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:07 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable_stdin] OUTPUT=/tmp/IntervalListTools8660093456031715299interval_list ACTION=CONCAT PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:07 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable_stdin] OUTPUT=/tmp/IntervalListTools8660093456031715299interval_list ACTION=CONCAT PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testAllActions[6](CONCAT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testAllActions[6](CONCAT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:07 IntervalListTools Unrecognized file extension, defaulting to .interval_list INFO 2024-07-02 12:01:07 IntervalListTools Unrecognized file extension, defaulting to .interval_list Test: Test method testAllActions[6](CONCAT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:07 IntervalListTools Produced 3 intervals totalling 200 bases. INFO 2024-07-02 12:01:07 IntervalListTools Produced 3 intervals totalling 200 bases. Test: Test method testAllActions[6](CONCAT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:07 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:07 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testAllActions[6](CONCAT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testAllActions[7](UNION, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) Test: Test method testAllActions[7](UNION, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:07 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testAllActions[7](UNION, testdata/picard/util/scatterable_stdin) STANDARD_ERROR INFO 2024-07-02 12:01:07 IntervalListTools Test: Test method testAllActions[7](UNION, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[7](UNION, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testAllActions[7](UNION, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[7](UNION, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testAllActions[7](UNION, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testAllActions[7](UNION, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[7](UNION, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testAllActions[7](UNION, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[7](UNION, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION UNION -INPUT testdata/picard/util/scatterable_stdin -OUTPUT /tmp/IntervalListTools18439316222734683947interval_list ********** IntervalListTools -ACTION UNION -INPUT testdata/picard/util/scatterable_stdin -OUTPUT /tmp/IntervalListTools18439316222734683947interval_list Test: Test method testAllActions[7](UNION, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[7](UNION, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[7](UNION, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[7](UNION, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.339 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:07.339 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAllActions[7](UNION, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.339 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:07.339 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAllActions[7](UNION, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.339 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:07.339 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAllActions[7](UNION, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.339 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:07.339 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAllActions[7](UNION, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:07 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable_stdin] OUTPUT=/tmp/IntervalListTools18439316222734683947interval_list ACTION=UNION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:07 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable_stdin] OUTPUT=/tmp/IntervalListTools18439316222734683947interval_list ACTION=UNION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testAllActions[7](UNION, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testAllActions[7](UNION, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:07 IntervalListTools Unrecognized file extension, defaulting to .interval_list INFO 2024-07-02 12:01:07 IntervalListTools Unrecognized file extension, defaulting to .interval_list Test: Test method testAllActions[7](UNION, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:07 IntervalListTools Produced 3 intervals totalling 200 bases. INFO 2024-07-02 12:01:07 IntervalListTools Produced 3 intervals totalling 200 bases. Test: Test method testAllActions[7](UNION, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:07 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:07 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testAllActions[7](UNION, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testAllActions[8](INTERSECT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) Test: Test method testAllActions[8](INTERSECT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:07 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testAllActions[8](INTERSECT, testdata/picard/util/scatterable_stdin) STANDARD_ERROR INFO 2024-07-02 12:01:07 IntervalListTools Test: Test method testAllActions[8](INTERSECT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[8](INTERSECT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testAllActions[8](INTERSECT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[8](INTERSECT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testAllActions[8](INTERSECT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testAllActions[8](INTERSECT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[8](INTERSECT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testAllActions[8](INTERSECT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[8](INTERSECT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION INTERSECT -INPUT testdata/picard/util/scatterable_stdin -OUTPUT /tmp/IntervalListTools1238825966903123768interval_list ********** IntervalListTools -ACTION INTERSECT -INPUT testdata/picard/util/scatterable_stdin -OUTPUT /tmp/IntervalListTools1238825966903123768interval_list Test: Test method testAllActions[8](INTERSECT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[8](INTERSECT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[8](INTERSECT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[8](INTERSECT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.482 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:07.482 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAllActions[8](INTERSECT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.482 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:07.482 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAllActions[8](INTERSECT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.483 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:07.483 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAllActions[8](INTERSECT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.483 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:07.483 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAllActions[8](INTERSECT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:07 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable_stdin] OUTPUT=/tmp/IntervalListTools1238825966903123768interval_list ACTION=INTERSECT PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:07 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable_stdin] OUTPUT=/tmp/IntervalListTools1238825966903123768interval_list ACTION=INTERSECT PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testAllActions[8](INTERSECT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testAllActions[8](INTERSECT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:07 IntervalListTools Unrecognized file extension, defaulting to .interval_list INFO 2024-07-02 12:01:07 IntervalListTools Unrecognized file extension, defaulting to .interval_list Test: Test method testAllActions[8](INTERSECT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:07 IntervalListTools Produced 3 intervals totalling 200 bases. INFO 2024-07-02 12:01:07 IntervalListTools Produced 3 intervals totalling 200 bases. Test: Test method testAllActions[8](INTERSECT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:07 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:07 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testAllActions[8](INTERSECT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testAllActions[9](SUBTRACT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) Test: Test method testAllActions[9](SUBTRACT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:07 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testAllActions[9](SUBTRACT, testdata/picard/util/scatterable_stdin) STANDARD_ERROR INFO 2024-07-02 12:01:07 IntervalListTools Test: Test method testAllActions[9](SUBTRACT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[9](SUBTRACT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testAllActions[9](SUBTRACT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[9](SUBTRACT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testAllActions[9](SUBTRACT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testAllActions[9](SUBTRACT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[9](SUBTRACT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testAllActions[9](SUBTRACT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[9](SUBTRACT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION SUBTRACT -INPUT testdata/picard/util/scatterable_stdin -SECOND_INPUT testdata/picard/util/secondInput.interval_list -OUTPUT /tmp/IntervalListTools9801201816599844280interval_list ********** IntervalListTools -ACTION SUBTRACT -INPUT testdata/picard/util/scatterable_stdin -SECOND_INPUT testdata/picard/util/secondInput.interval_list -OUTPUT /tmp/IntervalListTools9801201816599844280interval_list Test: Test method testAllActions[9](SUBTRACT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[9](SUBTRACT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[9](SUBTRACT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[9](SUBTRACT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.596 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:07.596 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAllActions[9](SUBTRACT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.596 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:07.596 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAllActions[9](SUBTRACT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.596 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:07.596 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAllActions[9](SUBTRACT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.596 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:07.596 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAllActions[9](SUBTRACT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:07 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable_stdin] OUTPUT=/tmp/IntervalListTools9801201816599844280interval_list ACTION=SUBTRACT SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:07 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable_stdin] OUTPUT=/tmp/IntervalListTools9801201816599844280interval_list ACTION=SUBTRACT SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testAllActions[9](SUBTRACT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testAllActions[9](SUBTRACT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:07 IntervalListTools Unrecognized file extension, defaulting to .interval_list INFO 2024-07-02 12:01:07 IntervalListTools Unrecognized file extension, defaulting to .interval_list Test: Test method testAllActions[9](SUBTRACT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:07 IntervalListTools Produced 2 intervals totalling 60 bases. INFO 2024-07-02 12:01:07 IntervalListTools Produced 2 intervals totalling 60 bases. Test: Test method testAllActions[9](SUBTRACT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:07 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:07 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testAllActions[9](SUBTRACT, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testAllActions[10](SYMDIFF, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) Test: Test method testAllActions[10](SYMDIFF, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:07 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testAllActions[10](SYMDIFF, testdata/picard/util/scatterable_stdin) STANDARD_ERROR INFO 2024-07-02 12:01:07 IntervalListTools Test: Test method testAllActions[10](SYMDIFF, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[10](SYMDIFF, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testAllActions[10](SYMDIFF, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[10](SYMDIFF, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testAllActions[10](SYMDIFF, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testAllActions[10](SYMDIFF, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[10](SYMDIFF, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testAllActions[10](SYMDIFF, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[10](SYMDIFF, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION SYMDIFF -INPUT testdata/picard/util/scatterable_stdin -SECOND_INPUT testdata/picard/util/secondInput.interval_list -OUTPUT /tmp/IntervalListTools8774444035638118350interval_list ********** IntervalListTools -ACTION SYMDIFF -INPUT testdata/picard/util/scatterable_stdin -SECOND_INPUT testdata/picard/util/secondInput.interval_list -OUTPUT /tmp/IntervalListTools8774444035638118350interval_list Test: Test method testAllActions[10](SYMDIFF, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[10](SYMDIFF, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[10](SYMDIFF, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[10](SYMDIFF, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:07.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAllActions[10](SYMDIFF, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.743 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:07.743 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAllActions[10](SYMDIFF, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:07.743 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAllActions[10](SYMDIFF, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.743 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:07.743 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAllActions[10](SYMDIFF, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:07 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable_stdin] OUTPUT=/tmp/IntervalListTools8774444035638118350interval_list ACTION=SYMDIFF SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:07 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable_stdin] OUTPUT=/tmp/IntervalListTools8774444035638118350interval_list ACTION=SYMDIFF SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testAllActions[10](SYMDIFF, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testAllActions[10](SYMDIFF, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:07 IntervalListTools Unrecognized file extension, defaulting to .interval_list INFO 2024-07-02 12:01:07 IntervalListTools Unrecognized file extension, defaulting to .interval_list Test: Test method testAllActions[10](SYMDIFF, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:07 IntervalListTools Produced 3 intervals totalling 61 bases. INFO 2024-07-02 12:01:07 IntervalListTools Produced 3 intervals totalling 61 bases. Test: Test method testAllActions[10](SYMDIFF, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:07 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:07 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testAllActions[10](SYMDIFF, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testAllActions[11](OVERLAPS, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) Test: Test method testAllActions[11](OVERLAPS, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:07 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testAllActions[11](OVERLAPS, testdata/picard/util/scatterable_stdin) STANDARD_ERROR INFO 2024-07-02 12:01:07 IntervalListTools Test: Test method testAllActions[11](OVERLAPS, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[11](OVERLAPS, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testAllActions[11](OVERLAPS, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[11](OVERLAPS, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testAllActions[11](OVERLAPS, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testAllActions[11](OVERLAPS, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[11](OVERLAPS, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testAllActions[11](OVERLAPS, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[11](OVERLAPS, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION OVERLAPS -INPUT testdata/picard/util/scatterable_stdin -SECOND_INPUT testdata/picard/util/secondInput.interval_list -OUTPUT /tmp/IntervalListTools11952910957347134984interval_list ********** IntervalListTools -ACTION OVERLAPS -INPUT testdata/picard/util/scatterable_stdin -SECOND_INPUT testdata/picard/util/secondInput.interval_list -OUTPUT /tmp/IntervalListTools11952910957347134984interval_list Test: Test method testAllActions[11](OVERLAPS, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testAllActions[11](OVERLAPS, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[11](OVERLAPS, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testAllActions[11](OVERLAPS, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.871 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:07.871 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAllActions[11](OVERLAPS, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.872 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:07.872 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAllActions[11](OVERLAPS, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.872 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:07.872 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testAllActions[11](OVERLAPS, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.872 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:07.872 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testAllActions[11](OVERLAPS, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:07 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable_stdin] OUTPUT=/tmp/IntervalListTools11952910957347134984interval_list ACTION=OVERLAPS SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:07 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/scatterable_stdin] OUTPUT=/tmp/IntervalListTools11952910957347134984interval_list ACTION=OVERLAPS SECOND_INPUT=[testdata/picard/util/secondInput.interval_list] PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testAllActions[11](OVERLAPS, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testAllActions[11](OVERLAPS, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:07 IntervalListTools Unrecognized file extension, defaulting to .interval_list INFO 2024-07-02 12:01:07 IntervalListTools Unrecognized file extension, defaulting to .interval_list Test: Test method testAllActions[11](OVERLAPS, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:07 IntervalListTools Produced 2 intervals totalling 150 bases. INFO 2024-07-02 12:01:07 IntervalListTools Produced 2 intervals totalling 150 bases. Test: Test method testAllActions[11](OVERLAPS, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:07 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:07 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testAllActions[11](OVERLAPS, testdata/picard/util/scatterable_stdin)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testCombineAbuttingIntervals[0](false, testdata/picard/util/abutting_combined.interval_list)(picard.util.IntervalListToolsTest) Test: Test method testCombineAbuttingIntervals[0](false, testdata/picard/util/abutting_combined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:07 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testCombineAbuttingIntervals[0](false, testdata/picard/util/abutting_combined.interval_list) STANDARD_ERROR INFO 2024-07-02 12:01:07 IntervalListTools Test: Test method testCombineAbuttingIntervals[0](false, testdata/picard/util/abutting_combined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testCombineAbuttingIntervals[0](false, testdata/picard/util/abutting_combined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCombineAbuttingIntervals[0](false, testdata/picard/util/abutting_combined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testCombineAbuttingIntervals[0](false, testdata/picard/util/abutting_combined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCombineAbuttingIntervals[0](false, testdata/picard/util/abutting_combined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCombineAbuttingIntervals[0](false, testdata/picard/util/abutting_combined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testCombineAbuttingIntervals[0](false, testdata/picard/util/abutting_combined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCombineAbuttingIntervals[0](false, testdata/picard/util/abutting_combined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testCombineAbuttingIntervals[0](false, testdata/picard/util/abutting_combined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -INPUT testdata/picard/util/abutting.interval_list -OUTPUT /tmp/IntervalListTools8871493379205327107.interval_list -ACTION UNION -DONT_MERGE_ABUTTING false ********** IntervalListTools -INPUT testdata/picard/util/abutting.interval_list -OUTPUT /tmp/IntervalListTools8871493379205327107.interval_list -ACTION UNION -DONT_MERGE_ABUTTING false Test: Test method testCombineAbuttingIntervals[0](false, testdata/picard/util/abutting_combined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testCombineAbuttingIntervals[0](false, testdata/picard/util/abutting_combined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testCombineAbuttingIntervals[0](false, testdata/picard/util/abutting_combined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testCombineAbuttingIntervals[0](false, testdata/picard/util/abutting_combined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.960 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:07.960 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCombineAbuttingIntervals[0](false, testdata/picard/util/abutting_combined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.960 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:07.960 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCombineAbuttingIntervals[0](false, testdata/picard/util/abutting_combined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.960 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:07.960 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCombineAbuttingIntervals[0](false, testdata/picard/util/abutting_combined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:07.960 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:07.960 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCombineAbuttingIntervals[0](false, testdata/picard/util/abutting_combined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:07 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list] OUTPUT=/tmp/IntervalListTools8871493379205327107.interval_list DONT_MERGE_ABUTTING=false ACTION=UNION PADDING=0 UNIQUE=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:07 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list] OUTPUT=/tmp/IntervalListTools8871493379205327107.interval_list DONT_MERGE_ABUTTING=false ACTION=UNION PADDING=0 UNIQUE=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCombineAbuttingIntervals[0](false, testdata/picard/util/abutting_combined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCombineAbuttingIntervals[0](false, testdata/picard/util/abutting_combined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:07 IntervalListTools Produced 2 intervals totalling 8 bases. INFO 2024-07-02 12:01:07 IntervalListTools Produced 2 intervals totalling 8 bases. Test: Test method testCombineAbuttingIntervals[0](false, testdata/picard/util/abutting_combined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:07 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:07 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testCombineAbuttingIntervals[0](false, testdata/picard/util/abutting_combined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testCombineAbuttingIntervals[1](true, testdata/picard/util/abutting_notcombined.interval_list)(picard.util.IntervalListToolsTest) Test: Test method testCombineAbuttingIntervals[1](true, testdata/picard/util/abutting_notcombined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:08 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testCombineAbuttingIntervals[1](true, testdata/picard/util/abutting_notcombined.interval_list) STANDARD_ERROR INFO 2024-07-02 12:01:08 IntervalListTools Test: Test method testCombineAbuttingIntervals[1](true, testdata/picard/util/abutting_notcombined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testCombineAbuttingIntervals[1](true, testdata/picard/util/abutting_notcombined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testCombineAbuttingIntervals[1](true, testdata/picard/util/abutting_notcombined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testCombineAbuttingIntervals[1](true, testdata/picard/util/abutting_notcombined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testCombineAbuttingIntervals[1](true, testdata/picard/util/abutting_notcombined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testCombineAbuttingIntervals[1](true, testdata/picard/util/abutting_notcombined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testCombineAbuttingIntervals[1](true, testdata/picard/util/abutting_notcombined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testCombineAbuttingIntervals[1](true, testdata/picard/util/abutting_notcombined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testCombineAbuttingIntervals[1](true, testdata/picard/util/abutting_notcombined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -INPUT testdata/picard/util/abutting.interval_list -OUTPUT /tmp/IntervalListTools8878537060180450840.interval_list -ACTION UNION -DONT_MERGE_ABUTTING true ********** IntervalListTools -INPUT testdata/picard/util/abutting.interval_list -OUTPUT /tmp/IntervalListTools8878537060180450840.interval_list -ACTION UNION -DONT_MERGE_ABUTTING true Test: Test method testCombineAbuttingIntervals[1](true, testdata/picard/util/abutting_notcombined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testCombineAbuttingIntervals[1](true, testdata/picard/util/abutting_notcombined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testCombineAbuttingIntervals[1](true, testdata/picard/util/abutting_notcombined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testCombineAbuttingIntervals[1](true, testdata/picard/util/abutting_notcombined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:08.006 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:08.006 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCombineAbuttingIntervals[1](true, testdata/picard/util/abutting_notcombined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:08.006 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:08.006 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCombineAbuttingIntervals[1](true, testdata/picard/util/abutting_notcombined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:08.006 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:08.006 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testCombineAbuttingIntervals[1](true, testdata/picard/util/abutting_notcombined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:08.006 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:08.006 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testCombineAbuttingIntervals[1](true, testdata/picard/util/abutting_notcombined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:08 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list] OUTPUT=/tmp/IntervalListTools8878537060180450840.interval_list DONT_MERGE_ABUTTING=true ACTION=UNION PADDING=0 UNIQUE=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:08 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/abutting.interval_list] OUTPUT=/tmp/IntervalListTools8878537060180450840.interval_list DONT_MERGE_ABUTTING=true ACTION=UNION PADDING=0 UNIQUE=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testCombineAbuttingIntervals[1](true, testdata/picard/util/abutting_notcombined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testCombineAbuttingIntervals[1](true, testdata/picard/util/abutting_notcombined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:08 IntervalListTools Produced 3 intervals totalling 8 bases. INFO 2024-07-02 12:01:08 IntervalListTools Produced 3 intervals totalling 8 bases. Test: Test method testCombineAbuttingIntervals[1](true, testdata/picard/util/abutting_notcombined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:08 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:08 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testCombineAbuttingIntervals[1](true, testdata/picard/util/abutting_notcombined.interval_list)(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testCountOutputValidation(picard.util.IntervalListToolsTest) Running Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:08 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testLargeScatters STANDARD_ERROR INFO 2024-07-02 12:01:08 IntervalListTools Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -SCATTER_COUNT 1000 -INPUT testdata/picard/util/large_scatterable.interval_list -OUTPUT /tmp/IntervalListTools16094285823574834445lists ********** IntervalListTools -SCATTER_COUNT 1000 -INPUT testdata/picard/util/large_scatterable.interval_list -OUTPUT /tmp/IntervalListTools16094285823574834445lists Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:08.371 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:08.371 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:08.381 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:08.381 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:08.382 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:08.382 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:08.382 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:08.382 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:08 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/large_scatterable.interval_list] OUTPUT=/tmp/IntervalListTools16094285823574834445lists SCATTER_COUNT=1000 PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true ACTION=CONCAT INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:08 GMT+14:00 2024] IntervalListTools INPUT=[testdata/picard/util/large_scatterable.interval_list] OUTPUT=/tmp/IntervalListTools16094285823574834445lists SCATTER_COUNT=1000 PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true ACTION=CONCAT INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:09 IntervalListTools Wrote 1000 scatter subdirectories to /tmp/IntervalListTools16094285823574834445lists. INFO 2024-07-02 12:01:09 IntervalListTools Wrote 1000 scatter subdirectories to /tmp/IntervalListTools16094285823574834445lists. Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:09 IntervalListTools Produced 1002 intervals totalling 53800 bases. INFO 2024-07-02 12:01:09 IntervalListTools Produced 1002 intervals totalling 53800 bases. Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:09 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.03 minutes. [Tue Jul 02 12:01:09 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.03 minutes. Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:10 IntervalListTools INFO 2024-07-02 12:01:10 IntervalListTools Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0594_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0176_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0608_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0671_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0511_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0639_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0596_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0257_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0158_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0485_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0868_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0603_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0920_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0418_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0122_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0796_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0197_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0838_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0555_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0050_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0783_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0047_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0698_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0324_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0724_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0656_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0970_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0949_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0277_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0252_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0001_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0283_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0058_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0148_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0909_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0155_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0139_of_1000/scattered.interval_list -INPUT 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/tmp/IntervalListTools16094285823574834445lists/temp_0593_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0095_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0788_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0733_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0021_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0499_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0780_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0759_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0443_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0133_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0055_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0374_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0464_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0020_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0562_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0194_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0857_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0526_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0420_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0089_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0363_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0974_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0495_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0071_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0952_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0440_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0417_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0360_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0408_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0586_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0219_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0881_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0233_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0705_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0351_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0540_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0398_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0545_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0955_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0720_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0719_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0516_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0473_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0906_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0948_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0676_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0370_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0168_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0354_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0871_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0681_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0962_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0173_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0254_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0087_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0236_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0829_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0882_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0180_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0070_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0715_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0213_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0030_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0023_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0287_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0390_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0896_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0855_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0619_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0742_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0550_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0276_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0686_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0162_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0789_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0835_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0645_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0591_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0469_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0271_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0616_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0191_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0307_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0661_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0613_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0075_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0064_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0781_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0518_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0801_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0335_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0067_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0463_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0745_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0493_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0837_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0231_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0622_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0329_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0312_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0407_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0985_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0358_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0241_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0966_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0737_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0502_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0691_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0582_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0956_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0606_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0170_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0313_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0647_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0636_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0345_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0895_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0014_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0721_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0132_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0960_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0975_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0342_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0249_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0732_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0514_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0617_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0043_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0117_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0414_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0242_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0554_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0569_of_1000/scattered.interval_list -OUTPUT /tmp/IntervalListTools12074713739530313075.interval_list -ACTION UNION ********** IntervalListTools -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0594_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0176_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0608_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0671_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0511_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0639_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0596_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0257_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0158_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0485_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0868_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0603_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0920_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0418_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0122_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0796_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0197_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0838_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0555_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0050_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0783_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0047_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0698_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0324_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0724_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0656_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0970_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0949_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0277_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0252_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0001_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0283_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0058_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0148_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0909_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0155_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0139_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0430_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0006_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0248_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0997_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0052_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0654_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0199_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0916_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0487_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0045_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0278_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0987_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0853_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0447_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0265_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0475_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0804_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0026_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0488_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0214_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0017_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0657_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0185_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0308_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0842_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0456_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0405_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0849_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0905_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0880_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0062_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0602_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0915_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0773_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0542_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0056_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0394_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0792_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0321_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0537_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0843_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0652_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0934_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0483_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0903_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0341_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0315_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0188_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0930_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0284_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0436_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0210_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0536_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0413_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0480_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0083_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0590_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0450_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0476_of_1000/scattered.interval_list -INPUT 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/tmp/IntervalListTools16094285823574834445lists/temp_0871_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0681_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0962_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0173_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0254_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0087_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0236_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0829_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0882_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0180_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0070_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0715_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0213_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0030_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0023_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0287_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0390_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0896_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0855_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0619_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0742_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0550_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0276_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0686_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0162_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0789_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0835_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0645_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0591_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0469_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0271_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0616_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0191_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0307_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0661_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0613_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0075_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0064_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0781_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0518_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0801_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0335_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0067_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0463_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0745_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0493_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0837_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0231_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0622_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0329_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0312_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0407_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0985_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0358_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0241_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0966_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0737_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0502_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0691_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0582_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0956_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0606_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0170_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0313_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0647_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0636_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0345_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0895_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0014_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0721_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0132_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0960_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0975_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0342_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0249_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0732_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0514_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0617_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0043_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0117_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0414_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0242_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0554_of_1000/scattered.interval_list -INPUT /tmp/IntervalListTools16094285823574834445lists/temp_0569_of_1000/scattered.interval_list -OUTPUT /tmp/IntervalListTools12074713739530313075.interval_list -ACTION UNION Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:10.105 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:10.105 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:10.105 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:10.105 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:10.106 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:10.106 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:10.106 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:10.106 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:10 GMT+14:00 2024] IntervalListTools INPUT=[/tmp/IntervalListTools16094285823574834445lists/temp_0594_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0176_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0608_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0671_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0511_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0639_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0596_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0257_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0158_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0485_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0868_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0603_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0920_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0418_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0122_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0796_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0197_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0838_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0555_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0050_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0783_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0047_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0698_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0324_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0724_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0656_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0970_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0949_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0277_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0252_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0001_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0283_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0058_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0148_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0909_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0155_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0139_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0430_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0006_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0248_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0997_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0052_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0654_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0199_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0916_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0487_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0045_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0278_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0987_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0853_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0447_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0265_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0475_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0804_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0026_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0488_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0214_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0017_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0657_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0185_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0308_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0842_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0456_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0405_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0849_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0905_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0880_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0062_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0602_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0915_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0773_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0542_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0056_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0394_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0792_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0321_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0537_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0843_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0652_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0934_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0483_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0903_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0341_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0315_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0188_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0930_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0284_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0436_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0210_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0536_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0413_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0480_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0083_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0590_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0450_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0476_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0207_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0451_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0588_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0816_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0585_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0239_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0371_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0669_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0933_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0340_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0396_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0917_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0926_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0584_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0461_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0224_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0234_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0564_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0678_of_1000/scattered.interval_list, 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/tmp/IntervalListTools16094285823574834445lists/temp_0288_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0465_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0044_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0428_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0018_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0547_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0104_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0704_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0723_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0777_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0840_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0327_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0973_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0377_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0372_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0677_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0092_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0039_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0710_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0404_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0727_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0114_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0556_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0904_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0320_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0178_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0438_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0620_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0938_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0100_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0373_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0989_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0033_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0574_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0836_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0336_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0763_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0832_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0498_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0546_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0130_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0182_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0433_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0505_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0644_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0806_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0770_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0105_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0402_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0258_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0111_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0246_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0598_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0611_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0635_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0883_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0142_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0032_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0525_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0332_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0073_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0793_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0264_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0680_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0561_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0625_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0400_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0831_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0972_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0862_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0593_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0095_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0788_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0733_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0021_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0499_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0780_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0759_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0443_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0133_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0055_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0374_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0464_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0020_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0562_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0194_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0857_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0526_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0420_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0089_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0363_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0974_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0495_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0071_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0952_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0440_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0417_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0360_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0408_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0586_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0219_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0881_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0233_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0705_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0351_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0540_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0398_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0545_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0955_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0720_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0719_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0516_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0473_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0906_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0948_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0676_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0370_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0168_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0354_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0871_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0681_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0962_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0173_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0254_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0087_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0236_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0829_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0882_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0180_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0070_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0715_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0213_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0030_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0023_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0287_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0390_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0896_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0855_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0619_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0742_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0550_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0276_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0686_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0162_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0789_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0835_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0645_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0591_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0469_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0271_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0616_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0191_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0307_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0661_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0613_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0075_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0064_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0781_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0518_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0801_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0335_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0067_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0463_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0745_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0493_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0837_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0231_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0622_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0329_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0312_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0407_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0985_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0358_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0241_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0966_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0737_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0502_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0691_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0582_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0956_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0606_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0170_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0313_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0647_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0636_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0345_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0895_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0014_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0721_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0132_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0960_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0975_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0342_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0249_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0732_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0514_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0617_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0043_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0117_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0414_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0242_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0554_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0569_of_1000/scattered.interval_list] OUTPUT=/tmp/IntervalListTools12074713739530313075.interval_list ACTION=UNION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:10 GMT+14:00 2024] IntervalListTools INPUT=[/tmp/IntervalListTools16094285823574834445lists/temp_0594_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0176_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0608_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0671_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0511_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0639_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0596_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0257_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0158_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0485_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0868_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0603_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0920_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0418_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0122_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0796_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0197_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0838_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0555_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0050_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0783_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0047_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0698_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0324_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0724_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0656_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0970_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0949_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0277_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0252_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0001_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0283_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0058_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0148_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0909_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0155_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0139_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0430_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0006_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0248_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0997_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0052_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0654_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0199_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0916_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0487_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0045_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0278_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0987_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0853_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0447_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0265_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0475_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0804_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0026_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0488_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0214_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0017_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0657_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0185_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0308_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0842_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0456_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0405_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0849_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0905_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0880_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0062_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0602_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0915_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0773_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0542_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0056_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0394_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0792_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0321_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0537_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0843_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0652_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0934_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0483_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0903_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0341_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0315_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0188_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0930_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0284_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0436_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0210_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0536_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0413_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0480_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0083_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0590_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0450_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0476_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0207_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0451_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0588_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0816_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0585_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0239_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0371_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0669_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0933_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0340_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0396_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0917_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0926_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0584_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0461_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0224_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0234_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0564_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0678_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0818_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0141_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0599_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0713_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0005_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0939_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0273_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0274_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0520_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0541_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0696_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0717_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0651_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0983_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0912_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0065_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0365_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0306_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0270_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0685_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0084_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0112_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0474_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0496_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0665_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0392_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0346_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0041_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0025_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0544_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0802_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0193_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0553_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0227_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0153_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0455_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0893_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0134_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0688_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0953_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0323_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0959_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0670_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0663_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0072_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0319_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0063_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0711_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0293_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0673_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0538_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0666_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0198_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0884_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0028_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0945_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0921_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0963_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0878_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0263_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0980_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0693_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0914_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0445_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0503_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0226_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0864_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0415_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0961_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0368_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0859_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0353_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0444_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0708_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0441_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0364_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0578_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0874_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0003_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0614_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0513_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0477_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0382_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0879_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0053_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0937_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0051_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0116_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0238_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0764_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0179_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0679_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0739_of_1000/scattered.interval_list, 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/tmp/IntervalListTools16094285823574834445lists/temp_0071_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0952_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0440_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0417_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0360_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0408_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0586_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0219_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0881_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0233_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0705_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0351_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0540_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0398_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0545_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0955_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0720_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0719_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0516_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0473_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0906_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0948_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0676_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0370_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0168_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0354_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0871_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0681_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0962_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0173_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0254_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0087_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0236_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0829_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0882_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0180_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0070_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0715_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0213_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0030_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0023_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0287_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0390_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0896_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0855_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0619_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0742_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0550_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0276_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0686_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0162_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0789_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0835_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0645_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0591_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0469_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0271_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0616_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0191_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0307_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0661_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0613_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0075_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0064_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0781_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0518_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0801_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0335_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0067_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0463_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0745_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0493_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0837_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0231_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0622_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0329_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0312_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0407_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0985_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0358_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0241_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0966_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0737_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0502_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0691_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0582_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0956_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0606_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0170_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0313_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0647_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0636_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0345_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0895_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0014_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0721_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0132_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0960_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0975_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0342_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0249_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0732_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0514_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0617_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0043_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0117_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0414_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0242_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0554_of_1000/scattered.interval_list, /tmp/IntervalListTools16094285823574834445lists/temp_0569_of_1000/scattered.interval_list] OUTPUT=/tmp/IntervalListTools12074713739530313075.interval_list ACTION=UNION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 SUBDIVISION_MODE=INTERVAL_SUBDIVISION INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:13 IntervalListTools Produced 3 intervals totalling 53800 bases. INFO 2024-07-02 12:01:13 IntervalListTools Produced 3 intervals totalling 53800 bases. Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:13 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.05 minutes. [Tue Jul 02 12:01:13 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.05 minutes. Test: Test method testLargeScatters(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatter[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) Test: Test method testScatter[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:13 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatter[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION}) STANDARD_ERROR INFO 2024-07-02 12:01:13 IntervalListTools Test: Test method testScatter[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatter[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatter[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatter[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatter[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools16929468552643253618lists -SCATTER_COUNT 2 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools16929468552643253618lists -SCATTER_COUNT 2 Test: Test method testScatter[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:13.668 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:13.668 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:13.668 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:13.668 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:13.668 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:13.668 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:13.668 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:13.668 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:13 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools16929468552643253618lists ACTION=CONCAT SCATTER_COUNT=2 SUBDIVISION_MODE=INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:13 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools16929468552643253618lists ACTION=CONCAT SCATTER_COUNT=2 SUBDIVISION_MODE=INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatter[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatter[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:13 IntervalListTools Wrote 2 scatter subdirectories to /tmp/IntervalListTools16929468552643253618lists. INFO 2024-07-02 12:01:13 IntervalListTools Wrote 2 scatter subdirectories to /tmp/IntervalListTools16929468552643253618lists. Test: Test method testScatter[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:13 IntervalListTools Produced 4 intervals totalling 200 bases. INFO 2024-07-02 12:01:13 IntervalListTools Produced 4 intervals totalling 200 bases. Test: Test method testScatter[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:13 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:13 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatter[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatter[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) Test: Test method testScatter[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:13 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatter[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION}) STANDARD_ERROR INFO 2024-07-02 12:01:13 IntervalListTools Test: Test method testScatter[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatter[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatter[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatter[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatter[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools13754569498310097992lists -SCATTER_COUNT 4 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools13754569498310097992lists -SCATTER_COUNT 4 Test: Test method testScatter[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:13.797 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:13.797 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:13.797 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:13.797 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:13.798 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:13.798 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:13.798 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:13.798 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:13 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools13754569498310097992lists ACTION=CONCAT SCATTER_COUNT=4 SUBDIVISION_MODE=INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:13 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools13754569498310097992lists ACTION=CONCAT SCATTER_COUNT=4 SUBDIVISION_MODE=INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatter[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatter[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:13 IntervalListTools Wrote 4 scatter subdirectories to /tmp/IntervalListTools13754569498310097992lists. INFO 2024-07-02 12:01:13 IntervalListTools Wrote 4 scatter subdirectories to /tmp/IntervalListTools13754569498310097992lists. Test: Test method testScatter[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:13 IntervalListTools Produced 5 intervals totalling 200 bases. INFO 2024-07-02 12:01:13 IntervalListTools Produced 5 intervals totalling 200 bases. Test: Test method testScatter[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:13 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:13 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatter[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatter[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) Test: Test method testScatter[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:13 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatter[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION}) STANDARD_ERROR INFO 2024-07-02 12:01:13 IntervalListTools Test: Test method testScatter[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatter[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatter[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatter[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatter[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools5329429799713722757lists -SCATTER_COUNT 5 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools5329429799713722757lists -SCATTER_COUNT 5 Test: Test method testScatter[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:13.904 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:13.904 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:13.904 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:13.904 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:13.904 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:13.904 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:13.904 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:13.904 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:13 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools5329429799713722757lists ACTION=CONCAT SCATTER_COUNT=5 SUBDIVISION_MODE=INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:13 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools5329429799713722757lists ACTION=CONCAT SCATTER_COUNT=5 SUBDIVISION_MODE=INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatter[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:13 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatter[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:13 IntervalListTools Wrote 5 scatter subdirectories to /tmp/IntervalListTools5329429799713722757lists. INFO 2024-07-02 12:01:13 IntervalListTools Wrote 5 scatter subdirectories to /tmp/IntervalListTools5329429799713722757lists. Test: Test method testScatter[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:13 IntervalListTools Produced 7 intervals totalling 200 bases. INFO 2024-07-02 12:01:13 IntervalListTools Produced 7 intervals totalling 200 bases. Test: Test method testScatter[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:13 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:13 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatter[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatter[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) Test: Test method testScatter[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:14 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatter[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION}) STANDARD_ERROR INFO 2024-07-02 12:01:14 IntervalListTools Test: Test method testScatter[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatter[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatter[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatter[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatter[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools6611739503579611971lists -SCATTER_COUNT 6 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools6611739503579611971lists -SCATTER_COUNT 6 Test: Test method testScatter[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.008 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:14.008 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.008 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:14.008 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.013 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:14.013 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.013 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:14.013 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:14 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools6611739503579611971lists ACTION=CONCAT SCATTER_COUNT=6 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:14 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools6611739503579611971lists ACTION=CONCAT SCATTER_COUNT=6 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatter[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatter[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:14 IntervalListTools Wrote 3 scatter subdirectories to /tmp/IntervalListTools6611739503579611971lists. INFO 2024-07-02 12:01:14 IntervalListTools Wrote 3 scatter subdirectories to /tmp/IntervalListTools6611739503579611971lists. Test: Test method testScatter[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: WARNING 2024-07-02 12:01:14 IntervalListTools Requested scatter width of 6, but only emitted 3. (This may be an expected consequence of running in BALANCING_WITHOUT_INTERVAL_SUBDIVISION mode.) WARNING 2024-07-02 12:01:14 IntervalListTools Requested scatter width of 6, but only emitted 3. (This may be an expected consequence of running in BALANCING_WITHOUT_INTERVAL_SUBDIVISION mode.) Test: Test method testScatter[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:14 IntervalListTools Produced 3 intervals totalling 200 bases. INFO 2024-07-02 12:01:14 IntervalListTools Produced 3 intervals totalling 200 bases. Test: Test method testScatter[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:14 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:14 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatter[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatter[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) Test: Test method testScatter[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:14 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatter[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW}) STANDARD_ERROR INFO 2024-07-02 12:01:14 IntervalListTools Test: Test method testScatter[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatter[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatter[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatter[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatter[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW -OUTPUT /tmp/IntervalListTools8557700398646941835lists -SCATTER_COUNT 2 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW -OUTPUT /tmp/IntervalListTools8557700398646941835lists -SCATTER_COUNT 2 Test: Test method testScatter[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.102 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:14.102 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.102 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:14.102 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.102 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:14.102 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.102 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:14.102 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:14 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools8557700398646941835lists ACTION=CONCAT SCATTER_COUNT=2 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:14 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools8557700398646941835lists ACTION=CONCAT SCATTER_COUNT=2 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatter[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatter[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:14 IntervalListTools Wrote 2 scatter subdirectories to /tmp/IntervalListTools8557700398646941835lists. INFO 2024-07-02 12:01:14 IntervalListTools Wrote 2 scatter subdirectories to /tmp/IntervalListTools8557700398646941835lists. Test: Test method testScatter[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:14 IntervalListTools Produced 3 intervals totalling 200 bases. INFO 2024-07-02 12:01:14 IntervalListTools Produced 3 intervals totalling 200 bases. Test: Test method testScatter[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:14 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:14 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatter[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatter[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) Test: Test method testScatter[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:14 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatter[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW}) STANDARD_ERROR INFO 2024-07-02 12:01:14 IntervalListTools Test: Test method testScatter[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatter[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatter[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatter[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatter[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW -OUTPUT /tmp/IntervalListTools13048587041940871989lists -SCATTER_COUNT 6 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW -OUTPUT /tmp/IntervalListTools13048587041940871989lists -SCATTER_COUNT 6 Test: Test method testScatter[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.230 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:14.230 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.230 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:14.230 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.230 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:14.230 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.230 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:14.230 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:14 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools13048587041940871989lists ACTION=CONCAT SCATTER_COUNT=6 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:14 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools13048587041940871989lists ACTION=CONCAT SCATTER_COUNT=6 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatter[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatter[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:14 IntervalListTools Wrote 3 scatter subdirectories to /tmp/IntervalListTools13048587041940871989lists. INFO 2024-07-02 12:01:14 IntervalListTools Wrote 3 scatter subdirectories to /tmp/IntervalListTools13048587041940871989lists. Test: Test method testScatter[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: WARNING 2024-07-02 12:01:14 IntervalListTools Requested scatter width of 6, but only emitted 3. (This may be an expected consequence of running in BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW mode.) WARNING 2024-07-02 12:01:14 IntervalListTools Requested scatter width of 6, but only emitted 3. (This may be an expected consequence of running in BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW mode.) Test: Test method testScatter[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:14 IntervalListTools Produced 3 intervals totalling 200 bases. INFO 2024-07-02 12:01:14 IntervalListTools Produced 3 intervals totalling 200 bases. Test: Test method testScatter[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:14 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:14 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatter[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatter[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) Test: Test method testScatter[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:14 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatter[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION}) STANDARD_ERROR INFO 2024-07-02 12:01:14 IntervalListTools Test: Test method testScatter[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatter[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatter[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatter[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatter[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools1441949368470444644lists -SCATTER_COUNT 2 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools1441949368470444644lists -SCATTER_COUNT 2 Test: Test method testScatter[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.344 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:14.344 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.345 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:14.345 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.345 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:14.345 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.345 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:14.345 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:14 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools1441949368470444644lists ACTION=CONCAT SCATTER_COUNT=2 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:14 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools1441949368470444644lists ACTION=CONCAT SCATTER_COUNT=2 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatter[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatter[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:14 IntervalListTools Wrote 2 scatter subdirectories to /tmp/IntervalListTools1441949368470444644lists. INFO 2024-07-02 12:01:14 IntervalListTools Wrote 2 scatter subdirectories to /tmp/IntervalListTools1441949368470444644lists. Test: Test method testScatter[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:14 IntervalListTools Produced 3 intervals totalling 200 bases. INFO 2024-07-02 12:01:14 IntervalListTools Produced 3 intervals totalling 200 bases. Test: Test method testScatter[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:14 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:14 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatter[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatter[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) Test: Test method testScatter[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:14 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatter[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION}) STANDARD_ERROR INFO 2024-07-02 12:01:14 IntervalListTools Test: Test method testScatter[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatter[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatter[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatter[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatter[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools5619385599160612177lists/temp_1_of_1/scattered.interval_list -SCATTER_COUNT 1 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools5619385599160612177lists/temp_1_of_1/scattered.interval_list -SCATTER_COUNT 1 Test: Test method testScatter[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.499 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:14.499 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.499 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:14.499 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.500 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:14.500 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.500 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:14.500 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:14 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools5619385599160612177lists/temp_1_of_1/scattered.interval_list ACTION=CONCAT SCATTER_COUNT=1 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:14 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools5619385599160612177lists/temp_1_of_1/scattered.interval_list ACTION=CONCAT SCATTER_COUNT=1 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatter[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatter[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:14 IntervalListTools Produced 3 intervals totalling 200 bases. INFO 2024-07-02 12:01:14 IntervalListTools Produced 3 intervals totalling 200 bases. Test: Test method testScatter[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:14 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:14 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatter[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatter[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) Test: Test method testScatter[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:14 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatter[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW}) STANDARD_ERROR INFO 2024-07-02 12:01:14 IntervalListTools Test: Test method testScatter[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatter[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatter[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatter[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatter[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW -OUTPUT /tmp/IntervalListTools3189323988467679044lists -SCATTER_COUNT 6 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW -OUTPUT /tmp/IntervalListTools3189323988467679044lists -SCATTER_COUNT 6 Test: Test method testScatter[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.600 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:14.600 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.600 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:14.600 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.600 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:14.600 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.601 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:14.601 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:14 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools3189323988467679044lists ACTION=CONCAT SCATTER_COUNT=6 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:14 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools3189323988467679044lists ACTION=CONCAT SCATTER_COUNT=6 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatter[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatter[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:14 IntervalListTools Wrote 3 scatter subdirectories to /tmp/IntervalListTools3189323988467679044lists. INFO 2024-07-02 12:01:14 IntervalListTools Wrote 3 scatter subdirectories to /tmp/IntervalListTools3189323988467679044lists. Test: Test method testScatter[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: WARNING 2024-07-02 12:01:14 IntervalListTools Requested scatter width of 6, but only emitted 3. (This may be an expected consequence of running in BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW mode.) WARNING 2024-07-02 12:01:14 IntervalListTools Requested scatter width of 6, but only emitted 3. (This may be an expected consequence of running in BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW mode.) Test: Test method testScatter[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:14 IntervalListTools Produced 3 intervals totalling 200 bases. INFO 2024-07-02 12:01:14 IntervalListTools Produced 3 intervals totalling 200 bases. Test: Test method testScatter[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:14 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:14 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatter[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatter[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) Test: Test method testScatter[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:14 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatter[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW}) STANDARD_ERROR INFO 2024-07-02 12:01:14 IntervalListTools Test: Test method testScatter[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatter[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatter[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatter[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatter[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW -OUTPUT /tmp/IntervalListTools16447793945732284528lists -SCATTER_COUNT 2 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW -OUTPUT /tmp/IntervalListTools16447793945732284528lists -SCATTER_COUNT 2 Test: Test method testScatter[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.714 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:14.714 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.715 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:14.715 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.715 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:14.715 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.715 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:14.715 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:14 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools16447793945732284528lists ACTION=CONCAT SCATTER_COUNT=2 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:14 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools16447793945732284528lists ACTION=CONCAT SCATTER_COUNT=2 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatter[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatter[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:14 IntervalListTools Wrote 2 scatter subdirectories to /tmp/IntervalListTools16447793945732284528lists. INFO 2024-07-02 12:01:14 IntervalListTools Wrote 2 scatter subdirectories to /tmp/IntervalListTools16447793945732284528lists. Test: Test method testScatter[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:14 IntervalListTools Produced 3 intervals totalling 200 bases. INFO 2024-07-02 12:01:14 IntervalListTools Produced 3 intervals totalling 200 bases. Test: Test method testScatter[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:14 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:14 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatter[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatter[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) Test: Test method testScatter[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:14 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatter[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW}) STANDARD_ERROR INFO 2024-07-02 12:01:14 IntervalListTools Test: Test method testScatter[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatter[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatter[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatter[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatter[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW -OUTPUT /tmp/IntervalListTools2724956121855903654lists/temp_1_of_1/scattered.interval_list -SCATTER_COUNT 1 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW -OUTPUT /tmp/IntervalListTools2724956121855903654lists/temp_1_of_1/scattered.interval_list -SCATTER_COUNT 1 Test: Test method testScatter[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.890 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:14.890 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.890 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:14.890 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.891 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:14.891 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:14.891 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:14.891 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:14 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools2724956121855903654lists/temp_1_of_1/scattered.interval_list ACTION=CONCAT SCATTER_COUNT=1 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:14 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools2724956121855903654lists/temp_1_of_1/scattered.interval_list ACTION=CONCAT SCATTER_COUNT=1 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatter[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:14 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatter[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:14 IntervalListTools Produced 3 intervals totalling 200 bases. INFO 2024-07-02 12:01:14 IntervalListTools Produced 3 intervals totalling 200 bases. Test: Test method testScatter[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:14 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:14 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatter[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatter[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) Test: Test method testScatter[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:15 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatter[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW}) STANDARD_ERROR INFO 2024-07-02 12:01:15 IntervalListTools Test: Test method testScatter[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatter[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatter[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatter[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatter[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW -OUTPUT /tmp/IntervalListTools1076222856997163421lists -SCATTER_COUNT 7 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW -OUTPUT /tmp/IntervalListTools1076222856997163421lists -SCATTER_COUNT 7 Test: Test method testScatter[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:15.060 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:15.060 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:15.060 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:15.060 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:15.061 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:15.061 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:15.061 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:15.061 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:15 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list] OUTPUT=/tmp/IntervalListTools1076222856997163421lists ACTION=CONCAT SCATTER_COUNT=7 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:15 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list] OUTPUT=/tmp/IntervalListTools1076222856997163421lists ACTION=CONCAT SCATTER_COUNT=7 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatter[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatter[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:15 IntervalListTools Wrote 7 scatter subdirectories to /tmp/IntervalListTools1076222856997163421lists. INFO 2024-07-02 12:01:15 IntervalListTools Wrote 7 scatter subdirectories to /tmp/IntervalListTools1076222856997163421lists. Test: Test method testScatter[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:15 IntervalListTools Produced 9 intervals totalling 80 bases. INFO 2024-07-02 12:01:15 IntervalListTools Produced 9 intervals totalling 80 bases. Test: Test method testScatter[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:15 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:15 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatter[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatter[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) Test: Test method testScatter[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:15 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatter[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION}) STANDARD_ERROR INFO 2024-07-02 12:01:15 IntervalListTools Test: Test method testScatter[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatter[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatter[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatter[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatter[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools4084801618763075381lists -SCATTER_COUNT 7 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools4084801618763075381lists -SCATTER_COUNT 7 Test: Test method testScatter[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:15.194 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:15.194 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:15.194 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:15.194 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:15.194 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:15.194 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:15.194 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:15.194 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:15 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list] OUTPUT=/tmp/IntervalListTools4084801618763075381lists ACTION=CONCAT SCATTER_COUNT=7 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:15 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list] OUTPUT=/tmp/IntervalListTools4084801618763075381lists ACTION=CONCAT SCATTER_COUNT=7 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatter[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatter[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:15 IntervalListTools Wrote 7 scatter subdirectories to /tmp/IntervalListTools4084801618763075381lists. INFO 2024-07-02 12:01:15 IntervalListTools Wrote 7 scatter subdirectories to /tmp/IntervalListTools4084801618763075381lists. Test: Test method testScatter[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:15 IntervalListTools Produced 9 intervals totalling 80 bases. INFO 2024-07-02 12:01:15 IntervalListTools Produced 9 intervals totalling 80 bases. Test: Test method testScatter[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:15 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:15 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatter[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatter[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) Test: Test method testScatter[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:15 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatter[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION}) STANDARD_ERROR INFO 2024-07-02 12:01:15 IntervalListTools Test: Test method testScatter[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatter[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatter[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatter[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatter[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools16185405831652018581lists -SCATTER_COUNT 8 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools16185405831652018581lists -SCATTER_COUNT 8 Test: Test method testScatter[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:15.489 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:15.489 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:15.489 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:15.489 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:15.490 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:15.490 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:15.490 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:15.490 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:15 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list] OUTPUT=/tmp/IntervalListTools16185405831652018581lists ACTION=CONCAT SCATTER_COUNT=8 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:15 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list] OUTPUT=/tmp/IntervalListTools16185405831652018581lists ACTION=CONCAT SCATTER_COUNT=8 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatter[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatter[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:15 IntervalListTools Wrote 8 scatter subdirectories to /tmp/IntervalListTools16185405831652018581lists. INFO 2024-07-02 12:01:15 IntervalListTools Wrote 8 scatter subdirectories to /tmp/IntervalListTools16185405831652018581lists. Test: Test method testScatter[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:15 IntervalListTools Produced 9 intervals totalling 80 bases. INFO 2024-07-02 12:01:15 IntervalListTools Produced 9 intervals totalling 80 bases. Test: Test method testScatter[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:15 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:15 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatter[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatter[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) Test: Test method testScatter[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:15 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatter[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION}) STANDARD_ERROR INFO 2024-07-02 12:01:15 IntervalListTools Test: Test method testScatter[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatter[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatter[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatter[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatter[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools8061646069164587771lists -SCATTER_COUNT 9 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools8061646069164587771lists -SCATTER_COUNT 9 Test: Test method testScatter[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:15.635 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:15.635 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:15.635 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:15.635 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:15.635 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:15.635 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:15.635 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:15.635 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:15 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list] OUTPUT=/tmp/IntervalListTools8061646069164587771lists ACTION=CONCAT SCATTER_COUNT=9 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:15 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list] OUTPUT=/tmp/IntervalListTools8061646069164587771lists ACTION=CONCAT SCATTER_COUNT=9 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatter[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatter[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:15 IntervalListTools Wrote 9 scatter subdirectories to /tmp/IntervalListTools8061646069164587771lists. INFO 2024-07-02 12:01:15 IntervalListTools Wrote 9 scatter subdirectories to /tmp/IntervalListTools8061646069164587771lists. Test: Test method testScatter[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:15 IntervalListTools Produced 9 intervals totalling 80 bases. INFO 2024-07-02 12:01:15 IntervalListTools Produced 9 intervals totalling 80 bases. Test: Test method testScatter[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:15 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:15 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatter[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatter[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) Test: Test method testScatter[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:15 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatter[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT}) STANDARD_ERROR INFO 2024-07-02 12:01:15 IntervalListTools Test: Test method testScatter[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatter[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatter[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatter[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatter[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_many_intervals.interval_list -SUBDIVISION_MODE INTERVAL_COUNT -OUTPUT /tmp/IntervalListTools12416472660822472627lists/temp_1_of_1/scattered.interval_list -SCATTER_COUNT 1 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_many_intervals.interval_list -SUBDIVISION_MODE INTERVAL_COUNT -OUTPUT /tmp/IntervalListTools12416472660822472627lists/temp_1_of_1/scattered.interval_list -SCATTER_COUNT 1 Test: Test method testScatter[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:15.763 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:15.763 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:15.763 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:15.763 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:15.763 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:15.763 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:15.763 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:15.763 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:15 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_many_intervals.interval_list] OUTPUT=/tmp/IntervalListTools12416472660822472627lists/temp_1_of_1/scattered.interval_list ACTION=CONCAT SCATTER_COUNT=1 SUBDIVISION_MODE=INTERVAL_COUNT PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:15 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_many_intervals.interval_list] OUTPUT=/tmp/IntervalListTools12416472660822472627lists/temp_1_of_1/scattered.interval_list ACTION=CONCAT SCATTER_COUNT=1 SUBDIVISION_MODE=INTERVAL_COUNT PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatter[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatter[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:15 IntervalListTools Produced 32 intervals totalling 64 bases. INFO 2024-07-02 12:01:15 IntervalListTools Produced 32 intervals totalling 64 bases. Test: Test method testScatter[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:15 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:15 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatter[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatter[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) Test: Test method testScatter[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:15 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatter[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT}) STANDARD_ERROR INFO 2024-07-02 12:01:15 IntervalListTools Test: Test method testScatter[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatter[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatter[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatter[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatter[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_many_intervals.interval_list -SUBDIVISION_MODE INTERVAL_COUNT -OUTPUT /tmp/IntervalListTools8840604081298885639lists -SCATTER_COUNT 2 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_many_intervals.interval_list -SUBDIVISION_MODE INTERVAL_COUNT -OUTPUT /tmp/IntervalListTools8840604081298885639lists -SCATTER_COUNT 2 Test: Test method testScatter[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:15.813 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:15.813 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:15.813 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:15.813 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:15.814 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:15.814 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:15.814 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:15.814 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:15 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_many_intervals.interval_list] OUTPUT=/tmp/IntervalListTools8840604081298885639lists ACTION=CONCAT SCATTER_COUNT=2 SUBDIVISION_MODE=INTERVAL_COUNT PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:15 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_many_intervals.interval_list] OUTPUT=/tmp/IntervalListTools8840604081298885639lists ACTION=CONCAT SCATTER_COUNT=2 SUBDIVISION_MODE=INTERVAL_COUNT PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatter[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatter[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:15 IntervalListTools Wrote 2 scatter subdirectories to /tmp/IntervalListTools8840604081298885639lists. INFO 2024-07-02 12:01:15 IntervalListTools Wrote 2 scatter subdirectories to /tmp/IntervalListTools8840604081298885639lists. Test: Test method testScatter[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:15 IntervalListTools Produced 32 intervals totalling 64 bases. INFO 2024-07-02 12:01:15 IntervalListTools Produced 32 intervals totalling 64 bases. Test: Test method testScatter[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:15 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:15 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatter[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatter[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) Test: Test method testScatter[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:15 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatter[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT}) STANDARD_ERROR INFO 2024-07-02 12:01:15 IntervalListTools Test: Test method testScatter[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatter[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatter[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatter[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatter[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_many_intervals.interval_list -SUBDIVISION_MODE INTERVAL_COUNT -OUTPUT /tmp/IntervalListTools8858625505788682109lists -SCATTER_COUNT 3 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_many_intervals.interval_list -SUBDIVISION_MODE INTERVAL_COUNT -OUTPUT /tmp/IntervalListTools8858625505788682109lists -SCATTER_COUNT 3 Test: Test method testScatter[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatter[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatter[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:15.910 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:15.910 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:15.910 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:15.910 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:15.910 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:15.910 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatter[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:15.910 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:15.910 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatter[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:15 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_many_intervals.interval_list] OUTPUT=/tmp/IntervalListTools8858625505788682109lists ACTION=CONCAT SCATTER_COUNT=3 SUBDIVISION_MODE=INTERVAL_COUNT PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:15 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_many_intervals.interval_list] OUTPUT=/tmp/IntervalListTools8858625505788682109lists ACTION=CONCAT SCATTER_COUNT=3 SUBDIVISION_MODE=INTERVAL_COUNT PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatter[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:15 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatter[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:15 IntervalListTools Wrote 3 scatter subdirectories to /tmp/IntervalListTools8858625505788682109lists. INFO 2024-07-02 12:01:15 IntervalListTools Wrote 3 scatter subdirectories to /tmp/IntervalListTools8858625505788682109lists. Test: Test method testScatter[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:15 IntervalListTools Produced 32 intervals totalling 64 bases. INFO 2024-07-02 12:01:15 IntervalListTools Produced 32 intervals totalling 64 bases. Test: Test method testScatter[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:15 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:15 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatter[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatterByContent[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) Test: Test method testScatterByContent[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:16 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatterByContent[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION}) STANDARD_ERROR INFO 2024-07-02 12:01:16 IntervalListTools Test: Test method testScatterByContent[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatterByContent[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatterByContent[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatterByContent[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatterByContent[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools13173026219856091945lists -SCATTER_CONTENT 100 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools13173026219856091945lists -SCATTER_CONTENT 100 Test: Test method testScatterByContent[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:16.067 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:16.067 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:16.067 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:16.067 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:16.067 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:16.067 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:16.067 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:16.067 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:16 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools13173026219856091945lists ACTION=CONCAT SCATTER_CONTENT=100 SUBDIVISION_MODE=INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:16 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools13173026219856091945lists ACTION=CONCAT SCATTER_CONTENT=100 SUBDIVISION_MODE=INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatterByContent[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatterByContent[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:16 IntervalListTools Using SCATTER_CONTENT = 100 and an interval of size 200, attempting to scatter into 2 intervals. INFO 2024-07-02 12:01:16 IntervalListTools Using SCATTER_CONTENT = 100 and an interval of size 200, attempting to scatter into 2 intervals. Test: Test method testScatterByContent[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:16 IntervalListTools Wrote 2 scatter subdirectories to /tmp/IntervalListTools13173026219856091945lists. INFO 2024-07-02 12:01:16 IntervalListTools Wrote 2 scatter subdirectories to /tmp/IntervalListTools13173026219856091945lists. Test: Test method testScatterByContent[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:16 IntervalListTools Produced 4 intervals totalling 200 bases. INFO 2024-07-02 12:01:16 IntervalListTools Produced 4 intervals totalling 200 bases. Test: Test method testScatterByContent[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:16 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:16 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatterByContent[0](Testcase{scatterWidth=2, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatterByContent[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) Test: Test method testScatterByContent[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:16 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatterByContent[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION}) STANDARD_ERROR INFO 2024-07-02 12:01:16 IntervalListTools Test: Test method testScatterByContent[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatterByContent[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatterByContent[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatterByContent[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatterByContent[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools1378784713738069443lists -SCATTER_CONTENT 50 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools1378784713738069443lists -SCATTER_CONTENT 50 Test: Test method testScatterByContent[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:16.191 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:16.191 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:16.191 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:16.191 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:16.191 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:16.191 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:16.191 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:16.191 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:16 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools1378784713738069443lists ACTION=CONCAT SCATTER_CONTENT=50 SUBDIVISION_MODE=INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:16 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools1378784713738069443lists ACTION=CONCAT SCATTER_CONTENT=50 SUBDIVISION_MODE=INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatterByContent[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatterByContent[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:16 IntervalListTools Using SCATTER_CONTENT = 50 and an interval of size 200, attempting to scatter into 4 intervals. INFO 2024-07-02 12:01:16 IntervalListTools Using SCATTER_CONTENT = 50 and an interval of size 200, attempting to scatter into 4 intervals. Test: Test method testScatterByContent[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:16 IntervalListTools Wrote 4 scatter subdirectories to /tmp/IntervalListTools1378784713738069443lists. INFO 2024-07-02 12:01:16 IntervalListTools Wrote 4 scatter subdirectories to /tmp/IntervalListTools1378784713738069443lists. Test: Test method testScatterByContent[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:16 IntervalListTools Produced 5 intervals totalling 200 bases. INFO 2024-07-02 12:01:16 IntervalListTools Produced 5 intervals totalling 200 bases. Test: Test method testScatterByContent[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:16 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:16 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatterByContent[1](Testcase{scatterWidth=4, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatterByContent[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) Test: Test method testScatterByContent[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:16 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatterByContent[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION}) STANDARD_ERROR INFO 2024-07-02 12:01:16 IntervalListTools Test: Test method testScatterByContent[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatterByContent[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatterByContent[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatterByContent[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatterByContent[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools16064252657267036855lists -SCATTER_CONTENT 40 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools16064252657267036855lists -SCATTER_CONTENT 40 Test: Test method testScatterByContent[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:16.296 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:16.296 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:16.296 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:16.296 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:16.296 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:16.296 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:16.296 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:16.296 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:16 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools16064252657267036855lists ACTION=CONCAT SCATTER_CONTENT=40 SUBDIVISION_MODE=INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:16 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools16064252657267036855lists ACTION=CONCAT SCATTER_CONTENT=40 SUBDIVISION_MODE=INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatterByContent[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatterByContent[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:16 IntervalListTools Using SCATTER_CONTENT = 40 and an interval of size 200, attempting to scatter into 5 intervals. INFO 2024-07-02 12:01:16 IntervalListTools Using SCATTER_CONTENT = 40 and an interval of size 200, attempting to scatter into 5 intervals. Test: Test method testScatterByContent[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:16 IntervalListTools Wrote 5 scatter subdirectories to /tmp/IntervalListTools16064252657267036855lists. INFO 2024-07-02 12:01:16 IntervalListTools Wrote 5 scatter subdirectories to /tmp/IntervalListTools16064252657267036855lists. Test: Test method testScatterByContent[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:16 IntervalListTools Produced 7 intervals totalling 200 bases. INFO 2024-07-02 12:01:16 IntervalListTools Produced 7 intervals totalling 200 bases. Test: Test method testScatterByContent[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:16 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:16 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatterByContent[2](Testcase{scatterWidth=5, mode=INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatterByContent[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) Test: Test method testScatterByContent[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:16 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatterByContent[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION}) STANDARD_ERROR INFO 2024-07-02 12:01:16 IntervalListTools Test: Test method testScatterByContent[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatterByContent[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatterByContent[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatterByContent[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatterByContent[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools10685431286164482116lists -SCATTER_CONTENT 66 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools10685431286164482116lists -SCATTER_CONTENT 66 Test: Test method testScatterByContent[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:16.500 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:16.500 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:16.500 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:16.500 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:16.501 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:16.501 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:16.501 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:16.501 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:16 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools10685431286164482116lists ACTION=CONCAT SCATTER_CONTENT=66 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:16 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools10685431286164482116lists ACTION=CONCAT SCATTER_CONTENT=66 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatterByContent[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatterByContent[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:16 IntervalListTools Using SCATTER_CONTENT = 66 and an interval of size 200, attempting to scatter into 3 intervals. INFO 2024-07-02 12:01:16 IntervalListTools Using SCATTER_CONTENT = 66 and an interval of size 200, attempting to scatter into 3 intervals. Test: Test method testScatterByContent[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:16 IntervalListTools Wrote 3 scatter subdirectories to /tmp/IntervalListTools10685431286164482116lists. INFO 2024-07-02 12:01:16 IntervalListTools Wrote 3 scatter subdirectories to /tmp/IntervalListTools10685431286164482116lists. Test: Test method testScatterByContent[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:16 IntervalListTools Produced 3 intervals totalling 200 bases. INFO 2024-07-02 12:01:16 IntervalListTools Produced 3 intervals totalling 200 bases. Test: Test method testScatterByContent[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:16 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:16 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatterByContent[3](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatterByContent[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) Test: Test method testScatterByContent[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:16 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatterByContent[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW}) STANDARD_ERROR INFO 2024-07-02 12:01:16 IntervalListTools Test: Test method testScatterByContent[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatterByContent[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatterByContent[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatterByContent[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatterByContent[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW -OUTPUT /tmp/IntervalListTools1832462345254806596lists -SCATTER_CONTENT 100 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW -OUTPUT /tmp/IntervalListTools1832462345254806596lists -SCATTER_CONTENT 100 Test: Test method testScatterByContent[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:16.662 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:16.662 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:16.662 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:16.662 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:16.662 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:16.662 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:16.662 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:16.662 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:16 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools1832462345254806596lists ACTION=CONCAT SCATTER_CONTENT=100 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:16 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools1832462345254806596lists ACTION=CONCAT SCATTER_CONTENT=100 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatterByContent[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatterByContent[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:16 IntervalListTools Using SCATTER_CONTENT = 100 and an interval of size 200, attempting to scatter into 2 intervals. INFO 2024-07-02 12:01:16 IntervalListTools Using SCATTER_CONTENT = 100 and an interval of size 200, attempting to scatter into 2 intervals. Test: Test method testScatterByContent[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:16 IntervalListTools Wrote 2 scatter subdirectories to /tmp/IntervalListTools1832462345254806596lists. INFO 2024-07-02 12:01:16 IntervalListTools Wrote 2 scatter subdirectories to /tmp/IntervalListTools1832462345254806596lists. Test: Test method testScatterByContent[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:16 IntervalListTools Produced 3 intervals totalling 200 bases. INFO 2024-07-02 12:01:16 IntervalListTools Produced 3 intervals totalling 200 bases. Test: Test method testScatterByContent[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:16 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:16 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatterByContent[4](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatterByContent[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) Test: Test method testScatterByContent[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:16 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatterByContent[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW}) STANDARD_ERROR INFO 2024-07-02 12:01:16 IntervalListTools Test: Test method testScatterByContent[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatterByContent[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatterByContent[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatterByContent[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatterByContent[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW -OUTPUT /tmp/IntervalListTools3656669258856665578lists -SCATTER_CONTENT 66 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW -OUTPUT /tmp/IntervalListTools3656669258856665578lists -SCATTER_CONTENT 66 Test: Test method testScatterByContent[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:16.828 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:16.828 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:16.828 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:16.828 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:16.828 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:16.828 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:16.828 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:16.828 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:16 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools3656669258856665578lists ACTION=CONCAT SCATTER_CONTENT=66 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:16 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools3656669258856665578lists ACTION=CONCAT SCATTER_CONTENT=66 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatterByContent[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatterByContent[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:16 IntervalListTools Using SCATTER_CONTENT = 66 and an interval of size 200, attempting to scatter into 3 intervals. INFO 2024-07-02 12:01:16 IntervalListTools Using SCATTER_CONTENT = 66 and an interval of size 200, attempting to scatter into 3 intervals. Test: Test method testScatterByContent[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:16 IntervalListTools Wrote 3 scatter subdirectories to /tmp/IntervalListTools3656669258856665578lists. INFO 2024-07-02 12:01:16 IntervalListTools Wrote 3 scatter subdirectories to /tmp/IntervalListTools3656669258856665578lists. Test: Test method testScatterByContent[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:16 IntervalListTools Produced 3 intervals totalling 200 bases. INFO 2024-07-02 12:01:16 IntervalListTools Produced 3 intervals totalling 200 bases. Test: Test method testScatterByContent[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:16 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:16 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatterByContent[5](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatterByContent[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) Test: Test method testScatterByContent[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:16 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatterByContent[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION}) STANDARD_ERROR INFO 2024-07-02 12:01:16 IntervalListTools Test: Test method testScatterByContent[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatterByContent[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatterByContent[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatterByContent[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatterByContent[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools14240174293786583013lists -SCATTER_CONTENT 100 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools14240174293786583013lists -SCATTER_CONTENT 100 Test: Test method testScatterByContent[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:16.957 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:16.957 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:16.957 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:16.957 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:16.957 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:16.957 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:16.957 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:16.957 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:16 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools14240174293786583013lists ACTION=CONCAT SCATTER_CONTENT=100 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:16 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools14240174293786583013lists ACTION=CONCAT SCATTER_CONTENT=100 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatterByContent[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:16 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatterByContent[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:16 IntervalListTools Using SCATTER_CONTENT = 100 and an interval of size 200, attempting to scatter into 2 intervals. INFO 2024-07-02 12:01:16 IntervalListTools Using SCATTER_CONTENT = 100 and an interval of size 200, attempting to scatter into 2 intervals. Test: Test method testScatterByContent[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:16 IntervalListTools Wrote 2 scatter subdirectories to /tmp/IntervalListTools14240174293786583013lists. INFO 2024-07-02 12:01:16 IntervalListTools Wrote 2 scatter subdirectories to /tmp/IntervalListTools14240174293786583013lists. Test: Test method testScatterByContent[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:16 IntervalListTools Produced 3 intervals totalling 200 bases. INFO 2024-07-02 12:01:16 IntervalListTools Produced 3 intervals totalling 200 bases. Test: Test method testScatterByContent[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:16 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:16 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatterByContent[6](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatterByContent[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) Test: Test method testScatterByContent[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatterByContent[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION}) STANDARD_ERROR INFO 2024-07-02 12:01:17 IntervalListTools Test: Test method testScatterByContent[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatterByContent[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatterByContent[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatterByContent[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatterByContent[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools9477490440162811028lists/temp_1_of_1/scattered.interval_list -SCATTER_CONTENT 200 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools9477490440162811028lists/temp_1_of_1/scattered.interval_list -SCATTER_CONTENT 200 Test: Test method testScatterByContent[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.048 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:17.048 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.048 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:17.048 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.048 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:17.048 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.048 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:17.048 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:17 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools9477490440162811028lists/temp_1_of_1/scattered.interval_list ACTION=CONCAT SCATTER_CONTENT=200 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:17 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools9477490440162811028lists/temp_1_of_1/scattered.interval_list ACTION=CONCAT SCATTER_CONTENT=200 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatterByContent[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatterByContent[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Using SCATTER_CONTENT = 200 and an interval of size 200, attempting to scatter into 1 intervals. INFO 2024-07-02 12:01:17 IntervalListTools Using SCATTER_CONTENT = 200 and an interval of size 200, attempting to scatter into 1 intervals. Test: Test method testScatterByContent[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Produced 3 intervals totalling 200 bases. INFO 2024-07-02 12:01:17 IntervalListTools Produced 3 intervals totalling 200 bases. Test: Test method testScatterByContent[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:17 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:17 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatterByContent[7](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatterByContent[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) Test: Test method testScatterByContent[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatterByContent[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW}) STANDARD_ERROR INFO 2024-07-02 12:01:17 IntervalListTools Test: Test method testScatterByContent[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatterByContent[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatterByContent[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatterByContent[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatterByContent[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW -OUTPUT /tmp/IntervalListTools13397824592741225179lists -SCATTER_CONTENT 66 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW -OUTPUT /tmp/IntervalListTools13397824592741225179lists -SCATTER_CONTENT 66 Test: Test method testScatterByContent[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.144 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:17.144 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.144 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:17.144 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.161 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:17.161 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.161 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:17.161 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:17 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools13397824592741225179lists ACTION=CONCAT SCATTER_CONTENT=66 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:17 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools13397824592741225179lists ACTION=CONCAT SCATTER_CONTENT=66 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatterByContent[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatterByContent[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Using SCATTER_CONTENT = 66 and an interval of size 200, attempting to scatter into 3 intervals. INFO 2024-07-02 12:01:17 IntervalListTools Using SCATTER_CONTENT = 66 and an interval of size 200, attempting to scatter into 3 intervals. Test: Test method testScatterByContent[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Wrote 3 scatter subdirectories to /tmp/IntervalListTools13397824592741225179lists. INFO 2024-07-02 12:01:17 IntervalListTools Wrote 3 scatter subdirectories to /tmp/IntervalListTools13397824592741225179lists. Test: Test method testScatterByContent[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Produced 3 intervals totalling 200 bases. INFO 2024-07-02 12:01:17 IntervalListTools Produced 3 intervals totalling 200 bases. Test: Test method testScatterByContent[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:17 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:17 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatterByContent[8](Testcase{scatterWidth=6, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatterByContent[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) Test: Test method testScatterByContent[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatterByContent[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW}) STANDARD_ERROR INFO 2024-07-02 12:01:17 IntervalListTools Test: Test method testScatterByContent[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatterByContent[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatterByContent[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatterByContent[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatterByContent[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW -OUTPUT /tmp/IntervalListTools10561308914979958161lists -SCATTER_CONTENT 100 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW -OUTPUT /tmp/IntervalListTools10561308914979958161lists -SCATTER_CONTENT 100 Test: Test method testScatterByContent[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.336 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:17.336 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.336 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:17.336 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.336 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:17.336 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.336 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:17.336 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:17 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools10561308914979958161lists ACTION=CONCAT SCATTER_CONTENT=100 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:17 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools10561308914979958161lists ACTION=CONCAT SCATTER_CONTENT=100 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatterByContent[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatterByContent[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Using SCATTER_CONTENT = 100 and an interval of size 200, attempting to scatter into 2 intervals. INFO 2024-07-02 12:01:17 IntervalListTools Using SCATTER_CONTENT = 100 and an interval of size 200, attempting to scatter into 2 intervals. Test: Test method testScatterByContent[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Wrote 2 scatter subdirectories to /tmp/IntervalListTools10561308914979958161lists. INFO 2024-07-02 12:01:17 IntervalListTools Wrote 2 scatter subdirectories to /tmp/IntervalListTools10561308914979958161lists. Test: Test method testScatterByContent[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Produced 3 intervals totalling 200 bases. INFO 2024-07-02 12:01:17 IntervalListTools Produced 3 intervals totalling 200 bases. Test: Test method testScatterByContent[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:17 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:17 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatterByContent[9](Testcase{scatterWidth=2, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatterByContent[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) Test: Test method testScatterByContent[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatterByContent[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW}) STANDARD_ERROR INFO 2024-07-02 12:01:17 IntervalListTools Test: Test method testScatterByContent[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatterByContent[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatterByContent[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatterByContent[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatterByContent[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW -OUTPUT /tmp/IntervalListTools2261665124969790954lists/temp_1_of_1/scattered.interval_list -SCATTER_CONTENT 200 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW -OUTPUT /tmp/IntervalListTools2261665124969790954lists/temp_1_of_1/scattered.interval_list -SCATTER_CONTENT 200 Test: Test method testScatterByContent[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.485 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:17.485 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.485 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:17.485 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.485 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:17.485 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.485 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:17.485 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:17 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools2261665124969790954lists/temp_1_of_1/scattered.interval_list ACTION=CONCAT SCATTER_CONTENT=200 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:17 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable.interval_list] OUTPUT=/tmp/IntervalListTools2261665124969790954lists/temp_1_of_1/scattered.interval_list ACTION=CONCAT SCATTER_CONTENT=200 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatterByContent[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatterByContent[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Using SCATTER_CONTENT = 200 and an interval of size 200, attempting to scatter into 1 intervals. INFO 2024-07-02 12:01:17 IntervalListTools Using SCATTER_CONTENT = 200 and an interval of size 200, attempting to scatter into 1 intervals. Test: Test method testScatterByContent[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Produced 3 intervals totalling 200 bases. INFO 2024-07-02 12:01:17 IntervalListTools Produced 3 intervals totalling 200 bases. Test: Test method testScatterByContent[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:17 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:17 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatterByContent[10](Testcase{scatterWidth=1, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatterByContent[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) Test: Test method testScatterByContent[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatterByContent[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW}) STANDARD_ERROR INFO 2024-07-02 12:01:17 IntervalListTools Test: Test method testScatterByContent[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatterByContent[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatterByContent[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatterByContent[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatterByContent[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW -OUTPUT /tmp/IntervalListTools5525186842451563818lists -SCATTER_CONTENT 11 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW -OUTPUT /tmp/IntervalListTools5525186842451563818lists -SCATTER_CONTENT 11 Test: Test method testScatterByContent[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.531 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:17.531 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.532 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:17.532 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.532 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:17.532 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.532 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:17.532 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:17 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list] OUTPUT=/tmp/IntervalListTools5525186842451563818lists ACTION=CONCAT SCATTER_CONTENT=11 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:17 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list] OUTPUT=/tmp/IntervalListTools5525186842451563818lists ACTION=CONCAT SCATTER_CONTENT=11 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatterByContent[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatterByContent[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Using SCATTER_CONTENT = 11 and an interval of size 80, attempting to scatter into 7 intervals. INFO 2024-07-02 12:01:17 IntervalListTools Using SCATTER_CONTENT = 11 and an interval of size 80, attempting to scatter into 7 intervals. Test: Test method testScatterByContent[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Wrote 7 scatter subdirectories to /tmp/IntervalListTools5525186842451563818lists. INFO 2024-07-02 12:01:17 IntervalListTools Wrote 7 scatter subdirectories to /tmp/IntervalListTools5525186842451563818lists. Test: Test method testScatterByContent[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Produced 9 intervals totalling 80 bases. INFO 2024-07-02 12:01:17 IntervalListTools Produced 9 intervals totalling 80 bases. Test: Test method testScatterByContent[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:17 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:17 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatterByContent[11](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatterByContent[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) Test: Test method testScatterByContent[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatterByContent[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION}) STANDARD_ERROR INFO 2024-07-02 12:01:17 IntervalListTools Test: Test method testScatterByContent[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatterByContent[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatterByContent[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatterByContent[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatterByContent[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools3265782888528092195lists -SCATTER_CONTENT 11 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools3265782888528092195lists -SCATTER_CONTENT 11 Test: Test method testScatterByContent[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.663 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:17.663 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.663 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:17.663 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.663 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:17.663 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.663 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:17.663 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:17 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list] OUTPUT=/tmp/IntervalListTools3265782888528092195lists ACTION=CONCAT SCATTER_CONTENT=11 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:17 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list] OUTPUT=/tmp/IntervalListTools3265782888528092195lists ACTION=CONCAT SCATTER_CONTENT=11 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatterByContent[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatterByContent[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Using SCATTER_CONTENT = 11 and an interval of size 80, attempting to scatter into 7 intervals. INFO 2024-07-02 12:01:17 IntervalListTools Using SCATTER_CONTENT = 11 and an interval of size 80, attempting to scatter into 7 intervals. Test: Test method testScatterByContent[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Wrote 7 scatter subdirectories to /tmp/IntervalListTools3265782888528092195lists. INFO 2024-07-02 12:01:17 IntervalListTools Wrote 7 scatter subdirectories to /tmp/IntervalListTools3265782888528092195lists. Test: Test method testScatterByContent[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Produced 9 intervals totalling 80 bases. INFO 2024-07-02 12:01:17 IntervalListTools Produced 9 intervals totalling 80 bases. Test: Test method testScatterByContent[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:17 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:17 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatterByContent[12](Testcase{scatterWidth=7, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatterByContent[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) Test: Test method testScatterByContent[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatterByContent[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION}) STANDARD_ERROR INFO 2024-07-02 12:01:17 IntervalListTools Test: Test method testScatterByContent[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatterByContent[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatterByContent[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatterByContent[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatterByContent[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools11004743729259635686lists -SCATTER_CONTENT 10 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools11004743729259635686lists -SCATTER_CONTENT 10 Test: Test method testScatterByContent[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.787 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:17.787 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.787 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:17.787 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.787 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:17.787 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.787 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:17.787 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:17 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list] OUTPUT=/tmp/IntervalListTools11004743729259635686lists ACTION=CONCAT SCATTER_CONTENT=10 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:17 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list] OUTPUT=/tmp/IntervalListTools11004743729259635686lists ACTION=CONCAT SCATTER_CONTENT=10 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatterByContent[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatterByContent[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Using SCATTER_CONTENT = 10 and an interval of size 80, attempting to scatter into 8 intervals. INFO 2024-07-02 12:01:17 IntervalListTools Using SCATTER_CONTENT = 10 and an interval of size 80, attempting to scatter into 8 intervals. Test: Test method testScatterByContent[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Wrote 8 scatter subdirectories to /tmp/IntervalListTools11004743729259635686lists. INFO 2024-07-02 12:01:17 IntervalListTools Wrote 8 scatter subdirectories to /tmp/IntervalListTools11004743729259635686lists. Test: Test method testScatterByContent[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Produced 9 intervals totalling 80 bases. INFO 2024-07-02 12:01:17 IntervalListTools Produced 9 intervals totalling 80 bases. Test: Test method testScatterByContent[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:17 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:17 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatterByContent[13](Testcase{scatterWidth=8, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatterByContent[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) Test: Test method testScatterByContent[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatterByContent[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION}) STANDARD_ERROR INFO 2024-07-02 12:01:17 IntervalListTools Test: Test method testScatterByContent[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatterByContent[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatterByContent[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatterByContent[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatterByContent[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools8539344802875055445lists -SCATTER_CONTENT 8 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list -SUBDIVISION_MODE BALANCING_WITHOUT_INTERVAL_SUBDIVISION -OUTPUT /tmp/IntervalListTools8539344802875055445lists -SCATTER_CONTENT 8 Test: Test method testScatterByContent[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.914 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:17.914 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.914 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:17.914 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.915 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:17.915 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:17.915 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:17.915 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:17 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list] OUTPUT=/tmp/IntervalListTools8539344802875055445lists ACTION=CONCAT SCATTER_CONTENT=8 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:17 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_with_overflow.interval_list] OUTPUT=/tmp/IntervalListTools8539344802875055445lists ACTION=CONCAT SCATTER_CONTENT=8 SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatterByContent[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:17 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatterByContent[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Using SCATTER_CONTENT = 8 and an interval of size 80, attempting to scatter into 10 intervals. INFO 2024-07-02 12:01:17 IntervalListTools Using SCATTER_CONTENT = 8 and an interval of size 80, attempting to scatter into 10 intervals. Test: Test method testScatterByContent[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Wrote 9 scatter subdirectories to /tmp/IntervalListTools8539344802875055445lists. INFO 2024-07-02 12:01:17 IntervalListTools Wrote 9 scatter subdirectories to /tmp/IntervalListTools8539344802875055445lists. Test: Test method testScatterByContent[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: WARNING 2024-07-02 12:01:17 IntervalListTools Requested scatter width of 10, but only emitted 9. (This may be an expected consequence of running in BALANCING_WITHOUT_INTERVAL_SUBDIVISION mode.) WARNING 2024-07-02 12:01:17 IntervalListTools Requested scatter width of 10, but only emitted 9. (This may be an expected consequence of running in BALANCING_WITHOUT_INTERVAL_SUBDIVISION mode.) Test: Test method testScatterByContent[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:17 IntervalListTools Produced 9 intervals totalling 80 bases. INFO 2024-07-02 12:01:17 IntervalListTools Produced 9 intervals totalling 80 bases. Test: Test method testScatterByContent[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:17 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:17 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatterByContent[14](Testcase{scatterWidth=9, mode=BALANCING_WITHOUT_INTERVAL_SUBDIVISION})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatterByContent[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) Test: Test method testScatterByContent[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:18 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatterByContent[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT}) STANDARD_ERROR INFO 2024-07-02 12:01:18 IntervalListTools Test: Test method testScatterByContent[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatterByContent[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatterByContent[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatterByContent[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatterByContent[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_many_intervals.interval_list -SUBDIVISION_MODE INTERVAL_COUNT -OUTPUT /tmp/IntervalListTools9201313474211828435lists/temp_1_of_1/scattered.interval_list -SCATTER_CONTENT 32 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_many_intervals.interval_list -SUBDIVISION_MODE INTERVAL_COUNT -OUTPUT /tmp/IntervalListTools9201313474211828435lists/temp_1_of_1/scattered.interval_list -SCATTER_CONTENT 32 Test: Test method testScatterByContent[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:18.044 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:18.044 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:18.044 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:18.044 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:18.044 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:18.044 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:18.044 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:18.044 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:18 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_many_intervals.interval_list] OUTPUT=/tmp/IntervalListTools9201313474211828435lists/temp_1_of_1/scattered.interval_list ACTION=CONCAT SCATTER_CONTENT=32 SUBDIVISION_MODE=INTERVAL_COUNT PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:18 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_many_intervals.interval_list] OUTPUT=/tmp/IntervalListTools9201313474211828435lists/temp_1_of_1/scattered.interval_list ACTION=CONCAT SCATTER_CONTENT=32 SUBDIVISION_MODE=INTERVAL_COUNT PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatterByContent[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatterByContent[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:18 IntervalListTools Using SCATTER_CONTENT = 32 and an interval of size 32, attempting to scatter into 1 intervals. INFO 2024-07-02 12:01:18 IntervalListTools Using SCATTER_CONTENT = 32 and an interval of size 32, attempting to scatter into 1 intervals. Test: Test method testScatterByContent[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:18 IntervalListTools Produced 32 intervals totalling 64 bases. INFO 2024-07-02 12:01:18 IntervalListTools Produced 32 intervals totalling 64 bases. Test: Test method testScatterByContent[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:18 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:18 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatterByContent[15](Testcase{scatterWidth=1, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatterByContent[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) Test: Test method testScatterByContent[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:18 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatterByContent[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT}) STANDARD_ERROR INFO 2024-07-02 12:01:18 IntervalListTools Test: Test method testScatterByContent[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatterByContent[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatterByContent[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatterByContent[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatterByContent[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_many_intervals.interval_list -SUBDIVISION_MODE INTERVAL_COUNT -OUTPUT /tmp/IntervalListTools14498187759234416674lists -SCATTER_CONTENT 16 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_many_intervals.interval_list -SUBDIVISION_MODE INTERVAL_COUNT -OUTPUT /tmp/IntervalListTools14498187759234416674lists -SCATTER_CONTENT 16 Test: Test method testScatterByContent[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:18.120 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:18.120 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:18.120 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:18.120 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:18.120 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:18.120 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:18.120 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:18.120 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:18 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_many_intervals.interval_list] OUTPUT=/tmp/IntervalListTools14498187759234416674lists ACTION=CONCAT SCATTER_CONTENT=16 SUBDIVISION_MODE=INTERVAL_COUNT PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:18 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_many_intervals.interval_list] OUTPUT=/tmp/IntervalListTools14498187759234416674lists ACTION=CONCAT SCATTER_CONTENT=16 SUBDIVISION_MODE=INTERVAL_COUNT PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatterByContent[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatterByContent[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:18 IntervalListTools Using SCATTER_CONTENT = 16 and an interval of size 32, attempting to scatter into 2 intervals. INFO 2024-07-02 12:01:18 IntervalListTools Using SCATTER_CONTENT = 16 and an interval of size 32, attempting to scatter into 2 intervals. Test: Test method testScatterByContent[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:18 IntervalListTools Wrote 2 scatter subdirectories to /tmp/IntervalListTools14498187759234416674lists. INFO 2024-07-02 12:01:18 IntervalListTools Wrote 2 scatter subdirectories to /tmp/IntervalListTools14498187759234416674lists. Test: Test method testScatterByContent[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:18 IntervalListTools Produced 32 intervals totalling 64 bases. INFO 2024-07-02 12:01:18 IntervalListTools Produced 32 intervals totalling 64 bases. Test: Test method testScatterByContent[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:18 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:18 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatterByContent[16](Testcase{scatterWidth=2, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testScatterByContent[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) Test: Test method testScatterByContent[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:18 IntervalListTools Gradle suite > Gradle test > picard.util.IntervalListToolsTest.testScatterByContent[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT}) STANDARD_ERROR INFO 2024-07-02 12:01:18 IntervalListTools Test: Test method testScatterByContent[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testScatterByContent[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testScatterByContent[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testScatterByContent[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testScatterByContent[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_many_intervals.interval_list -SUBDIVISION_MODE INTERVAL_COUNT -OUTPUT /tmp/IntervalListTools3770333377299826228lists -SCATTER_CONTENT 10 ********** IntervalListTools -ACTION CONCAT -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_many_intervals.interval_list -SUBDIVISION_MODE INTERVAL_COUNT -OUTPUT /tmp/IntervalListTools3770333377299826228lists -SCATTER_CONTENT 10 Test: Test method testScatterByContent[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: ********** ********** Test: Test method testScatterByContent[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: Test: Test method testScatterByContent[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:18.223 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:18.223 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:18.223 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:18.223 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:18.223 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:18.223 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testScatterByContent[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: 12:01:18.223 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:18.223 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testScatterByContent[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:18 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_many_intervals.interval_list] OUTPUT=/tmp/IntervalListTools3770333377299826228lists ACTION=CONCAT SCATTER_CONTENT=10 SUBDIVISION_MODE=INTERVAL_COUNT PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:18 GMT+14:00 2024] IntervalListTools INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/util/scatterable_many_intervals.interval_list] OUTPUT=/tmp/IntervalListTools3770333377299826228lists ACTION=CONCAT SCATTER_CONTENT=10 SUBDIVISION_MODE=INTERVAL_COUNT PADDING=0 UNIQUE=false DONT_MERGE_ABUTTING=false SORT=true SCATTER_COUNT=1 INCLUDE_FILTERED=false BREAK_BANDS_AT_MULTIPLES_OF=0 INVERT=false OUTPUT_VALUE=NONE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testScatterByContent[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testScatterByContent[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:18 IntervalListTools Using SCATTER_CONTENT = 10 and an interval of size 32, attempting to scatter into 3 intervals. INFO 2024-07-02 12:01:18 IntervalListTools Using SCATTER_CONTENT = 10 and an interval of size 32, attempting to scatter into 3 intervals. Test: Test method testScatterByContent[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:18 IntervalListTools Wrote 3 scatter subdirectories to /tmp/IntervalListTools3770333377299826228lists. INFO 2024-07-02 12:01:18 IntervalListTools Wrote 3 scatter subdirectories to /tmp/IntervalListTools3770333377299826228lists. Test: Test method testScatterByContent[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: INFO 2024-07-02 12:01:18 IntervalListTools Produced 32 intervals totalling 64 bases. INFO 2024-07-02 12:01:18 IntervalListTools Produced 32 intervals totalling 64 bases. Test: Test method testScatterByContent[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: [Tue Jul 02 12:01:18 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:18 GMT+14:00 2024] picard.util.IntervalListTools done. Elapsed time: 0.00 minutes. Test: Test method testScatterByContent[17](Testcase{scatterWidth=3, mode=INTERVAL_COUNT})(picard.util.IntervalListToolsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testSecondInputValidation(picard.util.IntervalListToolsTest) Running Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: INFO 2024-07-02 12:01:18 LiftOverHaplotypeMap Gradle suite > Gradle test > picard.fingerprint.LiftOverHaplotypeMapTest.testHaplotypeMapLiftover STANDARD_ERROR INFO 2024-07-02 12:01:18 LiftOverHaplotypeMap Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: ********** ********** Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: ********** ********** Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: ********** ********** Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: ********** LiftOverHaplotypeMap -INPUT testdata/picard/fingerprint/haplotypeMapHg18.txt -OUTPUT /tmp/hg19Map12096994940289528461.txt -SEQUENCE_DICTIONARY testdata/picard/fingerprint/Homo_sapiens_assembly19.dict -CHAIN testdata/picard/fingerprint/hg18ToHg19.clipped.over.chain ********** LiftOverHaplotypeMap -INPUT testdata/picard/fingerprint/haplotypeMapHg18.txt -OUTPUT /tmp/hg19Map12096994940289528461.txt -SEQUENCE_DICTIONARY testdata/picard/fingerprint/Homo_sapiens_assembly19.dict -CHAIN testdata/picard/fingerprint/hg18ToHg19.clipped.over.chain Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: ********** ********** Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: 12:01:18.258 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:18.258 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: 12:01:18.258 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:18.258 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: 12:01:18.259 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:18.259 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: 12:01:18.259 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:18.259 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: [Tue Jul 02 12:01:18 GMT+14:00 2024] LiftOverHaplotypeMap INPUT=testdata/picard/fingerprint/haplotypeMapHg18.txt OUTPUT=/tmp/hg19Map12096994940289528461.txt SEQUENCE_DICTIONARY=testdata/picard/fingerprint/Homo_sapiens_assembly19.dict CHAIN=testdata/picard/fingerprint/hg18ToHg19.clipped.over.chain VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:18 GMT+14:00 2024] LiftOverHaplotypeMap INPUT=testdata/picard/fingerprint/haplotypeMapHg18.txt OUTPUT=/tmp/hg19Map12096994940289528461.txt SEQUENCE_DICTIONARY=testdata/picard/fingerprint/Homo_sapiens_assembly19.dict CHAIN=testdata/picard/fingerprint/hg18ToHg19.clipped.over.chain VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: [Tue Jul 02 12:01:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs1106334(chr8:71175365) WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs1106334(chr8:71175365) Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs9572094(chr13:34150882) WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs9572094(chr13:34150882) Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs685449(chr6:153386224) WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs685449(chr6:153386224) Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs10943567(chr6:79459170) WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs10943567(chr6:79459170) Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs9343786(chr6:79471447) WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs9343786(chr6:79471447) Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs9352613(chr6:79481152) WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs9352613(chr6:79481152) Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs1155741(chr3:37602116) WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs1155741(chr3:37602116) Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs1155744(chr3:37602602) WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs1155744(chr3:37602602) Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs161792(chr3:153382394) WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs161792(chr3:153382394) Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs11655512(chr17:20792327) WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs11655512(chr17:20792327) Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs7808249(chr7:86821651) WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs7808249(chr7:86821651) Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs11940551(chr4:26771576) WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs11940551(chr4:26771576) Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs4775699(chr15:45660841) WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs4775699(chr15:45660841) Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs4905366(chr14:95172852) WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs4905366(chr14:95172852) Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs9293511(chr5:88452110) WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs9293511(chr5:88452110) Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs11017876(chr10:129090954) WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs11017876(chr10:129090954) Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs1528601(chr16:49655928) WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs1528601(chr16:49655928) Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs4793172(chr17:40487006) WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs4793172(chr17:40487006) Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs242076(chr22:31559830) WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs242076(chr22:31559830) Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs6603251(chrX:240580) WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs6603251(chrX:240580) Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs17272796(chr3:17052272) WARNING 2024-07-02 12:01:18 LiftOverHaplotypeMap Liftover failed for rs17272796(chr3:17052272) Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: [Tue Jul 02 12:01:18 GMT+14:00 2024] picard.fingerprint.LiftOverHaplotypeMap done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:18 GMT+14:00 2024] picard.fingerprint.LiftOverHaplotypeMap done. Elapsed time: 0.00 minutes. Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testHaplotypeMapLiftover(picard.fingerprint.LiftOverHaplotypeMapTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testAllelesToString[0]([A*, G], [A, G])(picard.util.LiftoverUtilsTest) Running Test: Test method testAllelesToString[1]([A, G], [A, G])(picard.util.LiftoverUtilsTest) Running Test: Test method testAllelesToString[2]([T*, T], [T, T])(picard.util.LiftoverUtilsTest) Running Test: Test method testAllelesToString[3]([*, G], [*, G])(picard.util.LiftoverUtilsTest) Running Test: Test method testAllelesToString[4]([ATG*, G], [ATG, G])(picard.util.LiftoverUtilsTest) Running Test: Test method testAllelesToString[5]([A*, GGGTGT], [A, GGGTGT])(picard.util.LiftoverUtilsTest) Running Test: Test method testAllelesToString[6]([A, A], [A, A])(picard.util.LiftoverUtilsTest) Running Test: Test method testAllelesToString[7]([., .], [., .])(picard.util.LiftoverUtilsTest) Running Test: Test method testAllelesToString[8]([*, A*], [*, A])(picard.util.LiftoverUtilsTest) Running Test: Test method testAllelesToString[9]([A*, .], [A, .])(picard.util.LiftoverUtilsTest) Running Test: Test method testAllelesToString[10]([TT*, .], [TT, .])(picard.util.LiftoverUtilsTest) Running Test: Test method testSwapRefAlt[0]([VC test1 @ chr1:2 Q. of type=SNP alleles=[A*, C] attr={} GT=[] filters=, [VC test1 @ chr1:2 Q. of type=SNP alleles=[C*, A] attr={SwappedAlleles=true} GT=[] filters=)(picard.util.LiftoverUtilsTest) Running Test: Test method testSwapRefAlt[1]([VC test2 @ chr1:2 Q. of type=SNP alleles=[A*, C] attr={AF=0.2} GT=[] filters=, [VC test2 @ chr1:2 Q. of type=SNP alleles=[C*, A] attr={AF=0.8, SwappedAlleles=true} GT=[] filters=)(picard.util.LiftoverUtilsTest) Running Test: Test method testSwapRefAlt[2]([VC test3 @ chr1:2 Q. of type=SNP alleles=[A*, C] attr={AF=.} GT=[] filters=, [VC test3 @ chr1:2 Q. of type=SNP alleles=[C*, A] attr={AF=., SwappedAlleles=true} GT=[] filters=)(picard.util.LiftoverUtilsTest) Running Test: Test method testSwapRefAlt[3]([VC test4 @ chr1:2 Q. of type=SNP alleles=[A*, C] attr={AF=1} GT=[] filters=, [VC test4 @ chr1:2 Q. of type=SNP alleles=[C*, A] attr={AF=0.0, SwappedAlleles=true} GT=[] filters=)(picard.util.LiftoverUtilsTest) Running Test: Test method testSwapRefAlt[4]([VC test5 @ chr1:2 Q. of type=SNP alleles=[A*, C] attr={AF=1, MAX_AF=1} GT=[] filters=, [VC test5 @ chr1:2 Q. of type=SNP alleles=[C*, A] attr={AF=0.0, SwappedAlleles=true} GT=[] filters=)(picard.util.LiftoverUtilsTest) Running Test: Test method testSwapRefAlt[5]([VC test5 @ chr1:2 Q. of type=SNP alleles=[A*, C] attr={AF=1, AF_MAX_shouldnt_be_dropped=1, MAX_AF=1} GT=[] filters=, [VC test5 @ chr1:2 Q. of type=SNP alleles=[C*, A] attr={AF=0.0, AF_MAX_shouldnt_be_dropped=1, SwappedAlleles=true} GT=[] filters=)(picard.util.LiftoverUtilsTest) Running Test: Test method snpWithChangedRef[0]([VC test1 @ chr1:12 Q. of type=SNP alleles=[A*, C] attr={} GT=[[test1 A*/C AD 5,4 PL 40,0,60]] filters=, [VC test1 @ chr1:12 Q. of type=SNP alleles=[C*, A] attr={SwappedAlleles=true} GT=[[test1 C*/A AD 4,5 PL 60,0,40]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method snpWithChangedRef[1]([VC test1 @ chr1:12 Q. of type=SNP alleles=[A*, C] attr={} GT=[[test1 C/C AD 0,10 PL 400,40,0]] filters=, [VC test1 @ chr1:12 Q. of type=SNP alleles=[C*, A] attr={SwappedAlleles=true} GT=[[test1 C*/C* AD 10,0 PL 0,40,400]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:18 LiftoverVcf Gradle suite > Gradle test > picard.util.LiftoverVcfTest.testChangingInfoFields STANDARD_ERROR INFO 2024-07-02 12:01:18 LiftoverVcf Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverFailingVariants.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN testdata/picard/vcf/LiftOver/test.over.chain -REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta -RECOVER_SWAPPED_REF_ALT true -CREATE_INDEX false ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverFailingVariants.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN testdata/picard/vcf/LiftOver/test.over.chain -REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta -RECOVER_SWAPPED_REF_ALT true -CREATE_INDEX false Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:18.504 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:18.504 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:18.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:18.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:18.504 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:18.504 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:18.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:18.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:18 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverFailingVariants.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/LiftOver/test.over.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf RECOVER_SWAPPED_REF_ALT=true CREATE_INDEX=false REFERENCE_SEQUENCE=testdata/picard/vcf/LiftOver/dummy.reference.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:18 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverFailingVariants.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/LiftOver/test.over.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf RECOVER_SWAPPED_REF_ALT=true CREATE_INDEX=false REFERENCE_SEQUENCE=testdata/picard/vcf/LiftOver/dummy.reference.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:18 LiftoverVcf Loading up the target reference genome. INFO 2024-07-02 12:01:18 LiftoverVcf Loading up the target reference genome. Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:18 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) INFO 2024-07-02 12:01:18 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:18 LiftoverVcf Processed 3 variants. INFO 2024-07-02 12:01:18 LiftoverVcf Processed 3 variants. Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:18 LiftoverVcf 0 variants failed to liftover. INFO 2024-07-02 12:01:18 LiftoverVcf 0 variants failed to liftover. Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:18 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over. INFO 2024-07-02 12:01:18 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over. Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:18 LiftoverVcf 0.0000% of variants were not successfully lifted over and written to the output. INFO 2024-07-02 12:01:18 LiftoverVcf 0.0000% of variants were not successfully lifted over and written to the output. Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:18 LiftoverVcf liftover success by source contig: INFO 2024-07-02 12:01:18 LiftoverVcf liftover success by source contig: Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:18 LiftoverVcf chr1: 3 / 3 (100.0000%) INFO 2024-07-02 12:01:18 LiftoverVcf chr1: 3 / 3 (100.0000%) Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:18 LiftoverVcf lifted variants by target contig: INFO 2024-07-02 12:01:18 LiftoverVcf lifted variants by target contig: Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:18 LiftoverVcf chr1: 3 INFO 2024-07-02 12:01:18 LiftoverVcf chr1: 3 Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:18 LiftoverVcf 2 variants were lifted by swapping REF/ALT alleles. INFO 2024-07-02 12:01:18 LiftoverVcf 2 variants were lifted by swapping REF/ALT alleles. Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:18 LiftoverVcf Writing out sorted records to final VCF. INFO 2024-07-02 12:01:18 LiftoverVcf Writing out sorted records to final VCF. Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:18 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:18 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. Test: Test method testChangingInfoFields(picard.util.LiftoverVcfTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:18 LiftoverVcf Gradle suite > Gradle test > picard.util.LiftoverVcfTest.testChangingTagArguments STANDARD_ERROR INFO 2024-07-02 12:01:18 LiftoverVcf Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverFailingVariants.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN testdata/picard/vcf/LiftOver/test.over.chain -REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta -TAGS_TO_REVERSE null -TAGS_TO_DROP null -CREATE_INDEX false ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverFailingVariants.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN testdata/picard/vcf/LiftOver/test.over.chain -REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta -TAGS_TO_REVERSE null -TAGS_TO_DROP null -CREATE_INDEX false Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:18.679 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:18.679 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:18.679 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:18.679 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:18.679 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:18.679 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:18.679 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:18.679 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:18 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverFailingVariants.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/LiftOver/test.over.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf TAGS_TO_REVERSE=[] TAGS_TO_DROP=[] CREATE_INDEX=false REFERENCE_SEQUENCE=testdata/picard/vcf/LiftOver/dummy.reference.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false RECOVER_SWAPPED_REF_ALT=false DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:18 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverFailingVariants.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/LiftOver/test.over.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf TAGS_TO_REVERSE=[] TAGS_TO_DROP=[] CREATE_INDEX=false REFERENCE_SEQUENCE=testdata/picard/vcf/LiftOver/dummy.reference.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false RECOVER_SWAPPED_REF_ALT=false DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:18 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:18 LiftoverVcf Loading up the target reference genome. INFO 2024-07-02 12:01:18 LiftoverVcf Loading up the target reference genome. Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:18 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) INFO 2024-07-02 12:01:18 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:18 LiftoverVcf Processed 3 variants. INFO 2024-07-02 12:01:18 LiftoverVcf Processed 3 variants. Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:18 LiftoverVcf 0 variants failed to liftover. INFO 2024-07-02 12:01:18 LiftoverVcf 0 variants failed to liftover. Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:18 LiftoverVcf 2 variants lifted over but had mismatching reference alleles after lift over. INFO 2024-07-02 12:01:18 LiftoverVcf 2 variants lifted over but had mismatching reference alleles after lift over. Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:18 LiftoverVcf 66.6667% of variants were not successfully lifted over and written to the output. INFO 2024-07-02 12:01:18 LiftoverVcf 66.6667% of variants were not successfully lifted over and written to the output. Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:18 LiftoverVcf liftover success by source contig: INFO 2024-07-02 12:01:18 LiftoverVcf liftover success by source contig: Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:18 LiftoverVcf chr1: 1 / 3 (33.3333%) INFO 2024-07-02 12:01:18 LiftoverVcf chr1: 1 / 3 (33.3333%) Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:18 LiftoverVcf lifted variants by target contig: INFO 2024-07-02 12:01:18 LiftoverVcf lifted variants by target contig: Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:18 LiftoverVcf chr1: 1 INFO 2024-07-02 12:01:18 LiftoverVcf chr1: 1 Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: WARNING 2024-07-02 12:01:18 LiftoverVcf 2 variants with a swapped REF/ALT were identified, but were not recovered. See RECOVER_SWAPPED_REF_ALT and associated caveats. WARNING 2024-07-02 12:01:18 LiftoverVcf 2 variants with a swapped REF/ALT were identified, but were not recovered. See RECOVER_SWAPPED_REF_ALT and associated caveats. Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:18 LiftoverVcf Writing out sorted records to final VCF. INFO 2024-07-02 12:01:18 LiftoverVcf Writing out sorted records to final VCF. Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:18 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:18 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. Test: Test method testChangingTagArguments(picard.util.LiftoverVcfTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testFlipIndel[0]([VC test1 @ chr1:537-539 Q. of type=INDEL alleles=[TTT*, T] attr={END=539} GT=[[test1 TTT*/T]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1-3 Q. of type=INDEL alleles=[CAA*, C] attr={END=3, ReverseComplementedAlleles=true} GT=[[test1 CAA*/C]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testFlipIndel[1]([VC test2 @ chr1:537 Q. of type=INDEL alleles=[T*, TTT] attr={} GT=[[test1 T*/TTT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CAA] attr={ReverseComplementedAlleles=true} GT=[[test1 C*/CAA]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testFlipIndel[2]([VC test3 @ chr1:527-530 Q. of type=INDEL alleles=[ACGT*, A] attr={} GT=[[test1 ACGT*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-13 Q. of type=INDEL alleles=[AACG*, A] attr={ReverseComplementedAlleles=true} GT=[[test1 AACG*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testFlipIndel[3]([VC test4 @ chr1:527 Q. of type=INDEL alleles=[A*, ACGT] attr={} GT=[[test1 A*/ACGT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10 Q. of type=INDEL alleles=[A*, AACG] attr={ReverseComplementedAlleles=true} GT=[[test1 A*/AACG]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testFlipIndel[4]([VC test5 @ chr1:540 Q. of type=INDEL alleles=[G*, GTT] attr={} GT=[[test1 G*/GTT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, AAC] attr={ReverseComplementedAlleles=true} GT=[[test1 C*/AAC]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testFlipIndel[5]([VC test6 @ chr1:541 Q. of type=INDEL alleles=[A*, ACGT] attr={} GT=[[test1 A*/ACGT]] filters=, ReferenceSequence chr1, null)(picard.util.LiftoverVcfTest) Running Test: Test method testFlipIndel[6]([VC test7 @ chr1:529-531 Q. of type=INDEL alleles=[GTT*, ACGT] attr={} GT=[[test1 GTT*/ACGT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:11-12 Q. of type=INDEL alleles=[AC*, CGT] attr={ReverseComplementedAlleles=true} GT=[[test1 AC*/CGT]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testFlipIndel[7]([VC test8 @ chr1:527-530 Q. of type=INDEL alleles=[ACGT*, ATT] attr={} GT=[[test1 ACGT*/ATT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:12-13 Q. of type=INDEL alleles=[CG*, A] attr={ReverseComplementedAlleles=true} GT=[[test1 CG*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testFlipIndel[8]([VC test9 @ chr1:511 Q. of type=INDEL alleles=[T*, TAG] attr={} GT=[[test1 T*/TAG]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19 Q. of type=INDEL alleles=[A*, ACT] attr={ReverseComplementedAlleles=true} GT=[[test1 A*/ACT]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testFlipIndel[9]([VC test10 @ chr1:540 Q. of type=INDEL alleles=[G*, GA] attr={} GT=[[test1 G*/GA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, TC] attr={ReverseComplementedAlleles=true} GT=[[test1 C*/TC]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testFlipIndel[10]([VC test11 @ chr1:540 Q. of type=INDEL alleles=[G*, GG] attr={} GT=[[test1 G*/GG]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CC] attr={ReverseComplementedAlleles=true} GT=[[test1 C*/CC]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testFlipIndel[11]([VC test12 @ chr1:536-539 Q. of type=INDEL alleles=[TTTT*, TTTTG] attr={} GT=[[test1 TTTT*/TTTTG]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CC] attr={ReverseComplementedAlleles=true} GT=[[test1 C*/CC]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testFlipIndel[12]([VC test13 @ chr1:536-539 Q. of type=INDEL alleles=[TTTT*, *, TTTTG] attr={} GT=[[test1 TTTT*/*/TTTTG]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=MIXED alleles=[C*, *, CC] attr={ReverseComplementedAlleles=true} GT=[[test1 C*/*/CC]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testFlipIndel[13]([VC test14 @ chr1:527-530 Q. of type=INDEL alleles=[ACGT*, *, A] attr={} GT=[[test1 ACGT*/*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-13 Q. of type=INDEL alleles=[AACG*, *, A] attr={ReverseComplementedAlleles=true} GT=[[test1 AACG*/*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testFlipIndelWithOriginalAlleles[0]([VC test1 @ chr1:537-539 Q. of type=INDEL alleles=[TTT*, T] attr={END=539} GT=[[test1 TTT*/T]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1-3 Q. of type=INDEL alleles=[CAA*, C] attr={END=3, OriginalAlleles=[TTT, T], ReverseComplementedAlleles=true} GT=[[test1 CAA*/C]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testFlipIndelWithOriginalAlleles[1]([VC test2 @ chr1:537 Q. of type=INDEL alleles=[T*, TTT] attr={} GT=[[test1 T*/TTT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CAA] attr={OriginalAlleles=[T, TTT], ReverseComplementedAlleles=true} GT=[[test1 C*/CAA]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testFlipIndelWithOriginalAlleles[2]([VC test3 @ chr1:527-530 Q. of type=INDEL alleles=[ACGT*, A] attr={} GT=[[test1 ACGT*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-13 Q. of type=INDEL alleles=[AACG*, A] attr={OriginalAlleles=[ACGT, A], ReverseComplementedAlleles=true} GT=[[test1 AACG*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testFlipIndelWithOriginalAlleles[3]([VC test4 @ chr1:527 Q. of type=INDEL alleles=[A*, ACGT] attr={} GT=[[test1 A*/ACGT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10 Q. of type=INDEL alleles=[A*, AACG] attr={OriginalAlleles=[A, ACGT], ReverseComplementedAlleles=true} GT=[[test1 A*/AACG]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testFlipIndelWithOriginalAlleles[4]([VC test5 @ chr1:540 Q. of type=INDEL alleles=[G*, GTT] attr={} GT=[[test1 G*/GTT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, AAC] attr={OriginalAlleles=[G, GTT], ReverseComplementedAlleles=true} GT=[[test1 C*/AAC]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testFlipIndelWithOriginalAlleles[5]([VC test6 @ chr1:541 Q. of type=INDEL alleles=[A*, ACGT] attr={} GT=[[test1 A*/ACGT]] filters=, ReferenceSequence chr1, null)(picard.util.LiftoverVcfTest) Running Test: Test method testFlipIndelWithOriginalAlleles[6]([VC test7 @ chr1:529-531 Q. of type=INDEL alleles=[GTT*, ACGT] attr={} GT=[[test1 GTT*/ACGT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:11-12 Q. of type=INDEL alleles=[AC*, CGT] attr={OriginalAlleles=[GTT, ACGT], ReverseComplementedAlleles=true} GT=[[test1 AC*/CGT]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testFlipIndelWithOriginalAlleles[7]([VC test8 @ chr1:527-530 Q. of type=INDEL alleles=[ACGT*, ATT] attr={} GT=[[test1 ACGT*/ATT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:12-13 Q. of type=INDEL alleles=[CG*, A] attr={OriginalAlleles=[ACGT, ATT], ReverseComplementedAlleles=true} GT=[[test1 CG*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testFlipIndelWithOriginalAlleles[8]([VC test9 @ chr1:511 Q. of type=INDEL alleles=[T*, TAG] attr={} GT=[[test1 T*/TAG]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19 Q. of type=INDEL alleles=[A*, ACT] attr={OriginalAlleles=[T, TAG], ReverseComplementedAlleles=true} GT=[[test1 A*/ACT]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testFlipIndelWithOriginalAlleles[9]([VC test10 @ chr1:540 Q. of type=INDEL alleles=[G*, GA] attr={} GT=[[test1 G*/GA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, TC] attr={OriginalAlleles=[G, GA], ReverseComplementedAlleles=true} GT=[[test1 C*/TC]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testFlipIndelWithOriginalAlleles[10]([VC test11 @ chr1:540 Q. of type=INDEL alleles=[G*, GG] attr={} GT=[[test1 G*/GG]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CC] attr={OriginalAlleles=[G, GG], ReverseComplementedAlleles=true} GT=[[test1 C*/CC]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testFlipIndelWithOriginalAlleles[11]([VC test12 @ chr1:536-539 Q. of type=INDEL alleles=[TTTT*, TTTTG] attr={} GT=[[test1 TTTT*/TTTTG]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CC] attr={OriginalAlleles=[TTTT, TTTTG], ReverseComplementedAlleles=true} GT=[[test1 C*/CC]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testFlipIndelWithOriginalAlleles[12]([VC test13 @ chr1:536-539 Q. of type=INDEL alleles=[TTTT*, *, TTTTG] attr={} GT=[[test1 TTTT*/*/TTTTG]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=MIXED alleles=[C*, *, CC] attr={OriginalAlleles=[TTTT, TTTTG, *], ReverseComplementedAlleles=true} GT=[[test1 C*/*/CC]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testFlipIndelWithOriginalAlleles[13]([VC test14 @ chr1:527-530 Q. of type=INDEL alleles=[ACGT*, *, A] attr={} GT=[[test1 ACGT*/*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-13 Q. of type=INDEL alleles=[AACG*, *, A] attr={OriginalAlleles=[ACGT, A, *], ReverseComplementedAlleles=true} GT=[[test1 AACG*/*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[0]([VC test1 @ chr1:1-4 Q. of type=INDEL alleles=[CAAA*, CCAAA] attr={} GT=[[test1 CAAA*/CCAAA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CC] attr={} GT=[[test1 C*/CC]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[1]([VC test1_5 @ chr1:13 Q. of type=SNP alleles=[G*, A] attr={} GT=[[test1 G*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:13 Q. of type=SNP alleles=[G*, A] attr={} GT=[[test1 G*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[2]([VC test1_5 @ chr1:13 Q. of type=MIXED alleles=[G*, <*>, A] attr={} GT=[[test1 G*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:13 Q. of type=MIXED alleles=[G*, <*>, A] attr={} GT=[[test1 G*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[3]([VC test2-1 @ chr1:1 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=, ReferenceSequence chr1, [VC test2-1 @ chr1:1 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[4]([VC test2-2 @ chr1:2 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, ReferenceSequence chr1, [VC test2-2 @ chr1:2 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[5]([VC test2-3 @ chr1:3 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, ReferenceSequence chr1, [VC test2-3 @ chr1:3 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[6]([VC test2-4 @ chr1:4 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, ReferenceSequence chr1, [VC test2-4 @ chr1:4 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[7]([VC test2-5 @ chr1:5 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, ReferenceSequence chr1, [VC test2-5 @ chr1:5 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[8]([VC test2-6 @ chr1:6 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, ReferenceSequence chr1, [VC test2-6 @ chr1:6 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[9]([VC test2-7 @ chr1:7 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, ReferenceSequence chr1, [VC test2-7 @ chr1:7 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[10]([VC test2-8 @ chr1:8 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, ReferenceSequence chr1, [VC test2-8 @ chr1:8 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[11]([VC test2-9 @ chr1:9 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, ReferenceSequence chr1, [VC test2-9 @ chr1:9 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[12]([VC test2-10 @ chr1:10 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, ReferenceSequence chr1, [VC test2-10 @ chr1:10 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[13]([VC test2-11 @ chr1:11 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, ReferenceSequence chr1, [VC test2-11 @ chr1:11 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[14]([VC test2-12 @ chr1:12 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=, ReferenceSequence chr1, [VC test2-12 @ chr1:12 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[15]([VC test2-13 @ chr1:13 Q. of type=SNP alleles=[G*, A] attr={} GT=[[test1 G*/A]] filters=, ReferenceSequence chr1, [VC test2-13 @ chr1:13 Q. of type=SNP alleles=[G*, A] attr={} GT=[[test1 G*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[16]([VC test2-14 @ chr1:14 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=, ReferenceSequence chr1, [VC test2-14 @ chr1:14 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[17]([VC test2-15 @ chr1:15 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, ReferenceSequence chr1, [VC test2-15 @ chr1:15 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[18]([VC test2-16 @ chr1:16 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=, ReferenceSequence chr1, [VC test2-16 @ chr1:16 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[19]([VC test2-17 @ chr1:17 Q. of type=SNP alleles=[G*, A] attr={} GT=[[test1 G*/A]] filters=, ReferenceSequence chr1, [VC test2-17 @ chr1:17 Q. of type=SNP alleles=[G*, A] attr={} GT=[[test1 G*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[20]([VC test2-18 @ chr1:18 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=, ReferenceSequence chr1, [VC test2-18 @ chr1:18 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[21]([VC test2-19 @ chr1:19 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, ReferenceSequence chr1, [VC test2-19 @ chr1:19 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[22]([VC test2-20 @ chr1:20 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=, ReferenceSequence chr1, [VC test2-20 @ chr1:20 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[23]([VC test2-21 @ chr1:21 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=, ReferenceSequence chr1, [VC test2-21 @ chr1:21 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[24]([VC test2-22 @ chr1:22 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=, ReferenceSequence chr1, [VC test2-22 @ chr1:22 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[25]([VC test2-23 @ chr1:23 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=, ReferenceSequence chr1, [VC test2-23 @ chr1:23 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[26]([VC test2-24 @ chr1:24 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=, ReferenceSequence chr1, [VC test2-24 @ chr1:24 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[27]([VC test2-25 @ chr1:25 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=, ReferenceSequence chr1, [VC test2-25 @ chr1:25 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[28]([VC test2-26 @ chr1:26 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=, ReferenceSequence chr1, [VC test2-26 @ chr1:26 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[29]([VC test2-27 @ chr1:27 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=, ReferenceSequence chr1, [VC test2-27 @ chr1:27 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[30]([VC test2-28 @ chr1:28 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=, ReferenceSequence chr1, [VC test2-28 @ chr1:28 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[31]([VC test2-29 @ chr1:29 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=, ReferenceSequence chr1, [VC test2-29 @ chr1:29 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[32]([VC test2-30 @ chr1:30 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, ReferenceSequence chr1, [VC test2-30 @ chr1:30 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[33]([VC test2-31 @ chr1:31 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=, ReferenceSequence chr1, [VC test2-31 @ chr1:31 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[34]([VC test2-32 @ chr1:32 Q. of type=SNP alleles=[G*, A] attr={} GT=[[test1 G*/A]] filters=, ReferenceSequence chr1, [VC test2-32 @ chr1:32 Q. of type=SNP alleles=[G*, A] attr={} GT=[[test1 G*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[35]([VC test2-33 @ chr1:33 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=, ReferenceSequence chr1, [VC test2-33 @ chr1:33 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[36]([VC test3-2 @ chr1:2-3 Q. of type=INDEL alleles=[AA*, A] attr={} GT=[[test1 AA*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1-2 Q. of type=INDEL alleles=[CA*, C] attr={} GT=[[test1 CA*/C]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[37]([VC test3-3 @ chr1:3-4 Q. of type=INDEL alleles=[AA*, A] attr={} GT=[[test1 AA*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1-2 Q. of type=INDEL alleles=[CA*, C] attr={} GT=[[test1 CA*/C]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[38]([VC test3-4 @ chr1:4-5 Q. of type=INDEL alleles=[AA*, A] attr={} GT=[[test1 AA*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1-2 Q. of type=INDEL alleles=[CA*, C] attr={} GT=[[test1 CA*/C]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[39]([VC test3-5 @ chr1:5-6 Q. of type=INDEL alleles=[AA*, A] attr={} GT=[[test1 AA*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1-2 Q. of type=INDEL alleles=[CA*, C] attr={} GT=[[test1 CA*/C]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[40]([VC test3-6 @ chr1:6-7 Q. of type=INDEL alleles=[AA*, A] attr={} GT=[[test1 AA*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1-2 Q. of type=INDEL alleles=[CA*, C] attr={} GT=[[test1 CA*/C]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[41]([VC test3-7 @ chr1:7-8 Q. of type=INDEL alleles=[AA*, A] attr={} GT=[[test1 AA*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1-2 Q. of type=INDEL alleles=[CA*, C] attr={} GT=[[test1 CA*/C]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[42]([VC test3-8 @ chr1:8-9 Q. of type=INDEL alleles=[AA*, A] attr={} GT=[[test1 AA*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1-2 Q. of type=INDEL alleles=[CA*, C] attr={} GT=[[test1 CA*/C]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[43]([VC test3-9 @ chr1:9-10 Q. of type=INDEL alleles=[AA*, A] attr={} GT=[[test1 AA*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1-2 Q. of type=INDEL alleles=[CA*, C] attr={} GT=[[test1 CA*/C]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[44]([VC test3-10 @ chr1:10-11 Q. of type=INDEL alleles=[AA*, A] attr={} GT=[[test1 AA*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1-2 Q. of type=INDEL alleles=[CA*, C] attr={} GT=[[test1 CA*/C]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[45]([VC test4-2 @ chr1:2 Q. of type=INDEL alleles=[A*, AA] attr={} GT=[[test1 A*/AA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CA] attr={} GT=[[test1 C*/CA]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[46]([VC test4-3 @ chr1:3 Q. of type=INDEL alleles=[A*, AA] attr={} GT=[[test1 A*/AA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CA] attr={} GT=[[test1 C*/CA]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[47]([VC test4-4 @ chr1:4 Q. of type=INDEL alleles=[A*, AA] attr={} GT=[[test1 A*/AA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CA] attr={} GT=[[test1 C*/CA]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[48]([VC test4-5 @ chr1:5 Q. of type=INDEL alleles=[A*, AA] attr={} GT=[[test1 A*/AA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CA] attr={} GT=[[test1 C*/CA]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[49]([VC test4-6 @ chr1:6 Q. of type=INDEL alleles=[A*, AA] attr={} GT=[[test1 A*/AA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CA] attr={} GT=[[test1 C*/CA]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[50]([VC test4-7 @ chr1:7 Q. of type=INDEL alleles=[A*, AA] attr={} GT=[[test1 A*/AA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CA] attr={} GT=[[test1 C*/CA]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[51]([VC test4-8 @ chr1:8 Q. of type=INDEL alleles=[A*, AA] attr={} GT=[[test1 A*/AA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CA] attr={} GT=[[test1 C*/CA]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[52]([VC test4-9 @ chr1:9 Q. of type=INDEL alleles=[A*, AA] attr={} GT=[[test1 A*/AA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CA] attr={} GT=[[test1 C*/CA]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[53]([VC test4-10 @ chr1:10 Q. of type=INDEL alleles=[A*, AA] attr={} GT=[[test1 A*/AA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CA] attr={} GT=[[test1 C*/CA]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[54]([VC test4-11 @ chr1:11 Q. of type=INDEL alleles=[A*, AA] attr={} GT=[[test1 A*/AA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CA] attr={} GT=[[test1 C*/CA]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[55]([VC test5-20 @ chr1:20-21 Q. of type=INDEL alleles=[CT*, CTCT] attr={} GT=[[test1 CT*/CTCT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19 Q. of type=INDEL alleles=[A*, ACT] attr={} GT=[[test1 A*/ACT]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[56]([VC test5-22 @ chr1:22-23 Q. of type=INDEL alleles=[CT*, CTCT] attr={} GT=[[test1 CT*/CTCT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19 Q. of type=INDEL alleles=[A*, ACT] attr={} GT=[[test1 A*/ACT]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[57]([VC test5-24 @ chr1:24-25 Q. of type=INDEL alleles=[CT*, CTCT] attr={} GT=[[test1 CT*/CTCT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19 Q. of type=INDEL alleles=[A*, ACT] attr={} GT=[[test1 A*/ACT]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[58]([VC test5-26 @ chr1:26-27 Q. of type=INDEL alleles=[CT*, CTCT] attr={} GT=[[test1 CT*/CTCT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19 Q. of type=INDEL alleles=[A*, ACT] attr={} GT=[[test1 A*/ACT]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[59]([VC test6-21 @ chr1:21-22 Q. of type=INDEL alleles=[TC*, TCTC] attr={} GT=[[test1 TC*/TCTC]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19 Q. of type=INDEL alleles=[A*, ACT] attr={} GT=[[test1 A*/ACT]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[60]([VC test6-23 @ chr1:23-24 Q. of type=INDEL alleles=[TC*, TCTC] attr={} GT=[[test1 TC*/TCTC]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19 Q. of type=INDEL alleles=[A*, ACT] attr={} GT=[[test1 A*/ACT]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[61]([VC test6-25 @ chr1:25-26 Q. of type=INDEL alleles=[TC*, TCTC] attr={} GT=[[test1 TC*/TCTC]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19 Q. of type=INDEL alleles=[A*, ACT] attr={} GT=[[test1 A*/ACT]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[62]([VC test6-27 @ chr1:27-28 Q. of type=INDEL alleles=[TC*, TCTC] attr={} GT=[[test1 TC*/TCTC]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19 Q. of type=INDEL alleles=[A*, ACT] attr={} GT=[[test1 A*/ACT]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[63]([VC test7-20 @ chr1:20-23 Q. of type=INDEL alleles=[CTCT*, CT] attr={} GT=[[test1 CTCT*/CT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19-21 Q. of type=INDEL alleles=[ACT*, A] attr={} GT=[[test1 ACT*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[64]([VC test7-22 @ chr1:22-25 Q. of type=INDEL alleles=[CTCT*, CT] attr={} GT=[[test1 CTCT*/CT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19-21 Q. of type=INDEL alleles=[ACT*, A] attr={} GT=[[test1 ACT*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[65]([VC test7-24 @ chr1:24-27 Q. of type=INDEL alleles=[CTCT*, CT] attr={} GT=[[test1 CTCT*/CT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19-21 Q. of type=INDEL alleles=[ACT*, A] attr={} GT=[[test1 ACT*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[66]([VC test7-26 @ chr1:26-29 Q. of type=INDEL alleles=[CTCT*, CT] attr={} GT=[[test1 CTCT*/CT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19-21 Q. of type=INDEL alleles=[ACT*, A] attr={} GT=[[test1 ACT*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[67]([VC test8-21 @ chr1:21-24 Q. of type=INDEL alleles=[TCTC*, TC] attr={} GT=[[test1 TCTC*/TC]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19-21 Q. of type=INDEL alleles=[ACT*, A] attr={} GT=[[test1 ACT*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[68]([VC test8-23 @ chr1:23-26 Q. of type=INDEL alleles=[TCTC*, TC] attr={} GT=[[test1 TCTC*/TC]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19-21 Q. of type=INDEL alleles=[ACT*, A] attr={} GT=[[test1 ACT*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[69]([VC test8-25 @ chr1:25-28 Q. of type=INDEL alleles=[TCTC*, TC] attr={} GT=[[test1 TCTC*/TC]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19-21 Q. of type=INDEL alleles=[ACT*, A] attr={} GT=[[test1 ACT*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[70]([VC test9-10-14 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[71]([VC test9-10-15 @ chr1:10-15 Q. of type=INDEL alleles=[AACGTA*, AA] attr={} GT=[[test1 AACGTA*/AA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[72]([VC test9-10-16 @ chr1:10-16 Q. of type=INDEL alleles=[AACGTAC*, AAC] attr={} GT=[[test1 AACGTAC*/AAC]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[73]([VC test9-10-17 @ chr1:10-17 Q. of type=INDEL alleles=[AACGTACG*, AACG] attr={} GT=[[test1 AACGTACG*/AACG]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[74]([VC test9-10-18 @ chr1:10-18 Q. of type=INDEL alleles=[AACGTACGT*, AACGT] attr={} GT=[[test1 AACGTACGT*/AACGT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[75]([VC test9-10-19 @ chr1:10-19 Q. of type=INDEL alleles=[AACGTACGTA*, AACGTA] attr={} GT=[[test1 AACGTACGTA*/AACGTA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[76]([VC test9-11-15 @ chr1:11-15 Q. of type=INDEL alleles=[ACGTA*, A] attr={} GT=[[test1 ACGTA*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[77]([VC test9-11-16 @ chr1:11-16 Q. of type=INDEL alleles=[ACGTAC*, AC] attr={} GT=[[test1 ACGTAC*/AC]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[78]([VC test9-11-17 @ chr1:11-17 Q. of type=INDEL alleles=[ACGTACG*, ACG] attr={} GT=[[test1 ACGTACG*/ACG]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[79]([VC test9-11-18 @ chr1:11-18 Q. of type=INDEL alleles=[ACGTACGT*, ACGT] attr={} GT=[[test1 ACGTACGT*/ACGT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[80]([VC test9-11-19 @ chr1:11-19 Q. of type=INDEL alleles=[ACGTACGTA*, ACGTA] attr={} GT=[[test1 ACGTACGTA*/ACGTA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[81]([VC test9-12-16 @ chr1:12-16 Q. of type=INDEL alleles=[CGTAC*, C] attr={} GT=[[test1 CGTAC*/C]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[82]([VC test9-12-17 @ chr1:12-17 Q. of type=INDEL alleles=[CGTACG*, CG] attr={} GT=[[test1 CGTACG*/CG]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[83]([VC test9-12-18 @ chr1:12-18 Q. of type=INDEL alleles=[CGTACGT*, CGT] attr={} GT=[[test1 CGTACGT*/CGT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[84]([VC test9-12-19 @ chr1:12-19 Q. of type=INDEL alleles=[CGTACGTA*, CGTA] attr={} GT=[[test1 CGTACGTA*/CGTA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[85]([VC test9-13-17 @ chr1:13-17 Q. of type=INDEL alleles=[GTACG*, G] attr={} GT=[[test1 GTACG*/G]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[86]([VC test9-13-18 @ chr1:13-18 Q. of type=INDEL alleles=[GTACGT*, GT] attr={} GT=[[test1 GTACGT*/GT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[87]([VC test9-13-19 @ chr1:13-19 Q. of type=INDEL alleles=[GTACGTA*, GTA] attr={} GT=[[test1 GTACGTA*/GTA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[88]([VC test9-14-18 @ chr1:14-18 Q. of type=INDEL alleles=[TACGT*, T] attr={} GT=[[test1 TACGT*/T]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[89]([VC test9-14-19 @ chr1:14-19 Q. of type=INDEL alleles=[TACGTA*, TA] attr={} GT=[[test1 TACGTA*/TA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[90]([VC test9-15-19 @ chr1:15-19 Q. of type=INDEL alleles=[ACGTA*, A] attr={} GT=[[test1 ACGTA*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLeftAlignVariants[91]([VC test12 @ chr1:9-18 Q. of type=INDEL alleles=[AAACGTACGT*, AAACGACGT, AAACGT, AAACGTACGTACGT] attr={} GT=[[sample1 AAACGTACGT*/AAACGT],[sample2 AAACGTACGT*/AAACGACGT],[sample3 AAACGTACGT*/AAACGTACGTACGT],[sample_non_ref_het AAACGACGT/AAACGT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A, AACG, AACGTACGT] attr={} GT=[[sample1 AACGT*/A],[sample2 AACGT*/AACG],[sample3 AACGT*/AACGTACGT],[sample_non_ref_het A/AACG]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverIndels[0](htsjdk.samtools.liftover.LiftOver@4fe4f205, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test1 @ chr1:1 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=, [VC test1 @ chr1:1 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverIndels[1](htsjdk.samtools.liftover.LiftOver@4fe4f205, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC testWithEND @ chr1:1-4 Q. of type=INDEL alleles=[CAAA*, CAA] attr={END=4} GT=[[test1 CAAA*/CAA]] filters=, [VC test1 @ chr1:1-4 Q. of type=INDEL alleles=[CAAA*, CAA] attr={END=4} GT=[[test1 CAAA*/CAA]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverIndels[2](htsjdk.samtools.liftover.LiftOver@4fe4f205, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test2 @ chr1:1-4 Q. of type=INDEL alleles=[CAAA*, CAA] attr={} GT=[[test1 CAAA*/CAA]] filters=, [VC test1 @ chr1:1-4 Q. of type=INDEL alleles=[CAAA*, CAA] attr={} GT=[[test1 CAAA*/CAA]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverIndels[3](htsjdk.samtools.liftover.LiftOver@4fe4f205, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test3 @ chr1:537-540 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, [VC test1 @ chr1:537-540 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverIndels[4](htsjdk.samtools.liftover.LiftOver@4fe4f205, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test4 @ chr1:540 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, [VC test1 @ chr1:540 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverIndels[5](htsjdk.samtools.liftover.LiftOver@4fe4f205, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test5_WITH_END @ chr1:538-541 Q. of type=INDEL alleles=[AAAA*, AAA] attr={END=541} GT=[[test1 AAAA*/AAA]] filters=, null)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverIndels[6](htsjdk.samtools.liftover.LiftOver@4fe4f205, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test6_withEND @ chr1:541 Q. of type=SNP alleles=[A*, T] attr={END=541} GT=[[test1 A*/T]] filters=, [VC test1 @ chr1:546 Q. of type=SNP alleles=[A*, T] attr={END=546} GT=[[test1 A*/T]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverIndels[7](htsjdk.samtools.liftover.LiftOver@4fe4f205, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test7 @ chr1:541 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, [VC test1 @ chr1:546 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverIndels[8](htsjdk.samtools.liftover.LiftOver@4fe4f205, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test8 @ chr1:1040 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, [VC test1 @ chr1:1045 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverIndels[9](htsjdk.samtools.liftover.LiftOver@4fe4f205, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test9 @ chr1:1037-1040 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, [VC test1 @ chr1:1042-1045 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverIndels[10](htsjdk.samtools.liftover.LiftOver@4fe4f205, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test9 @ chr1:1038-1041 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, null)(picard.util.LiftoverVcfTest) Test: Test method testLiftOverIndels[10](htsjdk.samtools.liftover.LiftOver@4fe4f205, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test9 @ chr1:1038-1041 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, null)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftOver Interval null failed to match chain 2 because intersection length 3 < minMatchSize 4.0 (0.75 < 1.0) Gradle suite > Gradle test > picard.util.LiftoverVcfTest.testLiftOverIndels[10](htsjdk.samtools.liftover.LiftOver@4fe4f205, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test9 @ chr1:1038-1041 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, null) STANDARD_ERROR INFO 2024-07-02 12:01:19 LiftOver Interval null failed to match chain 2 because intersection length 3 < minMatchSize 4.0 (0.75 < 1.0) Running Test: Test method testLiftOverIndels[11](htsjdk.samtools.liftover.LiftOver@4fe4f205, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test10 @ chr1:1045-1048 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, null)(picard.util.LiftoverVcfTest) Test: Test method testLiftOverIndels[11](htsjdk.samtools.liftover.LiftOver@4fe4f205, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test10 @ chr1:1045-1048 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, null)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftOver Interval null failed to match chain 2 because intersection length 3 < minMatchSize 4.0 (0.75 < 1.0) Gradle suite > Gradle test > picard.util.LiftoverVcfTest.testLiftOverIndels[11](htsjdk.samtools.liftover.LiftOver@4fe4f205, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test10 @ chr1:1045-1048 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, null) STANDARD_ERROR INFO 2024-07-02 12:01:19 LiftOver Interval null failed to match chain 2 because intersection length 3 < minMatchSize 4.0 (0.75 < 1.0) Running Test: Test method testLiftOverIndels[12](htsjdk.samtools.liftover.LiftOver@4fe4f205, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test11 @ chr1:1045 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, null)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverIndels[13](htsjdk.samtools.liftover.LiftOver@4fe4f205, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test12 @ chr1:1046-1049 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, [VC test1 @ chr1:1046-1049 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverIndels[14](htsjdk.samtools.liftover.LiftOver@4fe4f205, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test13 @ chr1:1046 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, [VC test1 @ chr1:1046 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverNoCallAndSymbolic[0](htsjdk.samtools.liftover.LiftOver@1e79a5f4, [VC test1 @ chr1:10 Q. of type=MIXED alleles=[C*, <*>, T] attr={TEST_ATTRIBUTE=1, TEST_ATTRIBUTE2=Hi, TEST_ATTRIBUTE3=[D@4b962322} GT=[[test1 ./.]] filters=, [VC test1 @ chr1:10 Q. of type=MIXED alleles=[C*, <*>, T] attr={OriginalContig=chr1, OriginalStart=10, TEST_ATTRIBUTE=1, TEST_ATTRIBUTE2=Hi, TEST_ATTRIBUTE3=[D@53f7e2c9} GT=[[test1 ./.]] filters=, false)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverNoCallAndSymbolic[1](htsjdk.samtools.liftover.LiftOver@1e79a5f4, [VC test2 @ chr1:10 Q. of type=SNP alleles=[C*, *, T] attr={TEST_ATTRIBUTE=1, TEST_ATTRIBUTE2=Hi, TEST_ATTRIBUTE3=[D@4b962322} GT=[[test1 */T]] filters=, [VC test1 @ chr1:10 Q. of type=SNP alleles=[C*, *, T] attr={OriginalContig=chr1, OriginalStart=10, TEST_ATTRIBUTE=1, TEST_ATTRIBUTE2=Hi, TEST_ATTRIBUTE3=[D@53f7e2c9} GT=[[test1 */T]] filters=, false)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverNoCallAndSymbolic[2](htsjdk.samtools.liftover.LiftOver@4cc3dba, [VC test3 @ chr1:537 Q. of type=MIXED alleles=[C*, <*>, *, T] attr={TEST_ATTRIBUTE=1, TEST_ATTRIBUTE2=Hi, TEST_ATTRIBUTE3=[D@4b962322} GT=[[test1 */T]] filters=, [VC test1 @ chr1:4 Q. of type=MIXED alleles=[G*, <*>, *, A] attr={OriginalAlleles=[C, T, *, <*>], OriginalContig=chr1, OriginalStart=537, ReverseComplementedAlleles=true, TEST_ATTRIBUTE=1, TEST_ATTRIBUTE2=Hi, TEST_ATTRIBUTE3=[D@53f7e2c9} GT=[[test1 */A]] filters=, true)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverNoCallAndSymbolic[3](htsjdk.samtools.liftover.LiftOver@4cc3dba, [VC test4 @ chr1:536 Q. of type=MIXED alleles=[C*, <*>, T] attr={TEST_ATTRIBUTE=1, TEST_ATTRIBUTE2=Hi, TEST_ATTRIBUTE3=[D@4b962322} GT=[[test1 ./T]] filters=, [VC test1 @ chr1:5 Q. of type=MIXED alleles=[G*, <*>, A] attr={OriginalAlleles=[C, T, <*>], OriginalContig=chr1, OriginalStart=536, ReverseComplementedAlleles=true, TEST_ATTRIBUTE=1, TEST_ATTRIBUTE2=Hi, TEST_ATTRIBUTE3=[D@53f7e2c9} GT=[[test1 ./A]] filters=, true)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverSimpleIndels[0](htsjdk.samtools.liftover.LiftOver@2b7dc5dd, [VC test1 @ chr1:1 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=, [VC test1 @ chr1:1 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverSimpleIndels[1](htsjdk.samtools.liftover.LiftOver@2b7dc5dd, [VC testWithEND @ chr1:1-4 Q. of type=INDEL alleles=[CAAA*, CAA] attr={} GT=[[test1 CAAA*/CAA]] filters=, [VC test1 @ chr1:1-4 Q. of type=INDEL alleles=[CAAA*, CAA] attr={} GT=[[test1 CAAA*/CAA]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverSimpleIndels[2](htsjdk.samtools.liftover.LiftOver@2b7dc5dd, [VC test2 @ chr1:1-4 Q. of type=INDEL alleles=[CAAA*, CAA] attr={} GT=[[test1 CAAA*/CAA]] filters=, [VC test1 @ chr1:1-4 Q. of type=INDEL alleles=[CAAA*, CAA] attr={} GT=[[test1 CAAA*/CAA]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverSimpleIndels[3](htsjdk.samtools.liftover.LiftOver@2b7dc5dd, [VC test3 @ chr1:537-540 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, [VC test1 @ chr1:537-540 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverSimpleIndels[4](htsjdk.samtools.liftover.LiftOver@2b7dc5dd, [VC test4 @ chr1:540 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, [VC test1 @ chr1:540 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverSimpleIndels[5](htsjdk.samtools.liftover.LiftOver@2b7dc5dd, [VC test5_WITH_END @ chr1:538-541 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, null)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverSimpleIndels[6](htsjdk.samtools.liftover.LiftOver@2b7dc5dd, [VC test6_withEND @ chr1:541 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, [VC test1 @ chr1:546 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverSimpleIndels[7](htsjdk.samtools.liftover.LiftOver@2b7dc5dd, [VC test7 @ chr1:541 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, [VC test1 @ chr1:546 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverSimpleIndels[8](htsjdk.samtools.liftover.LiftOver@2b7dc5dd, [VC test8 @ chr1:1040 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, [VC test1 @ chr1:1045 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverSimpleIndels[9](htsjdk.samtools.liftover.LiftOver@2b7dc5dd, [VC test9 @ chr1:1037-1040 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, [VC test1 @ chr1:1042-1045 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverSimpleIndels[10](htsjdk.samtools.liftover.LiftOver@2b7dc5dd, [VC test9 @ chr1:1038-1041 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, null)(picard.util.LiftoverVcfTest) Test: Test method testLiftOverSimpleIndels[10](htsjdk.samtools.liftover.LiftOver@2b7dc5dd, [VC test9 @ chr1:1038-1041 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, null)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftOver Interval null failed to match chain 2 because intersection length 3 < minMatchSize 4.0 (0.75 < 1.0) Gradle suite > Gradle test > picard.util.LiftoverVcfTest.testLiftOverSimpleIndels[10](htsjdk.samtools.liftover.LiftOver@2b7dc5dd, [VC test9 @ chr1:1038-1041 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, null) STANDARD_ERROR INFO 2024-07-02 12:01:19 LiftOver Interval null failed to match chain 2 because intersection length 3 < minMatchSize 4.0 (0.75 < 1.0) Running Test: Test method testLiftOverSimpleIndels[11](htsjdk.samtools.liftover.LiftOver@2b7dc5dd, [VC test10 @ chr1:1045-1048 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, null)(picard.util.LiftoverVcfTest) Test: Test method testLiftOverSimpleIndels[11](htsjdk.samtools.liftover.LiftOver@2b7dc5dd, [VC test10 @ chr1:1045-1048 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, null)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftOver Interval null failed to match chain 2 because intersection length 3 < minMatchSize 4.0 (0.75 < 1.0) Gradle suite > Gradle test > picard.util.LiftoverVcfTest.testLiftOverSimpleIndels[11](htsjdk.samtools.liftover.LiftOver@2b7dc5dd, [VC test10 @ chr1:1045-1048 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, null) STANDARD_ERROR INFO 2024-07-02 12:01:19 LiftOver Interval null failed to match chain 2 because intersection length 3 < minMatchSize 4.0 (0.75 < 1.0) Running Test: Test method testLiftOverSimpleIndels[12](htsjdk.samtools.liftover.LiftOver@2b7dc5dd, [VC test11 @ chr1:1045 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, null)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverSimpleIndels[13](htsjdk.samtools.liftover.LiftOver@2b7dc5dd, [VC test12 @ chr1:1046-1049 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, [VC test1 @ chr1:1046-1049 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testLiftOverSimpleIndels[14](htsjdk.samtools.liftover.LiftOver@2b7dc5dd, [VC test13 @ chr1:1046 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, [VC test1 @ chr1:1046 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=)(picard.util.LiftoverVcfTest) Running Test: Test method testMissingContigInReference[0](false, 1)(picard.util.LiftoverVcfTest) Test: Test method testMissingContigInReference[0](false, 1)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf Gradle suite > Gradle test > picard.util.LiftoverVcfTest.testMissingContigInReference[0](false, 1) STANDARD_ERROR INFO 2024-07-02 12:01:19 LiftoverVcf Test: Test method testMissingContigInReference[0](false, 1)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testMissingContigInReference[0](false, 1)(picard.util.LiftoverVcfTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingContigInReference[0](false, 1)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testMissingContigInReference[0](false, 1)(picard.util.LiftoverVcfTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingContigInReference[0](false, 1)(picard.util.LiftoverVcfTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingContigInReference[0](false, 1)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testMissingContigInReference[0](false, 1)(picard.util.LiftoverVcfTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingContigInReference[0](false, 1)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testMissingContigInReference[0](false, 1)(picard.util.LiftoverVcfTest) produced standard out/err: ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverUsingMissingContig.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN testdata/picard/vcf/LiftOver/test.over.badContig.chain -REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta -CREATE_INDEX false -WMC false ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverUsingMissingContig.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN testdata/picard/vcf/LiftOver/test.over.badContig.chain -REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta -CREATE_INDEX false -WMC false Test: Test method testMissingContigInReference[0](false, 1)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testMissingContigInReference[0](false, 1)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testMissingContigInReference[0](false, 1)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testMissingContigInReference[0](false, 1)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:19.247 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:19.247 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingContigInReference[0](false, 1)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:19.247 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:19.247 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingContigInReference[0](false, 1)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:19.247 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:19.247 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingContigInReference[0](false, 1)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:19.247 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:19.247 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingContigInReference[0](false, 1)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:19 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverUsingMissingContig.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/LiftOver/test.over.badContig.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf WARN_ON_MISSING_CONTIG=false CREATE_INDEX=false REFERENCE_SEQUENCE=testdata/picard/vcf/LiftOver/dummy.reference.fasta LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false RECOVER_SWAPPED_REF_ALT=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:19 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverUsingMissingContig.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/LiftOver/test.over.badContig.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf WARN_ON_MISSING_CONTIG=false CREATE_INDEX=false REFERENCE_SEQUENCE=testdata/picard/vcf/LiftOver/dummy.reference.fasta LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false RECOVER_SWAPPED_REF_ALT=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingContigInReference[0](false, 1)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingContigInReference[0](false, 1)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf Loading up the target reference genome. INFO 2024-07-02 12:01:19 LiftoverVcf Loading up the target reference genome. Test: Test method testMissingContigInReference[0](false, 1)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) INFO 2024-07-02 12:01:19 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) Test: Test method testMissingContigInReference[0](false, 1)(picard.util.LiftoverVcfTest) produced standard out/err: ERROR 2024-07-02 12:01:19 LiftoverVcf Encountered a contig, missingContig that is not part of the target reference. ERROR 2024-07-02 12:01:19 LiftoverVcf Encountered a contig, missingContig that is not part of the target reference. Test: Test method testMissingContigInReference[0](false, 1)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:19 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:19 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. Test: Test method testMissingContigInReference[0](false, 1)(picard.util.LiftoverVcfTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testMissingContigInReference[0](false, 1)(picard.util.LiftoverVcfTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf Gradle suite > Gradle test > picard.util.LiftoverVcfTest.testMissingContigInReference[1](true, 0) STANDARD_ERROR INFO 2024-07-02 12:01:19 LiftoverVcf Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverUsingMissingContig.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN testdata/picard/vcf/LiftOver/test.over.badContig.chain -REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta -CREATE_INDEX false -WMC true ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverUsingMissingContig.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN testdata/picard/vcf/LiftOver/test.over.badContig.chain -REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta -CREATE_INDEX false -WMC true Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:19.391 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:19.391 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:19.391 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:19.391 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:19.391 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:19.391 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:19.391 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:19.391 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:19 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverUsingMissingContig.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/LiftOver/test.over.badContig.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf WARN_ON_MISSING_CONTIG=true CREATE_INDEX=false REFERENCE_SEQUENCE=testdata/picard/vcf/LiftOver/dummy.reference.fasta LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false RECOVER_SWAPPED_REF_ALT=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:19 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverUsingMissingContig.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/LiftOver/test.over.badContig.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf WARN_ON_MISSING_CONTIG=true CREATE_INDEX=false REFERENCE_SEQUENCE=testdata/picard/vcf/LiftOver/dummy.reference.fasta LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false RECOVER_SWAPPED_REF_ALT=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf Loading up the target reference genome. INFO 2024-07-02 12:01:19 LiftoverVcf Loading up the target reference genome. Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) INFO 2024-07-02 12:01:19 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: WARNING 2024-07-02 12:01:19 LiftoverVcf Encountered a contig, missingContig that is not part of the target reference. WARNING 2024-07-02 12:01:19 LiftoverVcf Encountered a contig, missingContig that is not part of the target reference. Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf Processed 2 variants. INFO 2024-07-02 12:01:19 LiftoverVcf Processed 2 variants. Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf 2 variants failed to liftover. INFO 2024-07-02 12:01:19 LiftoverVcf 2 variants failed to liftover. Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over. INFO 2024-07-02 12:01:19 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over. Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf 100.0000% of variants were not successfully lifted over and written to the output. INFO 2024-07-02 12:01:19 LiftoverVcf 100.0000% of variants were not successfully lifted over and written to the output. Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf liftover success by source contig: INFO 2024-07-02 12:01:19 LiftoverVcf liftover success by source contig: Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf chr1: 0 / 1 (0.0000%) INFO 2024-07-02 12:01:19 LiftoverVcf chr1: 0 / 1 (0.0000%) Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf missingContig: 0 / 1 (0.0000%) INFO 2024-07-02 12:01:19 LiftoverVcf missingContig: 0 / 1 (0.0000%) Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf lifted variants by target contig: INFO 2024-07-02 12:01:19 LiftoverVcf lifted variants by target contig: Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf no successfully lifted variants INFO 2024-07-02 12:01:19 LiftoverVcf no successfully lifted variants Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: WARNING 2024-07-02 12:01:19 LiftoverVcf 0 variants with a swapped REF/ALT were identified, but were not recovered. See RECOVER_SWAPPED_REF_ALT and associated caveats. WARNING 2024-07-02 12:01:19 LiftoverVcf 0 variants with a swapped REF/ALT were identified, but were not recovered. See RECOVER_SWAPPED_REF_ALT and associated caveats. Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf Writing out sorted records to final VCF. INFO 2024-07-02 12:01:19 LiftoverVcf Writing out sorted records to final VCF. Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:19 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:19 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. Test: Test method testMissingContigInReference[1](true, 0)(picard.util.LiftoverVcfTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testNoDictionary(picard.util.LiftoverVcfTest) Test: Test method testNoDictionary(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf Gradle suite > Gradle test > picard.util.LiftoverVcfTest.testNoDictionary STANDARD_ERROR INFO 2024-07-02 12:01:19 LiftoverVcf Test: Test method testNoDictionary(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testNoDictionary(picard.util.LiftoverVcfTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testNoDictionary(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testNoDictionary(picard.util.LiftoverVcfTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testNoDictionary(picard.util.LiftoverVcfTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testNoDictionary(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testNoDictionary(picard.util.LiftoverVcfTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testNoDictionary(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testNoDictionary(picard.util.LiftoverVcfTest) produced standard out/err: ********** LiftoverVcf -INPUT testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf -OUTPUT /tmp/pbuilder2/tmpoutput2100348325173806917.vcf -REJECT /tmp/pbuilder2/tmpreject3477868165706143796.vcf -CHAIN testdata/picard/vcf/LiftOver/test.over.chain -REFERENCE_SEQUENCE /tmp/pbuilder2/copy14497951966987855651/refCopy.fasta ********** LiftoverVcf -INPUT testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf -OUTPUT /tmp/pbuilder2/tmpoutput2100348325173806917.vcf -REJECT /tmp/pbuilder2/tmpreject3477868165706143796.vcf -CHAIN testdata/picard/vcf/LiftOver/test.over.chain -REFERENCE_SEQUENCE /tmp/pbuilder2/copy14497951966987855651/refCopy.fasta Test: Test method testNoDictionary(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testNoDictionary(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testNoDictionary(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testNoDictionary(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:19.608 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:19.608 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoDictionary(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:19.608 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:19.608 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoDictionary(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:19.608 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:19.608 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoDictionary(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:19.608 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:19.608 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoDictionary(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:19 GMT+14:00 2024] LiftoverVcf INPUT=testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf OUTPUT=/tmp/pbuilder2/tmpoutput2100348325173806917.vcf CHAIN=testdata/picard/vcf/LiftOver/test.over.chain REJECT=/tmp/pbuilder2/tmpreject3477868165706143796.vcf REFERENCE_SEQUENCE=/tmp/pbuilder2/copy14497951966987855651/refCopy.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false RECOVER_SWAPPED_REF_ALT=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:19 GMT+14:00 2024] LiftoverVcf INPUT=testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf OUTPUT=/tmp/pbuilder2/tmpoutput2100348325173806917.vcf CHAIN=testdata/picard/vcf/LiftOver/test.over.chain REJECT=/tmp/pbuilder2/tmpreject3477868165706143796.vcf REFERENCE_SEQUENCE=/tmp/pbuilder2/copy14497951966987855651/refCopy.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false RECOVER_SWAPPED_REF_ALT=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testNoDictionary(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testNoDictionary(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf Loading up the target reference genome. INFO 2024-07-02 12:01:19 LiftoverVcf Loading up the target reference genome. Test: Test method testNoDictionary(picard.util.LiftoverVcfTest) produced standard out/err: ERROR 2024-07-02 12:01:19 LiftoverVcf Reference /tmp/pbuilder2/copy14497951966987855651/refCopy.fasta must have an associated Dictionary .dict file in the same directory. ERROR 2024-07-02 12:01:19 LiftoverVcf Reference /tmp/pbuilder2/copy14497951966987855651/refCopy.fasta must have an associated Dictionary .dict file in the same directory. Test: Test method testNoDictionary(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:19 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:19 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. Test: Test method testNoDictionary(picard.util.LiftoverVcfTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testNoDictionary(picard.util.LiftoverVcfTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testReverseComplementFailureDoesNotErrorOut(picard.util.LiftoverVcfTest) Running Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf Gradle suite > Gradle test > picard.util.LiftoverVcfTest.testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0) STANDARD_ERROR INFO 2024-07-02 12:01:19 LiftoverVcf Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN testdata/picard/vcf/LiftOver/test.over.chain -REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta -RECOVER_SWAPPED_REF_ALT true -CREATE_INDEX false ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN testdata/picard/vcf/LiftOver/test.over.chain -REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta -RECOVER_SWAPPED_REF_ALT true -CREATE_INDEX false Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:19.744 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:19.744 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:19.744 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:19.744 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:19.744 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:19.744 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:19.744 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:19.744 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:19 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/LiftOver/test.over.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf RECOVER_SWAPPED_REF_ALT=true CREATE_INDEX=false REFERENCE_SEQUENCE=testdata/picard/vcf/LiftOver/dummy.reference.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:19 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/LiftOver/test.over.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf RECOVER_SWAPPED_REF_ALT=true CREATE_INDEX=false REFERENCE_SEQUENCE=testdata/picard/vcf/LiftOver/dummy.reference.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf Loading up the target reference genome. INFO 2024-07-02 12:01:19 LiftoverVcf Loading up the target reference genome. Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) INFO 2024-07-02 12:01:19 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf Processed 5 variants. INFO 2024-07-02 12:01:19 LiftoverVcf Processed 5 variants. Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf 0 variants failed to liftover. INFO 2024-07-02 12:01:19 LiftoverVcf 0 variants failed to liftover. Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over. INFO 2024-07-02 12:01:19 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over. Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf 0.0000% of variants were not successfully lifted over and written to the output. INFO 2024-07-02 12:01:19 LiftoverVcf 0.0000% of variants were not successfully lifted over and written to the output. Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf liftover success by source contig: INFO 2024-07-02 12:01:19 LiftoverVcf liftover success by source contig: Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf chr1: 5 / 5 (100.0000%) INFO 2024-07-02 12:01:19 LiftoverVcf chr1: 5 / 5 (100.0000%) Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf lifted variants by target contig: INFO 2024-07-02 12:01:19 LiftoverVcf lifted variants by target contig: Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf chr1: 5 INFO 2024-07-02 12:01:19 LiftoverVcf chr1: 5 Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf 0 variants were lifted by swapping REF/ALT alleles. INFO 2024-07-02 12:01:19 LiftoverVcf 0 variants were lifted by swapping REF/ALT alleles. Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf Writing out sorted records to final VCF. INFO 2024-07-02 12:01:19 LiftoverVcf Writing out sorted records to final VCF. Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:19 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:19 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. Test: Test method testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0)(picard.util.LiftoverVcfTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf Gradle suite > Gradle test > picard.util.LiftoverVcfTest.testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0) STANDARD_ERROR INFO 2024-07-02 12:01:19 LiftoverVcf Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverMultiallelicIndels.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN testdata/picard/vcf/LiftOver/test.over.chain -REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta -RECOVER_SWAPPED_REF_ALT true -CREATE_INDEX false ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverMultiallelicIndels.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN testdata/picard/vcf/LiftOver/test.over.chain -REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta -RECOVER_SWAPPED_REF_ALT true -CREATE_INDEX false Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:19.929 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:19.929 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:19.929 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:19.929 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:19.929 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:19.929 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:19.929 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:19.929 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:19 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverMultiallelicIndels.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/LiftOver/test.over.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf RECOVER_SWAPPED_REF_ALT=true CREATE_INDEX=false REFERENCE_SEQUENCE=testdata/picard/vcf/LiftOver/dummy.reference.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:19 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverMultiallelicIndels.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/LiftOver/test.over.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf RECOVER_SWAPPED_REF_ALT=true CREATE_INDEX=false REFERENCE_SEQUENCE=testdata/picard/vcf/LiftOver/dummy.reference.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:19 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf Loading up the target reference genome. INFO 2024-07-02 12:01:19 LiftoverVcf Loading up the target reference genome. Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) INFO 2024-07-02 12:01:19 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf Processed 2 variants. INFO 2024-07-02 12:01:19 LiftoverVcf Processed 2 variants. Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf 0 variants failed to liftover. INFO 2024-07-02 12:01:19 LiftoverVcf 0 variants failed to liftover. Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over. INFO 2024-07-02 12:01:19 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over. Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf 0.0000% of variants were not successfully lifted over and written to the output. INFO 2024-07-02 12:01:19 LiftoverVcf 0.0000% of variants were not successfully lifted over and written to the output. Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf liftover success by source contig: INFO 2024-07-02 12:01:19 LiftoverVcf liftover success by source contig: Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf chr1: 2 / 2 (100.0000%) INFO 2024-07-02 12:01:19 LiftoverVcf chr1: 2 / 2 (100.0000%) Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf lifted variants by target contig: INFO 2024-07-02 12:01:19 LiftoverVcf lifted variants by target contig: Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf chr1: 2 INFO 2024-07-02 12:01:19 LiftoverVcf chr1: 2 Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf 0 variants were lifted by swapping REF/ALT alleles. INFO 2024-07-02 12:01:19 LiftoverVcf 0 variants were lifted by swapping REF/ALT alleles. Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:19 LiftoverVcf Writing out sorted records to final VCF. INFO 2024-07-02 12:01:19 LiftoverVcf Writing out sorted records to final VCF. Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:19 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:19 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. Test: Test method testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0)(picard.util.LiftoverVcfTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Gradle suite > Gradle test > picard.util.LiftoverVcfTest.testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0) STANDARD_ERROR INFO 2024-07-02 12:01:20 LiftoverVcf Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverFailingVariants.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN testdata/picard/vcf/LiftOver/test.over.chain -REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta -RECOVER_SWAPPED_REF_ALT true -CREATE_INDEX false ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverFailingVariants.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN testdata/picard/vcf/LiftOver/test.over.chain -REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta -RECOVER_SWAPPED_REF_ALT true -CREATE_INDEX false Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.093 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:20.093 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.093 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:20.093 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.093 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:20.093 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.093 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:20.093 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:20 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverFailingVariants.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/LiftOver/test.over.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf RECOVER_SWAPPED_REF_ALT=true CREATE_INDEX=false REFERENCE_SEQUENCE=testdata/picard/vcf/LiftOver/dummy.reference.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:20 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverFailingVariants.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/LiftOver/test.over.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf RECOVER_SWAPPED_REF_ALT=true CREATE_INDEX=false REFERENCE_SEQUENCE=testdata/picard/vcf/LiftOver/dummy.reference.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Loading up the target reference genome. INFO 2024-07-02 12:01:20 LiftoverVcf Loading up the target reference genome. Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) INFO 2024-07-02 12:01:20 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Processed 3 variants. INFO 2024-07-02 12:01:20 LiftoverVcf Processed 3 variants. Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants failed to liftover. INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants failed to liftover. Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over. INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over. Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf 0.0000% of variants were not successfully lifted over and written to the output. INFO 2024-07-02 12:01:20 LiftoverVcf 0.0000% of variants were not successfully lifted over and written to the output. Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf liftover success by source contig: INFO 2024-07-02 12:01:20 LiftoverVcf liftover success by source contig: Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf chr1: 3 / 3 (100.0000%) INFO 2024-07-02 12:01:20 LiftoverVcf chr1: 3 / 3 (100.0000%) Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf lifted variants by target contig: INFO 2024-07-02 12:01:20 LiftoverVcf lifted variants by target contig: Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf chr1: 3 INFO 2024-07-02 12:01:20 LiftoverVcf chr1: 3 Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf 2 variants were lifted by swapping REF/ALT alleles. INFO 2024-07-02 12:01:20 LiftoverVcf 2 variants were lifted by swapping REF/ALT alleles. Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Writing out sorted records to final VCF. INFO 2024-07-02 12:01:20 LiftoverVcf Writing out sorted records to final VCF. Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:20 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:20 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. Test: Test method testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0)(picard.util.LiftoverVcfTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Gradle suite > Gradle test > picard.util.LiftoverVcfTest.testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0) STANDARD_ERROR INFO 2024-07-02 12:01:20 LiftoverVcf Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN testdata/picard/vcf/LiftOver/test.over.chain -REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta -RECOVER_SWAPPED_REF_ALT true -CREATE_INDEX false ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN testdata/picard/vcf/LiftOver/test.over.chain -REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta -RECOVER_SWAPPED_REF_ALT true -CREATE_INDEX false Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.231 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:20.231 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.231 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:20.231 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.231 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:20.231 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.231 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:20.231 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:20 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/LiftOver/test.over.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf RECOVER_SWAPPED_REF_ALT=true CREATE_INDEX=false REFERENCE_SEQUENCE=testdata/picard/vcf/LiftOver/dummy.reference.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:20 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/LiftOver/test.over.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf RECOVER_SWAPPED_REF_ALT=true CREATE_INDEX=false REFERENCE_SEQUENCE=testdata/picard/vcf/LiftOver/dummy.reference.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Loading up the target reference genome. INFO 2024-07-02 12:01:20 LiftoverVcf Loading up the target reference genome. Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) INFO 2024-07-02 12:01:20 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Processed 4 variants. INFO 2024-07-02 12:01:20 LiftoverVcf Processed 4 variants. Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants failed to liftover. INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants failed to liftover. Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over. INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over. Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf 0.0000% of variants were not successfully lifted over and written to the output. INFO 2024-07-02 12:01:20 LiftoverVcf 0.0000% of variants were not successfully lifted over and written to the output. Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf liftover success by source contig: INFO 2024-07-02 12:01:20 LiftoverVcf liftover success by source contig: Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf chr1: 4 / 4 (100.0000%) INFO 2024-07-02 12:01:20 LiftoverVcf chr1: 4 / 4 (100.0000%) Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf lifted variants by target contig: INFO 2024-07-02 12:01:20 LiftoverVcf lifted variants by target contig: Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf chr1: 4 INFO 2024-07-02 12:01:20 LiftoverVcf chr1: 4 Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants were lifted by swapping REF/ALT alleles. INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants were lifted by swapping REF/ALT alleles. Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Writing out sorted records to final VCF. INFO 2024-07-02 12:01:20 LiftoverVcf Writing out sorted records to final VCF. Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:20 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:20 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. Test: Test method testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0)(picard.util.LiftoverVcfTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Gradle suite > Gradle test > picard.util.LiftoverVcfTest.testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1) STANDARD_ERROR INFO 2024-07-02 12:01:20 LiftoverVcf Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN testdata/picard/vcf/LiftOver/test.over.chain -REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta -RECOVER_SWAPPED_REF_ALT true -CREATE_INDEX false ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN testdata/picard/vcf/LiftOver/test.over.chain -REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta -RECOVER_SWAPPED_REF_ALT true -CREATE_INDEX false Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.302 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:20.302 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.302 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:20.302 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.302 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:20.302 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.302 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:20.302 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:20 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/LiftOver/test.over.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf RECOVER_SWAPPED_REF_ALT=true CREATE_INDEX=false REFERENCE_SEQUENCE=testdata/picard/vcf/LiftOver/dummy.reference.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:20 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/LiftOver/test.over.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf RECOVER_SWAPPED_REF_ALT=true CREATE_INDEX=false REFERENCE_SEQUENCE=testdata/picard/vcf/LiftOver/dummy.reference.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Loading up the target reference genome. INFO 2024-07-02 12:01:20 LiftoverVcf Loading up the target reference genome. Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) INFO 2024-07-02 12:01:20 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Processed 4 variants. INFO 2024-07-02 12:01:20 LiftoverVcf Processed 4 variants. Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants failed to liftover. INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants failed to liftover. Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf 1 variants lifted over but had mismatching reference alleles after lift over. INFO 2024-07-02 12:01:20 LiftoverVcf 1 variants lifted over but had mismatching reference alleles after lift over. Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf 25.0000% of variants were not successfully lifted over and written to the output. INFO 2024-07-02 12:01:20 LiftoverVcf 25.0000% of variants were not successfully lifted over and written to the output. Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf liftover success by source contig: INFO 2024-07-02 12:01:20 LiftoverVcf liftover success by source contig: Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf chr1: 3 / 4 (75.0000%) INFO 2024-07-02 12:01:20 LiftoverVcf chr1: 3 / 4 (75.0000%) Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf lifted variants by target contig: INFO 2024-07-02 12:01:20 LiftoverVcf lifted variants by target contig: Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf chr1: 3 INFO 2024-07-02 12:01:20 LiftoverVcf chr1: 3 Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants were lifted by swapping REF/ALT alleles. INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants were lifted by swapping REF/ALT alleles. Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Writing out sorted records to final VCF. INFO 2024-07-02 12:01:20 LiftoverVcf Writing out sorted records to final VCF. Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:20 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:20 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. Test: Test method testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1)(picard.util.LiftoverVcfTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Gradle suite > Gradle test > picard.util.LiftoverVcfTest.testVcfSorted[0](false) STANDARD_ERROR INFO 2024-07-02 12:01:20 LiftoverVcf Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN testdata/picard/vcf/LiftOver/test.over.chain -REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta -CREATE_INDEX true -DISABLE_SORT false ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN testdata/picard/vcf/LiftOver/test.over.chain -REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta -CREATE_INDEX true -DISABLE_SORT false Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.384 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:20.384 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.384 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:20.384 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.384 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:20.384 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.384 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:20.384 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:20 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/LiftOver/test.over.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf DISABLE_SORT=false CREATE_INDEX=true REFERENCE_SEQUENCE=testdata/picard/vcf/LiftOver/dummy.reference.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false RECOVER_SWAPPED_REF_ALT=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:20 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/LiftOver/test.over.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf DISABLE_SORT=false CREATE_INDEX=true REFERENCE_SEQUENCE=testdata/picard/vcf/LiftOver/dummy.reference.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false RECOVER_SWAPPED_REF_ALT=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Loading up the target reference genome. INFO 2024-07-02 12:01:20 LiftoverVcf Loading up the target reference genome. Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) INFO 2024-07-02 12:01:20 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Processed 5 variants. INFO 2024-07-02 12:01:20 LiftoverVcf Processed 5 variants. Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants failed to liftover. INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants failed to liftover. Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over. INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over. Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf 0.0000% of variants were not successfully lifted over and written to the output. INFO 2024-07-02 12:01:20 LiftoverVcf 0.0000% of variants were not successfully lifted over and written to the output. Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf liftover success by source contig: INFO 2024-07-02 12:01:20 LiftoverVcf liftover success by source contig: Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf chr1: 5 / 5 (100.0000%) INFO 2024-07-02 12:01:20 LiftoverVcf chr1: 5 / 5 (100.0000%) Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf lifted variants by target contig: INFO 2024-07-02 12:01:20 LiftoverVcf lifted variants by target contig: Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf chr1: 5 INFO 2024-07-02 12:01:20 LiftoverVcf chr1: 5 Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: WARNING 2024-07-02 12:01:20 LiftoverVcf 0 variants with a swapped REF/ALT were identified, but were not recovered. See RECOVER_SWAPPED_REF_ALT and associated caveats. WARNING 2024-07-02 12:01:20 LiftoverVcf 0 variants with a swapped REF/ALT were identified, but were not recovered. See RECOVER_SWAPPED_REF_ALT and associated caveats. Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Writing out sorted records to final VCF. INFO 2024-07-02 12:01:20 LiftoverVcf Writing out sorted records to final VCF. Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:20 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:20 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. Test: Test method testVcfSorted[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Gradle suite > Gradle test > picard.util.LiftoverVcfTest.testVcfSorted[1](true) STANDARD_ERROR INFO 2024-07-02 12:01:20 LiftoverVcf Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN testdata/picard/vcf/LiftOver/test.over.chain -REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta -CREATE_INDEX false -DISABLE_SORT true ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN testdata/picard/vcf/LiftOver/test.over.chain -REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta -CREATE_INDEX false -DISABLE_SORT true Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.552 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:20.552 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.552 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:20.552 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.552 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:20.552 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.552 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:20.552 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:20 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/LiftOver/test.over.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf DISABLE_SORT=true CREATE_INDEX=false REFERENCE_SEQUENCE=testdata/picard/vcf/LiftOver/dummy.reference.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false RECOVER_SWAPPED_REF_ALT=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:20 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/LiftOver/test.over.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf DISABLE_SORT=true CREATE_INDEX=false REFERENCE_SEQUENCE=testdata/picard/vcf/LiftOver/dummy.reference.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false RECOVER_SWAPPED_REF_ALT=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Loading up the target reference genome. INFO 2024-07-02 12:01:20 LiftoverVcf Loading up the target reference genome. Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Lifting variants over and writing the output file. Variants will not be sorted. INFO 2024-07-02 12:01:20 LiftoverVcf Lifting variants over and writing the output file. Variants will not be sorted. Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Processed 5 variants. INFO 2024-07-02 12:01:20 LiftoverVcf Processed 5 variants. Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants failed to liftover. INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants failed to liftover. Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over. INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over. Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf 0.0000% of variants were not successfully lifted over and written to the output. INFO 2024-07-02 12:01:20 LiftoverVcf 0.0000% of variants were not successfully lifted over and written to the output. Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf liftover success by source contig: INFO 2024-07-02 12:01:20 LiftoverVcf liftover success by source contig: Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf chr1: 5 / 5 (100.0000%) INFO 2024-07-02 12:01:20 LiftoverVcf chr1: 5 / 5 (100.0000%) Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf lifted variants by target contig: INFO 2024-07-02 12:01:20 LiftoverVcf lifted variants by target contig: Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf chr1: 5 INFO 2024-07-02 12:01:20 LiftoverVcf chr1: 5 Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: WARNING 2024-07-02 12:01:20 LiftoverVcf 0 variants with a swapped REF/ALT were identified, but were not recovered. See RECOVER_SWAPPED_REF_ALT and associated caveats. WARNING 2024-07-02 12:01:20 LiftoverVcf 0 variants with a swapped REF/ALT were identified, but were not recovered. See RECOVER_SWAPPED_REF_ALT and associated caveats. Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:20 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:20 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. Test: Test method testVcfSorted[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Gradle suite > Gradle test > picard.util.LiftoverVcfTest.testWriteOriginalPosition[0](false) STANDARD_ERROR INFO 2024-07-02 12:01:20 LiftoverVcf Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN testdata/picard/vcf/LiftOver/test.over.chain -REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta -CREATE_INDEX false -WRITE_ORIGINAL_POSITION false ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN testdata/picard/vcf/LiftOver/test.over.chain -REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta -CREATE_INDEX false -WRITE_ORIGINAL_POSITION false Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.677 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:20.677 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.689 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:20.689 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.689 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:20.689 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.689 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:20.689 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:20 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/LiftOver/test.over.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf WRITE_ORIGINAL_POSITION=false CREATE_INDEX=false REFERENCE_SEQUENCE=testdata/picard/vcf/LiftOver/dummy.reference.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false RECOVER_SWAPPED_REF_ALT=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:20 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/LiftOver/test.over.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf WRITE_ORIGINAL_POSITION=false CREATE_INDEX=false REFERENCE_SEQUENCE=testdata/picard/vcf/LiftOver/dummy.reference.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false RECOVER_SWAPPED_REF_ALT=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Loading up the target reference genome. INFO 2024-07-02 12:01:20 LiftoverVcf Loading up the target reference genome. Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) INFO 2024-07-02 12:01:20 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Processed 5 variants. INFO 2024-07-02 12:01:20 LiftoverVcf Processed 5 variants. Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants failed to liftover. INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants failed to liftover. Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over. INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over. Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf 0.0000% of variants were not successfully lifted over and written to the output. INFO 2024-07-02 12:01:20 LiftoverVcf 0.0000% of variants were not successfully lifted over and written to the output. Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf liftover success by source contig: INFO 2024-07-02 12:01:20 LiftoverVcf liftover success by source contig: Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf chr1: 5 / 5 (100.0000%) INFO 2024-07-02 12:01:20 LiftoverVcf chr1: 5 / 5 (100.0000%) Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf lifted variants by target contig: INFO 2024-07-02 12:01:20 LiftoverVcf lifted variants by target contig: Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf chr1: 5 INFO 2024-07-02 12:01:20 LiftoverVcf chr1: 5 Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: WARNING 2024-07-02 12:01:20 LiftoverVcf 0 variants with a swapped REF/ALT were identified, but were not recovered. See RECOVER_SWAPPED_REF_ALT and associated caveats. WARNING 2024-07-02 12:01:20 LiftoverVcf 0 variants with a swapped REF/ALT were identified, but were not recovered. See RECOVER_SWAPPED_REF_ALT and associated caveats. Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Writing out sorted records to final VCF. INFO 2024-07-02 12:01:20 LiftoverVcf Writing out sorted records to final VCF. Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:20 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:20 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. Test: Test method testWriteOriginalPosition[0](false)(picard.util.LiftoverVcfTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Gradle suite > Gradle test > picard.util.LiftoverVcfTest.testWriteOriginalPosition[1](true) STANDARD_ERROR INFO 2024-07-02 12:01:20 LiftoverVcf Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN testdata/picard/vcf/LiftOver/test.over.chain -REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta -CREATE_INDEX false -WRITE_ORIGINAL_POSITION true ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN testdata/picard/vcf/LiftOver/test.over.chain -REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta -CREATE_INDEX false -WRITE_ORIGINAL_POSITION true Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.820 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:20.820 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.820 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:20.820 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.820 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:20.820 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.820 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:20.820 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:20 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/LiftOver/test.over.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf WRITE_ORIGINAL_POSITION=true CREATE_INDEX=false REFERENCE_SEQUENCE=testdata/picard/vcf/LiftOver/dummy.reference.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false RECOVER_SWAPPED_REF_ALT=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:20 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/LiftOver/test.over.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf WRITE_ORIGINAL_POSITION=true CREATE_INDEX=false REFERENCE_SEQUENCE=testdata/picard/vcf/LiftOver/dummy.reference.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false RECOVER_SWAPPED_REF_ALT=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Loading up the target reference genome. INFO 2024-07-02 12:01:20 LiftoverVcf Loading up the target reference genome. Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) INFO 2024-07-02 12:01:20 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Processed 5 variants. INFO 2024-07-02 12:01:20 LiftoverVcf Processed 5 variants. Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants failed to liftover. INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants failed to liftover. Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over. INFO 2024-07-02 12:01:20 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over. Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf 0.0000% of variants were not successfully lifted over and written to the output. INFO 2024-07-02 12:01:20 LiftoverVcf 0.0000% of variants were not successfully lifted over and written to the output. Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf liftover success by source contig: INFO 2024-07-02 12:01:20 LiftoverVcf liftover success by source contig: Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf chr1: 5 / 5 (100.0000%) INFO 2024-07-02 12:01:20 LiftoverVcf chr1: 5 / 5 (100.0000%) Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf lifted variants by target contig: INFO 2024-07-02 12:01:20 LiftoverVcf lifted variants by target contig: Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf chr1: 5 INFO 2024-07-02 12:01:20 LiftoverVcf chr1: 5 Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: WARNING 2024-07-02 12:01:20 LiftoverVcf 0 variants with a swapped REF/ALT were identified, but were not recovered. See RECOVER_SWAPPED_REF_ALT and associated caveats. WARNING 2024-07-02 12:01:20 LiftoverVcf 0 variants with a swapped REF/ALT were identified, but were not recovered. See RECOVER_SWAPPED_REF_ALT and associated caveats. Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Writing out sorted records to final VCF. INFO 2024-07-02 12:01:20 LiftoverVcf Writing out sorted records to final VCF. Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:20 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:20 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. Test: Test method testWriteOriginalPosition[1](true)(picard.util.LiftoverVcfTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Gradle suite > Gradle test > picard.util.LiftoverVcfTest.testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain) STANDARD_ERROR INFO 2024-07-02 12:01:20 LiftoverVcf Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/test.two.block.over.chain -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta -RECOVER_SWAPPED_REF_ALT true -CREATE_INDEX false ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/test.two.block.over.chain -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta -RECOVER_SWAPPED_REF_ALT true -CREATE_INDEX false Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.993 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:20.993 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.993 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:20.993 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.993 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:20.993 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:20.993 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:20.993 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:20 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/test.two.block.over.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf RECOVER_SWAPPED_REF_ALT=true CREATE_INDEX=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:20 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/test.two.block.over.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf RECOVER_SWAPPED_REF_ALT=true CREATE_INDEX=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:20 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:20 LiftoverVcf Loading up the target reference genome. INFO 2024-07-02 12:01:20 LiftoverVcf Loading up the target reference genome. Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) INFO 2024-07-02 12:01:21 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf Processed 4 variants. INFO 2024-07-02 12:01:21 LiftoverVcf Processed 4 variants. Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf 0 variants failed to liftover. INFO 2024-07-02 12:01:21 LiftoverVcf 0 variants failed to liftover. Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf 2 variants lifted over but had mismatching reference alleles after lift over. INFO 2024-07-02 12:01:21 LiftoverVcf 2 variants lifted over but had mismatching reference alleles after lift over. Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf 50.0000% of variants were not successfully lifted over and written to the output. INFO 2024-07-02 12:01:21 LiftoverVcf 50.0000% of variants were not successfully lifted over and written to the output. Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf liftover success by source contig: INFO 2024-07-02 12:01:21 LiftoverVcf liftover success by source contig: Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf chr1: 2 / 4 (50.0000%) INFO 2024-07-02 12:01:21 LiftoverVcf chr1: 2 / 4 (50.0000%) Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf lifted variants by target contig: INFO 2024-07-02 12:01:21 LiftoverVcf lifted variants by target contig: Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf chr1: 2 INFO 2024-07-02 12:01:21 LiftoverVcf chr1: 2 Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf 1 variants were lifted by swapping REF/ALT alleles. INFO 2024-07-02 12:01:21 LiftoverVcf 1 variants were lifted by swapping REF/ALT alleles. Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf Writing out sorted records to final VCF. INFO 2024-07-02 12:01:21 LiftoverVcf Writing out sorted records to final VCF. Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:21 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:21 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. Test: Test method testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf Gradle suite > Gradle test > picard.util.LiftoverVcfTest.testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain) STANDARD_ERROR INFO 2024-07-02 12:01:21 LiftoverVcf Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/test.over.chain -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/dummy.reference.fasta -RECOVER_SWAPPED_REF_ALT true -CREATE_INDEX false ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/test.over.chain -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/dummy.reference.fasta -RECOVER_SWAPPED_REF_ALT true -CREATE_INDEX false Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:21.212 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:21.212 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:21.212 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:21.212 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:21.212 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:21.212 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:21.212 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:21.212 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:21 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/test.over.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf RECOVER_SWAPPED_REF_ALT=true CREATE_INDEX=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/dummy.reference.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:21 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/test.over.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf RECOVER_SWAPPED_REF_ALT=true CREATE_INDEX=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/dummy.reference.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf Loading up the target reference genome. INFO 2024-07-02 12:01:21 LiftoverVcf Loading up the target reference genome. Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) INFO 2024-07-02 12:01:21 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf Processed 4 variants. INFO 2024-07-02 12:01:21 LiftoverVcf Processed 4 variants. Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf 0 variants failed to liftover. INFO 2024-07-02 12:01:21 LiftoverVcf 0 variants failed to liftover. Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf 1 variants lifted over but had mismatching reference alleles after lift over. INFO 2024-07-02 12:01:21 LiftoverVcf 1 variants lifted over but had mismatching reference alleles after lift over. Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf 25.0000% of variants were not successfully lifted over and written to the output. INFO 2024-07-02 12:01:21 LiftoverVcf 25.0000% of variants were not successfully lifted over and written to the output. Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf liftover success by source contig: INFO 2024-07-02 12:01:21 LiftoverVcf liftover success by source contig: Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf chr1: 3 / 4 (75.0000%) INFO 2024-07-02 12:01:21 LiftoverVcf chr1: 3 / 4 (75.0000%) Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf lifted variants by target contig: INFO 2024-07-02 12:01:21 LiftoverVcf lifted variants by target contig: Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf chr1: 3 INFO 2024-07-02 12:01:21 LiftoverVcf chr1: 3 Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf 0 variants were lifted by swapping REF/ALT alleles. INFO 2024-07-02 12:01:21 LiftoverVcf 0 variants were lifted by swapping REF/ALT alleles. Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf Writing out sorted records to final VCF. INFO 2024-07-02 12:01:21 LiftoverVcf Writing out sorted records to final VCF. Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:21 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:21 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. Test: Test method testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf Gradle suite > Gradle test > picard.util.LiftoverVcfTest.testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain) STANDARD_ERROR INFO 2024-07-02 12:01:21 LiftoverVcf Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/test.over.chain -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/dummy.reference.fasta -RECOVER_SWAPPED_REF_ALT true -CREATE_INDEX false ********** LiftoverVcf -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf -OUTPUT /tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf -REJECT /tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf -CHAIN /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/test.over.chain -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/dummy.reference.fasta -RECOVER_SWAPPED_REF_ALT true -CREATE_INDEX false Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: ********** ********** Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:21.413 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:21.413 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:21.413 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:21.413 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:21.414 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:21.414 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: 12:01:21.414 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:21.414 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:21 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/test.over.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf RECOVER_SWAPPED_REF_ALT=true CREATE_INDEX=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/dummy.reference.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:21 GMT+14:00 2024] LiftoverVcf INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf OUTPUT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/lift-delete-me.vcf CHAIN=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/test.over.chain REJECT=/tmp/LiftoverVcfsTest9700599110103934936.tmp/reject-delete-me.vcf RECOVER_SWAPPED_REF_ALT=true CREATE_INDEX=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/LiftOver/dummy.reference.fasta WARN_ON_MISSING_CONTIG=false LOG_FAILED_INTERVALS=true WRITE_ORIGINAL_POSITION=false WRITE_ORIGINAL_ALLELES=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false TAGS_TO_REVERSE=[AF] TAGS_TO_DROP=[MAX_AF] DISABLE_SORT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf Loading up the target reference genome. INFO 2024-07-02 12:01:21 LiftoverVcf Loading up the target reference genome. Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) INFO 2024-07-02 12:01:21 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.) Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf Processed 4 variants. INFO 2024-07-02 12:01:21 LiftoverVcf Processed 4 variants. Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf 0 variants failed to liftover. INFO 2024-07-02 12:01:21 LiftoverVcf 0 variants failed to liftover. Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over. INFO 2024-07-02 12:01:21 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over. Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf 0.0000% of variants were not successfully lifted over and written to the output. INFO 2024-07-02 12:01:21 LiftoverVcf 0.0000% of variants were not successfully lifted over and written to the output. Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf liftover success by source contig: INFO 2024-07-02 12:01:21 LiftoverVcf liftover success by source contig: Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf chr1: 4 / 4 (100.0000%) INFO 2024-07-02 12:01:21 LiftoverVcf chr1: 4 / 4 (100.0000%) Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf lifted variants by target contig: INFO 2024-07-02 12:01:21 LiftoverVcf lifted variants by target contig: Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf chr1: 4 INFO 2024-07-02 12:01:21 LiftoverVcf chr1: 4 Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf 0 variants were lifted by swapping REF/ALT alleles. INFO 2024-07-02 12:01:21 LiftoverVcf 0 variants were lifted by swapping REF/ALT alleles. Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: INFO 2024-07-02 12:01:21 LiftoverVcf Writing out sorted records to final VCF. INFO 2024-07-02 12:01:21 LiftoverVcf Writing out sorted records to final VCF. Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: [Tue Jul 02 12:01:21 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:21 GMT+14:00 2024] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes. Test: Test method testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain)(picard.util.LiftoverVcfTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method invalidFilesTest[0](s_1_7.locs)(picard.illumina.parser.readers.LocsFileReaderTest) Running Test: Test method invalidFilesTest[1](s_1_8.locs)(picard.illumina.parser.readers.LocsFileReaderTest) Running Test: Test method invalidFilesTest[2](s_1_9.locs)(picard.illumina.parser.readers.LocsFileReaderTest) Running Test: Test method invalidFilesTest[3](s_1_10.locs)(picard.illumina.parser.readers.LocsFileReaderTest) Running Test: Test method invalidFilesTest[4](s_f2af.locs)(picard.illumina.parser.readers.LocsFileReaderTest) Running Test: Test method passingFileTest(picard.illumina.parser.readers.LocsFileReaderTest) Running Test: Test method invalidFileSizeTests[0](1, 12)(picard.illumina.parser.readers.MMapBackedIteratorFactoryTest) Running Test: Test method invalidFileSizeTests[1](3, 11)(picard.illumina.parser.readers.MMapBackedIteratorFactoryTest) Running Test: Test method negativeHeaderTest(picard.illumina.parser.readers.MMapBackedIteratorFactoryTest) Running Test: Test method onlyHeaderTest(picard.illumina.parser.readers.MMapBackedIteratorFactoryTest) Running Test: Test method testValidConfigurations[0](picard.illumina.parser.readers.MMapBackedIteratorFactoryTest$1@f7753a0)(picard.illumina.parser.readers.MMapBackedIteratorFactoryTest) Running Test: Test method testValidConfigurations[1](picard.illumina.parser.readers.MMapBackedIteratorFactoryTest$2@270e90af)(picard.illumina.parser.readers.MMapBackedIteratorFactoryTest) Running Test: Test method testValidConfigurations[2](picard.illumina.parser.readers.MMapBackedIteratorFactoryTest$3@30d5ca62)(picard.illumina.parser.readers.MMapBackedIteratorFactoryTest) Running Test: Test method tooLargeHeaderTest(picard.illumina.parser.readers.MMapBackedIteratorFactoryTest) Running Test: Test method testFailMultiSampleVcf(picard.vcf.MakeVcfSampleNameMapTest) Test: Test method testFailMultiSampleVcf(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: INFO 2024-07-02 12:01:21 MakeVcfSampleNameMap Gradle suite > Gradle test > picard.vcf.MakeVcfSampleNameMapTest.testFailMultiSampleVcf STANDARD_ERROR INFO 2024-07-02 12:01:21 MakeVcfSampleNameMap Test: Test method testFailMultiSampleVcf(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: Test: Test method testFailMultiSampleVcf(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFailMultiSampleVcf(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: ********** ********** Test: Test method testFailMultiSampleVcf(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFailMultiSampleVcf(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFailMultiSampleVcf(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: ********** ********** Test: Test method testFailMultiSampleVcf(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFailMultiSampleVcf(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: ********** ********** Test: Test method testFailMultiSampleVcf(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: ********** MakeVcfSampleNameMap -I testdata/picard/vcf/mini.vcf -O testdata/picard/vcf/MakeVcfSampleNameMap/not-used ********** MakeVcfSampleNameMap -I testdata/picard/vcf/mini.vcf -O testdata/picard/vcf/MakeVcfSampleNameMap/not-used Test: Test method testFailMultiSampleVcf(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: ********** ********** Test: Test method testFailMultiSampleVcf(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: Test: Test method testFailMultiSampleVcf(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: Test: Test method testFailMultiSampleVcf(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: 12:01:21.602 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:21.602 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFailMultiSampleVcf(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: 12:01:21.602 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:21.602 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFailMultiSampleVcf(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: 12:01:21.603 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:21.603 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFailMultiSampleVcf(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: 12:01:21.603 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:21.603 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFailMultiSampleVcf(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: [Tue Jul 02 12:01:21 GMT+14:00 2024] MakeVcfSampleNameMap INPUT=[testdata/picard/vcf/mini.vcf] OUTPUT=testdata/picard/vcf/MakeVcfSampleNameMap/not-used VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:21 GMT+14:00 2024] MakeVcfSampleNameMap INPUT=[testdata/picard/vcf/mini.vcf] OUTPUT=testdata/picard/vcf/MakeVcfSampleNameMap/not-used VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFailMultiSampleVcf(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: [Tue Jul 02 12:01:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFailMultiSampleVcf(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: [Tue Jul 02 12:01:21 GMT+14:00 2024] picard.vcf.MakeVcfSampleNameMap done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:21 GMT+14:00 2024] picard.vcf.MakeVcfSampleNameMap done. Elapsed time: 0.00 minutes. Test: Test method testFailMultiSampleVcf(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testFailMultiSampleVcf(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMakeMap(picard.vcf.MakeVcfSampleNameMapTest) Test: Test method testMakeMap(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: INFO 2024-07-02 12:01:21 MakeVcfSampleNameMap Gradle suite > Gradle test > picard.vcf.MakeVcfSampleNameMapTest.testMakeMap STANDARD_ERROR INFO 2024-07-02 12:01:21 MakeVcfSampleNameMap Test: Test method testMakeMap(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: Test: Test method testMakeMap(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMakeMap(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: ********** ********** Test: Test method testMakeMap(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMakeMap(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMakeMap(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: ********** ********** Test: Test method testMakeMap(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMakeMap(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: ********** ********** Test: Test method testMakeMap(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: ********** MakeVcfSampleNameMap -I testdata/picard/vcf/MakeVcfSampleNameMap/NA12878.vcf -I testdata/picard/vcf/MakeVcfSampleNameMap/NA12891.vcf -I testdata/picard/vcf/MakeVcfSampleNameMap/NA12892.vcf -O /tmp/MakeMap9222954719717804634test.sample_map ********** MakeVcfSampleNameMap -I testdata/picard/vcf/MakeVcfSampleNameMap/NA12878.vcf -I testdata/picard/vcf/MakeVcfSampleNameMap/NA12891.vcf -I testdata/picard/vcf/MakeVcfSampleNameMap/NA12892.vcf -O /tmp/MakeMap9222954719717804634test.sample_map Test: Test method testMakeMap(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: ********** ********** Test: Test method testMakeMap(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: Test: Test method testMakeMap(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: Test: Test method testMakeMap(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: 12:01:21.627 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:21.627 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMakeMap(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: 12:01:21.627 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:21.627 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMakeMap(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: 12:01:21.627 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:21.627 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMakeMap(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: 12:01:21.628 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:21.628 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMakeMap(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: [Tue Jul 02 12:01:21 GMT+14:00 2024] MakeVcfSampleNameMap INPUT=[testdata/picard/vcf/MakeVcfSampleNameMap/NA12878.vcf, testdata/picard/vcf/MakeVcfSampleNameMap/NA12891.vcf, testdata/picard/vcf/MakeVcfSampleNameMap/NA12892.vcf] OUTPUT=/tmp/MakeMap9222954719717804634test.sample_map VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:21 GMT+14:00 2024] MakeVcfSampleNameMap INPUT=[testdata/picard/vcf/MakeVcfSampleNameMap/NA12878.vcf, testdata/picard/vcf/MakeVcfSampleNameMap/NA12891.vcf, testdata/picard/vcf/MakeVcfSampleNameMap/NA12892.vcf] OUTPUT=/tmp/MakeMap9222954719717804634test.sample_map VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMakeMap(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: [Tue Jul 02 12:01:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMakeMap(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: [Tue Jul 02 12:01:21 GMT+14:00 2024] picard.vcf.MakeVcfSampleNameMap done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:21 GMT+14:00 2024] picard.vcf.MakeVcfSampleNameMap done. Elapsed time: 0.00 minutes. Test: Test method testMakeMap(picard.vcf.MakeVcfSampleNameMapTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method getProbabilityFromLogTest[0]([D@43b624d3, [D@4756c1c0)(picard.util.MathUtilTest) Running Test: Test method getProbabilityFromLogTest[1]([D@79ee6ffa, [D@b8c5ca8)(picard.util.MathUtilTest) Running Test: Test method getProbabilityFromLogTest[2]([D@5cee4df4, [D@56f5682c)(picard.util.MathUtilTest) Running Test: Test method getProbabilityFromLogTest[3]([D@6b229764, [D@458de619)(picard.util.MathUtilTest) Running Test: Test method logMathTest(picard.util.MathUtilTest) Running Test: Test method pNormalizeLogProbabilityTest[0]([D@50fa96d5, [D@7aed0ffd)(picard.util.MathUtilTest) Running Test: Test method pNormalizeLogProbabilityTest[1]([D@2a9e98fa, [D@2e56ef42)(picard.util.MathUtilTest) Running Test: Test method pNormalizeLogProbabilityTest[2]([D@673aad04, [D@39bdb051)(picard.util.MathUtilTest) Running Test: Test method pNormalizeLogProbabilityTest[3]([D@282a5547, [D@1aca8fcb)(picard.util.MathUtilTest) Running Test: Test method pNormalizeLogProbabilityTest[4]([D@2d6c0058, [D@5796e8df)(picard.util.MathUtilTest) Running Test: Test method pNormalizeLogProbabilityTest[5]([D@5b50afb4, [D@16730a46)(picard.util.MathUtilTest) Running Test: Test method testDivide[0]([D@b5b3ab7, [D@55a81967, [D@5b0718ae)(picard.util.MathUtilTest) Running Test: Test method testDivide[1]([D@61b2f831, [D@7444b641, [D@17e5020f)(picard.util.MathUtilTest) Running Test: Test method testDivide[2]([D@2559ce9a, [D@747e92ce, [D@4b341334)(picard.util.MathUtilTest) Running Test: Test method testDivide[3]([D@1526107d, [D@154e18f5, [D@7e8814db)(picard.util.MathUtilTest) Running Test: Test method testDivideDouble[0](15.0, 3.0, 5.0)(picard.util.MathUtilTest) Running Test: Test method testDivideDouble[1](15.0, 0.0, 0.0)(picard.util.MathUtilTest) Running Test: Test method testDivideFail[0]([D@7f8a04ff, [D@4a3ccee3)(picard.util.MathUtilTest) Running Test: Test method testDivideFail[1]([D@4ebabb12, [D@61b8e3c6)(picard.util.MathUtilTest) Running Test: Test method testMaxOfArray[0]([D@1697aa5a, 3.0)(picard.util.MathUtilTest) Running Test: Test method testMaxOfArray[1]([D@2bee8509, 3.0)(picard.util.MathUtilTest) Running Test: Test method testMaxOfArray[2]([D@367fb770, 3.0)(picard.util.MathUtilTest) Running Test: Test method testMaxOfArray[3]([D@13ffa93f, 3.0)(picard.util.MathUtilTest) Running Test: Test method testMaxOfByteArray[0]([B@4d2b1dba, 1)(picard.util.MathUtilTest) Running Test: Test method testMaxOfByteArray[1]([B@5ab75b08, 1)(picard.util.MathUtilTest) Running Test: Test method testMaxOfByteArray[2]([B@6e90274e, 1)(picard.util.MathUtilTest) Running Test: Test method testMaxOfByteArray[3]([B@47ee00ea, 1)(picard.util.MathUtilTest) Running Test: Test method testMaxWithArrayAndScalar[0]([D@4a1083de, 2.0, [D@665db3c1)(picard.util.MathUtilTest) Running Test: Test method testMaxWithArrayAndScalar[1]([D@5f8b08ef, 2.0, [D@114b7eb3)(picard.util.MathUtilTest) Running Test: Test method testMaxWithArrayAndScalar[2]([D@53fc2796, 2.0, [D@54379176)(picard.util.MathUtilTest) Running Test: Test method testMaxWithArrayAndScalar[3]([D@1ce56099, 2.0, [D@2e972404)(picard.util.MathUtilTest) Running Test: Test method testMaxWithArrayAndScalar[4]([D@461d1117, 2.0, [D@714b50e5)(picard.util.MathUtilTest) Running Test: Test method testMinOfArray[0]([D@3d976234, 1.0)(picard.util.MathUtilTest) Running Test: Test method testMinOfArray[1]([D@38cbffd0, 1.0)(picard.util.MathUtilTest) Running Test: Test method testMinOfArray[2]([D@7f7a440, 1.0)(picard.util.MathUtilTest) Running Test: Test method testMinOfArray[3]([D@11b18c6c, 1.0)(picard.util.MathUtilTest) Running Test: Test method testMinOfIntArray[0]([I@159339f9, 1)(picard.util.MathUtilTest) Running Test: Test method testMinOfIntArray[1]([I@609719df, 1)(picard.util.MathUtilTest) Running Test: Test method testMinOfIntArray[2]([I@21996343, 1)(picard.util.MathUtilTest) Running Test: Test method testMinOfIntArray[3]([I@453bdb05, 1)(picard.util.MathUtilTest) Running Test: Test method testMinOfShortArray[0]([S@4c27627a, 1)(picard.util.MathUtilTest) Running Test: Test method testMinOfShortArray[1]([S@19afd5ce, 1)(picard.util.MathUtilTest) Running Test: Test method testMinOfShortArray[2]([S@3c842516, 1)(picard.util.MathUtilTest) Running Test: Test method testMinOfShortArray[3]([S@6722bfc2, 1)(picard.util.MathUtilTest) Running Test: Test method testMinWithArrayAndScalar[0]([D@c778021, 2.0, [D@2cce1b1d)(picard.util.MathUtilTest) Running Test: Test method testMinWithArrayAndScalar[1]([D@7ade1744, 2.0, [D@4a98f6b6)(picard.util.MathUtilTest) Running Test: Test method testMinWithArrayAndScalar[2]([D@4b00b21d, 2.0, [D@416ef80e)(picard.util.MathUtilTest) Running Test: Test method testMinWithArrayAndScalar[3]([D@4acac203, 2.0, [D@494011d)(picard.util.MathUtilTest) Running Test: Test method testMinWithArrayAndScalar[4]([D@a243298, 2.0, [D@16e22305)(picard.util.MathUtilTest) Running Test: Test method testRandomSublist(picard.util.MathUtilTest) Running Test: Test method testSeqGeneration[0](0.0, 5.0, 1.0, [D@4a26475d)(picard.util.MathUtilTest) Running Test: Test method testSeqGeneration[1](0.0, 0.5, 0.1, [D@24bc889c)(picard.util.MathUtilTest) Running Test: Test method testSeqGeneration[2](0.0, 0.5, 0.11, [D@660c5d5b)(picard.util.MathUtilTest) Running Test: Test method testSeqGeneration[3](50.0, 55.0, 1.25, [D@3b0e85a6)(picard.util.MathUtilTest) Running Test: Test method testSeqGeneration[4](10.0, 0.0, 2.0, [D@2f941c05)(picard.util.MathUtilTest) Running Test: Test method testSeqGeneration[5](10.0, 0.0, -2.0, [D@60c794ce)(picard.util.MathUtilTest) Running Test: Test method testSubtractMax[0]([D@7787368f, [D@62ed10)(picard.util.MathUtilTest) Running Test: Test method testSubtractMax[1]([D@47f5236d, [D@9884652)(picard.util.MathUtilTest) Running Test: Test method testSubtractMax[2]([D@392ce522, [D@57ac4721)(picard.util.MathUtilTest) Running Test: Test method testSubtractMax[3]([D@2bffe715, [D@75a402bd)(picard.util.MathUtilTest) Running Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:21 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1) STANDARD_ERROR INFO 2024-07-02 12:01:21 MergeBamAlignment Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.9887445413360564071.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.18037592730395086011.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.singleAlignmentFirstEndincludeSecondary18203171066705448606.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS true ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.9887445413360564071.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.18037592730395086011.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.singleAlignmentFirstEndincludeSecondary18203171066705448606.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS true Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:21.920 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:21.920 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:21.920 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:21.920 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:21.920 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:21.920 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:21.920 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:21.920 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:21 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.9887445413360564071.sam ALIGNED_BAM=[/tmp/aligned.18037592730395086011.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleAlignmentFirstEndincludeSecondary18203171066705448606.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:21 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.9887445413360564071.sam ALIGNED_BAM=[/tmp/aligned.18037592730395086011.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleAlignmentFirstEndincludeSecondary18203171066705448606.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:21 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:21 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.18037592730395086011.sam] INFO 2024-07-02 12:01:21 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.18037592730395086011.sam] Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:21 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:21 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:21 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:21 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:21 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:21 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:21 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:21 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:21 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:21 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:21 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:21 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:21 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:21 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:21 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:21 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:21 AbstractAlignmentMerger Wrote 1 alignment records and 1 unmapped reads. INFO 2024-07-02 12:01:21 AbstractAlignmentMerger Wrote 1 alignment records and 1 unmapped reads. Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:21 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:21 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:22 MergeBamAlignment INFO 2024-07-02 12:01:22 MergeBamAlignment Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.13572750419854061565.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.1325639468935982923.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.singleAlignmentFirstEndexcludeSecondary9978599403301622441.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS false ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.13572750419854061565.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.1325639468935982923.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.singleAlignmentFirstEndexcludeSecondary9978599403301622441.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS false Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:22.111 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:22.111 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:22.111 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:22.111 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:22.111 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:22.111 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:22.111 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:22.111 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:22 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.13572750419854061565.sam ALIGNED_BAM=[/tmp/aligned.1325639468935982923.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleAlignmentFirstEndexcludeSecondary9978599403301622441.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:22 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.13572750419854061565.sam ALIGNED_BAM=[/tmp/aligned.1325639468935982923.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleAlignmentFirstEndexcludeSecondary9978599403301622441.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:22 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.1325639468935982923.sam] INFO 2024-07-02 12:01:22 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.1325639468935982923.sam] Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:22 AbstractAlignmentMerger Wrote 1 alignment records and 1 unmapped reads. INFO 2024-07-02 12:01:22 AbstractAlignmentMerger Wrote 1 alignment records and 1 unmapped reads. Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:22 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:22 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@61353678, [I@34517109, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:22 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12) STANDARD_ERROR INFO 2024-07-02 12:01:22 MergeBamAlignment Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.12662172094306168212.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.1254518071599744584.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.singleAlignmentSecondEndincludeSecondary1580247679728919693.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS true ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.12662172094306168212.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.1254518071599744584.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.singleAlignmentSecondEndincludeSecondary1580247679728919693.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS true Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:22.399 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:22.399 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:22.400 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:22.400 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:22.400 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:22.400 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:22.400 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:22.400 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:22 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.12662172094306168212.sam ALIGNED_BAM=[/tmp/aligned.1254518071599744584.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleAlignmentSecondEndincludeSecondary1580247679728919693.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:22 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.12662172094306168212.sam ALIGNED_BAM=[/tmp/aligned.1254518071599744584.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleAlignmentSecondEndincludeSecondary1580247679728919693.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:22 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.1254518071599744584.sam] INFO 2024-07-02 12:01:22 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.1254518071599744584.sam] Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:22 AbstractAlignmentMerger Wrote 1 alignment records and 1 unmapped reads. INFO 2024-07-02 12:01:22 AbstractAlignmentMerger Wrote 1 alignment records and 1 unmapped reads. Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:22 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:22 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:22 MergeBamAlignment INFO 2024-07-02 12:01:22 MergeBamAlignment Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.16868053931238048628.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.18326444959284400369.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.singleAlignmentSecondEndexcludeSecondary6605117654482346738.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS false ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.16868053931238048628.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.18326444959284400369.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.singleAlignmentSecondEndexcludeSecondary6605117654482346738.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS false Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:22.746 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:22.746 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:22.746 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:22.746 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:22.746 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:22.746 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:22.746 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:22.746 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:22 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.16868053931238048628.sam ALIGNED_BAM=[/tmp/aligned.18326444959284400369.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleAlignmentSecondEndexcludeSecondary6605117654482346738.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:22 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.16868053931238048628.sam ALIGNED_BAM=[/tmp/aligned.18326444959284400369.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleAlignmentSecondEndexcludeSecondary6605117654482346738.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:22 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.18326444959284400369.sam] INFO 2024-07-02 12:01:22 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.18326444959284400369.sam] Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:22 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:22 AbstractAlignmentMerger Wrote 1 alignment records and 1 unmapped reads. INFO 2024-07-02 12:01:22 AbstractAlignmentMerger Wrote 1 alignment records and 1 unmapped reads. Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:22 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:22 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@3f848a22, [I@18a5b933, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:22 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12) STANDARD_ERROR INFO 2024-07-02 12:01:22 MergeBamAlignment Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.11547622155968367237.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.7757776989992607887.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.singleAlignmentBothEndincludeSecondary6342323889720744761.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS true ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.11547622155968367237.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.7757776989992607887.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.singleAlignmentBothEndincludeSecondary6342323889720744761.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS true Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:22.998 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:22.998 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:22.998 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:22.998 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:22.998 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:22.998 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:22.998 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:22.998 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:22 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.11547622155968367237.sam ALIGNED_BAM=[/tmp/aligned.7757776989992607887.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleAlignmentBothEndincludeSecondary6342323889720744761.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:22 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.11547622155968367237.sam ALIGNED_BAM=[/tmp/aligned.7757776989992607887.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleAlignmentBothEndincludeSecondary6342323889720744761.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:22 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:22 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.7757776989992607887.sam] INFO 2024-07-02 12:01:22 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.7757776989992607887.sam] Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:23 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:23 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:23 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:23 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:23 MergeBamAlignment INFO 2024-07-02 12:01:23 MergeBamAlignment Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.13575532286361210519.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.6657642073412449657.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.singleAlignmentBothEndexcludeSecondary17985462905078725317.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS false ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.13575532286361210519.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.6657642073412449657.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.singleAlignmentBothEndexcludeSecondary17985462905078725317.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS false Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.210 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:23.210 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.210 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:23.210 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.210 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:23.210 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.210 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:23.210 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:23 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.13575532286361210519.sam ALIGNED_BAM=[/tmp/aligned.6657642073412449657.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleAlignmentBothEndexcludeSecondary17985462905078725317.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:23 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.13575532286361210519.sam ALIGNED_BAM=[/tmp/aligned.6657642073412449657.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleAlignmentBothEndexcludeSecondary17985462905078725317.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:23 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.6657642073412449657.sam] INFO 2024-07-02 12:01:23 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.6657642073412449657.sam] Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:23 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:23 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:23 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:23 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@1313c4fc, [I@2c54ff67, 13, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:23 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14) STANDARD_ERROR INFO 2024-07-02 12:01:23 MergeBamAlignment Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.18218594054333731636.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.226139991109406787.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.multipleBothEnds1includeSecondary5619681953924509674.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS true ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.18218594054333731636.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.226139991109406787.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.multipleBothEnds1includeSecondary5619681953924509674.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS true Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.311 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:23.311 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.311 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:23.311 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.312 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:23.312 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.312 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:23.312 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:23 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.18218594054333731636.sam ALIGNED_BAM=[/tmp/aligned.226139991109406787.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleBothEnds1includeSecondary5619681953924509674.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:23 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.18218594054333731636.sam ALIGNED_BAM=[/tmp/aligned.226139991109406787.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleBothEnds1includeSecondary5619681953924509674.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:23 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.226139991109406787.sam] INFO 2024-07-02 12:01:23 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.226139991109406787.sam] Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:23 AbstractAlignmentMerger Wrote 10 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:23 AbstractAlignmentMerger Wrote 10 alignment records and 0 unmapped reads. Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:23 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:23 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:23 MergeBamAlignment INFO 2024-07-02 12:01:23 MergeBamAlignment Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.1022457813206966843.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.5200758028835363362.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.multipleBothEnds1excludeSecondary15940171012808704174.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS false ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.1022457813206966843.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.5200758028835363362.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.multipleBothEnds1excludeSecondary15940171012808704174.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS false Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.395 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:23.395 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.395 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:23.395 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.396 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:23.396 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.396 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:23.396 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:23 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.1022457813206966843.sam ALIGNED_BAM=[/tmp/aligned.5200758028835363362.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleBothEnds1excludeSecondary15940171012808704174.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:23 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.1022457813206966843.sam ALIGNED_BAM=[/tmp/aligned.5200758028835363362.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleBothEnds1excludeSecondary15940171012808704174.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:23 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.5200758028835363362.sam] INFO 2024-07-02 12:01:23 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.5200758028835363362.sam] Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:23 AbstractAlignmentMerger Wrote 10 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:23 AbstractAlignmentMerger Wrote 10 alignment records and 0 unmapped reads. Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:23 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:23 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@1b405ed, [I@792ddb46, 11, 14)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:23 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255) STANDARD_ERROR INFO 2024-07-02 12:01:23 MergeBamAlignment Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.1808671810851999531.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.5898979996816177698.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.multipleBothEnds2includeSecondary7885277809150043329.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS true ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.1808671810851999531.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.5898979996816177698.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.multipleBothEnds2includeSecondary7885277809150043329.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS true Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.532 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:23.532 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.532 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:23.532 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.532 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:23.532 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.532 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:23.532 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:23 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.1808671810851999531.sam ALIGNED_BAM=[/tmp/aligned.5898979996816177698.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleBothEnds2includeSecondary7885277809150043329.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:23 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.1808671810851999531.sam ALIGNED_BAM=[/tmp/aligned.5898979996816177698.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleBothEnds2includeSecondary7885277809150043329.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:23 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.5898979996816177698.sam] INFO 2024-07-02 12:01:23 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.5898979996816177698.sam] Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:23 AbstractAlignmentMerger Wrote 5 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:23 AbstractAlignmentMerger Wrote 5 alignment records and 0 unmapped reads. Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:23 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:23 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:23 MergeBamAlignment INFO 2024-07-02 12:01:23 MergeBamAlignment Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.10814169557875943205.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.3517934108872626974.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.multipleBothEnds2excludeSecondary12828677945910068107.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS false ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.10814169557875943205.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.3517934108872626974.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.multipleBothEnds2excludeSecondary12828677945910068107.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS false Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.622 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:23.622 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.622 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:23.622 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.622 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:23.622 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.622 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:23.622 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:23 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.10814169557875943205.sam ALIGNED_BAM=[/tmp/aligned.3517934108872626974.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleBothEnds2excludeSecondary12828677945910068107.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:23 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.10814169557875943205.sam ALIGNED_BAM=[/tmp/aligned.3517934108872626974.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleBothEnds2excludeSecondary12828677945910068107.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:23 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.3517934108872626974.sam] INFO 2024-07-02 12:01:23 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.3517934108872626974.sam] Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:23 AbstractAlignmentMerger Wrote 5 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:23 AbstractAlignmentMerger Wrote 5 alignment records and 0 unmapped reads. Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:23 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:23 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@32f9b4b0, [I@5b52a702, 255, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:23 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1) STANDARD_ERROR INFO 2024-07-02 12:01:23 MergeBamAlignment Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.1026440113428908481.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.4985348900862898855.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.multipleFirstEndincludeSecondary3053392485733642854.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS true ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.1026440113428908481.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.4985348900862898855.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.multipleFirstEndincludeSecondary3053392485733642854.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS true Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.735 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:23.735 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.735 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:23.735 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.745 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:23.745 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.745 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:23.745 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:23 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.1026440113428908481.sam ALIGNED_BAM=[/tmp/aligned.4985348900862898855.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleFirstEndincludeSecondary3053392485733642854.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:23 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.1026440113428908481.sam ALIGNED_BAM=[/tmp/aligned.4985348900862898855.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleFirstEndincludeSecondary3053392485733642854.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:23 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.4985348900862898855.sam] INFO 2024-07-02 12:01:23 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.4985348900862898855.sam] Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:23 AbstractAlignmentMerger Wrote 5 alignment records and 1 unmapped reads. INFO 2024-07-02 12:01:23 AbstractAlignmentMerger Wrote 5 alignment records and 1 unmapped reads. Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:23 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:23 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:23 MergeBamAlignment INFO 2024-07-02 12:01:23 MergeBamAlignment Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.4119833175583889152.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.11059301624435857371.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.multipleFirstEndexcludeSecondary6214173575427793917.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS false ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.4119833175583889152.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.11059301624435857371.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.multipleFirstEndexcludeSecondary6214173575427793917.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS false Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.873 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:23.873 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.873 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:23.873 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.874 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:23.874 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.874 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:23.874 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:23 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.4119833175583889152.sam ALIGNED_BAM=[/tmp/aligned.11059301624435857371.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleFirstEndexcludeSecondary6214173575427793917.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:23 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.4119833175583889152.sam ALIGNED_BAM=[/tmp/aligned.11059301624435857371.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleFirstEndexcludeSecondary6214173575427793917.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:23 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.11059301624435857371.sam] INFO 2024-07-02 12:01:23 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.11059301624435857371.sam] Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:23 AbstractAlignmentMerger Wrote 5 alignment records and 1 unmapped reads. INFO 2024-07-02 12:01:23 AbstractAlignmentMerger Wrote 5 alignment records and 1 unmapped reads. Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:23 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:23 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@161766b, [I@1011aab0, 12, -1)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:23 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12) STANDARD_ERROR INFO 2024-07-02 12:01:23 MergeBamAlignment Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.9639941421454486532.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.17049196605773834466.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.multipleSecondEndincludeSecondary12534929936198949244.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS true ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.9639941421454486532.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.17049196605773834466.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.multipleSecondEndincludeSecondary12534929936198949244.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS true Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.989 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:23.989 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.990 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:23.990 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.990 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:23.990 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:23.990 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:23.990 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:23 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.9639941421454486532.sam ALIGNED_BAM=[/tmp/aligned.17049196605773834466.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleSecondEndincludeSecondary12534929936198949244.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:23 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.9639941421454486532.sam ALIGNED_BAM=[/tmp/aligned.17049196605773834466.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleSecondEndincludeSecondary12534929936198949244.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:23 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:23 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.17049196605773834466.sam] INFO 2024-07-02 12:01:23 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.17049196605773834466.sam] Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:23 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:24 AbstractAlignmentMerger Wrote 5 alignment records and 1 unmapped reads. INFO 2024-07-02 12:01:24 AbstractAlignmentMerger Wrote 5 alignment records and 1 unmapped reads. Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:24 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:24 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:24 MergeBamAlignment INFO 2024-07-02 12:01:24 MergeBamAlignment Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.17511607983879448879.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.449301860613685555.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.multipleSecondEndexcludeSecondary9149109736984745674.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS false ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.17511607983879448879.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.449301860613685555.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.multipleSecondEndexcludeSecondary9149109736984745674.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS false Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:24.158 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:24.158 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:24.158 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:24.158 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:24.158 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:24.158 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:24.158 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:24.158 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:24 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.17511607983879448879.sam ALIGNED_BAM=[/tmp/aligned.449301860613685555.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleSecondEndexcludeSecondary9149109736984745674.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:24 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.17511607983879448879.sam ALIGNED_BAM=[/tmp/aligned.449301860613685555.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleSecondEndexcludeSecondary9149109736984745674.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:24 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.449301860613685555.sam] INFO 2024-07-02 12:01:24 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.449301860613685555.sam] Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:24 AbstractAlignmentMerger Wrote 5 alignment records and 1 unmapped reads. INFO 2024-07-02 12:01:24 AbstractAlignmentMerger Wrote 5 alignment records and 1 unmapped reads. Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:24 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:24 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@2d896020, [I@e638b6, -1, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:24 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255) STANDARD_ERROR INFO 2024-07-02 12:01:24 MergeBamAlignment Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.15685202648205628218.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.6391580677506202423.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.multipleFirstEndSingleSecondEndincludeSecondary7195468915400564447.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS true ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.15685202648205628218.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.6391580677506202423.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.multipleFirstEndSingleSecondEndincludeSecondary7195468915400564447.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS true Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:24.450 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:24.450 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:24.450 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:24.450 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:24.450 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:24.450 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:24.450 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:24.450 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:24 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.15685202648205628218.sam ALIGNED_BAM=[/tmp/aligned.6391580677506202423.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleFirstEndSingleSecondEndincludeSecondary7195468915400564447.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:24 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.15685202648205628218.sam ALIGNED_BAM=[/tmp/aligned.6391580677506202423.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleFirstEndSingleSecondEndincludeSecondary7195468915400564447.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:24 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.6391580677506202423.sam] INFO 2024-07-02 12:01:24 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.6391580677506202423.sam] Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:24 AbstractAlignmentMerger Wrote 6 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:24 AbstractAlignmentMerger Wrote 6 alignment records and 0 unmapped reads. Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:24 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:24 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:24 MergeBamAlignment INFO 2024-07-02 12:01:24 MergeBamAlignment Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.18052744184098787820.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.7903210734530049105.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.multipleFirstEndSingleSecondEndexcludeSecondary12455239074307255082.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS false ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.18052744184098787820.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.7903210734530049105.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.multipleFirstEndSingleSecondEndexcludeSecondary12455239074307255082.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS false Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:24.704 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:24.704 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:24.704 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:24.704 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:24.704 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:24.704 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:24.704 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:24.704 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:24 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.18052744184098787820.sam ALIGNED_BAM=[/tmp/aligned.7903210734530049105.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleFirstEndSingleSecondEndexcludeSecondary12455239074307255082.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:24 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.18052744184098787820.sam ALIGNED_BAM=[/tmp/aligned.7903210734530049105.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleFirstEndSingleSecondEndexcludeSecondary12455239074307255082.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:24 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.7903210734530049105.sam] INFO 2024-07-02 12:01:24 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.7903210734530049105.sam] Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:24 AbstractAlignmentMerger Wrote 6 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:24 AbstractAlignmentMerger Wrote 6 alignment records and 0 unmapped reads. Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:24 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:24 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@191eac87, [I@6ede7d8b, 12, 255)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:24 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12) STANDARD_ERROR INFO 2024-07-02 12:01:24 MergeBamAlignment Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.8645948185320895802.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.479970502810016142.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.singleFirstEndMultipleSecondEndincludeSecondary9039779776504124445.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS true ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.8645948185320895802.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.479970502810016142.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.singleFirstEndMultipleSecondEndincludeSecondary9039779776504124445.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS true Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:24.833 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:24.833 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:24.833 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:24.833 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:24.834 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:24.834 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:24.834 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:24.834 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:24 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.8645948185320895802.sam ALIGNED_BAM=[/tmp/aligned.479970502810016142.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleFirstEndMultipleSecondEndincludeSecondary9039779776504124445.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:24 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.8645948185320895802.sam ALIGNED_BAM=[/tmp/aligned.479970502810016142.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleFirstEndMultipleSecondEndincludeSecondary9039779776504124445.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:24 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:24 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.479970502810016142.sam] INFO 2024-07-02 12:01:24 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.479970502810016142.sam] Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:24 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:24 AbstractAlignmentMerger Wrote 6 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:24 AbstractAlignmentMerger Wrote 6 alignment records and 0 unmapped reads. Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:24 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:24 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:25 MergeBamAlignment INFO 2024-07-02 12:01:25 MergeBamAlignment Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.14267083672107807165.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.15598301869347243997.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.singleFirstEndMultipleSecondEndexcludeSecondary16604049969920065894.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS false ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.14267083672107807165.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.15598301869347243997.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testBestFragmentMapqStrategy.singleFirstEndMultipleSecondEndexcludeSecondary16604049969920065894.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY BestEndMapq -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS false Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:25.082 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:25.082 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:25.082 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:25.082 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:25.082 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:25.082 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:25.082 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:25.082 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:25 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.14267083672107807165.sam ALIGNED_BAM=[/tmp/aligned.15598301869347243997.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleFirstEndMultipleSecondEndexcludeSecondary16604049969920065894.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:25 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.14267083672107807165.sam ALIGNED_BAM=[/tmp/aligned.15598301869347243997.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleFirstEndMultipleSecondEndexcludeSecondary16604049969920065894.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:25 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.15598301869347243997.sam] INFO 2024-07-02 12:01:25 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.15598301869347243997.sam] Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:25 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:25 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:25 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:25 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:25 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:25 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:25 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:25 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:25 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:25 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:25 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:25 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:25 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:25 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:25 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:25 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:25 AbstractAlignmentMerger Wrote 6 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:25 AbstractAlignmentMerger Wrote 6 alignment records and 0 unmapped reads. Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:25 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:25 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@5f582d6d, [I@28a3173c, 0, 12)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:25 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam) STANDARD_ERROR INFO 2024-07-02 12:01:25 MergeBamAlignment Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta -OUTPUT /tmp/merged7604136097501859916.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS true -UNMAPPED_READ_STRATEGY DO_NOT_CHANGE -SORT_ORDER coordinate ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta -OUTPUT /tmp/merged7604136097501859916.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS true -UNMAPPED_READ_STRATEGY DO_NOT_CHANGE -SORT_ORDER coordinate Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:25.199 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:25.199 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:25.199 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:25.199 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:25.199 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:25.199 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:25.199 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:25.199 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:25 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam] OUTPUT=/tmp/merged7604136097501859916.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] SORT_ORDER=coordinate UNMAP_CONTAMINANT_READS=true UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:25 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam] OUTPUT=/tmp/merged7604136097501859916.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] SORT_ORDER=coordinate UNMAP_CONTAMINANT_READS=true UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:25 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam] INFO 2024-07-02 12:01:25 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam] Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:25 AbstractAlignmentMerger Wrote 4 alignment records and 11 unmapped reads. INFO 2024-07-02 12:01:25 AbstractAlignmentMerger Wrote 4 alignment records and 11 unmapped reads. Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:25 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:25 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:25 ValidateSamFile INFO 2024-07-02 12:01:25 ValidateSamFile Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ValidateSamFile -I /tmp/merged7604136097501859916.sam ********** ValidateSamFile -I /tmp/merged7604136097501859916.sam Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:25.464 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:25.464 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:25.464 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:25.464 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:25.481 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:25.481 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:25.481 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:25.481 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:25 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged7604136097501859916.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:25 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged7604136097501859916.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:25 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:25 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam) STANDARD_OUT No errors found Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:25 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam) STANDARD_ERROR [Tue Jul 02 12:01:25 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testContaminationDetection[1](DO_NOT_CHANGE_INVALID, contam.expected.NO_CHANGE_INVALID.sam)(picard.sam.MergeBamAlignmentTest) Test: Test method testContaminationDetection[1](DO_NOT_CHANGE_INVALID, contam.expected.NO_CHANGE_INVALID.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:25 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testContaminationDetection[1](DO_NOT_CHANGE_INVALID, contam.expected.NO_CHANGE_INVALID.sam) STANDARD_ERROR INFO 2024-07-02 12:01:25 MergeBamAlignment Test: Test method testContaminationDetection[1](DO_NOT_CHANGE_INVALID, contam.expected.NO_CHANGE_INVALID.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testContaminationDetection[1](DO_NOT_CHANGE_INVALID, contam.expected.NO_CHANGE_INVALID.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testContaminationDetection[1](DO_NOT_CHANGE_INVALID, contam.expected.NO_CHANGE_INVALID.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[1](DO_NOT_CHANGE_INVALID, contam.expected.NO_CHANGE_INVALID.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testContaminationDetection[1](DO_NOT_CHANGE_INVALID, contam.expected.NO_CHANGE_INVALID.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testContaminationDetection[1](DO_NOT_CHANGE_INVALID, contam.expected.NO_CHANGE_INVALID.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[1](DO_NOT_CHANGE_INVALID, contam.expected.NO_CHANGE_INVALID.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testContaminationDetection[1](DO_NOT_CHANGE_INVALID, contam.expected.NO_CHANGE_INVALID.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[1](DO_NOT_CHANGE_INVALID, contam.expected.NO_CHANGE_INVALID.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta -OUTPUT /tmp/merged5315297644011861591.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS true -UNMAPPED_READ_STRATEGY DO_NOT_CHANGE_INVALID -SORT_ORDER coordinate ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta -OUTPUT /tmp/merged5315297644011861591.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS true -UNMAPPED_READ_STRATEGY DO_NOT_CHANGE_INVALID -SORT_ORDER coordinate Test: Test method testContaminationDetection[1](DO_NOT_CHANGE_INVALID, contam.expected.NO_CHANGE_INVALID.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[1](DO_NOT_CHANGE_INVALID, contam.expected.NO_CHANGE_INVALID.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testContaminationDetection[1](DO_NOT_CHANGE_INVALID, contam.expected.NO_CHANGE_INVALID.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testContaminationDetection[1](DO_NOT_CHANGE_INVALID, contam.expected.NO_CHANGE_INVALID.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:25.645 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:25.645 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testContaminationDetection[1](DO_NOT_CHANGE_INVALID, contam.expected.NO_CHANGE_INVALID.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:25.653 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:25.653 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testContaminationDetection[1](DO_NOT_CHANGE_INVALID, contam.expected.NO_CHANGE_INVALID.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:25.653 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:25.653 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testContaminationDetection[1](DO_NOT_CHANGE_INVALID, contam.expected.NO_CHANGE_INVALID.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:25.653 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:25.653 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testContaminationDetection[1](DO_NOT_CHANGE_INVALID, contam.expected.NO_CHANGE_INVALID.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:25 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam] OUTPUT=/tmp/merged5315297644011861591.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] SORT_ORDER=coordinate UNMAP_CONTAMINANT_READS=true UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE_INVALID REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:25 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam] OUTPUT=/tmp/merged5315297644011861591.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] SORT_ORDER=coordinate UNMAP_CONTAMINANT_READS=true UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE_INVALID REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testContaminationDetection[1](DO_NOT_CHANGE_INVALID, contam.expected.NO_CHANGE_INVALID.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testContaminationDetection[1](DO_NOT_CHANGE_INVALID, contam.expected.NO_CHANGE_INVALID.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:25 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam] INFO 2024-07-02 12:01:25 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam] Test: Test method testContaminationDetection[1](DO_NOT_CHANGE_INVALID, contam.expected.NO_CHANGE_INVALID.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:25 AbstractAlignmentMerger Wrote 4 alignment records and 11 unmapped reads. INFO 2024-07-02 12:01:25 AbstractAlignmentMerger Wrote 4 alignment records and 11 unmapped reads. Test: Test method testContaminationDetection[1](DO_NOT_CHANGE_INVALID, contam.expected.NO_CHANGE_INVALID.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:25 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:25 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testContaminationDetection[1](DO_NOT_CHANGE_INVALID, contam.expected.NO_CHANGE_INVALID.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:25 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam) STANDARD_ERROR INFO 2024-07-02 12:01:25 MergeBamAlignment Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta -OUTPUT /tmp/merged6834066998155445419.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS true -SORT_ORDER coordinate ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta -OUTPUT /tmp/merged6834066998155445419.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS true -SORT_ORDER coordinate Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:25.811 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:25.811 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:25.811 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:25.811 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:25.812 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:25.812 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:25.812 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:25.812 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:25 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam] OUTPUT=/tmp/merged6834066998155445419.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] SORT_ORDER=coordinate UNMAP_CONTAMINANT_READS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:25 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam] OUTPUT=/tmp/merged6834066998155445419.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] SORT_ORDER=coordinate UNMAP_CONTAMINANT_READS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:25 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam] INFO 2024-07-02 12:01:25 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam] Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:25 AbstractAlignmentMerger Wrote 4 alignment records and 11 unmapped reads. INFO 2024-07-02 12:01:25 AbstractAlignmentMerger Wrote 4 alignment records and 11 unmapped reads. Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:25 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:25 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:25 ValidateSamFile INFO 2024-07-02 12:01:25 ValidateSamFile Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ValidateSamFile -I /tmp/merged6834066998155445419.sam ********** ValidateSamFile -I /tmp/merged6834066998155445419.sam Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:25.939 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:25.939 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:25.939 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:25.939 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:25.940 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:25.940 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:25.940 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:25.940 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:25 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged6834066998155445419.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:25 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged6834066998155445419.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:25 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:25 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:25 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam) STANDARD_OUT No errors found Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:25 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam) STANDARD_ERROR [Tue Jul 02 12:01:25 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:26 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam) STANDARD_ERROR INFO 2024-07-02 12:01:26 MergeBamAlignment Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta -OUTPUT /tmp/merged6808306645071574674.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS true -UNMAPPED_READ_STRATEGY COPY_TO_TAG -SORT_ORDER coordinate ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta -OUTPUT /tmp/merged6808306645071574674.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS true -UNMAPPED_READ_STRATEGY COPY_TO_TAG -SORT_ORDER coordinate Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:26.051 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:26.051 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:26.051 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:26.051 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:26.052 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:26.052 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:26.052 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:26.052 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:26 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam] OUTPUT=/tmp/merged6808306645071574674.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] SORT_ORDER=coordinate UNMAP_CONTAMINANT_READS=true UNMAPPED_READ_STRATEGY=COPY_TO_TAG REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:26 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam] OUTPUT=/tmp/merged6808306645071574674.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] SORT_ORDER=coordinate UNMAP_CONTAMINANT_READS=true UNMAPPED_READ_STRATEGY=COPY_TO_TAG REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:26 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam] INFO 2024-07-02 12:01:26 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam] Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:26 AbstractAlignmentMerger Wrote 4 alignment records and 11 unmapped reads. INFO 2024-07-02 12:01:26 AbstractAlignmentMerger Wrote 4 alignment records and 11 unmapped reads. Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:26 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:26 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:26 ValidateSamFile INFO 2024-07-02 12:01:26 ValidateSamFile Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ValidateSamFile -I /tmp/merged6808306645071574674.sam ********** ValidateSamFile -I /tmp/merged6808306645071574674.sam Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:26.211 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:26.211 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:26.211 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:26.211 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:26.212 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:26.212 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:26.212 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:26.212 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:26 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged6808306645071574674.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:26 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged6808306645071574674.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:26 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:26 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam) STANDARD_OUT No errors found Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:26 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam) STANDARD_ERROR [Tue Jul 02 12:01:26 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:26 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam) STANDARD_ERROR INFO 2024-07-02 12:01:26 MergeBamAlignment Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta -OUTPUT /tmp/merged18305715574211747334.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS true -UNMAPPED_READ_STRATEGY MOVE_TO_TAG -SORT_ORDER coordinate ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta -OUTPUT /tmp/merged18305715574211747334.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS true -UNMAPPED_READ_STRATEGY MOVE_TO_TAG -SORT_ORDER coordinate Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:26.379 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:26.379 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:26.379 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:26.379 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:26.379 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:26.379 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:26.379 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:26.379 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:26 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam] OUTPUT=/tmp/merged18305715574211747334.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] SORT_ORDER=coordinate UNMAP_CONTAMINANT_READS=true UNMAPPED_READ_STRATEGY=MOVE_TO_TAG REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:26 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam] OUTPUT=/tmp/merged18305715574211747334.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] SORT_ORDER=coordinate UNMAP_CONTAMINANT_READS=true UNMAPPED_READ_STRATEGY=MOVE_TO_TAG REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:26 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam] INFO 2024-07-02 12:01:26 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam] Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:26 AbstractAlignmentMerger Wrote 4 alignment records and 11 unmapped reads. INFO 2024-07-02 12:01:26 AbstractAlignmentMerger Wrote 4 alignment records and 11 unmapped reads. Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:26 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:26 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:26 ValidateSamFile INFO 2024-07-02 12:01:26 ValidateSamFile Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ValidateSamFile -I /tmp/merged18305715574211747334.sam ********** ValidateSamFile -I /tmp/merged18305715574211747334.sam Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:26.594 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:26.594 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:26.594 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:26.594 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:26.594 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:26.594 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:26.594 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:26.594 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:26 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged18305715574211747334.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:26 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged18305715574211747334.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:26 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:26 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam) STANDARD_OUT No errors found Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:26 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam) STANDARD_ERROR [Tue Jul 02 12:01:26 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:26 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc) STANDARD_ERROR INFO 2024-07-02 12:01:26 MergeBamAlignment Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.18177322548993257812.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.6176000061819544716.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/simpleForward4206977226865161863.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY EarliestFragment -ATTRIBUTES_TO_RETAIN YB -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS false ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.18177322548993257812.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.6176000061819544716.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/simpleForward4206977226865161863.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY EarliestFragment -ATTRIBUTES_TO_RETAIN YB -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS false Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:26.811 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:26.811 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:26.812 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:26.812 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:26.812 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:26.812 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:26.812 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:26.812 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:26 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.18177322548993257812.sam ALIGNED_BAM=[/tmp/aligned.6176000061819544716.sam] OUTPUT=/tmp/simpleForward4206977226865161863.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:26 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.18177322548993257812.sam ALIGNED_BAM=[/tmp/aligned.6176000061819544716.sam] OUTPUT=/tmp/simpleForward4206977226865161863.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:26 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:26 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.6176000061819544716.sam] INFO 2024-07-02 12:01:26 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.6176000061819544716.sam] Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:26 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:26 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:26 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:26 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:26 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:26 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:26 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:26 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:26 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:26 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:26 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:26 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:26 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:26 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:26 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:26 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:26 AbstractAlignmentMerger Wrote 1 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:26 AbstractAlignmentMerger Wrote 1 alignment records and 0 unmapped reads. Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:26 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:26 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@30fbf9cc)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:27 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b) STANDARD_ERROR INFO 2024-07-02 12:01:27 MergeBamAlignment Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.9889010913014736615.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.7510146706912301759.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/simpleReverse309569327311380308.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY EarliestFragment -ATTRIBUTES_TO_RETAIN YB -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS false ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.9889010913014736615.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.7510146706912301759.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/simpleReverse309569327311380308.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY EarliestFragment -ATTRIBUTES_TO_RETAIN YB -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS false Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:27.014 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:27.014 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:27.014 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:27.014 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:27.014 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:27.014 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:27.014 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:27.014 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:27 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.9889010913014736615.sam ALIGNED_BAM=[/tmp/aligned.7510146706912301759.sam] OUTPUT=/tmp/simpleReverse309569327311380308.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:27 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.9889010913014736615.sam ALIGNED_BAM=[/tmp/aligned.7510146706912301759.sam] OUTPUT=/tmp/simpleReverse309569327311380308.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:27 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.7510146706912301759.sam] INFO 2024-07-02 12:01:27 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.7510146706912301759.sam] Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:27 AbstractAlignmentMerger Wrote 1 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:27 AbstractAlignmentMerger Wrote 1 alignment records and 0 unmapped reads. Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:27 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:27 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@77e2522b)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:27 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd) STANDARD_ERROR INFO 2024-07-02 12:01:27 MergeBamAlignment Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.17235643698950661671.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.20416800630375869.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/2 forward one earlier7530435553087922059.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY EarliestFragment -ATTRIBUTES_TO_RETAIN YB -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS false ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.17235643698950661671.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.20416800630375869.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/2 forward one earlier7530435553087922059.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY EarliestFragment -ATTRIBUTES_TO_RETAIN YB -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS false Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:27.144 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:27.144 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:27.144 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:27.144 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:27.144 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:27.144 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:27.144 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:27.144 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:27 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.17235643698950661671.sam ALIGNED_BAM=[/tmp/aligned.20416800630375869.sam] OUTPUT=/tmp/2 forward one earlier7530435553087922059.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:27 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.17235643698950661671.sam ALIGNED_BAM=[/tmp/aligned.20416800630375869.sam] OUTPUT=/tmp/2 forward one earlier7530435553087922059.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:27 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.20416800630375869.sam] INFO 2024-07-02 12:01:27 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.20416800630375869.sam] Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:27 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:27 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:27 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:27 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@17deadfd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:27 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd) STANDARD_ERROR INFO 2024-07-02 12:01:27 MergeBamAlignment Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.516150770506609473.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.10679186344273079856.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/forward earlier than reverse2529709917020855658.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY EarliestFragment -ATTRIBUTES_TO_RETAIN YB -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS false ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.516150770506609473.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.10679186344273079856.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/forward earlier than reverse2529709917020855658.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY EarliestFragment -ATTRIBUTES_TO_RETAIN YB -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS false Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:27.387 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:27.387 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:27.387 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:27.387 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:27.387 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:27.387 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:27.387 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:27.387 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:27 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.516150770506609473.sam ALIGNED_BAM=[/tmp/aligned.10679186344273079856.sam] OUTPUT=/tmp/forward earlier than reverse2529709917020855658.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:27 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.516150770506609473.sam ALIGNED_BAM=[/tmp/aligned.10679186344273079856.sam] OUTPUT=/tmp/forward earlier than reverse2529709917020855658.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:27 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.10679186344273079856.sam] INFO 2024-07-02 12:01:27 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.10679186344273079856.sam] Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:27 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:27 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:27 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:27 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@260996bd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:27 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd) STANDARD_ERROR INFO 2024-07-02 12:01:27 MergeBamAlignment Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.460049935574159041.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.13754734102773402203.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/reverse earlier than forward10568015182023095803.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY EarliestFragment -ATTRIBUTES_TO_RETAIN YB -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS false ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.460049935574159041.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.13754734102773402203.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/reverse earlier than forward10568015182023095803.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY EarliestFragment -ATTRIBUTES_TO_RETAIN YB -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS false Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:27.555 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:27.555 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:27.555 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:27.555 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:27.555 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:27.555 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:27.555 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:27.555 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:27 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.460049935574159041.sam ALIGNED_BAM=[/tmp/aligned.13754734102773402203.sam] OUTPUT=/tmp/reverse earlier than forward10568015182023095803.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:27 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.460049935574159041.sam ALIGNED_BAM=[/tmp/aligned.13754734102773402203.sam] OUTPUT=/tmp/reverse earlier than forward10568015182023095803.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:27 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.13754734102773402203.sam] INFO 2024-07-02 12:01:27 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.13754734102773402203.sam] Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:27 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:27 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:27 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:27 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1892a1fd)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:27 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2) STANDARD_ERROR INFO 2024-07-02 12:01:27 MergeBamAlignment Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.5362028660510819081.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.9097755859414114999.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/tie resolved via MAPQ1491014889534212292.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY EarliestFragment -ATTRIBUTES_TO_RETAIN YB -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS false ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.5362028660510819081.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.9097755859414114999.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/tie resolved via MAPQ1491014889534212292.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY EarliestFragment -ATTRIBUTES_TO_RETAIN YB -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS false Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:27.738 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:27.738 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:27.738 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:27.738 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:27.739 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:27.739 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:27.739 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:27.739 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:27 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.5362028660510819081.sam ALIGNED_BAM=[/tmp/aligned.9097755859414114999.sam] OUTPUT=/tmp/tie resolved via MAPQ1491014889534212292.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:27 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.5362028660510819081.sam ALIGNED_BAM=[/tmp/aligned.9097755859414114999.sam] OUTPUT=/tmp/tie resolved via MAPQ1491014889534212292.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:27 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.9097755859414114999.sam] INFO 2024-07-02 12:01:27 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.9097755859414114999.sam] Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:27 AbstractAlignmentMerger Wrote 4 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:27 AbstractAlignmentMerger Wrote 4 alignment records and 0 unmapped reads. Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:27 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:27 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@422ea6c2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:27 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57) STANDARD_ERROR INFO 2024-07-02 12:01:27 MergeBamAlignment Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.15935812833767829624.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.11920071948387273763.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/tie with same MAPQ resolved arbitrarily8981946803345435505.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY EarliestFragment -ATTRIBUTES_TO_RETAIN YB -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS false ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.15935812833767829624.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.11920071948387273763.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/tie with same MAPQ resolved arbitrarily8981946803345435505.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY EarliestFragment -ATTRIBUTES_TO_RETAIN YB -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS false Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:27.925 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:27.925 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:27.925 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:27.925 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:27.925 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:27.925 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:27.925 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:27.925 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:27 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.15935812833767829624.sam ALIGNED_BAM=[/tmp/aligned.11920071948387273763.sam] OUTPUT=/tmp/tie with same MAPQ resolved arbitrarily8981946803345435505.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:27 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.15935812833767829624.sam ALIGNED_BAM=[/tmp/aligned.11920071948387273763.sam] OUTPUT=/tmp/tie with same MAPQ resolved arbitrarily8981946803345435505.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:27 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:27 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.11920071948387273763.sam] INFO 2024-07-02 12:01:27 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.11920071948387273763.sam] Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:27 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:27 AbstractAlignmentMerger Wrote 4 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:27 AbstractAlignmentMerger Wrote 4 alignment records and 0 unmapped reads. Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:27 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:27 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5333cb57)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:28 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2) STANDARD_ERROR INFO 2024-07-02 12:01:28 MergeBamAlignment Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.15914096785489528699.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.2274232104443828428.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/one cigar with deletion and higher MAPQ10840785031593025597.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY EarliestFragment -ATTRIBUTES_TO_RETAIN YB -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS false ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.15914096785489528699.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.2274232104443828428.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/one cigar with deletion and higher MAPQ10840785031593025597.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY EarliestFragment -ATTRIBUTES_TO_RETAIN YB -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS false Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:28.115 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:28.115 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:28.115 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:28.115 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:28.116 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:28.116 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:28.116 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:28.116 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:28 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.15914096785489528699.sam ALIGNED_BAM=[/tmp/aligned.2274232104443828428.sam] OUTPUT=/tmp/one cigar with deletion and higher MAPQ10840785031593025597.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:28 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.15914096785489528699.sam ALIGNED_BAM=[/tmp/aligned.2274232104443828428.sam] OUTPUT=/tmp/one cigar with deletion and higher MAPQ10840785031593025597.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:28 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.2274232104443828428.sam] INFO 2024-07-02 12:01:28 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.2274232104443828428.sam] Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:28 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:28 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:28 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:28 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@237236a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:28 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489) STANDARD_ERROR INFO 2024-07-02 12:01:28 MergeBamAlignment Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.11286339663551979832.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.13633760160695987996.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/one cigar with deletion and lower MAPQ9703211778593968080.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY EarliestFragment -ATTRIBUTES_TO_RETAIN YB -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS false ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.11286339663551979832.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.13633760160695987996.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/one cigar with deletion and lower MAPQ9703211778593968080.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY EarliestFragment -ATTRIBUTES_TO_RETAIN YB -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS false Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:28.340 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:28.340 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:28.340 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:28.340 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:28.340 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:28.340 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:28.340 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:28.340 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:28 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.11286339663551979832.sam ALIGNED_BAM=[/tmp/aligned.13633760160695987996.sam] OUTPUT=/tmp/one cigar with deletion and lower MAPQ9703211778593968080.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:28 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.11286339663551979832.sam ALIGNED_BAM=[/tmp/aligned.13633760160695987996.sam] OUTPUT=/tmp/one cigar with deletion and lower MAPQ9703211778593968080.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:28 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.13633760160695987996.sam] INFO 2024-07-02 12:01:28 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.13633760160695987996.sam] Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:28 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:28 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:28 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:28 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ec7d489)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:28 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77) STANDARD_ERROR INFO 2024-07-02 12:01:28 MergeBamAlignment Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.11117723643806692102.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.6426506285261079472.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/Insertion makes alignment later2692101243683270599.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY EarliestFragment -ATTRIBUTES_TO_RETAIN YB -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS false ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.11117723643806692102.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.6426506285261079472.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/Insertion makes alignment later2692101243683270599.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY EarliestFragment -ATTRIBUTES_TO_RETAIN YB -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS false Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:28.494 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:28.494 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:28.494 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:28.494 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:28.495 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:28.495 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:28.495 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:28.495 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:28 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.11117723643806692102.sam ALIGNED_BAM=[/tmp/aligned.6426506285261079472.sam] OUTPUT=/tmp/Insertion makes alignment later2692101243683270599.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:28 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.11117723643806692102.sam ALIGNED_BAM=[/tmp/aligned.6426506285261079472.sam] OUTPUT=/tmp/Insertion makes alignment later2692101243683270599.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:28 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.6426506285261079472.sam] INFO 2024-07-02 12:01:28 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.6426506285261079472.sam] Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:28 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:28 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:28 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:28 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1352ba77)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:28 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d) STANDARD_ERROR INFO 2024-07-02 12:01:28 MergeBamAlignment Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.3732089653585125418.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.5310304781828364589.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/one cigar with deletion and higher MAPQ -- reverse5818123466903064840.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY EarliestFragment -ATTRIBUTES_TO_RETAIN YB -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS false ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.3732089653585125418.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.5310304781828364589.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/one cigar with deletion and higher MAPQ -- reverse5818123466903064840.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY EarliestFragment -ATTRIBUTES_TO_RETAIN YB -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS false Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:28.726 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:28.726 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:28.726 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:28.726 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:28.726 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:28.726 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:28.726 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:28.726 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:28 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.3732089653585125418.sam ALIGNED_BAM=[/tmp/aligned.5310304781828364589.sam] OUTPUT=/tmp/one cigar with deletion and higher MAPQ -- reverse5818123466903064840.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:28 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.3732089653585125418.sam ALIGNED_BAM=[/tmp/aligned.5310304781828364589.sam] OUTPUT=/tmp/one cigar with deletion and higher MAPQ -- reverse5818123466903064840.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:28 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.5310304781828364589.sam] INFO 2024-07-02 12:01:28 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.5310304781828364589.sam] Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:28 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:28 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:28 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:28 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@34188d3d)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:28 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2) STANDARD_ERROR INFO 2024-07-02 12:01:28 MergeBamAlignment Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.3160639714158713935.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.13584776571251183553.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/one cigar with deletion and lower MAPQ -- reverse14558349973391132116.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY EarliestFragment -ATTRIBUTES_TO_RETAIN YB -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS false ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.3160639714158713935.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.13584776571251183553.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/one cigar with deletion and lower MAPQ -- reverse14558349973391132116.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY EarliestFragment -ATTRIBUTES_TO_RETAIN YB -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS false Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:28.862 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:28.862 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:28.862 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:28.862 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:28.863 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:28.863 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:28.863 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:28.863 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:28 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.3160639714158713935.sam ALIGNED_BAM=[/tmp/aligned.13584776571251183553.sam] OUTPUT=/tmp/one cigar with deletion and lower MAPQ -- reverse14558349973391132116.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:28 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.3160639714158713935.sam ALIGNED_BAM=[/tmp/aligned.13584776571251183553.sam] OUTPUT=/tmp/one cigar with deletion and lower MAPQ -- reverse14558349973391132116.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:28 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:28 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.13584776571251183553.sam] INFO 2024-07-02 12:01:28 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.13584776571251183553.sam] Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:28 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:29 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:29 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:29 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:29 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@fbe44d2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:29 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4) STANDARD_ERROR INFO 2024-07-02 12:01:29 MergeBamAlignment Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.15880143694745846100.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.16918752792651328828.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/Insertion makes alignment later -- reverse11778618504847163304.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY EarliestFragment -ATTRIBUTES_TO_RETAIN YB -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS false ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.15880143694745846100.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.16918752792651328828.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/Insertion makes alignment later -- reverse11778618504847163304.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY EarliestFragment -ATTRIBUTES_TO_RETAIN YB -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS false Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.108 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:29.108 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.108 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:29.108 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.108 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:29.108 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.108 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:29.108 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:29 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.15880143694745846100.sam ALIGNED_BAM=[/tmp/aligned.16918752792651328828.sam] OUTPUT=/tmp/Insertion makes alignment later -- reverse11778618504847163304.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:29 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.15880143694745846100.sam ALIGNED_BAM=[/tmp/aligned.16918752792651328828.sam] OUTPUT=/tmp/Insertion makes alignment later -- reverse11778618504847163304.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:29 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.16918752792651328828.sam] INFO 2024-07-02 12:01:29 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.16918752792651328828.sam] Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:29 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:29 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:29 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:29 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:29 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:29 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:29 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:29 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:29 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:29 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:29 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:29 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:29 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:29 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:29 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2024-07-02 12:01:29 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:29 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:29 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:29 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:29 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@14a70a4)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testEarliestFragmentStrategyPaired(picard.sam.MergeBamAlignmentTest) Test: Test method testEarliestFragmentStrategyPaired(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:29 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testEarliestFragmentStrategyPaired STANDARD_ERROR INFO 2024-07-02 12:01:29 MergeBamAlignment Test: Test method testEarliestFragmentStrategyPaired(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategyPaired(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testEarliestFragmentStrategyPaired(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategyPaired(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testEarliestFragmentStrategyPaired(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testEarliestFragmentStrategyPaired(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategyPaired(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testEarliestFragmentStrategyPaired(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategyPaired(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.11591416070122411595.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.4426225640786768598.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/mergeTest9651163665050360566.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY EarliestFragment -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.11591416070122411595.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.4426225640786768598.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/mergeTest9651163665050360566.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY EarliestFragment -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testEarliestFragmentStrategyPaired(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testEarliestFragmentStrategyPaired(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategyPaired(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testEarliestFragmentStrategyPaired(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.243 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:29.243 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEarliestFragmentStrategyPaired(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.243 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:29.243 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEarliestFragmentStrategyPaired(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.244 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:29.244 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testEarliestFragmentStrategyPaired(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.244 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:29.244 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testEarliestFragmentStrategyPaired(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:29 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.11591416070122411595.sam ALIGNED_BAM=[/tmp/aligned.4426225640786768598.sam] OUTPUT=/tmp/mergeTest9651163665050360566.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:29 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.11591416070122411595.sam ALIGNED_BAM=[/tmp/aligned.4426225640786768598.sam] OUTPUT=/tmp/mergeTest9651163665050360566.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testEarliestFragmentStrategyPaired(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testEarliestFragmentStrategyPaired(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:29 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.4426225640786768598.sam] INFO 2024-07-02 12:01:29 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.4426225640786768598.sam] Test: Test method testEarliestFragmentStrategyPaired(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:29 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:29 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testEarliestFragmentStrategyPaired(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testEarliestFragmentStrategyPaired(picard.sam.MergeBamAlignmentTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:29 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8) STANDARD_ERROR INFO 2024-07-02 12:01:29 MergeBamAlignment Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.1907513063001640234.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN false -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.4560020123405886015.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.1907513063001640234.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN false -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.4560020123405886015.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.323 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:29.323 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.323 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:29.323 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.324 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:29.324 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.324 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:29.324 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:29 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam ALIGNED_BAM=[/tmp/aligned.1907513063001640234.sam] OUTPUT=/tmp/merged.4560020123405886015.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=false CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:29 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam ALIGNED_BAM=[/tmp/aligned.1907513063001640234.sam] OUTPUT=/tmp/merged.4560020123405886015.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=false CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:29 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.1907513063001640234.sam] INFO 2024-07-02 12:01:29 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.1907513063001640234.sam] Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:29 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:29 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:29 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:29 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:29 ValidateSamFile INFO 2024-07-02 12:01:29 ValidateSamFile Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ValidateSamFile -I /tmp/merged.4560020123405886015.sam ********** ValidateSamFile -I /tmp/merged.4560020123405886015.sam Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.413 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:29.413 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.413 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:29.413 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.413 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:29.413 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.413 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:29.413 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:29 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.4560020123405886015.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:29 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.4560020123405886015.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:29 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:29 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8) STANDARD_OUT No errors found Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:29 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8) STANDARD_ERROR [Tue Jul 02 12:01:29 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1cee3d53, picard.sam.MergeBamAlignmentTest$HitSpec@484239aa, picard.sam.MergeBamAlignmentTest$HitSpec@1628f3a6], -1, 2, 8)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:29 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11) STANDARD_ERROR INFO 2024-07-02 12:01:29 MergeBamAlignment Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.10202399062964926877.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN false -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.12617460827366154037.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.10202399062964926877.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN false -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.12617460827366154037.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.487 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:29.487 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.487 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:29.487 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.487 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:29.487 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.487 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:29.487 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:29 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam ALIGNED_BAM=[/tmp/aligned.10202399062964926877.sam] OUTPUT=/tmp/merged.12617460827366154037.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=false CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:29 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam ALIGNED_BAM=[/tmp/aligned.10202399062964926877.sam] OUTPUT=/tmp/merged.12617460827366154037.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=false CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:29 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.10202399062964926877.sam] INFO 2024-07-02 12:01:29 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.10202399062964926877.sam] Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:29 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:29 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:29 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:29 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:29 ValidateSamFile INFO 2024-07-02 12:01:29 ValidateSamFile Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ValidateSamFile -I /tmp/merged.12617460827366154037.sam ********** ValidateSamFile -I /tmp/merged.12617460827366154037.sam Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.595 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:29.595 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.595 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:29.595 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.595 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:29.595 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.595 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:29.595 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:29 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.12617460827366154037.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:29 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.12617460827366154037.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:29 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:29 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11) STANDARD_OUT No errors found Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:29 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11) STANDARD_ERROR [Tue Jul 02 12:01:29 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6fc47b69, picard.sam.MergeBamAlignmentTest$HitSpec@171a3bc4, picard.sam.MergeBamAlignmentTest$HitSpec@652f4746], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:29 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11) STANDARD_ERROR INFO 2024-07-02 12:01:29 MergeBamAlignment Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.10197838041025513957.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN false -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.1336386216569215742.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.10197838041025513957.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN false -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.1336386216569215742.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.711 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:29.711 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.711 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:29.711 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.712 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:29.712 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.712 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:29.712 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:29 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam ALIGNED_BAM=[/tmp/aligned.10197838041025513957.sam] OUTPUT=/tmp/merged.1336386216569215742.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=false CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:29 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam ALIGNED_BAM=[/tmp/aligned.10197838041025513957.sam] OUTPUT=/tmp/merged.1336386216569215742.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=false CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:29 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.10197838041025513957.sam] INFO 2024-07-02 12:01:29 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.10197838041025513957.sam] Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:29 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:29 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:29 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:29 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:29 ValidateSamFile INFO 2024-07-02 12:01:29 ValidateSamFile Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ValidateSamFile -I /tmp/merged.1336386216569215742.sam ********** ValidateSamFile -I /tmp/merged.1336386216569215742.sam Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.866 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:29.866 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.866 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:29.866 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.866 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:29.866 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.866 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:29.866 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:29 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.1336386216569215742.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:29 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.1336386216569215742.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:29 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:29 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:29 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11) STANDARD_OUT No errors found Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:29 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11) STANDARD_ERROR [Tue Jul 02 12:01:29 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@23ce00f2, picard.sam.MergeBamAlignmentTest$HitSpec@3b4ecb5, picard.sam.MergeBamAlignmentTest$HitSpec@d8c0347], -1, 2, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:29 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9) STANDARD_ERROR INFO 2024-07-02 12:01:29 MergeBamAlignment Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.15687228491152758144.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN false -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.376280226427555802.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.15687228491152758144.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN false -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.376280226427555802.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:29.988 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:29.988 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.001 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:30.001 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.002 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:30.002 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.002 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:30.002 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:30 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam ALIGNED_BAM=[/tmp/aligned.15687228491152758144.sam] OUTPUT=/tmp/merged.376280226427555802.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=false CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:30 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam ALIGNED_BAM=[/tmp/aligned.15687228491152758144.sam] OUTPUT=/tmp/merged.376280226427555802.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=false CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:30 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.15687228491152758144.sam] INFO 2024-07-02 12:01:30 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.15687228491152758144.sam] Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:30 AbstractAlignmentMerger Wrote 1 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:30 AbstractAlignmentMerger Wrote 1 alignment records and 0 unmapped reads. Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:30 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:30 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:30 ValidateSamFile INFO 2024-07-02 12:01:30 ValidateSamFile Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ValidateSamFile -I /tmp/merged.376280226427555802.sam ********** ValidateSamFile -I /tmp/merged.376280226427555802.sam Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.135 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:30.135 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.135 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:30.135 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.135 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:30.135 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.135 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:30.135 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:30 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.376280226427555802.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:30 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.376280226427555802.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:30 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:30 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9) STANDARD_OUT No errors found Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:30 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9) STANDARD_ERROR [Tue Jul 02 12:01:30 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@287e5895, picard.sam.MergeBamAlignmentTest$HitSpec@338eb4d3, picard.sam.MergeBamAlignmentTest$HitSpec@7c73b319], -1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:30 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0) STANDARD_ERROR INFO 2024-07-02 12:01:30 MergeBamAlignment Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.4646152802635599034.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN false -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.9235914248121477525.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.4646152802635599034.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN false -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.9235914248121477525.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.263 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:30.263 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.263 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:30.263 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.263 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:30.263 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.263 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:30.263 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:30 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam ALIGNED_BAM=[/tmp/aligned.4646152802635599034.sam] OUTPUT=/tmp/merged.9235914248121477525.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=false CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:30 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam ALIGNED_BAM=[/tmp/aligned.4646152802635599034.sam] OUTPUT=/tmp/merged.9235914248121477525.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=false CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:30 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.4646152802635599034.sam] INFO 2024-07-02 12:01:30 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.4646152802635599034.sam] Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:30 AbstractAlignmentMerger Wrote 0 alignment records and 1 unmapped reads. INFO 2024-07-02 12:01:30 AbstractAlignmentMerger Wrote 0 alignment records and 1 unmapped reads. Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:30 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:30 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:30 ValidateSamFile INFO 2024-07-02 12:01:30 ValidateSamFile Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ValidateSamFile -I /tmp/merged.9235914248121477525.sam ********** ValidateSamFile -I /tmp/merged.9235914248121477525.sam Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.396 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:30.396 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.396 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:30.396 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.397 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:30.397 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.405 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:30.405 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:30 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.9235914248121477525.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:30 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.9235914248121477525.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:30 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:30 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0) STANDARD_OUT No errors found Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:30 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0) STANDARD_ERROR [Tue Jul 02 12:01:30 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@6c5069c4, picard.sam.MergeBamAlignmentTest$HitSpec@454a9bd5, picard.sam.MergeBamAlignmentTest$HitSpec@7cf7167d], null, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testHeaderFromMappedBreaks[0](specialHeader.aligned.breaks.length.sam)(picard.sam.MergeBamAlignmentTest) Test: Test method testHeaderFromMappedBreaks[0](specialHeader.aligned.breaks.length.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:30 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testHeaderFromMappedBreaks[0](specialHeader.aligned.breaks.length.sam) STANDARD_ERROR INFO 2024-07-02 12:01:30 MergeBamAlignment Test: Test method testHeaderFromMappedBreaks[0](specialHeader.aligned.breaks.length.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testHeaderFromMappedBreaks[0](specialHeader.aligned.breaks.length.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testHeaderFromMappedBreaks[0](specialHeader.aligned.breaks.length.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testHeaderFromMappedBreaks[0](specialHeader.aligned.breaks.length.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testHeaderFromMappedBreaks[0](specialHeader.aligned.breaks.length.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testHeaderFromMappedBreaks[0](specialHeader.aligned.breaks.length.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testHeaderFromMappedBreaks[0](specialHeader.aligned.breaks.length.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testHeaderFromMappedBreaks[0](specialHeader.aligned.breaks.length.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testHeaderFromMappedBreaks[0](specialHeader.aligned.breaks.length.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.breaks.length.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.fasta -OUTPUT /tmp/merged9446436263780028650.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS true ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.breaks.length.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.fasta -OUTPUT /tmp/merged9446436263780028650.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS true Test: Test method testHeaderFromMappedBreaks[0](specialHeader.aligned.breaks.length.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testHeaderFromMappedBreaks[0](specialHeader.aligned.breaks.length.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testHeaderFromMappedBreaks[0](specialHeader.aligned.breaks.length.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testHeaderFromMappedBreaks[0](specialHeader.aligned.breaks.length.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.505 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:30.505 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testHeaderFromMappedBreaks[0](specialHeader.aligned.breaks.length.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.513 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:30.513 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testHeaderFromMappedBreaks[0](specialHeader.aligned.breaks.length.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.513 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:30.513 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testHeaderFromMappedBreaks[0](specialHeader.aligned.breaks.length.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.513 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:30.513 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testHeaderFromMappedBreaks[0](specialHeader.aligned.breaks.length.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:30 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.breaks.length.sam] OUTPUT=/tmp/merged9446436263780028650.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] UNMAP_CONTAMINANT_READS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:30 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.breaks.length.sam] OUTPUT=/tmp/merged9446436263780028650.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] UNMAP_CONTAMINANT_READS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testHeaderFromMappedBreaks[0](specialHeader.aligned.breaks.length.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testHeaderFromMappedBreaks[0](specialHeader.aligned.breaks.length.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:30 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.breaks.length.sam] INFO 2024-07-02 12:01:30 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.breaks.length.sam] Test: Test method testHeaderFromMappedBreaks[0](specialHeader.aligned.breaks.length.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:30 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:30 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testHeaderFromMappedBreaks[0](specialHeader.aligned.breaks.length.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testHeaderFromMappedBreaks[0](specialHeader.aligned.breaks.length.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testHeaderFromMappedBreaks[1](specialHeader.aligned.breaks.md5.sam)(picard.sam.MergeBamAlignmentTest) Test: Test method testHeaderFromMappedBreaks[1](specialHeader.aligned.breaks.md5.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:30 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testHeaderFromMappedBreaks[1](specialHeader.aligned.breaks.md5.sam) STANDARD_ERROR INFO 2024-07-02 12:01:30 MergeBamAlignment Test: Test method testHeaderFromMappedBreaks[1](specialHeader.aligned.breaks.md5.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testHeaderFromMappedBreaks[1](specialHeader.aligned.breaks.md5.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testHeaderFromMappedBreaks[1](specialHeader.aligned.breaks.md5.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testHeaderFromMappedBreaks[1](specialHeader.aligned.breaks.md5.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testHeaderFromMappedBreaks[1](specialHeader.aligned.breaks.md5.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testHeaderFromMappedBreaks[1](specialHeader.aligned.breaks.md5.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testHeaderFromMappedBreaks[1](specialHeader.aligned.breaks.md5.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testHeaderFromMappedBreaks[1](specialHeader.aligned.breaks.md5.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testHeaderFromMappedBreaks[1](specialHeader.aligned.breaks.md5.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.breaks.md5.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.fasta -OUTPUT /tmp/merged13469339181061486267.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS true ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.breaks.md5.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.fasta -OUTPUT /tmp/merged13469339181061486267.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS true Test: Test method testHeaderFromMappedBreaks[1](specialHeader.aligned.breaks.md5.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testHeaderFromMappedBreaks[1](specialHeader.aligned.breaks.md5.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testHeaderFromMappedBreaks[1](specialHeader.aligned.breaks.md5.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testHeaderFromMappedBreaks[1](specialHeader.aligned.breaks.md5.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.634 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:30.634 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testHeaderFromMappedBreaks[1](specialHeader.aligned.breaks.md5.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.634 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:30.634 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testHeaderFromMappedBreaks[1](specialHeader.aligned.breaks.md5.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.634 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:30.634 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testHeaderFromMappedBreaks[1](specialHeader.aligned.breaks.md5.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.634 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:30.634 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testHeaderFromMappedBreaks[1](specialHeader.aligned.breaks.md5.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:30 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.breaks.md5.sam] OUTPUT=/tmp/merged13469339181061486267.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] UNMAP_CONTAMINANT_READS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:30 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.breaks.md5.sam] OUTPUT=/tmp/merged13469339181061486267.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] UNMAP_CONTAMINANT_READS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testHeaderFromMappedBreaks[1](specialHeader.aligned.breaks.md5.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testHeaderFromMappedBreaks[1](specialHeader.aligned.breaks.md5.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:30 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.breaks.md5.sam] INFO 2024-07-02 12:01:30 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.breaks.md5.sam] Test: Test method testHeaderFromMappedBreaks[1](specialHeader.aligned.breaks.md5.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ERROR 2024-07-02 12:01:30 SAMSequenceDictionary Cannot merge dictionaries. Found sequence entry for which tags differ: chr1_alt and tag M5 has the two values: dummy! and 8e0c728a0fb8a73feb55f9a447f4b144. ERROR 2024-07-02 12:01:30 SAMSequenceDictionary Cannot merge dictionaries. Found sequence entry for which tags differ: chr1_alt and tag M5 has the two values: dummy! and 8e0c728a0fb8a73feb55f9a447f4b144. Test: Test method testHeaderFromMappedBreaks[1](specialHeader.aligned.breaks.md5.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:30 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:30 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testHeaderFromMappedBreaks[1](specialHeader.aligned.breaks.md5.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testHeaderFromMappedBreaks[1](specialHeader.aligned.breaks.md5.sam)(picard.sam.MergeBamAlignmentTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMappedReadInUnmappedBam[0](false, false, false, true)(picard.sam.MergeBamAlignmentTest) Test: Test method testMappedReadInUnmappedBam[0](false, false, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:30 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testMappedReadInUnmappedBam[0](false, false, false, true) STANDARD_ERROR INFO 2024-07-02 12:01:30 MergeBamAlignment Test: Test method testMappedReadInUnmappedBam[0](false, false, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMappedReadInUnmappedBam[0](false, false, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedReadInUnmappedBam[0](false, false, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMappedReadInUnmappedBam[0](false, false, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedReadInUnmappedBam[0](false, false, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedReadInUnmappedBam[0](false, false, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMappedReadInUnmappedBam[0](false, false, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedReadInUnmappedBam[0](false, false, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMappedReadInUnmappedBam[0](false, false, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.1128578681670919739.sam -ALIGNED_BAM /tmp/aligned.666803930325983036.sam -OUTPUT /tmp/output834442561035201621.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.1128578681670919739.sam -ALIGNED_BAM /tmp/aligned.666803930325983036.sam -OUTPUT /tmp/output834442561035201621.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta Test: Test method testMappedReadInUnmappedBam[0](false, false, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMappedReadInUnmappedBam[0](false, false, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMappedReadInUnmappedBam[0](false, false, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMappedReadInUnmappedBam[0](false, false, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.794 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:30.794 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedReadInUnmappedBam[0](false, false, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.794 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:30.794 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedReadInUnmappedBam[0](false, false, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.794 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:30.794 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedReadInUnmappedBam[0](false, false, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.794 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:30.794 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedReadInUnmappedBam[0](false, false, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:30 GMT+14:00 2024] MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.1128578681670919739.sam ALIGNED_BAM=[/tmp/aligned.666803930325983036.sam] OUTPUT=/tmp/output834442561035201621.sam REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta ADD_PG_TAG_TO_READS=true PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ] READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:30 GMT+14:00 2024] MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.1128578681670919739.sam ALIGNED_BAM=[/tmp/aligned.666803930325983036.sam] OUTPUT=/tmp/output834442561035201621.sam REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta ADD_PG_TAG_TO_READS=true PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ] READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedReadInUnmappedBam[0](false, false, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedReadInUnmappedBam[0](false, false, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:30 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.666803930325983036.sam] INFO 2024-07-02 12:01:30 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.666803930325983036.sam] Test: Test method testMappedReadInUnmappedBam[0](false, false, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:30 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:30 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testMappedReadInUnmappedBam[0](false, false, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testMappedReadInUnmappedBam[0](false, false, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMappedReadInUnmappedBam[1](true, true, false, true)(picard.sam.MergeBamAlignmentTest) Test: Test method testMappedReadInUnmappedBam[1](true, true, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:30 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testMappedReadInUnmappedBam[1](true, true, false, true) STANDARD_ERROR INFO 2024-07-02 12:01:30 MergeBamAlignment Test: Test method testMappedReadInUnmappedBam[1](true, true, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMappedReadInUnmappedBam[1](true, true, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedReadInUnmappedBam[1](true, true, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMappedReadInUnmappedBam[1](true, true, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedReadInUnmappedBam[1](true, true, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedReadInUnmappedBam[1](true, true, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMappedReadInUnmappedBam[1](true, true, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedReadInUnmappedBam[1](true, true, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMappedReadInUnmappedBam[1](true, true, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.12968178587292829666.sam -ALIGNED_BAM /tmp/aligned.7220619594281473997.sam -OUTPUT /tmp/output12418425376151080861.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.12968178587292829666.sam -ALIGNED_BAM /tmp/aligned.7220619594281473997.sam -OUTPUT /tmp/output12418425376151080861.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta Test: Test method testMappedReadInUnmappedBam[1](true, true, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMappedReadInUnmappedBam[1](true, true, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMappedReadInUnmappedBam[1](true, true, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMappedReadInUnmappedBam[1](true, true, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.971 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:30.971 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedReadInUnmappedBam[1](true, true, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.971 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:30.971 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedReadInUnmappedBam[1](true, true, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.971 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:30.971 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedReadInUnmappedBam[1](true, true, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:30.971 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:30.971 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedReadInUnmappedBam[1](true, true, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:30 GMT+14:00 2024] MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.12968178587292829666.sam ALIGNED_BAM=[/tmp/aligned.7220619594281473997.sam] OUTPUT=/tmp/output12418425376151080861.sam REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta ADD_PG_TAG_TO_READS=true PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ] READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:30 GMT+14:00 2024] MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.12968178587292829666.sam ALIGNED_BAM=[/tmp/aligned.7220619594281473997.sam] OUTPUT=/tmp/output12418425376151080861.sam REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta ADD_PG_TAG_TO_READS=true PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ] READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedReadInUnmappedBam[1](true, true, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:30 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedReadInUnmappedBam[1](true, true, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:30 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.7220619594281473997.sam] INFO 2024-07-02 12:01:30 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.7220619594281473997.sam] Test: Test method testMappedReadInUnmappedBam[1](true, true, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:30 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:30 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testMappedReadInUnmappedBam[1](true, true, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testMappedReadInUnmappedBam[1](true, true, false, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMappedReadInUnmappedBam[2](true, false, true, true)(picard.sam.MergeBamAlignmentTest) Test: Test method testMappedReadInUnmappedBam[2](true, false, true, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testMappedReadInUnmappedBam[2](true, false, true, true) STANDARD_ERROR INFO 2024-07-02 12:01:31 MergeBamAlignment Test: Test method testMappedReadInUnmappedBam[2](true, false, true, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMappedReadInUnmappedBam[2](true, false, true, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedReadInUnmappedBam[2](true, false, true, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMappedReadInUnmappedBam[2](true, false, true, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedReadInUnmappedBam[2](true, false, true, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedReadInUnmappedBam[2](true, false, true, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMappedReadInUnmappedBam[2](true, false, true, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedReadInUnmappedBam[2](true, false, true, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMappedReadInUnmappedBam[2](true, false, true, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.11370132422105698106.sam -ALIGNED_BAM /tmp/aligned.5442442639064941820.sam -OUTPUT /tmp/output17956448046583411900.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.11370132422105698106.sam -ALIGNED_BAM /tmp/aligned.5442442639064941820.sam -OUTPUT /tmp/output17956448046583411900.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta Test: Test method testMappedReadInUnmappedBam[2](true, false, true, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMappedReadInUnmappedBam[2](true, false, true, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMappedReadInUnmappedBam[2](true, false, true, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMappedReadInUnmappedBam[2](true, false, true, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.175 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.175 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedReadInUnmappedBam[2](true, false, true, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.175 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.175 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedReadInUnmappedBam[2](true, false, true, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.175 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.175 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedReadInUnmappedBam[2](true, false, true, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.175 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.175 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedReadInUnmappedBam[2](true, false, true, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.11370132422105698106.sam ALIGNED_BAM=[/tmp/aligned.5442442639064941820.sam] OUTPUT=/tmp/output17956448046583411900.sam REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta ADD_PG_TAG_TO_READS=true PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ] READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:31 GMT+14:00 2024] MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.11370132422105698106.sam ALIGNED_BAM=[/tmp/aligned.5442442639064941820.sam] OUTPUT=/tmp/output17956448046583411900.sam REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta ADD_PG_TAG_TO_READS=true PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ] READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedReadInUnmappedBam[2](true, false, true, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedReadInUnmappedBam[2](true, false, true, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.5442442639064941820.sam] INFO 2024-07-02 12:01:31 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.5442442639064941820.sam] Test: Test method testMappedReadInUnmappedBam[2](true, false, true, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:31 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testMappedReadInUnmappedBam[2](true, false, true, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testMappedReadInUnmappedBam[2](true, false, true, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testMappedReadInUnmappedBam[3](true, true, true, false)(picard.sam.MergeBamAlignmentTest) Test: Test method testMappedReadInUnmappedBam[3](true, true, true, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testMappedReadInUnmappedBam[3](true, true, true, false) STANDARD_ERROR INFO 2024-07-02 12:01:31 MergeBamAlignment Test: Test method testMappedReadInUnmappedBam[3](true, true, true, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMappedReadInUnmappedBam[3](true, true, true, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedReadInUnmappedBam[3](true, true, true, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMappedReadInUnmappedBam[3](true, true, true, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedReadInUnmappedBam[3](true, true, true, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedReadInUnmappedBam[3](true, true, true, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMappedReadInUnmappedBam[3](true, true, true, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedReadInUnmappedBam[3](true, true, true, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMappedReadInUnmappedBam[3](true, true, true, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.11546677850940764137.sam -ALIGNED_BAM /tmp/aligned.1608437678334820655.sam -OUTPUT /tmp/output15701678475334980976.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.11546677850940764137.sam -ALIGNED_BAM /tmp/aligned.1608437678334820655.sam -OUTPUT /tmp/output15701678475334980976.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta Test: Test method testMappedReadInUnmappedBam[3](true, true, true, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMappedReadInUnmappedBam[3](true, true, true, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMappedReadInUnmappedBam[3](true, true, true, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMappedReadInUnmappedBam[3](true, true, true, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.273 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.273 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedReadInUnmappedBam[3](true, true, true, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.273 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.273 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedReadInUnmappedBam[3](true, true, true, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.274 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.274 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedReadInUnmappedBam[3](true, true, true, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.274 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.274 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedReadInUnmappedBam[3](true, true, true, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.11546677850940764137.sam ALIGNED_BAM=[/tmp/aligned.1608437678334820655.sam] OUTPUT=/tmp/output15701678475334980976.sam REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta ADD_PG_TAG_TO_READS=true PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ] READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:31 GMT+14:00 2024] MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.11546677850940764137.sam ALIGNED_BAM=[/tmp/aligned.1608437678334820655.sam] OUTPUT=/tmp/output15701678475334980976.sam REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta ADD_PG_TAG_TO_READS=true PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ] READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedReadInUnmappedBam[3](true, true, true, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedReadInUnmappedBam[3](true, true, true, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.1608437678334820655.sam] INFO 2024-07-02 12:01:31 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.1608437678334820655.sam] Test: Test method testMappedReadInUnmappedBam[3](true, true, true, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:31 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. Test: Test method testMappedReadInUnmappedBam[3](true, true, true, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:31 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testMappedReadInUnmappedBam[3](true, true, true, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testMappedToMultipleStrands(picard.sam.MergeBamAlignmentTest) Test: Test method testMappedToMultipleStrands(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testMappedToMultipleStrands STANDARD_ERROR INFO 2024-07-02 12:01:31 MergeBamAlignment Test: Test method testMappedToMultipleStrands(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMappedToMultipleStrands(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMappedToMultipleStrands(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMappedToMultipleStrands(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMappedToMultipleStrands(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMappedToMultipleStrands(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMappedToMultipleStrands(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMappedToMultipleStrands(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMappedToMultipleStrands(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/aligned.both.strands.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/mappedToMultipleStrands14959524176439922838.sam -EXPECTED_ORIENTATIONS FR -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/aligned.both.strands.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/mappedToMultipleStrands14959524176439922838.sam -EXPECTED_ORIENTATIONS FR -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testMappedToMultipleStrands(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMappedToMultipleStrands(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMappedToMultipleStrands(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMappedToMultipleStrands(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.310 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.310 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedToMultipleStrands(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.310 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.310 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedToMultipleStrands(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.311 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.311 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMappedToMultipleStrands(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.311 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.311 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMappedToMultipleStrands(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/aligned.both.strands.sam] OUTPUT=/tmp/mappedToMultipleStrands14959524176439922838.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:31 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/aligned.both.strands.sam] OUTPUT=/tmp/mappedToMultipleStrands14959524176439922838.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMappedToMultipleStrands(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMappedToMultipleStrands(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/aligned.both.strands.sam] INFO 2024-07-02 12:01:31 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/aligned.both.strands.sam] Test: Test method testMappedToMultipleStrands(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 AbstractAlignmentMerger Wrote 6 alignment records and 9 unmapped reads. INFO 2024-07-02 12:01:31 AbstractAlignmentMerger Wrote 6 alignment records and 9 unmapped reads. Test: Test method testMappedToMultipleStrands(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:31 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testMappedToMultipleStrands(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testMergeHeaderMappedAndReference STANDARD_ERROR INFO 2024-07-02 12:01:31 MergeBamAlignment Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.fasta -OUTPUT /tmp/merged16839763619026962228.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS true ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.fasta -OUTPUT /tmp/merged16839763619026962228.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS true Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.345 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.345 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.345 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.345 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.345 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.345 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.345 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.345 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.sam] OUTPUT=/tmp/merged16839763619026962228.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] UNMAP_CONTAMINANT_READS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:31 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.sam] OUTPUT=/tmp/merged16839763619026962228.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] UNMAP_CONTAMINANT_READS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.sam] INFO 2024-07-02 12:01:31 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.sam] Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 AbstractAlignmentMerger Wrote 4 alignment records and 11 unmapped reads. INFO 2024-07-02 12:01:31 AbstractAlignmentMerger Wrote 4 alignment records and 11 unmapped reads. Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:31 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 ValidateSamFile INFO 2024-07-02 12:01:31 ValidateSamFile Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ValidateSamFile -I /tmp/merged16839763619026962228.sam ********** ValidateSamFile -I /tmp/merged16839763619026962228.sam Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.380 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.380 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.380 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.380 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.380 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.380 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.380 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.380 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged16839763619026962228.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:31 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged16839763619026962228.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:31 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:31 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testMergeHeaderMappedAndReference STANDARD_OUT No errors found Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testMergeHeaderMappedAndReference STANDARD_ERROR [Tue Jul 02 12:01:31 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testMergeHeaderMappedAndReference(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by picard.sam.MergeBamAlignmentTest (file:/build/reproducible-path/picard-tools-2.24.1+dfsg/build/classes/java/test/) to field java.io.FileDescriptor.fd WARNING: Please consider reporting this to the maintainers of picard.sam.MergeBamAlignmentTest WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream STANDARD_ERROR INFO 2024-07-02 12:01:31 MergeBamAlignment Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /dev/fd/2466 -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.fasta -OUTPUT /tmp/merged7901710826292698742.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS true ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /dev/fd/2466 -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.fasta -OUTPUT /tmp/merged7901710826292698742.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS true Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.409 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.409 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.409 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.409 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.409 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.409 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.409 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.409 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.unmapped.sam ALIGNED_BAM=[/dev/fd/2466] OUTPUT=/tmp/merged7901710826292698742.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] UNMAP_CONTAMINANT_READS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:31 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.unmapped.sam ALIGNED_BAM=[/dev/fd/2466] OUTPUT=/tmp/merged7901710826292698742.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] UNMAP_CONTAMINANT_READS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 SamAlignmentMerger Processing SAM file(s): [/dev/fd/2466] INFO 2024-07-02 12:01:31 SamAlignmentMerger Processing SAM file(s): [/dev/fd/2466] Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 AbstractAlignmentMerger Wrote 4 alignment records and 11 unmapped reads. INFO 2024-07-02 12:01:31 AbstractAlignmentMerger Wrote 4 alignment records and 11 unmapped reads. Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:31 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 ValidateSamFile INFO 2024-07-02 12:01:31 ValidateSamFile Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ValidateSamFile -I /tmp/merged7901710826292698742.sam ********** ValidateSamFile -I /tmp/merged7901710826292698742.sam Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.444 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.444 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.444 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.444 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.444 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.444 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.444 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.444 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged7901710826292698742.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:31 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged7901710826292698742.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:31 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:31 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream STANDARD_OUT No errors found Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream STANDARD_ERROR [Tue Jul 02 12:01:31 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream STANDARD_ERROR INFO 2024-07-02 12:01:31 MergeBamAlignment Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /dev/fd/2470 -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.fasta -OUTPUT /tmp/merged10383566503487316419.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS true ********** MergeBamAlignment -UNMAPPED_BAM /dev/fd/2470 -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.fasta -OUTPUT /tmp/merged10383566503487316419.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -UNMAP_CONTAMINANT_READS true Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.470 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.470 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.470 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.470 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.470 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.470 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.470 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.470 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/dev/fd/2470 ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.sam] OUTPUT=/tmp/merged10383566503487316419.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] UNMAP_CONTAMINANT_READS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:31 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/dev/fd/2470 ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.sam] OUTPUT=/tmp/merged10383566503487316419.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] UNMAP_CONTAMINANT_READS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.sam] INFO 2024-07-02 12:01:31 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.sam] Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 AbstractAlignmentMerger Wrote 4 alignment records and 11 unmapped reads. INFO 2024-07-02 12:01:31 AbstractAlignmentMerger Wrote 4 alignment records and 11 unmapped reads. Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:31 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 ValidateSamFile INFO 2024-07-02 12:01:31 ValidateSamFile Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ValidateSamFile -I /tmp/merged10383566503487316419.sam ********** ValidateSamFile -I /tmp/merged10383566503487316419.sam Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.500 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.500 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.500 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.500 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.500 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.500 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.500 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.500 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged10383566503487316419.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:31 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged10383566503487316419.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:31 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:31 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream STANDARD_OUT No errors found Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream STANDARD_ERROR [Tue Jul 02 12:01:31 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testMerger STANDARD_ERROR INFO 2024-07-02 12:01:31 MergeBamAlignment Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/aligned.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/mergeTest17254971585746912123.sam -EXPECTED_ORIENTATIONS FR -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/aligned.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/mergeTest17254971585746912123.sam -EXPECTED_ORIENTATIONS FR -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.526 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.526 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.526 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.526 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.526 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.526 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.526 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.526 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/aligned.sam] OUTPUT=/tmp/mergeTest17254971585746912123.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:31 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/aligned.sam] OUTPUT=/tmp/mergeTest17254971585746912123.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/aligned.sam] INFO 2024-07-02 12:01:31 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/aligned.sam] Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:31 SamAlignmentMerger Exception merging bam alignment - attempting to sort aligned reads and try again: Underlying iterator is not queryname sorted: read_2_too_many_gaps 1/2 101b aligned to chr7:1-101. > both_reads_align_clip_adapter 2/2 101b aligned to chr7:16-116. WARNING 2024-07-02 12:01:31 SamAlignmentMerger Exception merging bam alignment - attempting to sort aligned reads and try again: Underlying iterator is not queryname sorted: read_2_too_many_gaps 1/2 101b aligned to chr7:1-101. > both_reads_align_clip_adapter 2/2 101b aligned to chr7:16-116. Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 SamAlignmentMerger Finished reading 8 total records from alignment SAM/BAM. INFO 2024-07-02 12:01:31 SamAlignmentMerger Finished reading 8 total records from alignment SAM/BAM. Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 AbstractAlignmentMerger Wrote 6 alignment records and 4 unmapped reads. INFO 2024-07-02 12:01:31 AbstractAlignmentMerger Wrote 6 alignment records and 4 unmapped reads. Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:31 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 MergeBamAlignment INFO 2024-07-02 12:01:31 MergeBamAlignment Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/aligned.sam -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/mergeTest17254971585746912123.sam -EXPECTED_ORIENTATIONS FR -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/aligned.sam -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/mergeTest17254971585746912123.sam -EXPECTED_ORIENTATIONS FR -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.568 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.568 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.568 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.568 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.568 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.568 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.568 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.568 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/aligned.sam] OUTPUT=/tmp/mergeTest17254971585746912123.sam PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:31 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/aligned.sam] OUTPUT=/tmp/mergeTest17254971585746912123.sam PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/aligned.sam] INFO 2024-07-02 12:01:31 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/aligned.sam] Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:31 SamAlignmentMerger Exception merging bam alignment - attempting to sort aligned reads and try again: Underlying iterator is not queryname sorted: read_2_too_many_gaps 1/2 101b aligned to chr7:1-101. > both_reads_align_clip_adapter 2/2 101b aligned to chr7:16-116. WARNING 2024-07-02 12:01:31 SamAlignmentMerger Exception merging bam alignment - attempting to sort aligned reads and try again: Underlying iterator is not queryname sorted: read_2_too_many_gaps 1/2 101b aligned to chr7:1-101. > both_reads_align_clip_adapter 2/2 101b aligned to chr7:16-116. Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 SamAlignmentMerger Finished reading 8 total records from alignment SAM/BAM. INFO 2024-07-02 12:01:31 SamAlignmentMerger Finished reading 8 total records from alignment SAM/BAM. Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 AbstractAlignmentMerger Wrote 6 alignment records and 4 unmapped reads. INFO 2024-07-02 12:01:31 AbstractAlignmentMerger Wrote 6 alignment records and 4 unmapped reads. Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:31 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testMerger(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testMergerFromMultipleFiles(picard.sam.MergeBamAlignmentTest) Test: Test method testMergerFromMultipleFiles(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testMergerFromMultipleFiles STANDARD_ERROR INFO 2024-07-02 12:01:31 MergeBamAlignment Test: Test method testMergerFromMultipleFiles(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergerFromMultipleFiles(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMergerFromMultipleFiles(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergerFromMultipleFiles(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMergerFromMultipleFiles(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMergerFromMultipleFiles(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergerFromMultipleFiles(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMergerFromMultipleFiles(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergerFromMultipleFiles(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/onehalfaligned.sam -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/otherhalfaligned.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/mergeTest2656813433930521683.sam -EXPECTED_ORIENTATIONS FR -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/onehalfaligned.sam -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/otherhalfaligned.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/mergeTest2656813433930521683.sam -EXPECTED_ORIENTATIONS FR -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testMergerFromMultipleFiles(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergerFromMultipleFiles(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergerFromMultipleFiles(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergerFromMultipleFiles(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.614 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.614 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMergerFromMultipleFiles(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.614 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.614 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMergerFromMultipleFiles(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.614 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.614 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMergerFromMultipleFiles(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.614 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.614 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMergerFromMultipleFiles(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/onehalfaligned.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/otherhalfaligned.sam] OUTPUT=/tmp/mergeTest2656813433930521683.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:31 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/onehalfaligned.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/otherhalfaligned.sam] OUTPUT=/tmp/mergeTest2656813433930521683.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMergerFromMultipleFiles(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMergerFromMultipleFiles(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/onehalfaligned.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/otherhalfaligned.sam] INFO 2024-07-02 12:01:31 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/onehalfaligned.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/otherhalfaligned.sam] Test: Test method testMergerFromMultipleFiles(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:31 SamAlignmentMerger Exception merging bam alignment - attempting to sort aligned reads and try again: Underlying iterator is not queryname sorted: both_reads_present_only_first_aligns 1/2 101b aligned to chr7:1-101. > both_reads_align_clip_adapter 2/2 101b aligned to chr7:16-116. WARNING 2024-07-02 12:01:31 SamAlignmentMerger Exception merging bam alignment - attempting to sort aligned reads and try again: Underlying iterator is not queryname sorted: both_reads_present_only_first_aligns 1/2 101b aligned to chr7:1-101. > both_reads_align_clip_adapter 2/2 101b aligned to chr7:16-116. Test: Test method testMergerFromMultipleFiles(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 SamAlignmentMerger Finished reading 8 total records from alignment SAM/BAM. INFO 2024-07-02 12:01:31 SamAlignmentMerger Finished reading 8 total records from alignment SAM/BAM. Test: Test method testMergerFromMultipleFiles(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 AbstractAlignmentMerger Wrote 6 alignment records and 4 unmapped reads. INFO 2024-07-02 12:01:31 AbstractAlignmentMerger Wrote 6 alignment records and 4 unmapped reads. Test: Test method testMergerFromMultipleFiles(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:31 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testMergerFromMultipleFiles(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testMergerWithSupplemental(picard.sam.MergeBamAlignmentTest) Test: Test method testMergerWithSupplemental(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testMergerWithSupplemental STANDARD_ERROR INFO 2024-07-02 12:01:31 MergeBamAlignment Test: Test method testMergerWithSupplemental(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergerWithSupplemental(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMergerWithSupplemental(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergerWithSupplemental(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMergerWithSupplemental(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMergerWithSupplemental(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergerWithSupplemental(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMergerWithSupplemental(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergerWithSupplemental(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/aligned.supplement.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/mergeWithSupplementalTest2936802381996916195.sam -EXPECTED_ORIENTATIONS FR -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/aligned.supplement.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/mergeWithSupplementalTest2936802381996916195.sam -EXPECTED_ORIENTATIONS FR -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testMergerWithSupplemental(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergerWithSupplemental(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergerWithSupplemental(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergerWithSupplemental(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.683 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.683 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMergerWithSupplemental(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.683 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.683 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMergerWithSupplemental(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.683 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.683 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMergerWithSupplemental(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.683 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.683 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMergerWithSupplemental(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/aligned.supplement.sam] OUTPUT=/tmp/mergeWithSupplementalTest2936802381996916195.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:31 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/aligned.supplement.sam] OUTPUT=/tmp/mergeWithSupplementalTest2936802381996916195.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMergerWithSupplemental(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMergerWithSupplemental(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/aligned.supplement.sam] INFO 2024-07-02 12:01:31 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/aligned.supplement.sam] Test: Test method testMergerWithSupplemental(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 AbstractAlignmentMerger Wrote 8 alignment records and 4 unmapped reads. INFO 2024-07-02 12:01:31 AbstractAlignmentMerger Wrote 8 alignment records and 4 unmapped reads. Test: Test method testMergerWithSupplemental(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:31 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testMergerWithSupplemental(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testMergingFromSeparatedReadTrimmedAlignments[0](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam], 17, 20, one file per read)(picard.sam.MergeBamAlignmentTest) Test: Test method testMergingFromSeparatedReadTrimmedAlignments[0](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam], 17, 20, one file per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testMergingFromSeparatedReadTrimmedAlignments[0](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam], 17, 20, one file per read) STANDARD_ERROR INFO 2024-07-02 12:01:31 MergeBamAlignment Test: Test method testMergingFromSeparatedReadTrimmedAlignments[0](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam], 17, 20, one file per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergingFromSeparatedReadTrimmedAlignments[0](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam], 17, 20, one file per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMergingFromSeparatedReadTrimmedAlignments[0](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam], 17, 20, one file per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergingFromSeparatedReadTrimmedAlignments[0](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam], 17, 20, one file per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMergingFromSeparatedReadTrimmedAlignments[0](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam], 17, 20, one file per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMergingFromSeparatedReadTrimmedAlignments[0](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam], 17, 20, one file per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergingFromSeparatedReadTrimmedAlignments[0](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam], 17, 20, one file per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMergingFromSeparatedReadTrimmedAlignments[0](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam], 17, 20, one file per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergingFromSeparatedReadTrimmedAlignments[0](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam], 17, 20, one file per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -READ1_ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam -READ2_ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam -READ1_TRIM 17 -READ2_TRIM 20 -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/mergeMultipleAlignmentsTest13078988206937775076.sam -EXPECTED_ORIENTATIONS FR -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -READ1_ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam -READ2_ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam -READ1_TRIM 17 -READ2_TRIM 20 -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/mergeMultipleAlignmentsTest13078988206937775076.sam -EXPECTED_ORIENTATIONS FR -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testMergingFromSeparatedReadTrimmedAlignments[0](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam], 17, 20, one file per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergingFromSeparatedReadTrimmedAlignments[0](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam], 17, 20, one file per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergingFromSeparatedReadTrimmedAlignments[0](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam], 17, 20, one file per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergingFromSeparatedReadTrimmedAlignments[0](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam], 17, 20, one file per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.782 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.782 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMergingFromSeparatedReadTrimmedAlignments[0](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam], 17, 20, one file per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.782 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.782 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMergingFromSeparatedReadTrimmedAlignments[0](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam], 17, 20, one file per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.783 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.783 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMergingFromSeparatedReadTrimmedAlignments[0](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam], 17, 20, one file per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.783 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.783 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMergingFromSeparatedReadTrimmedAlignments[0](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam], 17, 20, one file per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/unmapped.sam READ1_ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam] READ2_ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam] OUTPUT=/tmp/mergeMultipleAlignmentsTest13078988206937775076.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] READ1_TRIM=17 READ2_TRIM=20 EXPECTED_ORIENTATIONS=[FR] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:31 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/unmapped.sam READ1_ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam] READ2_ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam] OUTPUT=/tmp/mergeMultipleAlignmentsTest13078988206937775076.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] READ1_TRIM=17 READ2_TRIM=20 EXPECTED_ORIENTATIONS=[FR] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMergingFromSeparatedReadTrimmedAlignments[0](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam], 17, 20, one file per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMergingFromSeparatedReadTrimmedAlignments[0](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam], 17, 20, one file per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 SamAlignmentMerger Processing SAM file(s): [] INFO 2024-07-02 12:01:31 SamAlignmentMerger Processing SAM file(s): [] Test: Test method testMergingFromSeparatedReadTrimmedAlignments[0](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam], 17, 20, one file per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 AbstractAlignmentMerger Wrote 8 alignment records and 4 unmapped reads. INFO 2024-07-02 12:01:31 AbstractAlignmentMerger Wrote 8 alignment records and 4 unmapped reads. Test: Test method testMergingFromSeparatedReadTrimmedAlignments[0](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam], 17, 20, one file per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:31 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testMergingFromSeparatedReadTrimmedAlignments[0](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam], 17, 20, one file per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testMergingFromSeparatedReadTrimmedAlignments[1](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, two files per read)(picard.sam.MergeBamAlignmentTest) Test: Test method testMergingFromSeparatedReadTrimmedAlignments[1](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, two files per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testMergingFromSeparatedReadTrimmedAlignments[1](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, two files per read) STANDARD_ERROR INFO 2024-07-02 12:01:31 MergeBamAlignment Test: Test method testMergingFromSeparatedReadTrimmedAlignments[1](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, two files per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergingFromSeparatedReadTrimmedAlignments[1](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, two files per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMergingFromSeparatedReadTrimmedAlignments[1](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, two files per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergingFromSeparatedReadTrimmedAlignments[1](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, two files per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMergingFromSeparatedReadTrimmedAlignments[1](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, two files per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMergingFromSeparatedReadTrimmedAlignments[1](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, two files per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergingFromSeparatedReadTrimmedAlignments[1](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, two files per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMergingFromSeparatedReadTrimmedAlignments[1](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, two files per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergingFromSeparatedReadTrimmedAlignments[1](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, two files per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -READ1_ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam -READ1_ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam -READ2_ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam -READ2_ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam -READ1_TRIM 17 -READ2_TRIM 20 -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/mergeMultipleAlignmentsTest6002441027203080052.sam -EXPECTED_ORIENTATIONS FR -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -READ1_ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam -READ1_ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam -READ2_ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam -READ2_ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam -READ1_TRIM 17 -READ2_TRIM 20 -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/mergeMultipleAlignmentsTest6002441027203080052.sam -EXPECTED_ORIENTATIONS FR -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testMergingFromSeparatedReadTrimmedAlignments[1](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, two files per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMergingFromSeparatedReadTrimmedAlignments[1](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, two files per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergingFromSeparatedReadTrimmedAlignments[1](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, two files per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMergingFromSeparatedReadTrimmedAlignments[1](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, two files per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.916 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.916 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMergingFromSeparatedReadTrimmedAlignments[1](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, two files per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.916 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.916 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMergingFromSeparatedReadTrimmedAlignments[1](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, two files per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.916 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:31.916 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMergingFromSeparatedReadTrimmedAlignments[1](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, two files per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:31.916 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:31.916 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMergingFromSeparatedReadTrimmedAlignments[1](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, two files per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/unmapped.sam READ1_ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam] READ2_ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam] OUTPUT=/tmp/mergeMultipleAlignmentsTest6002441027203080052.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] READ1_TRIM=17 READ2_TRIM=20 EXPECTED_ORIENTATIONS=[FR] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:31 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/unmapped.sam READ1_ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam] READ2_ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam] OUTPUT=/tmp/mergeMultipleAlignmentsTest6002441027203080052.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] READ1_TRIM=17 READ2_TRIM=20 EXPECTED_ORIENTATIONS=[FR] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMergingFromSeparatedReadTrimmedAlignments[1](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, two files per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:31 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMergingFromSeparatedReadTrimmedAlignments[1](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, two files per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 SamAlignmentMerger Processing SAM file(s): [] INFO 2024-07-02 12:01:31 SamAlignmentMerger Processing SAM file(s): [] Test: Test method testMergingFromSeparatedReadTrimmedAlignments[1](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, two files per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:31 SamAlignmentMerger Exception merging bam alignment - attempting to sort aligned reads and try again: Underlying iterator is not queryname sorted: test:6 1/2 36b aligned to chr1:15-50. > test:2 1/2 36b aligned to chr7:50-85. WARNING 2024-07-02 12:01:31 SamAlignmentMerger Exception merging bam alignment - attempting to sort aligned reads and try again: Underlying iterator is not queryname sorted: test:6 1/2 36b aligned to chr1:15-50. > test:2 1/2 36b aligned to chr7:50-85. Test: Test method testMergingFromSeparatedReadTrimmedAlignments[1](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, two files per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:31 SamAlignmentMerger Finished reading 12 total records from alignment SAM/BAM. INFO 2024-07-02 12:01:31 SamAlignmentMerger Finished reading 12 total records from alignment SAM/BAM. Test: Test method testMergingFromSeparatedReadTrimmedAlignments[1](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, two files per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:32 AbstractAlignmentMerger Wrote 8 alignment records and 4 unmapped reads. INFO 2024-07-02 12:01:32 AbstractAlignmentMerger Wrote 8 alignment records and 4 unmapped reads. Test: Test method testMergingFromSeparatedReadTrimmedAlignments[1](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, two files per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:32 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:32 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testMergingFromSeparatedReadTrimmedAlignments[1](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, two files per read)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:32 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948) STANDARD_ERROR INFO 2024-07-02 12:01:32 MergeBamAlignment Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.14139796877128794942.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.3128938027870406531.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testMostDistantStrategy.multipleAlignmentsBothEnds.includeSecondary16668575316730152801.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY MostDistant -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS true ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.14139796877128794942.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.3128938027870406531.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testMostDistantStrategy.multipleAlignmentsBothEnds.includeSecondary16668575316730152801.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY MostDistant -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS true Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:32.133 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:32.133 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:32.133 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:32.133 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:32.133 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:32.133 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:32.133 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:32.133 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:32 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.14139796877128794942.sam ALIGNED_BAM=[/tmp/aligned.3128938027870406531.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsBothEnds.includeSecondary16668575316730152801.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:32 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.14139796877128794942.sam ALIGNED_BAM=[/tmp/aligned.3128938027870406531.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsBothEnds.includeSecondary16668575316730152801.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:32 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.3128938027870406531.sam] INFO 2024-07-02 12:01:32 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.3128938027870406531.sam] Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:32 AbstractAlignmentMerger Wrote 14 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:32 AbstractAlignmentMerger Wrote 14 alignment records and 0 unmapped reads. Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:32 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:32 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:32 MergeBamAlignment INFO 2024-07-02 12:01:32 MergeBamAlignment Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.4397907114520501715.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.17884199837582427289.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testMostDistantStrategy.multipleAlignmentsBothEnds.excludeSecondary12832658148106522303.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY MostDistant -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS false ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.4397907114520501715.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.17884199837582427289.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testMostDistantStrategy.multipleAlignmentsBothEnds.excludeSecondary12832658148106522303.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY MostDistant -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS false Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:32.420 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:32.420 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:32.420 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:32.420 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:32.430 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:32.430 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:32.430 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:32.430 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:32 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.4397907114520501715.sam ALIGNED_BAM=[/tmp/aligned.17884199837582427289.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsBothEnds.excludeSecondary12832658148106522303.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:32 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.4397907114520501715.sam ALIGNED_BAM=[/tmp/aligned.17884199837582427289.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsBothEnds.excludeSecondary12832658148106522303.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:32 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.17884199837582427289.sam] INFO 2024-07-02 12:01:32 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.17884199837582427289.sam] Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:32 AbstractAlignmentMerger Wrote 14 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:32 AbstractAlignmentMerger Wrote 14 alignment records and 0 unmapped reads. Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:32 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:32 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75668016, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@4ece5948)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:32 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2) STANDARD_ERROR INFO 2024-07-02 12:01:32 MergeBamAlignment Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.10980674056689947715.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.14899046818165465358.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testMostDistantStrategy.multipleAlignmentsAllChimeric.includeSecondary4611634706115725138.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY MostDistant -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS true ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.10980674056689947715.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.14899046818165465358.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testMostDistantStrategy.multipleAlignmentsAllChimeric.includeSecondary4611634706115725138.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY MostDistant -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS true Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:32.552 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:32.552 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:32.552 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:32.552 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:32.552 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:32.552 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:32.552 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:32.552 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:32 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.10980674056689947715.sam ALIGNED_BAM=[/tmp/aligned.14899046818165465358.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsAllChimeric.includeSecondary4611634706115725138.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:32 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.10980674056689947715.sam ALIGNED_BAM=[/tmp/aligned.14899046818165465358.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsAllChimeric.includeSecondary4611634706115725138.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:32 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.14899046818165465358.sam] INFO 2024-07-02 12:01:32 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.14899046818165465358.sam] Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:32 AbstractAlignmentMerger Wrote 14 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:32 AbstractAlignmentMerger Wrote 14 alignment records and 0 unmapped reads. Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:32 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:32 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:32 MergeBamAlignment INFO 2024-07-02 12:01:32 MergeBamAlignment Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.622117350973025410.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.1669008153716627877.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testMostDistantStrategy.multipleAlignmentsAllChimeric.excludeSecondary5702181608164923679.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY MostDistant -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS false ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.622117350973025410.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.1669008153716627877.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testMostDistantStrategy.multipleAlignmentsAllChimeric.excludeSecondary5702181608164923679.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY MostDistant -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS false Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:32.888 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:32.888 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:32.888 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:32.888 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:32.888 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:32.888 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:32.888 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:32.888 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:32 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.622117350973025410.sam ALIGNED_BAM=[/tmp/aligned.1669008153716627877.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsAllChimeric.excludeSecondary5702181608164923679.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:32 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.622117350973025410.sam ALIGNED_BAM=[/tmp/aligned.1669008153716627877.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsAllChimeric.excludeSecondary5702181608164923679.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:32 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.1669008153716627877.sam] INFO 2024-07-02 12:01:32 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.1669008153716627877.sam] Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:32 AbstractAlignmentMerger Wrote 14 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:32 AbstractAlignmentMerger Wrote 14 alignment records and 0 unmapped reads. Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:32 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:32 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ead3d2b, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2ec401a2)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c) STANDARD_ERROR INFO 2024-07-02 12:01:33 MergeBamAlignment Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.5356063198771513176.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.341177910446996235.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testMostDistantStrategy.multipleAlignmentsFirstEnd.includeSecondary11710299463840681089.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY MostDistant -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS true ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.5356063198771513176.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.341177910446996235.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testMostDistantStrategy.multipleAlignmentsFirstEnd.includeSecondary11710299463840681089.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY MostDistant -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS true Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.050 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:33.050 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.050 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:33.050 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.051 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:33.051 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.051 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:33.051 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.5356063198771513176.sam ALIGNED_BAM=[/tmp/aligned.341177910446996235.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsFirstEnd.includeSecondary11710299463840681089.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:33 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.5356063198771513176.sam ALIGNED_BAM=[/tmp/aligned.341177910446996235.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsFirstEnd.includeSecondary11710299463840681089.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.341177910446996235.sam] INFO 2024-07-02 12:01:33 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.341177910446996235.sam] Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 AbstractAlignmentMerger Wrote 8 alignment records and 1 unmapped reads. INFO 2024-07-02 12:01:33 AbstractAlignmentMerger Wrote 8 alignment records and 1 unmapped reads. Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:33 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 MergeBamAlignment INFO 2024-07-02 12:01:33 MergeBamAlignment Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.1478503985921496963.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.14989628690266519678.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testMostDistantStrategy.multipleAlignmentsFirstEnd.excludeSecondary16188265680734496214.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY MostDistant -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS false ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.1478503985921496963.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.14989628690266519678.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testMostDistantStrategy.multipleAlignmentsFirstEnd.excludeSecondary16188265680734496214.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY MostDistant -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS false Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.183 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:33.183 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.183 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:33.183 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.184 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:33.184 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.184 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:33.184 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.1478503985921496963.sam ALIGNED_BAM=[/tmp/aligned.14989628690266519678.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsFirstEnd.excludeSecondary16188265680734496214.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:33 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.1478503985921496963.sam ALIGNED_BAM=[/tmp/aligned.14989628690266519678.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsFirstEnd.excludeSecondary16188265680734496214.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.14989628690266519678.sam] INFO 2024-07-02 12:01:33 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.14989628690266519678.sam] Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 AbstractAlignmentMerger Wrote 8 alignment records and 1 unmapped reads. INFO 2024-07-02 12:01:33 AbstractAlignmentMerger Wrote 8 alignment records and 1 unmapped reads. Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:33 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@523e5ab0, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3413273c)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f) STANDARD_ERROR INFO 2024-07-02 12:01:33 MergeBamAlignment Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.11287803516090577493.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.944553402218615387.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testMostDistantStrategy.multipleAlignmentsSecondEnd.includeSecondary10738391328355916197.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY MostDistant -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS true ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.11287803516090577493.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.944553402218615387.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testMostDistantStrategy.multipleAlignmentsSecondEnd.includeSecondary10738391328355916197.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY MostDistant -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS true Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.309 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:33.309 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.309 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:33.309 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.309 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:33.309 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.310 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:33.310 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.11287803516090577493.sam ALIGNED_BAM=[/tmp/aligned.944553402218615387.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsSecondEnd.includeSecondary10738391328355916197.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:33 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.11287803516090577493.sam ALIGNED_BAM=[/tmp/aligned.944553402218615387.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsSecondEnd.includeSecondary10738391328355916197.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.944553402218615387.sam] INFO 2024-07-02 12:01:33 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.944553402218615387.sam] Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 AbstractAlignmentMerger Wrote 8 alignment records and 1 unmapped reads. INFO 2024-07-02 12:01:33 AbstractAlignmentMerger Wrote 8 alignment records and 1 unmapped reads. Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:33 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 MergeBamAlignment INFO 2024-07-02 12:01:33 MergeBamAlignment Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.13685291394772804136.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.3314759976862079879.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testMostDistantStrategy.multipleAlignmentsSecondEnd.excludeSecondary13404904510850886571.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY MostDistant -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS false ********** MergeBamAlignment -UNMAPPED_BAM /tmp/unmapped.13685291394772804136.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.3314759976862079879.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/testMostDistantStrategy.multipleAlignmentsSecondEnd.excludeSecondary13404904510850886571.sam -EXPECTED_ORIENTATIONS FR -PRIMARY_ALIGNMENT_STRATEGY MostDistant -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -INCLUDE_SECONDARY_ALIGNMENTS false Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.408 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:33.408 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.408 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:33.408 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.409 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:33.409 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.409 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:33.409 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.13685291394772804136.sam ALIGNED_BAM=[/tmp/aligned.3314759976862079879.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsSecondEnd.excludeSecondary13404904510850886571.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:33 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/tmp/unmapped.13685291394772804136.sam ALIGNED_BAM=[/tmp/aligned.3314759976862079879.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsSecondEnd.excludeSecondary13404904510850886571.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=false REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.3314759976862079879.sam] INFO 2024-07-02 12:01:33 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.3314759976862079879.sam] Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 AbstractAlignmentMerger Wrote 8 alignment records and 1 unmapped reads. INFO 2024-07-02 12:01:33 AbstractAlignmentMerger Wrote 8 alignment records and 1 unmapped reads. Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:33 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@139bc4ad, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@5b506c8f)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testMultiHit STANDARD_ERROR INFO 2024-07-02 12:01:33 MergeBamAlignment Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.aligned.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged1047403277281285614.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.aligned.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged1047403277281285614.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.477 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:33.477 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.477 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:33.477 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.478 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:33.478 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.478 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:33.478 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.aligned.sam] OUTPUT=/tmp/merged1047403277281285614.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:33 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.aligned.sam] OUTPUT=/tmp/merged1047403277281285614.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.aligned.sam] INFO 2024-07-02 12:01:33 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.aligned.sam] Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 AbstractAlignmentMerger Wrote 20 alignment records and 7 unmapped reads. INFO 2024-07-02 12:01:33 AbstractAlignmentMerger Wrote 20 alignment records and 7 unmapped reads. Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:33 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 ValidateSamFile INFO 2024-07-02 12:01:33 ValidateSamFile Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ValidateSamFile -I /tmp/merged1047403277281285614.sam ********** ValidateSamFile -I /tmp/merged1047403277281285614.sam Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.540 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:33.540 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.540 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:33.540 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.540 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:33.540 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.540 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:33.540 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged1047403277281285614.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:33 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged1047403277281285614.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:33 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:33 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testMultiHit STANDARD_OUT No errors found Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testMultiHit STANDARD_ERROR [Tue Jul 02 12:01:33 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testMultiHit(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testOldQuerynameSortFails(picard.sam.MergeBamAlignmentTest) Test: Test method testOldQuerynameSortFails(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testOldQuerynameSortFails STANDARD_ERROR INFO 2024-07-02 12:01:33 MergeBamAlignment Test: Test method testOldQuerynameSortFails(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testOldQuerynameSortFails(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOldQuerynameSortFails(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testOldQuerynameSortFails(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOldQuerynameSortFails(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOldQuerynameSortFails(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testOldQuerynameSortFails(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOldQuerynameSortFails(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testOldQuerynameSortFails(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/unmapped.badorder.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/aligned.badorder.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged15601126920461301832.bam -EXPECTED_ORIENTATIONS FR -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/unmapped.badorder.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/aligned.badorder.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged15601126920461301832.bam -EXPECTED_ORIENTATIONS FR -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testOldQuerynameSortFails(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testOldQuerynameSortFails(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testOldQuerynameSortFails(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testOldQuerynameSortFails(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.603 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:33.603 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOldQuerynameSortFails(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.603 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:33.603 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOldQuerynameSortFails(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.603 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:33.603 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOldQuerynameSortFails(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.603 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:33.603 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOldQuerynameSortFails(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/unmapped.badorder.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/aligned.badorder.sam] OUTPUT=/tmp/merged15601126920461301832.bam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:33 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/unmapped.badorder.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/aligned.badorder.sam] OUTPUT=/tmp/merged15601126920461301832.bam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOldQuerynameSortFails(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOldQuerynameSortFails(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/aligned.badorder.sam] INFO 2024-07-02 12:01:33 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/aligned.badorder.sam] Test: Test method testOldQuerynameSortFails(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:33 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testOldQuerynameSortFails(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testOldQuerynameSortFails(picard.sam.MergeBamAlignmentTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9) STANDARD_ERROR INFO 2024-07-02 12:01:33 MergeBamAlignment Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.15246790460068295240.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.2484879877138239676.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.15246790460068295240.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.2484879877138239676.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.655 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:33.655 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.656 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:33.656 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.656 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:33.656 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.656 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:33.656 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.15246790460068295240.sam] OUTPUT=/tmp/merged.2484879877138239676.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:33 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.15246790460068295240.sam] OUTPUT=/tmp/merged.2484879877138239676.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.15246790460068295240.sam] INFO 2024-07-02 12:01:33 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.15246790460068295240.sam] Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 AbstractAlignmentMerger Wrote 1 alignment records and 1 unmapped reads. INFO 2024-07-02 12:01:33 AbstractAlignmentMerger Wrote 1 alignment records and 1 unmapped reads. Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:33 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 ValidateSamFile INFO 2024-07-02 12:01:33 ValidateSamFile Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ValidateSamFile -I /tmp/merged.2484879877138239676.sam ********** ValidateSamFile -I /tmp/merged.2484879877138239676.sam Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.707 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:33.707 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.707 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:33.707 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.707 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:33.707 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.707 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:33.707 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.2484879877138239676.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:33 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.2484879877138239676.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:33 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:33 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9) STANDARD_OUT No errors found Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9) STANDARD_ERROR [Tue Jul 02 12:01:33 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1c1799e4, picard.sam.MergeBamAlignmentTest$HitSpec@554eba9e, picard.sam.MergeBamAlignmentTest$HitSpec@172479c8], [], -1, 1, 1, 9)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11) STANDARD_ERROR INFO 2024-07-02 12:01:33 MergeBamAlignment Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.12196131332129464517.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.7147858157970510627.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.12196131332129464517.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.7147858157970510627.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.763 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:33.763 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.763 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:33.763 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.763 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:33.763 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.763 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:33.763 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.12196131332129464517.sam] OUTPUT=/tmp/merged.7147858157970510627.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:33 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.12196131332129464517.sam] OUTPUT=/tmp/merged.7147858157970510627.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.12196131332129464517.sam] INFO 2024-07-02 12:01:33 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.12196131332129464517.sam] Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 AbstractAlignmentMerger Wrote 1 alignment records and 1 unmapped reads. INFO 2024-07-02 12:01:33 AbstractAlignmentMerger Wrote 1 alignment records and 1 unmapped reads. Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:33 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 ValidateSamFile INFO 2024-07-02 12:01:33 ValidateSamFile Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ValidateSamFile -I /tmp/merged.7147858157970510627.sam ********** ValidateSamFile -I /tmp/merged.7147858157970510627.sam Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.807 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:33.807 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.807 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:33.807 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.808 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:33.808 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.808 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:33.808 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.7147858157970510627.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:33 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.7147858157970510627.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:33 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:33 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11) STANDARD_OUT No errors found Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11) STANDARD_ERROR [Tue Jul 02 12:01:33 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@4bc1516a, picard.sam.MergeBamAlignmentTest$HitSpec@a4537c, picard.sam.MergeBamAlignmentTest$HitSpec@6952b4ff], -1, 1, 1, 11)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0) STANDARD_ERROR INFO 2024-07-02 12:01:33 MergeBamAlignment Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.13811250576169649772.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.14288657389222471071.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.13811250576169649772.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.14288657389222471071.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.858 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:33.858 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.858 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:33.858 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.858 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:33.858 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.858 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:33.858 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.13811250576169649772.sam] OUTPUT=/tmp/merged.14288657389222471071.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:33 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.13811250576169649772.sam] OUTPUT=/tmp/merged.14288657389222471071.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.13811250576169649772.sam] INFO 2024-07-02 12:01:33 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.13811250576169649772.sam] Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 AbstractAlignmentMerger Wrote 0 alignment records and 2 unmapped reads. INFO 2024-07-02 12:01:33 AbstractAlignmentMerger Wrote 0 alignment records and 2 unmapped reads. Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:33 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 ValidateSamFile INFO 2024-07-02 12:01:33 ValidateSamFile Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ValidateSamFile -I /tmp/merged.14288657389222471071.sam ********** ValidateSamFile -I /tmp/merged.14288657389222471071.sam Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.912 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:33.912 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.912 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:33.912 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.920 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:33.920 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.920 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:33.920 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.14288657389222471071.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:33 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.14288657389222471071.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:33 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:33 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0) STANDARD_OUT No errors found Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0) STANDARD_ERROR [Tue Jul 02 12:01:33 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@45bcab00, picard.sam.MergeBamAlignmentTest$HitSpec@6b69a024, picard.sam.MergeBamAlignmentTest$HitSpec@4a7b3b4d], [], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0) STANDARD_ERROR INFO 2024-07-02 12:01:33 MergeBamAlignment Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.11906883472562678759.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.12687519415122572825.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.11906883472562678759.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.12687519415122572825.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.983 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:33.983 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.983 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:33.983 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.983 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:33.983 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:33.983 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:33.983 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.11906883472562678759.sam] OUTPUT=/tmp/merged.12687519415122572825.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:33 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.11906883472562678759.sam] OUTPUT=/tmp/merged.12687519415122572825.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.11906883472562678759.sam] INFO 2024-07-02 12:01:33 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.11906883472562678759.sam] Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:33 AbstractAlignmentMerger Wrote 0 alignment records and 2 unmapped reads. INFO 2024-07-02 12:01:33 AbstractAlignmentMerger Wrote 0 alignment records and 2 unmapped reads. Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:33 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:33 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:34 ValidateSamFile INFO 2024-07-02 12:01:34 ValidateSamFile Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ValidateSamFile -I /tmp/merged.12687519415122572825.sam ********** ValidateSamFile -I /tmp/merged.12687519415122572825.sam Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.032 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:34.032 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.032 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:34.032 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.032 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:34.032 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.032 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:34.032 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:34 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.12687519415122572825.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:34 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.12687519415122572825.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0) STANDARD_OUT No errors found Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:34 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0) STANDARD_ERROR [Tue Jul 02 12:01:34 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@53355fb3, picard.sam.MergeBamAlignmentTest$HitSpec@6f314ec1, picard.sam.MergeBamAlignmentTest$HitSpec@1e7cc730], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:34 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30) STANDARD_ERROR INFO 2024-07-02 12:01:34 MergeBamAlignment Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.17198195634923960667.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.2278480567179132830.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.17198195634923960667.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.2278480567179132830.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.116 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:34.116 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.116 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:34.116 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.116 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:34.116 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.116 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:34.116 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:34 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.17198195634923960667.sam] OUTPUT=/tmp/merged.2278480567179132830.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:34 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.17198195634923960667.sam] OUTPUT=/tmp/merged.2278480567179132830.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:34 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.17198195634923960667.sam] INFO 2024-07-02 12:01:34 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.17198195634923960667.sam] Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:34 AbstractAlignmentMerger Wrote 5 alignment records and 1 unmapped reads. INFO 2024-07-02 12:01:34 AbstractAlignmentMerger Wrote 5 alignment records and 1 unmapped reads. Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:34 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:34 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:34 ValidateSamFile INFO 2024-07-02 12:01:34 ValidateSamFile Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ValidateSamFile -I /tmp/merged.2278480567179132830.sam ********** ValidateSamFile -I /tmp/merged.2278480567179132830.sam Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.216 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:34.216 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.216 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:34.216 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.216 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:34.216 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.216 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:34.216 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:34 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.2278480567179132830.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:34 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.2278480567179132830.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30) STANDARD_OUT No errors found Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:34 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30) STANDARD_ERROR [Tue Jul 02 12:01:34 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@792fc3f3, picard.sam.MergeBamAlignmentTest$HitSpec@7537d2fb, picard.sam.MergeBamAlignmentTest$HitSpec@1182c907], [picard.sam.MergeBamAlignmentTest$HitSpec@19dddd7c, picard.sam.MergeBamAlignmentTest$HitSpec@1eeab5ef, picard.sam.MergeBamAlignmentTest$HitSpec@55811cc3], -1, 3, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:34 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30) STANDARD_ERROR INFO 2024-07-02 12:01:34 MergeBamAlignment Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.18314290825650721509.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.12760333927200056404.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.18314290825650721509.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.12760333927200056404.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.330 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:34.330 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.339 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:34.339 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.339 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:34.339 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.339 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:34.339 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:34 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.18314290825650721509.sam] OUTPUT=/tmp/merged.12760333927200056404.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:34 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.18314290825650721509.sam] OUTPUT=/tmp/merged.12760333927200056404.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:34 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.18314290825650721509.sam] INFO 2024-07-02 12:01:34 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.18314290825650721509.sam] Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:34 AbstractAlignmentMerger Wrote 4 alignment records and 1 unmapped reads. INFO 2024-07-02 12:01:34 AbstractAlignmentMerger Wrote 4 alignment records and 1 unmapped reads. Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:34 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:34 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:34 ValidateSamFile INFO 2024-07-02 12:01:34 ValidateSamFile Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ValidateSamFile -I /tmp/merged.12760333927200056404.sam ********** ValidateSamFile -I /tmp/merged.12760333927200056404.sam Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.435 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:34.435 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.435 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:34.435 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.435 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:34.435 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.435 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:34.435 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:34 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.12760333927200056404.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:34 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.12760333927200056404.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30) STANDARD_OUT No errors found Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:34 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30) STANDARD_ERROR [Tue Jul 02 12:01:34 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@42cbc29d, picard.sam.MergeBamAlignmentTest$HitSpec@15590227, picard.sam.MergeBamAlignmentTest$HitSpec@27e1daee], [picard.sam.MergeBamAlignmentTest$HitSpec@648e001d, picard.sam.MergeBamAlignmentTest$HitSpec@78cde93b, picard.sam.MergeBamAlignmentTest$HitSpec@25d8943f], -1, 2, 3, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:34 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21) STANDARD_ERROR INFO 2024-07-02 12:01:34 MergeBamAlignment Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.1108860727693019994.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.5057299072669603106.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.1108860727693019994.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.5057299072669603106.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.539 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:34.539 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.539 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:34.539 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.539 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:34.539 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.540 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:34.540 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:34 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.1108860727693019994.sam] OUTPUT=/tmp/merged.5057299072669603106.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:34 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.1108860727693019994.sam] OUTPUT=/tmp/merged.5057299072669603106.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:34 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.1108860727693019994.sam] INFO 2024-07-02 12:01:34 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.1108860727693019994.sam] Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:34 AbstractAlignmentMerger Wrote 4 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:34 AbstractAlignmentMerger Wrote 4 alignment records and 0 unmapped reads. Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:34 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:34 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:34 ValidateSamFile INFO 2024-07-02 12:01:34 ValidateSamFile Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ValidateSamFile -I /tmp/merged.5057299072669603106.sam ********** ValidateSamFile -I /tmp/merged.5057299072669603106.sam Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.672 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:34.672 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.672 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:34.672 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.672 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:34.672 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.672 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:34.672 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:34 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.5057299072669603106.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:34 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.5057299072669603106.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21) STANDARD_OUT No errors found Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:34 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21) STANDARD_ERROR [Tue Jul 02 12:01:34 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@82c97a3, picard.sam.MergeBamAlignmentTest$HitSpec@4966745f, picard.sam.MergeBamAlignmentTest$HitSpec@677793d4], [picard.sam.MergeBamAlignmentTest$HitSpec@60c8d509, picard.sam.MergeBamAlignmentTest$HitSpec@c35c73c, picard.sam.MergeBamAlignmentTest$HitSpec@768b8e69], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:34 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21) STANDARD_ERROR INFO 2024-07-02 12:01:34 MergeBamAlignment Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.7815354523314169090.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.17708501557640626555.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.7815354523314169090.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.17708501557640626555.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.793 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:34.793 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.793 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:34.793 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.794 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:34.794 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.794 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:34.794 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:34 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.7815354523314169090.sam] OUTPUT=/tmp/merged.17708501557640626555.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:34 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.7815354523314169090.sam] OUTPUT=/tmp/merged.17708501557640626555.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:34 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.7815354523314169090.sam] INFO 2024-07-02 12:01:34 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.7815354523314169090.sam] Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:34 AbstractAlignmentMerger Wrote 4 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:34 AbstractAlignmentMerger Wrote 4 alignment records and 0 unmapped reads. Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:34 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:34 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:34 ValidateSamFile INFO 2024-07-02 12:01:34 ValidateSamFile Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ValidateSamFile -I /tmp/merged.17708501557640626555.sam ********** ValidateSamFile -I /tmp/merged.17708501557640626555.sam Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.911 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:34.911 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.911 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:34.911 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.911 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:34.911 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:34.911 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:34.911 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:34 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.17708501557640626555.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:34 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.17708501557640626555.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21) STANDARD_OUT No errors found Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:34 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21) STANDARD_ERROR [Tue Jul 02 12:01:34 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@29a0519f, picard.sam.MergeBamAlignmentTest$HitSpec@3264f1c1, picard.sam.MergeBamAlignmentTest$HitSpec@a080312], [picard.sam.MergeBamAlignmentTest$HitSpec@310bc115, picard.sam.MergeBamAlignmentTest$HitSpec@1a0c5202, picard.sam.MergeBamAlignmentTest$HitSpec@ff3527b], 1, 2, 2, 21)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:35 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30) STANDARD_ERROR INFO 2024-07-02 12:01:35 MergeBamAlignment Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.2623429773112800598.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.16714747940698874695.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.2623429773112800598.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.16714747940698874695.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:35.022 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:35.022 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:35.022 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:35.022 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:35.022 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:35.022 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:35.022 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:35.022 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:35 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.2623429773112800598.sam] OUTPUT=/tmp/merged.16714747940698874695.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:35 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.2623429773112800598.sam] OUTPUT=/tmp/merged.16714747940698874695.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:35 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.2623429773112800598.sam] INFO 2024-07-02 12:01:35 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.2623429773112800598.sam] Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:35 AbstractAlignmentMerger Wrote 3 alignment records and 1 unmapped reads. INFO 2024-07-02 12:01:35 AbstractAlignmentMerger Wrote 3 alignment records and 1 unmapped reads. Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:35 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:35 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:35 ValidateSamFile INFO 2024-07-02 12:01:35 ValidateSamFile Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ValidateSamFile -I /tmp/merged.16714747940698874695.sam ********** ValidateSamFile -I /tmp/merged.16714747940698874695.sam Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:35.150 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:35.150 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:35.150 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:35.150 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:35.150 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:35.150 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:35.150 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:35.150 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:35 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.16714747940698874695.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:35 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.16714747940698874695.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:35 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:35 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30) STANDARD_OUT No errors found Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:35 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30) STANDARD_ERROR [Tue Jul 02 12:01:35 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@71e87b3c, picard.sam.MergeBamAlignmentTest$HitSpec@b276847, picard.sam.MergeBamAlignmentTest$HitSpec@569f7c34], [picard.sam.MergeBamAlignmentTest$HitSpec@63c64da7, picard.sam.MergeBamAlignmentTest$HitSpec@5145eb78, picard.sam.MergeBamAlignmentTest$HitSpec@6110c447], -1, 2, 2, 30)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:35 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40) STANDARD_ERROR INFO 2024-07-02 12:01:35 MergeBamAlignment Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.8781562466209570055.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.17349355923595055252.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.8781562466209570055.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.17349355923595055252.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:35.298 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:35.298 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:35.298 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:35.298 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:35.298 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:35.298 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:35.298 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:35.298 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:35 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.8781562466209570055.sam] OUTPUT=/tmp/merged.17349355923595055252.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:35 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.8781562466209570055.sam] OUTPUT=/tmp/merged.17349355923595055252.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:35 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.8781562466209570055.sam] INFO 2024-07-02 12:01:35 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.8781562466209570055.sam] Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:35 AbstractAlignmentMerger Wrote 4 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:35 AbstractAlignmentMerger Wrote 4 alignment records and 0 unmapped reads. Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:35 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:35 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:35 ValidateSamFile INFO 2024-07-02 12:01:35 ValidateSamFile Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ValidateSamFile -I /tmp/merged.17349355923595055252.sam ********** ValidateSamFile -I /tmp/merged.17349355923595055252.sam Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:35.573 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:35.573 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:35.573 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:35.573 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:35.573 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:35.573 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:35.573 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:35.573 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:35 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.17349355923595055252.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:35 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.17349355923595055252.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:35 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:35 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40) STANDARD_OUT No errors found Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:35 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40) STANDARD_ERROR [Tue Jul 02 12:01:35 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4a419021, picard.sam.MergeBamAlignmentTest$HitSpec@7bdb1620, picard.sam.MergeBamAlignmentTest$HitSpec@24e940b9], [picard.sam.MergeBamAlignmentTest$HitSpec@2cb9e354, picard.sam.MergeBamAlignmentTest$HitSpec@6abfbe7a, picard.sam.MergeBamAlignmentTest$HitSpec@4976df1b], 1, 2, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:35 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40) STANDARD_ERROR INFO 2024-07-02 12:01:35 MergeBamAlignment Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.11130964109075124629.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.6695183742362531894.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.11130964109075124629.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.6695183742362531894.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:35.690 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:35.690 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:35.690 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:35.690 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:35.690 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:35.690 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:35.690 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:35.690 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:35 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.11130964109075124629.sam] OUTPUT=/tmp/merged.6695183742362531894.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:35 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.11130964109075124629.sam] OUTPUT=/tmp/merged.6695183742362531894.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:35 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.11130964109075124629.sam] INFO 2024-07-02 12:01:35 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.11130964109075124629.sam] Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:35 AbstractAlignmentMerger Wrote 5 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:35 AbstractAlignmentMerger Wrote 5 alignment records and 0 unmapped reads. Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:35 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:35 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:35 ValidateSamFile INFO 2024-07-02 12:01:35 ValidateSamFile Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ValidateSamFile -I /tmp/merged.6695183742362531894.sam ********** ValidateSamFile -I /tmp/merged.6695183742362531894.sam Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:35.814 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:35.814 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:35.814 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:35.814 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:35.814 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:35.814 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:35.814 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:35.814 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:35 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.6695183742362531894.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:35 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.6695183742362531894.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:35 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:35 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40) STANDARD_OUT No errors found Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:35 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40) STANDARD_ERROR [Tue Jul 02 12:01:35 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@3b8440e9, picard.sam.MergeBamAlignmentTest$HitSpec@55f21bc6, picard.sam.MergeBamAlignmentTest$HitSpec@74eea0f3], [picard.sam.MergeBamAlignmentTest$HitSpec@595171dc, picard.sam.MergeBamAlignmentTest$HitSpec@404bf117, picard.sam.MergeBamAlignmentTest$HitSpec@522eef3], 2, 3, 2, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:35 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40) STANDARD_ERROR INFO 2024-07-02 12:01:35 MergeBamAlignment Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.5530725463111293903.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.16753704838442196234.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.5530725463111293903.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.16753704838442196234.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:35.942 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:35.942 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:35.942 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:35.942 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:35.942 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:35.942 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:35.942 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:35.942 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:35 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.5530725463111293903.sam] OUTPUT=/tmp/merged.16753704838442196234.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:35 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.5530725463111293903.sam] OUTPUT=/tmp/merged.16753704838442196234.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:35 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.5530725463111293903.sam] INFO 2024-07-02 12:01:35 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.5530725463111293903.sam] Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:36 AbstractAlignmentMerger Wrote 5 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:36 AbstractAlignmentMerger Wrote 5 alignment records and 0 unmapped reads. Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:36 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:36 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:36 ValidateSamFile INFO 2024-07-02 12:01:36 ValidateSamFile Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ValidateSamFile -I /tmp/merged.16753704838442196234.sam ********** ValidateSamFile -I /tmp/merged.16753704838442196234.sam Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:36.107 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:36.107 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:36.107 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:36.107 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:36.108 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:36.108 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:36.108 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:36.108 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:36 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.16753704838442196234.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:36 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.16753704838442196234.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:36 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:36 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40) STANDARD_OUT No errors found Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:36 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40) STANDARD_ERROR [Tue Jul 02 12:01:36 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@48265e12, picard.sam.MergeBamAlignmentTest$HitSpec@3f240b6f, picard.sam.MergeBamAlignmentTest$HitSpec@22859451], [picard.sam.MergeBamAlignmentTest$HitSpec@3168a28f, picard.sam.MergeBamAlignmentTest$HitSpec@4b44bc7e, picard.sam.MergeBamAlignmentTest$HitSpec@54a4a90a], 2, 2, 3, 40)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:36 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0) STANDARD_ERROR INFO 2024-07-02 12:01:36 MergeBamAlignment Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.17583945416787385135.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.14079321355349832050.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /tmp/aligned.17583945416787385135.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta -OUTPUT /tmp/merged.14079321355349832050.sam -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:36.251 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:36.251 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:36.251 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:36.251 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:36.252 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:36.252 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:36.252 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:36.252 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:36 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.17583945416787385135.sam] OUTPUT=/tmp/merged.14079321355349832050.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:36 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.17583945416787385135.sam] OUTPUT=/tmp/merged.14079321355349832050.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/merger.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:36 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.17583945416787385135.sam] INFO 2024-07-02 12:01:36 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.17583945416787385135.sam] Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:36 AbstractAlignmentMerger Wrote 0 alignment records and 2 unmapped reads. INFO 2024-07-02 12:01:36 AbstractAlignmentMerger Wrote 0 alignment records and 2 unmapped reads. Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:36 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:36 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:36 ValidateSamFile INFO 2024-07-02 12:01:36 ValidateSamFile Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ValidateSamFile -I /tmp/merged.14079321355349832050.sam ********** ValidateSamFile -I /tmp/merged.14079321355349832050.sam Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:36.407 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:36.407 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:36.408 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:36.408 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:36.408 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:36.408 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:36.408 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:36.408 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:36 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.14079321355349832050.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:36 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/merged.14079321355349832050.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:36 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:36 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0) STANDARD_OUT No errors found Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:36 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0) STANDARD_ERROR [Tue Jul 02 12:01:36 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@196b86f8, picard.sam.MergeBamAlignmentTest$HitSpec@7afd4b48, picard.sam.MergeBamAlignmentTest$HitSpec@7b904d7b], [picard.sam.MergeBamAlignmentTest$HitSpec@47c11c65, picard.sam.MergeBamAlignmentTest$HitSpec@2d81e23, picard.sam.MergeBamAlignmentTest$HitSpec@126fa23b], null, 1, 1, 0)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testRemoveNmMdAndUqOnOverlappingReads(picard.sam.MergeBamAlignmentTest) Test: Test method testRemoveNmMdAndUqOnOverlappingReads(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:36 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testRemoveNmMdAndUqOnOverlappingReads STANDARD_ERROR INFO 2024-07-02 12:01:36 MergeBamAlignment Test: Test method testRemoveNmMdAndUqOnOverlappingReads(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testRemoveNmMdAndUqOnOverlappingReads(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testRemoveNmMdAndUqOnOverlappingReads(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testRemoveNmMdAndUqOnOverlappingReads(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testRemoveNmMdAndUqOnOverlappingReads(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testRemoveNmMdAndUqOnOverlappingReads(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testRemoveNmMdAndUqOnOverlappingReads(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testRemoveNmMdAndUqOnOverlappingReads(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testRemoveNmMdAndUqOnOverlappingReads(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/removetags.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/removetags.aligned.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/removetags.fasta -OUTPUT /tmp/testRemoveNmMdAndUqOnOverlappingReads6318702943562649696.sam -EXPECTED_ORIENTATIONS FR -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -SORT_ORDER queryname ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/removetags.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/removetags.aligned.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/removetags.fasta -OUTPUT /tmp/testRemoveNmMdAndUqOnOverlappingReads6318702943562649696.sam -EXPECTED_ORIENTATIONS FR -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af -SORT_ORDER queryname Test: Test method testRemoveNmMdAndUqOnOverlappingReads(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testRemoveNmMdAndUqOnOverlappingReads(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testRemoveNmMdAndUqOnOverlappingReads(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testRemoveNmMdAndUqOnOverlappingReads(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:36.553 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:36.553 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRemoveNmMdAndUqOnOverlappingReads(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:36.553 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:36.553 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRemoveNmMdAndUqOnOverlappingReads(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:36.553 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:36.553 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testRemoveNmMdAndUqOnOverlappingReads(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:36.553 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:36.553 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testRemoveNmMdAndUqOnOverlappingReads(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:36 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/removetags.unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/removetags.aligned.sam] OUTPUT=/tmp/testRemoveNmMdAndUqOnOverlappingReads6318702943562649696.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] SORT_ORDER=queryname REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/removetags.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:36 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/removetags.unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/removetags.aligned.sam] OUTPUT=/tmp/testRemoveNmMdAndUqOnOverlappingReads6318702943562649696.sam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] SORT_ORDER=queryname REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/removetags.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testRemoveNmMdAndUqOnOverlappingReads(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testRemoveNmMdAndUqOnOverlappingReads(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:36 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/removetags.aligned.sam] INFO 2024-07-02 12:01:36 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/removetags.aligned.sam] Test: Test method testRemoveNmMdAndUqOnOverlappingReads(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:36 AbstractAlignmentMerger Wrote 8 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:36 AbstractAlignmentMerger Wrote 8 alignment records and 0 unmapped reads. Test: Test method testRemoveNmMdAndUqOnOverlappingReads(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:36 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:36 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testRemoveNmMdAndUqOnOverlappingReads(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testShortFragmentClipping(picard.sam.MergeBamAlignmentTest) Test: Test method testShortFragmentClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:36 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testShortFragmentClipping STANDARD_ERROR INFO 2024-07-02 12:01:36 MergeBamAlignment Test: Test method testShortFragmentClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testShortFragmentClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testShortFragmentClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testShortFragmentClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testShortFragmentClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testShortFragmentClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testShortFragmentClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testShortFragmentClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testShortFragmentClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.aligned.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta -OUTPUT /tmp/testShortFragmentClipping5068535450423992763.bam -EXPECTED_ORIENTATIONS FR -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.unmapped.sam -ALIGNED_READS_ONLY false -CLIP_ADAPTERS true -IS_BISULFITE_SEQUENCE false -MAX_INSERTIONS_OR_DELETIONS 1 -ADD_PG_TAG_TO_READS true -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.aligned.sam -PROGRAM_RECORD_ID 0 -PROGRAM_GROUP_VERSION 1.0 -PROGRAM_GROUP_COMMAND_LINE align! -PROGRAM_GROUP_NAME myAligner -PAIRED_RUN true -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta -OUTPUT /tmp/testShortFragmentClipping5068535450423992763.bam -EXPECTED_ORIENTATIONS FR -ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 -ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ -ATTRIBUTES_TO_REVERSE_COMPLEMENT ab -ATTRIBUTES_TO_REVERSE OQ -ATTRIBUTES_TO_REVERSE U2 -ATTRIBUTES_TO_REVERSE aa -ATTRIBUTES_TO_REVERSE ac -ATTRIBUTES_TO_REVERSE as -ATTRIBUTES_TO_REVERSE ai -ATTRIBUTES_TO_REVERSE af Test: Test method testShortFragmentClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testShortFragmentClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testShortFragmentClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testShortFragmentClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:36.682 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:36.682 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testShortFragmentClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:36.682 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:36.682 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testShortFragmentClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:36.682 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:36.682 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testShortFragmentClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:36.682 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:36.682 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testShortFragmentClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:36 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.aligned.sam] OUTPUT=/tmp/testShortFragmentClipping5068535450423992763.bam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:36 GMT+14:00 2024] MergeBamAlignment ADD_PG_TAG_TO_READS=true UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.aligned.sam] OUTPUT=/tmp/testShortFragmentClipping5068535450423992763.bam PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2, aa, ac, af, ai, as] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ, ab] EXPECTED_ORIENTATIONS=[FR] REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true HARD_CLIP_OVERLAPPING_READS=false INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testShortFragmentClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testShortFragmentClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:36 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.aligned.sam] INFO 2024-07-02 12:01:36 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.aligned.sam] Test: Test method testShortFragmentClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:36 AbstractAlignmentMerger Wrote 10 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:36 AbstractAlignmentMerger Wrote 10 alignment records and 0 unmapped reads. Test: Test method testShortFragmentClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:36 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:36 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testShortFragmentClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testShortFragmentHardClipping(picard.sam.MergeBamAlignmentTest) Test: Test method testShortFragmentHardClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:36 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testShortFragmentHardClipping STANDARD_ERROR INFO 2024-07-02 12:01:36 MergeBamAlignment Test: Test method testShortFragmentHardClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testShortFragmentHardClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testShortFragmentHardClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testShortFragmentHardClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testShortFragmentHardClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testShortFragmentHardClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testShortFragmentHardClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testShortFragmentHardClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testShortFragmentHardClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/hardclip.unmapped.sam -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/hardclip.aligned.sam -OUTPUT /tmp/testShortFragmentClipping571222793652074331.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta -HARD_CLIP_OVERLAPPING_READS true ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/hardclip.unmapped.sam -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/hardclip.aligned.sam -OUTPUT /tmp/testShortFragmentClipping571222793652074331.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta -HARD_CLIP_OVERLAPPING_READS true Test: Test method testShortFragmentHardClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testShortFragmentHardClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testShortFragmentHardClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testShortFragmentHardClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:36.812 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:36.812 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testShortFragmentHardClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:36.812 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:36.812 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testShortFragmentHardClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:36.812 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:36.812 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testShortFragmentHardClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:36.812 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:36.812 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testShortFragmentHardClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:36 GMT+14:00 2024] MergeBamAlignment UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/hardclip.unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/hardclip.aligned.sam] OUTPUT=/tmp/testShortFragmentClipping571222793652074331.sam HARD_CLIP_OVERLAPPING_READS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta ADD_PG_TAG_TO_READS=true PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ] READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:36 GMT+14:00 2024] MergeBamAlignment UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/hardclip.unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/hardclip.aligned.sam] OUTPUT=/tmp/testShortFragmentClipping571222793652074331.sam HARD_CLIP_OVERLAPPING_READS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta ADD_PG_TAG_TO_READS=true PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ] READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testShortFragmentHardClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testShortFragmentHardClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:36 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/hardclip.aligned.sam] INFO 2024-07-02 12:01:36 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/hardclip.aligned.sam] Test: Test method testShortFragmentHardClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:36 AbstractAlignmentMerger Wrote 10 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:36 AbstractAlignmentMerger Wrote 10 alignment records and 0 unmapped reads. Test: Test method testShortFragmentHardClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:36 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:36 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testShortFragmentHardClipping(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testShortFragmentWithIndelsClipping[0](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected.sam, false)(picard.sam.MergeBamAlignmentTest) Test: Test method testShortFragmentWithIndelsClipping[0](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected.sam, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:36 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testShortFragmentWithIndelsClipping[0](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected.sam, false) STANDARD_ERROR INFO 2024-07-02 12:01:36 MergeBamAlignment Test: Test method testShortFragmentWithIndelsClipping[0](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected.sam, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testShortFragmentWithIndelsClipping[0](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected.sam, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testShortFragmentWithIndelsClipping[0](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected.sam, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testShortFragmentWithIndelsClipping[0](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected.sam, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testShortFragmentWithIndelsClipping[0](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected.sam, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testShortFragmentWithIndelsClipping[0](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected.sam, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testShortFragmentWithIndelsClipping[0](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected.sam, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testShortFragmentWithIndelsClipping[0](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected.sam, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testShortFragmentWithIndelsClipping[0](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected.sam, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/indel_reads_unmapped.sam -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/indel_reads_aligned.sam -OUTPUT /tmp/testShortFragmentClipping4836301604651990444.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta -HARD_CLIP_OVERLAPPING_READS true -SORT_ORDER queryname ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/indel_reads_unmapped.sam -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/indel_reads_aligned.sam -OUTPUT /tmp/testShortFragmentClipping4836301604651990444.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta -HARD_CLIP_OVERLAPPING_READS true -SORT_ORDER queryname Test: Test method testShortFragmentWithIndelsClipping[0](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected.sam, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testShortFragmentWithIndelsClipping[0](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected.sam, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testShortFragmentWithIndelsClipping[0](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected.sam, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testShortFragmentWithIndelsClipping[0](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected.sam, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:36.922 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:36.922 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testShortFragmentWithIndelsClipping[0](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected.sam, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:36.922 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:36.922 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testShortFragmentWithIndelsClipping[0](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected.sam, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:36.922 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:36.922 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testShortFragmentWithIndelsClipping[0](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected.sam, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:36.922 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:36.922 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testShortFragmentWithIndelsClipping[0](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected.sam, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:36 GMT+14:00 2024] MergeBamAlignment UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/indel_reads_unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/indel_reads_aligned.sam] OUTPUT=/tmp/testShortFragmentClipping4836301604651990444.sam SORT_ORDER=queryname HARD_CLIP_OVERLAPPING_READS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta ADD_PG_TAG_TO_READS=true PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ] READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:36 GMT+14:00 2024] MergeBamAlignment UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/indel_reads_unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/indel_reads_aligned.sam] OUTPUT=/tmp/testShortFragmentClipping4836301604651990444.sam SORT_ORDER=queryname HARD_CLIP_OVERLAPPING_READS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta ADD_PG_TAG_TO_READS=true PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ] READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testShortFragmentWithIndelsClipping[0](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected.sam, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testShortFragmentWithIndelsClipping[0](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected.sam, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:36 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/indel_reads_aligned.sam] INFO 2024-07-02 12:01:36 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/indel_reads_aligned.sam] Test: Test method testShortFragmentWithIndelsClipping[0](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected.sam, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:36 AbstractAlignmentMerger Wrote 26 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:36 AbstractAlignmentMerger Wrote 26 alignment records and 0 unmapped reads. Test: Test method testShortFragmentWithIndelsClipping[0](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected.sam, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:36 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:36 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testShortFragmentWithIndelsClipping[0](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected.sam, false)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testShortFragmentWithIndelsClipping[1](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected_with_hardclips.sam, true)(picard.sam.MergeBamAlignmentTest) Test: Test method testShortFragmentWithIndelsClipping[1](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected_with_hardclips.sam, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:37 MergeBamAlignment Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testShortFragmentWithIndelsClipping[1](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected_with_hardclips.sam, true) STANDARD_ERROR INFO 2024-07-02 12:01:37 MergeBamAlignment Test: Test method testShortFragmentWithIndelsClipping[1](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected_with_hardclips.sam, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testShortFragmentWithIndelsClipping[1](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected_with_hardclips.sam, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testShortFragmentWithIndelsClipping[1](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected_with_hardclips.sam, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testShortFragmentWithIndelsClipping[1](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected_with_hardclips.sam, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testShortFragmentWithIndelsClipping[1](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected_with_hardclips.sam, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testShortFragmentWithIndelsClipping[1](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected_with_hardclips.sam, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testShortFragmentWithIndelsClipping[1](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected_with_hardclips.sam, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testShortFragmentWithIndelsClipping[1](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected_with_hardclips.sam, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testShortFragmentWithIndelsClipping[1](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected_with_hardclips.sam, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/indel_reads_unmapped.sam -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/indel_reads_aligned.sam -OUTPUT /tmp/testShortFragmentClipping3458696521630281095.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta -HARD_CLIP_OVERLAPPING_READS true -SORT_ORDER queryname ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/indel_reads_unmapped.sam -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/indel_reads_aligned.sam -OUTPUT /tmp/testShortFragmentClipping3458696521630281095.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta -HARD_CLIP_OVERLAPPING_READS true -SORT_ORDER queryname Test: Test method testShortFragmentWithIndelsClipping[1](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected_with_hardclips.sam, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: ********** ********** Test: Test method testShortFragmentWithIndelsClipping[1](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected_with_hardclips.sam, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testShortFragmentWithIndelsClipping[1](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected_with_hardclips.sam, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Test: Test method testShortFragmentWithIndelsClipping[1](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected_with_hardclips.sam, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:37.031 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:37.031 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testShortFragmentWithIndelsClipping[1](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected_with_hardclips.sam, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:37.031 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:37.031 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testShortFragmentWithIndelsClipping[1](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected_with_hardclips.sam, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:37.031 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:37.031 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testShortFragmentWithIndelsClipping[1](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected_with_hardclips.sam, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: 12:01:37.031 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:37.031 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testShortFragmentWithIndelsClipping[1](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected_with_hardclips.sam, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:37 GMT+14:00 2024] MergeBamAlignment UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/indel_reads_unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/indel_reads_aligned.sam] OUTPUT=/tmp/testShortFragmentClipping3458696521630281095.sam SORT_ORDER=queryname HARD_CLIP_OVERLAPPING_READS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta ADD_PG_TAG_TO_READS=true PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ] READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:37 GMT+14:00 2024] MergeBamAlignment UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/indel_reads_unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/indel_reads_aligned.sam] OUTPUT=/tmp/testShortFragmentClipping3458696521630281095.sam SORT_ORDER=queryname HARD_CLIP_OVERLAPPING_READS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta ADD_PG_TAG_TO_READS=true PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ] READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testShortFragmentWithIndelsClipping[1](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected_with_hardclips.sam, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testShortFragmentWithIndelsClipping[1](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected_with_hardclips.sam, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:37 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/indel_reads_aligned.sam] INFO 2024-07-02 12:01:37 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/indel_reads_aligned.sam] Test: Test method testShortFragmentWithIndelsClipping[1](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected_with_hardclips.sam, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:37 AbstractAlignmentMerger Wrote 26 alignment records and 0 unmapped reads. INFO 2024-07-02 12:01:37 AbstractAlignmentMerger Wrote 26 alignment records and 0 unmapped reads. Test: Test method testShortFragmentWithIndelsClipping[1](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected_with_hardclips.sam, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: [Tue Jul 02 12:01:37 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:37 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testShortFragmentWithIndelsClipping[1](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected_with_hardclips.sam, true)(picard.sam.MergeBamAlignmentTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testSortingOnSamAlignmentMerger[0](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned_queryname_sorted.sam, true, true, Basic test with pre-sorted alignment)(picard.sam.MergeBamAlignmentTest) Test: Test method testSortingOnSamAlignmentMerger[0](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned_queryname_sorted.sam, true, true, Basic test with pre-sorted alignment)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:37 SamAlignmentMerger Processing SAM file(s): [testdata/picard/sam/aligned_queryname_sorted.sam] Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testSortingOnSamAlignmentMerger[0](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned_queryname_sorted.sam, true, true, Basic test with pre-sorted alignment) STANDARD_ERROR INFO 2024-07-02 12:01:37 SamAlignmentMerger Processing SAM file(s): [testdata/picard/sam/aligned_queryname_sorted.sam] Test: Test method testSortingOnSamAlignmentMerger[0](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned_queryname_sorted.sam, true, true, Basic test with pre-sorted alignment)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:37 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/target13800262037809115088bam INFO 2024-07-02 12:01:37 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/target13800262037809115088bam Test: Test method testSortingOnSamAlignmentMerger[0](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned_queryname_sorted.sam, true, true, Basic test with pre-sorted alignment)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:37 AbstractAlignmentMerger Wrote 6 alignment records and 4 unmapped reads. INFO 2024-07-02 12:01:37 AbstractAlignmentMerger Wrote 6 alignment records and 4 unmapped reads. Running Test: Test method testSortingOnSamAlignmentMerger[1](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned.sam, false, true, Basic test with unsorted alignment)(picard.sam.MergeBamAlignmentTest) Test: Test method testSortingOnSamAlignmentMerger[1](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned.sam, false, true, Basic test with unsorted alignment)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:37 SamAlignmentMerger Processing SAM file(s): [testdata/picard/sam/aligned.sam] Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testSortingOnSamAlignmentMerger[1](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned.sam, false, true, Basic test with unsorted alignment) STANDARD_ERROR INFO 2024-07-02 12:01:37 SamAlignmentMerger Processing SAM file(s): [testdata/picard/sam/aligned.sam] Test: Test method testSortingOnSamAlignmentMerger[1](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned.sam, false, true, Basic test with unsorted alignment)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:37 SamAlignmentMerger Exception merging bam alignment - attempting to sort aligned reads and try again: Underlying iterator is not queryname sorted: read_2_too_many_gaps 1/2 101b aligned to chr7:1-101. > both_reads_align_clip_adapter 2/2 101b aligned to chr7:16-116. WARNING 2024-07-02 12:01:37 SamAlignmentMerger Exception merging bam alignment - attempting to sort aligned reads and try again: Underlying iterator is not queryname sorted: read_2_too_many_gaps 1/2 101b aligned to chr7:1-101. > both_reads_align_clip_adapter 2/2 101b aligned to chr7:16-116. Test: Test method testSortingOnSamAlignmentMerger[1](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned.sam, false, true, Basic test with unsorted alignment)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:37 SamAlignmentMerger Finished reading 8 total records from alignment SAM/BAM. INFO 2024-07-02 12:01:37 SamAlignmentMerger Finished reading 8 total records from alignment SAM/BAM. Test: Test method testSortingOnSamAlignmentMerger[1](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned.sam, false, true, Basic test with unsorted alignment)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:37 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/target16305266479115901013bam INFO 2024-07-02 12:01:37 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/target16305266479115901013bam Test: Test method testSortingOnSamAlignmentMerger[1](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned.sam, false, true, Basic test with unsorted alignment)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:37 AbstractAlignmentMerger Wrote 6 alignment records and 4 unmapped reads. INFO 2024-07-02 12:01:37 AbstractAlignmentMerger Wrote 6 alignment records and 4 unmapped reads. Running Test: Test method testSortingOnSamAlignmentMerger[2](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned_queryname_sorted.sam, true, false, Basic test with pre-sorted alignment)(picard.sam.MergeBamAlignmentTest) Test: Test method testSortingOnSamAlignmentMerger[2](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned_queryname_sorted.sam, true, false, Basic test with pre-sorted alignment)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:37 SamAlignmentMerger Processing SAM file(s): [testdata/picard/sam/aligned_queryname_sorted.sam] Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testSortingOnSamAlignmentMerger[2](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned_queryname_sorted.sam, true, false, Basic test with pre-sorted alignment) STANDARD_ERROR INFO 2024-07-02 12:01:37 SamAlignmentMerger Processing SAM file(s): [testdata/picard/sam/aligned_queryname_sorted.sam] Test: Test method testSortingOnSamAlignmentMerger[2](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned_queryname_sorted.sam, true, false, Basic test with pre-sorted alignment)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:37 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/target13633197373724578713bam INFO 2024-07-02 12:01:37 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/target13633197373724578713bam Test: Test method testSortingOnSamAlignmentMerger[2](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned_queryname_sorted.sam, true, false, Basic test with pre-sorted alignment)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:37 AbstractAlignmentMerger Wrote 6 alignment records and 4 unmapped reads. INFO 2024-07-02 12:01:37 AbstractAlignmentMerger Wrote 6 alignment records and 4 unmapped reads. Running Test: Test method testSortingOnSamAlignmentMerger[3](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned.sam, false, false, Basic test with unsorted alignment)(picard.sam.MergeBamAlignmentTest) Test: Test method testSortingOnSamAlignmentMerger[3](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned.sam, false, false, Basic test with unsorted alignment)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:37 SamAlignmentMerger Processing SAM file(s): [testdata/picard/sam/aligned.sam] Gradle suite > Gradle test > picard.sam.MergeBamAlignmentTest.testSortingOnSamAlignmentMerger[3](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned.sam, false, false, Basic test with unsorted alignment) STANDARD_ERROR INFO 2024-07-02 12:01:37 SamAlignmentMerger Processing SAM file(s): [testdata/picard/sam/aligned.sam] Test: Test method testSortingOnSamAlignmentMerger[3](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned.sam, false, false, Basic test with unsorted alignment)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:37 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/target16942433508236510554bam INFO 2024-07-02 12:01:37 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/target16942433508236510554bam Test: Test method testSortingOnSamAlignmentMerger[3](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned.sam, false, false, Basic test with unsorted alignment)(picard.sam.MergeBamAlignmentTest) produced standard out/err: WARNING 2024-07-02 12:01:37 SamAlignmentMerger Exception merging bam alignment - attempting to sort aligned reads and try again: Underlying iterator is not queryname sorted: read_2_too_many_gaps 1/2 101b aligned to chr7:1-101. > both_reads_align_clip_adapter 2/2 101b aligned to chr7:16-116. WARNING 2024-07-02 12:01:37 SamAlignmentMerger Exception merging bam alignment - attempting to sort aligned reads and try again: Underlying iterator is not queryname sorted: read_2_too_many_gaps 1/2 101b aligned to chr7:1-101. > both_reads_align_clip_adapter 2/2 101b aligned to chr7:16-116. Test: Test method testSortingOnSamAlignmentMerger[3](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned.sam, false, false, Basic test with unsorted alignment)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:37 SamAlignmentMerger Finished reading 8 total records from alignment SAM/BAM. INFO 2024-07-02 12:01:37 SamAlignmentMerger Finished reading 8 total records from alignment SAM/BAM. Test: Test method testSortingOnSamAlignmentMerger[3](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned.sam, false, false, Basic test with unsorted alignment)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:37 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/target16942433508236510554bam INFO 2024-07-02 12:01:37 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/target16942433508236510554bam Test: Test method testSortingOnSamAlignmentMerger[3](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned.sam, false, false, Basic test with unsorted alignment)(picard.sam.MergeBamAlignmentTest) produced standard out/err: INFO 2024-07-02 12:01:37 AbstractAlignmentMerger Wrote 6 alignment records and 4 unmapped reads. INFO 2024-07-02 12:01:37 AbstractAlignmentMerger Wrote 6 alignment records and 4 unmapped reads. Running Test: Test method testMergePedIntoVcf(picard.arrays.MergePedIntoVcfTest) Running Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: INFO 2024-07-02 12:01:37 MergeSamFiles Gradle suite > Gradle test > picard.sam.MergeSamFilesTest.unsortedInputSortedOutputTest STANDARD_ERROR INFO 2024-07-02 12:01:37 MergeSamFiles Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: ********** ********** Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: ********** ********** Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: ********** ********** Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: ********** MergeSamFiles -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeSamFiles/unsorted_input/1.sam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeSamFiles/unsorted_input/2.sam -O /tmp/unsortedInputSortedOutputTest.10058447869646235323.bam -CREATE_INDEX true -SO coordinate ********** MergeSamFiles -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeSamFiles/unsorted_input/1.sam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeSamFiles/unsorted_input/2.sam -O /tmp/unsortedInputSortedOutputTest.10058447869646235323.bam -CREATE_INDEX true -SO coordinate Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: ********** ********** Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: 12:01:37.605 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:37.605 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: 12:01:37.605 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:37.605 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: 12:01:37.606 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:37.606 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: 12:01:37.606 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:37.606 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: [Tue Jul 02 12:01:37 GMT+14:00 2024] MergeSamFiles INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeSamFiles/unsorted_input/1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeSamFiles/unsorted_input/2.sam] OUTPUT=/tmp/unsortedInputSortedOutputTest.10058447869646235323.bam SORT_ORDER=coordinate CREATE_INDEX=true ASSUME_SORTED=false MERGE_SEQUENCE_DICTIONARIES=false USE_THREADING=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:37 GMT+14:00 2024] MergeSamFiles INPUT=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeSamFiles/unsorted_input/1.sam, /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeSamFiles/unsorted_input/2.sam] OUTPUT=/tmp/unsortedInputSortedOutputTest.10058447869646235323.bam SORT_ORDER=coordinate CREATE_INDEX=true ASSUME_SORTED=false MERGE_SEQUENCE_DICTIONARIES=false USE_THREADING=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: [Tue Jul 02 12:01:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: INFO 2024-07-02 12:01:37 MergeSamFiles Sorting input files using temp directory [/tmp/pbuilder2] INFO 2024-07-02 12:01:37 MergeSamFiles Sorting input files using temp directory [/tmp/pbuilder2] Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: INFO 2024-07-02 12:01:37 MergeSamFiles Finished reading inputs. INFO 2024-07-02 12:01:37 MergeSamFiles Finished reading inputs. Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: [Tue Jul 02 12:01:37 GMT+14:00 2024] picard.sam.MergeSamFiles done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:37 GMT+14:00 2024] picard.sam.MergeSamFiles done. Elapsed time: 0.00 minutes. Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: INFO 2024-07-02 12:01:37 ValidateSamFile INFO 2024-07-02 12:01:37 ValidateSamFile Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: ********** ********** Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: ********** ********** Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: ********** ********** Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: ********** ValidateSamFile -I /tmp/unsortedInputSortedOutputTest.10058447869646235323.bam ********** ValidateSamFile -I /tmp/unsortedInputSortedOutputTest.10058447869646235323.bam Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: ********** ********** Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: 12:01:37.735 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:37.735 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: 12:01:37.735 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:37.735 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: 12:01:37.735 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:37.735 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: 12:01:37.735 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:37.735 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: [Tue Jul 02 12:01:37 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/unsortedInputSortedOutputTest.10058447869646235323.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:37 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/unsortedInputSortedOutputTest.10058447869646235323.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: [Tue Jul 02 12:01:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: WARNING 2024-07-02 12:01:37 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:37 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.MergeSamFilesTest.unsortedInputSortedOutputTest STANDARD_OUT No errors found Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: [Tue Jul 02 12:01:37 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.MergeSamFilesTest.unsortedInputSortedOutputTest STANDARD_ERROR [Tue Jul 02 12:01:37 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method unsortedInputSortedOutputTest(picard.sam.MergeSamFilesTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method TestCanMerge(picard.analysis.MergeableMetricBaseTest) Running Test: Test method TestMergingDerivedClass(picard.analysis.MergeableMetricBaseTest) Running Test: Test method TestMergingSuperClass(picard.analysis.MergeableMetricBaseTest) Running Test: Test method testIllegalClass(picard.analysis.MergeableMetricBaseTest) Running Test: Test method testMerging(picard.analysis.MergeableMetricBaseTest) Running Test: Test method testMergingANull(picard.analysis.MergeableMetricBaseTest) Running Test: Test method testMergingUnequalBoolean(picard.analysis.MergeableMetricBaseTest) Running Test: Test method testMergingUnequalDouble(picard.analysis.MergeableMetricBaseTest) Running Test: Test method testMergingUnequalString(picard.analysis.MergeableMetricBaseTest) Running Test: Test method testMergingWithRestrictedMembers(picard.analysis.MergeableMetricBaseTest) Running Test: Test method testMergingWithRestrictedMembersUsingBaseClass(picard.analysis.MergeableMetricBaseTest) Running Test: Test method testMergingWithStaticAnnotatedMembers(picard.analysis.MergeableMetricBaseTest) Running Test: Test method testMergingWithStaticMembers(picard.analysis.MergeableMetricBaseTest) Running Test: Test method testIteratorsOfUnevenLength(picard.util.MergingIteratorTest) Running Test: Test method testOrderingAndCompleteness(picard.util.MergingIteratorTest) Running Test: Test method testOutOfOrderIterators(picard.util.MergingIteratorTest) Running Test: Test method testUniqueFields[0](class picard.analysis.CollectWgsMetricsWithNonZeroCoverage$WgsMetricsWithNonZeroCoverage)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[1](class picard.analysis.MergeableMetricBaseTest$TestMergeableMetric)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[2](class picard.sam.DuplicationMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[3](class picard.analysis.FingerprintingSummaryMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[4](class picard.analysis.artifacts.SequencingArtifactMetrics$BaitBiasDetailMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[5](class picard.sam.SamErrorMetric.OverlappingErrorMetric)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[6](class picard.vcf.CollectVariantCallingMetrics$VariantCallingDetailMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[7](class picard.illumina.IlluminaBasecallingMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[8](class picard.arrays.CollectArraysVariantCallingMetrics$ArraysVariantCallingSummaryMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[9](class picard.sam.SamErrorMetric.BaseErrorMetric)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[10](class picard.analysis.MergeableMetricBaseTest$TestMergeableMetricWithRestrictedMembers)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[11](class picard.sam.SamErrorMetric.IndelErrorMetric)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[12](class picard.analysis.RrbsSummaryMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[13](class picard.metrics.MultilevelMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[14](class picard.analysis.WgsMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[15](class picard.analysis.MergeableMetricBaseTest$TestMergeableMetricIllegal)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[16](class picard.analysis.MergeableMetricBaseTest$TestMergeableMetricWithStaticAnnotatedMembers)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[17](class picard.vcf.MendelianViolations.MendelianViolationMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[18](class picard.analysis.GcBiasSummaryMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[19](class picard.analysis.RrbsMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[20](class picard.metrics.GcBiasMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[21](class picard.analysis.RnaSeqMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[22](class picard.analysis.TheoreticalSensitivityMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[23](class picard.analysis.MergeableMetricBaseTest$TestDerivedMergableMetric)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[24](class picard.analysis.MergeableMetricBase)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[25](class picard.analysis.CollectRawWgsMetrics$RawWgsMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[26](class picard.sam.SamComparisonMetric)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[27](class picard.analysis.directed.PanelMetricsBase)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[28](class picard.analysis.CollectOxoGMetrics$CpcgMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[29](class picard.sam.markduplicates.UmiMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[30](class picard.analysis.replicates.IndependentReplicateMetric)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[31](class picard.illumina.ExtractIlluminaBarcodes$BarcodeMetric)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[32](class picard.analysis.directed.TargetedPcrMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[33](class picard.fingerprint.ClusteredCrosscheckMetric)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[34](class picard.analysis.MultiLevelCollectorTest$TotalNumberMetric)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[35](class picard.analysis.JumpingLibraryMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[36](class picard.illumina.IlluminaLaneMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[37](class picard.arrays.CollectArraysVariantCallingMetrics$ArraysVariantCallingDetailMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[38](class picard.fingerprint.CrosscheckMetric)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[39](class picard.analysis.artifacts.SequencingArtifactMetrics$BaitBiasSummaryMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[40](class picard.vcf.GenotypeConcordanceSummaryMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[41](class picard.illumina.quality.CollectHiSeqXPfFailMetrics$PFFailDetailedMetric)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[42](class picard.analysis.RrbsCpgDetailMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[43](class picard.analysis.AlignmentSummaryMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[44](class picard.analysis.MergeableMetricBaseTest$TestMergeableMetricWithStaticMembers)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[45](class picard.analysis.directed.TargetMetricsBase)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[46](class picard.analysis.CollectQualityYieldMetrics$QualityYieldMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[47](class picard.sam.SamErrorMetric.ErrorMetric)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[48](class picard.analysis.directed.TargetMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[49](class picard.arrays.CollectArraysVariantCallingMetrics$ArraysControlCodesSummaryMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[50](class picard.fingerprint.FingerprintMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[51](class picard.analysis.InsertSizeMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[52](class picard.analysis.BaseDistributionByCycleMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[53](class picard.analysis.artifacts.SequencingArtifactMetrics$PreAdapterSummaryMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[54](class picard.analysis.artifacts.SequencingArtifactMetrics$PreAdapterDetailMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[55](class picard.analysis.directed.HsMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[56](class picard.vcf.GenotypeConcordanceDetailMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[57](class picard.vcf.CollectVariantCallingMetrics$VariantCallingSummaryMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[58](class picard.analysis.GcBiasDetailMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[59](class picard.analysis.artifacts.ErrorSummaryMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[60](class picard.vcf.GenotypeConcordanceContingencyMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[61](class picard.illumina.IlluminaPhasingMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[62](class picard.arrays.VerifyIDIntensityContaminationMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[63](class picard.analysis.FingerprintingDetailMetrics)(picard.metrics.MetricBaseTest) Running Test: Test method testUniqueFields[64](class picard.illumina.quality.CollectHiSeqXPfFailMetrics$PFFailSummaryMetric)(picard.metrics.MetricBaseTest) Running Test: Test method canWriteToDevNull(picard.util.MiscTest) Running Test: Test method multilevelCollectorTest[0]([ALL_READS])(picard.analysis.MultiLevelCollectorTest) Running Test: Test method multilevelCollectorTest[1]([SAMPLE, ALL_READS])(picard.analysis.MultiLevelCollectorTest) Running Test: Test method multilevelCollectorTest[2]([LIBRARY, SAMPLE])(picard.analysis.MultiLevelCollectorTest) Running Test: Test method multilevelCollectorTest[3]([READ_GROUP, LIBRARY])(picard.analysis.MultiLevelCollectorTest) Running Test: Test method multilevelCollectorTest[4]([READ_GROUP, LIBRARY, SAMPLE])(picard.analysis.MultiLevelCollectorTest) Running Test: Test method multilevelCollectorTest[5]([READ_GROUP, LIBRARY, SAMPLE, ALL_READS])(picard.analysis.MultiLevelCollectorTest) Running Test: Test method noIntervals(picard.reference.NonNFastaSizeTest) Test: Test method noIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: INFO 2024-07-02 12:01:37 NonNFastaSize Gradle suite > Gradle test > picard.reference.NonNFastaSizeTest.noIntervals STANDARD_ERROR INFO 2024-07-02 12:01:37 NonNFastaSize Test: Test method noIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: Test: Test method noIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method noIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: ********** ********** Test: Test method noIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method noIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method noIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: ********** ********** Test: Test method noIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method noIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: ********** ********** Test: Test method noIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: ********** NonNFastaSize -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/test.fasta -OUTPUT /tmp/nonNcount268913351168228379.txt ********** NonNFastaSize -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/test.fasta -OUTPUT /tmp/nonNcount268913351168228379.txt Test: Test method noIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: ********** ********** Test: Test method noIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: Test: Test method noIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: Test: Test method noIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: 12:01:37.990 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:37.990 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method noIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: 12:01:37.990 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:37.990 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method noIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: 12:01:37.990 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:37.990 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method noIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: 12:01:37.990 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:37.990 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method noIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: [Tue Jul 02 12:01:37 GMT+14:00 2024] NonNFastaSize INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/test.fasta OUTPUT=/tmp/nonNcount268913351168228379.txt VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:37 GMT+14:00 2024] NonNFastaSize INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/test.fasta OUTPUT=/tmp/nonNcount268913351168228379.txt VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method noIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: [Tue Jul 02 12:01:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method noIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: [Tue Jul 02 12:01:37 GMT+14:00 2024] picard.reference.NonNFastaSize done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:37 GMT+14:00 2024] picard.reference.NonNFastaSize done. Elapsed time: 0.00 minutes. Test: Test method noIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method withIntervals(picard.reference.NonNFastaSizeTest) Test: Test method withIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: INFO 2024-07-02 12:01:38 NonNFastaSize Gradle suite > Gradle test > picard.reference.NonNFastaSizeTest.withIntervals STANDARD_ERROR INFO 2024-07-02 12:01:38 NonNFastaSize Test: Test method withIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: Test: Test method withIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method withIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: ********** ********** Test: Test method withIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method withIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method withIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: ********** ********** Test: Test method withIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method withIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: ********** ********** Test: Test method withIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: ********** NonNFastaSize -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/test.fasta -OUTPUT /tmp/nonNcount13588057113161642015.txt -INTERVALS /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/test.intervals ********** NonNFastaSize -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/test.fasta -OUTPUT /tmp/nonNcount13588057113161642015.txt -INTERVALS /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/test.intervals Test: Test method withIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: ********** ********** Test: Test method withIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: Test: Test method withIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: Test: Test method withIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: 12:01:38.007 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:38.007 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method withIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: 12:01:38.007 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:38.007 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method withIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: 12:01:38.007 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:38.007 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method withIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: 12:01:38.007 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:38.007 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method withIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: [Tue Jul 02 12:01:38 GMT+14:00 2024] NonNFastaSize INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/test.fasta OUTPUT=/tmp/nonNcount13588057113161642015.txt INTERVALS=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/test.intervals VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:38 GMT+14:00 2024] NonNFastaSize INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/test.fasta OUTPUT=/tmp/nonNcount13588057113161642015.txt INTERVALS=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/reference/test.intervals VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method withIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: [Tue Jul 02 12:01:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method withIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: [Tue Jul 02 12:01:38 GMT+14:00 2024] picard.reference.NonNFastaSize done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:38 GMT+14:00 2024] picard.reference.NonNFastaSize done. Elapsed time: 0.00 minutes. Test: Test method withIntervals(picard.reference.NonNFastaSizeTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testDefaultRegex(picard.sam.markduplicates.util.OpticalDuplicateFinderTest) Running Test: Test method testKeeper(picard.sam.markduplicates.util.OpticalDuplicateFinderTest) Running Test: Test method testKeeperAtEndWithinCliqueOfAllOpticalDuplicates(picard.sam.markduplicates.util.OpticalDuplicateFinderTest) Running Test: Test method testKeeperNotInList(picard.sam.markduplicates.util.OpticalDuplicateFinderTest) Running Test: Test method testKeeperOrderDependence(picard.sam.markduplicates.util.OpticalDuplicateFinderTest) Running Test: Test method testKeeperOrderDependenceTwoDistinctClusters(picard.sam.markduplicates.util.OpticalDuplicateFinderTest) Running Test: Test method testKeeperOrderIndependenceTwoDistinctClusters(picard.sam.markduplicates.util.OpticalDuplicateFinderTest) Running Test: Test method testMaxSetSize(picard.sam.markduplicates.util.OpticalDuplicateFinderTest) Running Test: Test method testVeryLongReadNames(picard.sam.markduplicates.util.OpticalDuplicateFinderTest) Running Test: Test method testFromSexMap[0]([], [])(picard.pedigree.PedFileTest) Running Test: Test method testFromSexMap[1]([female1, female2, female3], [male1, male2, male3])(picard.pedigree.PedFileTest) Running Test: Test method testFromSexMap[2]([female1, female2, female3], [])(picard.pedigree.PedFileTest) Running Test: Test method testFromSexMap[3]([female1], [male1, male2, male3])(picard.pedigree.PedFileTest) Running Test: Test method basicIterationTest(picard.illumina.parser.PerTileParserTest) Running Test: Test method failVerifyTestMissingTile(picard.illumina.parser.PerTileParserTest) Running Test: Test method failVerifyTestTooManyTiles(picard.illumina.parser.PerTileParserTest) Running Test: Test method missingTileTest[0](-1)(picard.illumina.parser.PerTileParserTest) Running Test: Test method missingTileTest[1](10)(picard.illumina.parser.PerTileParserTest) Running Test: Test method missingTileTest[2](2147483647)(picard.illumina.parser.PerTileParserTest) Running Test: Test method missingTileTest[3](-2147483648)(picard.illumina.parser.PerTileParserTest) Running Test: Test method passVerifyTest(picard.illumina.parser.PerTileParserTest) Running Test: Test method seekToTileTest[0](1, 4, null, null)(picard.illumina.parser.PerTileParserTest) Running Test: Test method seekToTileTest[1](15, 1, null, null)(picard.illumina.parser.PerTileParserTest) Running Test: Test method seekToTileTest[2](25, 3, null, null)(picard.illumina.parser.PerTileParserTest) Running Test: Test method seekToTileTest[3](24, 5, null, null)(picard.illumina.parser.PerTileParserTest) Running Test: Test method seekToTileTest[4](1, 3, 10, 1)(picard.illumina.parser.PerTileParserTest) Running Test: Test method seekToTileTest[5](1, 3, 15, 2)(picard.illumina.parser.PerTileParserTest) Running Test: Test method seekToTileTest[6](12, 2, 15, 4)(picard.illumina.parser.PerTileParserTest) Running Test: Test method seekToTileTest[7](6, 3, 12, 5)(picard.illumina.parser.PerTileParserTest) Running Test: Test method seekToTileTest[8](14, 5, 25, 2)(picard.illumina.parser.PerTileParserTest) Running Test: Test method basicIterationTest(picard.illumina.parser.PerTilePerCycleParserTest) Running Test: Test method seekingIterationTest[0](1, 3, null, null)(picard.illumina.parser.PerTilePerCycleParserTest) Running Test: Test method seekingIterationTest[1](22, 1, null, null)(picard.illumina.parser.PerTilePerCycleParserTest) Running Test: Test method seekingIterationTest[2](38, 2, null, null)(picard.illumina.parser.PerTilePerCycleParserTest) Running Test: Test method seekingIterationTest[3](75, 4, null, null)(picard.illumina.parser.PerTilePerCycleParserTest) Running Test: Test method seekingIterationTest[4](1, 3, 70, 1)(picard.illumina.parser.PerTilePerCycleParserTest) Running Test: Test method seekingIterationTest[5](1, 3, 45, 2)(picard.illumina.parser.PerTilePerCycleParserTest) Running Test: Test method seekingIterationTest[6](12, 2, 59, 4)(picard.illumina.parser.PerTilePerCycleParserTest) Running Test: Test method seekingIterationTest[7](45, 3, 70, 3)(picard.illumina.parser.PerTilePerCycleParserTest) Running Test: Test method seekingIterationTest[8](14, 1, 5, 2)(picard.illumina.parser.PerTilePerCycleParserTest) Running Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: USAGE: PicardCommandLine  [-h] Gradle suite > Gradle test > picard.cmdline.PicardCommandLineTest.TestPicardPublic STANDARD_ERROR USAGE: PicardCommandLine  [-h] Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: Available Programs: Available Programs: Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: -------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------- Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: Base Calling: Tools that process sequencing machine data, e.g. Illumina base calls, and detect sequencing level attributes, e.g. adapters Base Calling: Tools that process sequencing machine data, e.g. Illumina base calls, and detect sequencing level attributes, e.g. adapters Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CheckIlluminaDirectory Asserts the validity for specified Illumina basecalling data.   CheckIlluminaDirectory Asserts the validity for specified Illumina basecalling data.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectIlluminaBasecallingMetrics Collects Illumina Basecalling metrics for a sequencing run.   CollectIlluminaBasecallingMetrics Collects Illumina Basecalling metrics for a sequencing run.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectIlluminaLaneMetrics Collects Illumina lane metrics for the given BaseCalling analysis directory.   CollectIlluminaLaneMetrics Collects Illumina lane metrics for the given BaseCalling analysis directory.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  ExtractIlluminaBarcodes Tool determines the barcode for each read in an Illumina lane.   ExtractIlluminaBarcodes Tool determines the barcode for each read in an Illumina lane.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  IlluminaBasecallsToFastq Generate FASTQ file(s) from Illumina basecall read data.   IlluminaBasecallsToFastq Generate FASTQ file(s) from Illumina basecall read data.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  IlluminaBasecallsToSam Transforms raw Illumina sequencing data into an unmapped SAM or BAM file.  IlluminaBasecallsToSam Transforms raw Illumina sequencing data into an unmapped SAM or BAM file. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  MarkIlluminaAdapters Reads a SAM or BAM file and rewrites it with new adapter-trimming tags.   MarkIlluminaAdapters Reads a SAM or BAM file and rewrites it with new adapter-trimming tags.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: -------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------- Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: Diagnostics and Quality Control: Tools that collect sequencing quality related and comparative metrics Diagnostics and Quality Control: Tools that collect sequencing quality related and comparative metrics Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  AccumulateVariantCallingMetrics Combines multiple Variant Calling Metrics files into a single file  AccumulateVariantCallingMetrics Combines multiple Variant Calling Metrics files into a single file Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  BamIndexStats Generate index statistics from a BAM file  BamIndexStats Generate index statistics from a BAM file Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CalculateFingerprintMetrics Calculate statistics on fingerprints, checking their viability  CalculateFingerprintMetrics Calculate statistics on fingerprints, checking their viability Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CalculateReadGroupChecksum Creates a hash code based on the read groups (RG).   CalculateReadGroupChecksum Creates a hash code based on the read groups (RG).  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CheckDuplicateMarking Checks the consistency of duplicate markings.  CheckDuplicateMarking Checks the consistency of duplicate markings. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CheckFingerprint Computes a fingerprint from the supplied input (SAM/BAM/CRAM or VCF) file and compares it to the provided genotypes  CheckFingerprint Computes a fingerprint from the supplied input (SAM/BAM/CRAM or VCF) file and compares it to the provided genotypes Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CheckTerminatorBlock Asserts the provided gzip file's (e.g., BAM) last block is well-formed; RC 100 otherwise  CheckTerminatorBlock Asserts the provided gzip file's (e.g., BAM) last block is well-formed; RC 100 otherwise Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  ClusterCrosscheckMetrics Clusters the results of a CrosscheckFingerprints run by LOD score  ClusterCrosscheckMetrics Clusters the results of a CrosscheckFingerprints run by LOD score Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectAlignmentSummaryMetrics Produces a summary of alignment metrics from a SAM or BAM file.   CollectAlignmentSummaryMetrics Produces a summary of alignment metrics from a SAM or BAM file.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectArraysVariantCallingMetrics Collects summary and per-sample from the provided arrays VCF file  CollectArraysVariantCallingMetrics Collects summary and per-sample from the provided arrays VCF file Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectBaseDistributionByCycle Chart the nucleotide distribution per cycle in a SAM or BAM file  CollectBaseDistributionByCycle Chart the nucleotide distribution per cycle in a SAM or BAM file Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectGcBiasMetrics Collect metrics regarding GC bias.   CollectGcBiasMetrics Collect metrics regarding GC bias.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectHiSeqXPfFailMetrics Classify PF-Failing reads in a HiSeqX Illumina Basecalling directory into various categories.  CollectHiSeqXPfFailMetrics Classify PF-Failing reads in a HiSeqX Illumina Basecalling directory into various categories. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectHsMetrics Collects hybrid-selection (HS) metrics for a SAM or BAM file.   CollectHsMetrics Collects hybrid-selection (HS) metrics for a SAM or BAM file.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectIndependentReplicateMetrics **EXPERIMENTAL - USE AT YOUR OWN RISK** Estimates the rate of independent replication rate of reads within a bam.  CollectIndependentReplicateMetrics **EXPERIMENTAL - USE AT YOUR OWN RISK** Estimates the rate of independent replication rate of reads within a bam. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:   Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectInsertSizeMetrics Collect metrics about the insert size distribution of a paired-end library.   CollectInsertSizeMetrics Collect metrics about the insert size distribution of a paired-end library.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectJumpingLibraryMetrics Collect jumping library metrics.   CollectJumpingLibraryMetrics Collect jumping library metrics.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectMultipleMetrics Collect multiple classes of metrics.   CollectMultipleMetrics Collect multiple classes of metrics.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectOxoGMetrics Collect metrics to assess oxidative artifacts.  CollectOxoGMetrics Collect metrics to assess oxidative artifacts. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectQualityYieldMetrics Collect metrics about reads that pass quality thresholds and Illumina-specific filters.   CollectQualityYieldMetrics Collect metrics about reads that pass quality thresholds and Illumina-specific filters.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectRawWgsMetrics Collect whole genome sequencing-related metrics.   CollectRawWgsMetrics Collect whole genome sequencing-related metrics.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectRnaSeqMetrics Produces RNA alignment metrics for a SAM or BAM file.   CollectRnaSeqMetrics Produces RNA alignment metrics for a SAM or BAM file.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectRrbsMetrics Collects metrics from reduced representation bisulfite sequencing (Rrbs) data.   CollectRrbsMetrics Collects metrics from reduced representation bisulfite sequencing (Rrbs) data.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectSamErrorMetrics Program to collect error metrics on bases stratified in various ways.  CollectSamErrorMetrics Program to collect error metrics on bases stratified in various ways. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectSequencingArtifactMetrics Collect metrics to quantify single-base sequencing artifacts.   CollectSequencingArtifactMetrics Collect metrics to quantify single-base sequencing artifacts.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectTargetedPcrMetrics Calculate PCR-related metrics from targeted sequencing data.   CollectTargetedPcrMetrics Calculate PCR-related metrics from targeted sequencing data.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectVariantCallingMetrics Collects per-sample and aggregate (spanning all samples) metrics from the provided VCF file  CollectVariantCallingMetrics Collects per-sample and aggregate (spanning all samples) metrics from the provided VCF file Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectWgsMetrics Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.  CollectWgsMetrics Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectWgsMetricsWithNonZeroCoverage **EXPERIMENTAL - USE AT YOUR OWN RISK** Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.   CollectWgsMetricsWithNonZeroCoverage **EXPERIMENTAL - USE AT YOUR OWN RISK** Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CompareMetrics Compare two metrics files.  CompareMetrics Compare two metrics files. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CompareSAMs Compare two input ".sam" or ".bam" files.   CompareSAMs Compare two input ".sam" or ".bam" files.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  ConvertSequencingArtifactToOxoG Extract OxoG metrics from generalized artifacts metrics.   ConvertSequencingArtifactToOxoG Extract OxoG metrics from generalized artifacts metrics.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CrosscheckFingerprints Checks that all data in the input files appear to have come from the same individual  CrosscheckFingerprints Checks that all data in the input files appear to have come from the same individual Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CrosscheckReadGroupFingerprints DEPRECATED: USE CrosscheckFingerprints.   CrosscheckReadGroupFingerprints DEPRECATED: USE CrosscheckFingerprints.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  EstimateLibraryComplexity Estimates the numbers of unique molecules in a sequencing library.   EstimateLibraryComplexity Estimates the numbers of unique molecules in a sequencing library.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  ExtractFingerprint Computes a fingerprint from the input file.  ExtractFingerprint Computes a fingerprint from the input file. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  IdentifyContaminant Computes a fingerprint from the supplied SAM/BAM file, given a contamination estimate.  IdentifyContaminant Computes a fingerprint from the supplied SAM/BAM file, given a contamination estimate. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  LiftOverHaplotypeMap Lifts over a haplotype database from one reference to another  LiftOverHaplotypeMap Lifts over a haplotype database from one reference to another Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  MeanQualityByCycle Collect mean quality by cycle.  MeanQualityByCycle Collect mean quality by cycle. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  QualityScoreDistribution Chart the distribution of quality scores.   QualityScoreDistribution Chart the distribution of quality scores.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  ValidateSamFile Validates a SAM or BAM file.  ValidateSamFile Validates a SAM or BAM file. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  ViewSam Prints a SAM or BAM file to the screen  ViewSam Prints a SAM or BAM file to the screen Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: -------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------- Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: Genotyping Arrays Manipulation: Tools that manipulate data generated by Genotyping arrays Genotyping Arrays Manipulation: Tools that manipulate data generated by Genotyping arrays Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  BpmToNormalizationManifestCsv Program to convert an Illumina bpm file into a bpm.csv file.  BpmToNormalizationManifestCsv Program to convert an Illumina bpm file into a bpm.csv file. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CombineGenotypingArrayVcfs Program to combine multiple genotyping array VCF files into one VCF.  CombineGenotypingArrayVcfs Program to combine multiple genotyping array VCF files into one VCF. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CompareGtcFiles Compares two GTC files.  CompareGtcFiles Compares two GTC files. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CreateVerifyIDIntensityContaminationMetricsFile Program to generate a picard metrics file from the output of the VerifyIDIntensity tool.  CreateVerifyIDIntensityContaminationMetricsFile Program to generate a picard metrics file from the output of the VerifyIDIntensity tool. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  GtcToVcf Program to convert an Illumina GTC file to a VCF  GtcToVcf Program to convert an Illumina GTC file to a VCF Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  MergePedIntoVcf Program to merge a single-sample ped file from zCall into a single-sample VCF.  MergePedIntoVcf Program to merge a single-sample ped file from zCall into a single-sample VCF. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  VcfToAdpc Program to convert an Arrays VCF to an ADPC file.  VcfToAdpc Program to convert an Arrays VCF to an ADPC file. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: -------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------- Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: Intervals Manipulation: Tools that process genomic intervals in various formats Intervals Manipulation: Tools that process genomic intervals in various formats Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  BedToIntervalList Converts a BED file to a Picard Interval List.   BedToIntervalList Converts a BED file to a Picard Interval List.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  IntervalListToBed Converts an Picard IntervalList file to a BED file.  IntervalListToBed Converts an Picard IntervalList file to a BED file. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  IntervalListTools A tool for performing various IntervalList manipulations  IntervalListTools A tool for performing various IntervalList manipulations Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  LiftOverIntervalList Lifts over an interval list from one reference build to another.   LiftOverIntervalList Lifts over an interval list from one reference build to another.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: -------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------- Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: Other: Miscellaneous tools, e.g. those that aid in data streaming Other: Miscellaneous tools, e.g. those that aid in data streaming Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  FifoBuffer Provides a large, FIFO buffer that can be used to buffer input and output streams between programs.  FifoBuffer Provides a large, FIFO buffer that can be used to buffer input and output streams between programs. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: -------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------- Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: Read Data Manipulation: Tools that manipulate read data in SAM, BAM or CRAM format Read Data Manipulation: Tools that manipulate read data in SAM, BAM or CRAM format Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  AddCommentsToBam Adds comments to the header of a BAM file.  AddCommentsToBam Adds comments to the header of a BAM file. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  AddOATag Record current alignment information to OA tag.  AddOATag Record current alignment information to OA tag. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  AddOrReplaceReadGroups Assigns all the reads in a file to a single new read-group.  AddOrReplaceReadGroups Assigns all the reads in a file to a single new read-group. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  BamToBfq Converts a BAM file into a BFQ (binary fastq formatted) file  BamToBfq Converts a BAM file into a BFQ (binary fastq formatted) file Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  BuildBamIndex Generates a BAM index ".bai" file.   BuildBamIndex Generates a BAM index ".bai" file.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CleanSam Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads  CleanSam Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectDuplicateMetrics Collect Duplicate metrics from marked file.  CollectDuplicateMetrics Collect Duplicate metrics from marked file. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  DownsampleSam Downsample a SAM or BAM file.  DownsampleSam Downsample a SAM or BAM file. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  FastqToSam Converts a FASTQ file to an unaligned BAM or SAM file  FastqToSam Converts a FASTQ file to an unaligned BAM or SAM file Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  FilterSamReads Subsets reads from a SAM or BAM file by applying one of several filters.  FilterSamReads Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  FixMateInformation Verify mate-pair information between mates and fix if needed.  FixMateInformation Verify mate-pair information between mates and fix if needed. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  GatherBamFiles Concatenate efficiently BAM files that resulted from a scattered parallel analysis  GatherBamFiles Concatenate efficiently BAM files that resulted from a scattered parallel analysis Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  MarkDuplicates Identifies duplicate reads.   MarkDuplicates Identifies duplicate reads.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  MarkDuplicatesWithMateCigar Identifies duplicate reads, accounting for mate CIGAR.   MarkDuplicatesWithMateCigar Identifies duplicate reads, accounting for mate CIGAR.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  MergeBamAlignment Merge alignment data from a SAM or BAM with data in an unmapped BAM file.   MergeBamAlignment Merge alignment data from a SAM or BAM with data in an unmapped BAM file.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  MergeSamFiles Merges multiple SAM and/or BAM files into a single file.   MergeSamFiles Merges multiple SAM and/or BAM files into a single file.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  PositionBasedDownsampleSam Downsample a SAM or BAM file to retain a subset of the reads based on the reads location in each tile in the flowcell.  PositionBasedDownsampleSam Downsample a SAM or BAM file to retain a subset of the reads based on the reads location in each tile in the flowcell. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  ReorderSam Reorders reads in a SAM or BAM file to match ordering in a second reference file.  ReorderSam Reorders reads in a SAM or BAM file to match ordering in a second reference file. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  ReplaceSamHeader Replaces the SAMFileHeader in a SAM or BAM file.   ReplaceSamHeader Replaces the SAMFileHeader in a SAM or BAM file.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  RevertOriginalBaseQualitiesAndAddMateCigar Reverts the original base qualities and adds the mate cigar tag to read-group BAMs  RevertOriginalBaseQualitiesAndAddMateCigar Reverts the original base qualities and adds the mate cigar tag to read-group BAMs Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  RevertSam Reverts SAM or BAM files to a previous state.   RevertSam Reverts SAM or BAM files to a previous state.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  SamFormatConverter Convert a BAM file to a SAM file, or a SAM to a BAM  SamFormatConverter Convert a BAM file to a SAM file, or a SAM to a BAM Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  SamToFastq Converts a SAM or BAM file to FASTQ.  SamToFastq Converts a SAM or BAM file to FASTQ. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  SamToFastqWithTags Converts a SAM or BAM file to FASTQ alongside FASTQs created from tags.  SamToFastqWithTags Converts a SAM or BAM file to FASTQ alongside FASTQs created from tags. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  SetNmAndUqTags DEPRECATED: Use SetNmMdAndUqTags instead.  SetNmAndUqTags DEPRECATED: Use SetNmMdAndUqTags instead. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  SetNmMdAndUqTags Fixes the NM, MD, and UQ tags in a SAM file   SetNmMdAndUqTags Fixes the NM, MD, and UQ tags in a SAM file  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  SimpleMarkDuplicatesWithMateCigar **EXPERIMENTAL - USE AT YOUR OWN RISK** Examines aligned records in the supplied SAM or BAM file to locate duplicate molecules.  SimpleMarkDuplicatesWithMateCigar **EXPERIMENTAL - USE AT YOUR OWN RISK** Examines aligned records in the supplied SAM or BAM file to locate duplicate molecules. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  SortSam Sorts a SAM or BAM file  SortSam Sorts a SAM or BAM file Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  SplitSamByLibrary Splits a SAM or BAM file into individual files by library  SplitSamByLibrary Splits a SAM or BAM file into individual files by library Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  SplitSamByNumberOfReads Splits a SAM or BAM file to multiple BAMs.  SplitSamByNumberOfReads Splits a SAM or BAM file to multiple BAMs. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  UmiAwareMarkDuplicatesWithMateCigar **EXPERIMENTAL - USE AT YOUR OWN RISK** Identifies duplicate reads using information from read positions and UMIs.   UmiAwareMarkDuplicatesWithMateCigar **EXPERIMENTAL - USE AT YOUR OWN RISK** Identifies duplicate reads using information from read positions and UMIs.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: -------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------- Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: Reference: Tools that analyze and manipulate FASTA format references Reference: Tools that analyze and manipulate FASTA format references Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  BaitDesigner Designs oligonucleotide baits for hybrid selection reactions.  BaitDesigner Designs oligonucleotide baits for hybrid selection reactions. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CreateSequenceDictionary Creates a sequence dictionary for a reference sequence.   CreateSequenceDictionary Creates a sequence dictionary for a reference sequence.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  ExtractSequences Subsets intervals from a reference sequence to a new FASTA file.  ExtractSequences Subsets intervals from a reference sequence to a new FASTA file. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  NonNFastaSize Counts the number of non-N bases in a fasta file.  NonNFastaSize Counts the number of non-N bases in a fasta file. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  NormalizeFasta Normalizes lines of sequence in a FASTA file to be of the same length.  NormalizeFasta Normalizes lines of sequence in a FASTA file to be of the same length. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  ScatterIntervalsByNs Writes an interval list created by splitting a reference at Ns.  ScatterIntervalsByNs Writes an interval list created by splitting a reference at Ns. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: -------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------- Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: Test Tools: Tools for internal test purposes  Test Tools: Tools for internal test purposes  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  MockCLP No-op CLP for testing initialization behavior.  MockCLP No-op CLP for testing initialization behavior. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: -------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------- Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: Variant Evaluation and Refinement: Tools that evaluate and refine variant calls, e.g. with annotations not offered by the engine Variant Evaluation and Refinement: Tools that evaluate and refine variant calls, e.g. with annotations not offered by the engine Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  FindMendelianViolations Finds mendelian violations of all types within a VCF  FindMendelianViolations Finds mendelian violations of all types within a VCF Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  GenotypeConcordance Calculates the concordance between genotype data of one sample in each of two VCFs - truth (or reference) vs. calls.  GenotypeConcordance Calculates the concordance between genotype data of one sample in each of two VCFs - truth (or reference) vs. calls. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: -------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------- Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: Variant Filtering: Tools that filter variants by annotating the FILTER column Variant Filtering: Tools that filter variants by annotating the FILTER column Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  FilterVcf Hard filters a VCF.  FilterVcf Hard filters a VCF. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: -------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------- Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: Variant Manipulation: Tools that manipulate variant call format (VCF) data Variant Manipulation: Tools that manipulate variant call format (VCF) data Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  FixVcfHeader Replaces or fixes a VCF header.  FixVcfHeader Replaces or fixes a VCF header. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  GatherVcfs Gathers multiple VCF files from a scatter operation into a single VCF file  GatherVcfs Gathers multiple VCF files from a scatter operation into a single VCF file Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  LiftoverVcf Lifts over a VCF file from one reference build to another.   LiftoverVcf Lifts over a VCF file from one reference build to another.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  MakeSitesOnlyVcf Creates a VCF that contains all the site-level information for all records in the input VCF but no genotype information.  MakeSitesOnlyVcf Creates a VCF that contains all the site-level information for all records in the input VCF but no genotype information. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  MakeVcfSampleNameMap Creates a TSV from sample name to VCF/GVCF path, with one line per input.  MakeVcfSampleNameMap Creates a TSV from sample name to VCF/GVCF path, with one line per input. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  MergeVcfs Combines multiple variant files into a single variant file  MergeVcfs Combines multiple variant files into a single variant file Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  RenameSampleInVcf Renames a sample within a VCF or BCF.  RenameSampleInVcf Renames a sample within a VCF or BCF. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  SortVcf Sorts one or more VCF files.   SortVcf Sorts one or more VCF files.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  SplitVcfs Splits SNPs and INDELs into separate files.   SplitVcfs Splits SNPs and INDELs into separate files.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  UpdateVcfSequenceDictionary Takes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary.  UpdateVcfSequenceDictionary Takes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary. Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  VcfFormatConverter Converts VCF to BCF or BCF to VCF.   VcfFormatConverter Converts VCF to BCF or BCF to VCF.  Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err:  VcfToIntervalList Converts a VCF or BCF file to a Picard Interval List  VcfToIntervalList Converts a VCF or BCF file to a Picard Interval List Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: -------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------- Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: Test: Test method TestPicardPublic(picard.cmdline.PicardCommandLineTest) produced standard out/err: '' is not a valid command. See PicardCommandLine -h for more information. '' is not a valid command. See PicardCommandLine -h for more information. Running Test: Test method testCommandlineProgramPropertiesOneLineSummaryLength(picard.cmdline.PicardCommandLineTest) Running Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: USAGE: PicardCommandLine  [-h] Gradle suite > Gradle test > picard.cmdline.PicardCommandLineTest.testPrintUsage STANDARD_ERROR USAGE: PicardCommandLine  [-h] Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: Available Programs: Available Programs: Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: -------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------- Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: Base Calling: Tools that process sequencing machine data, e.g. Illumina base calls, and detect sequencing level attributes, e.g. adapters Base Calling: Tools that process sequencing machine data, e.g. Illumina base calls, and detect sequencing level attributes, e.g. adapters Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CheckIlluminaDirectory Asserts the validity for specified Illumina basecalling data.   CheckIlluminaDirectory Asserts the validity for specified Illumina basecalling data.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectIlluminaBasecallingMetrics Collects Illumina Basecalling metrics for a sequencing run.   CollectIlluminaBasecallingMetrics Collects Illumina Basecalling metrics for a sequencing run.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectIlluminaLaneMetrics Collects Illumina lane metrics for the given BaseCalling analysis directory.   CollectIlluminaLaneMetrics Collects Illumina lane metrics for the given BaseCalling analysis directory.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  ExtractIlluminaBarcodes Tool determines the barcode for each read in an Illumina lane.   ExtractIlluminaBarcodes Tool determines the barcode for each read in an Illumina lane.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  IlluminaBasecallsToFastq Generate FASTQ file(s) from Illumina basecall read data.   IlluminaBasecallsToFastq Generate FASTQ file(s) from Illumina basecall read data.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  IlluminaBasecallsToSam Transforms raw Illumina sequencing data into an unmapped SAM or BAM file.  IlluminaBasecallsToSam Transforms raw Illumina sequencing data into an unmapped SAM or BAM file. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  MarkIlluminaAdapters Reads a SAM or BAM file and rewrites it with new adapter-trimming tags.   MarkIlluminaAdapters Reads a SAM or BAM file and rewrites it with new adapter-trimming tags.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: -------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------- Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: Diagnostics and Quality Control: Tools that collect sequencing quality related and comparative metrics Diagnostics and Quality Control: Tools that collect sequencing quality related and comparative metrics Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  AccumulateVariantCallingMetrics Combines multiple Variant Calling Metrics files into a single file  AccumulateVariantCallingMetrics Combines multiple Variant Calling Metrics files into a single file Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  BamIndexStats Generate index statistics from a BAM file  BamIndexStats Generate index statistics from a BAM file Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CalculateFingerprintMetrics Calculate statistics on fingerprints, checking their viability  CalculateFingerprintMetrics Calculate statistics on fingerprints, checking their viability Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CalculateReadGroupChecksum Creates a hash code based on the read groups (RG).   CalculateReadGroupChecksum Creates a hash code based on the read groups (RG).  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CheckDuplicateMarking Checks the consistency of duplicate markings.  CheckDuplicateMarking Checks the consistency of duplicate markings. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CheckFingerprint Computes a fingerprint from the supplied input (SAM/BAM/CRAM or VCF) file and compares it to the provided genotypes  CheckFingerprint Computes a fingerprint from the supplied input (SAM/BAM/CRAM or VCF) file and compares it to the provided genotypes Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CheckTerminatorBlock Asserts the provided gzip file's (e.g., BAM) last block is well-formed; RC 100 otherwise  CheckTerminatorBlock Asserts the provided gzip file's (e.g., BAM) last block is well-formed; RC 100 otherwise Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  ClusterCrosscheckMetrics Clusters the results of a CrosscheckFingerprints run by LOD score  ClusterCrosscheckMetrics Clusters the results of a CrosscheckFingerprints run by LOD score Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectAlignmentSummaryMetrics Produces a summary of alignment metrics from a SAM or BAM file.   CollectAlignmentSummaryMetrics Produces a summary of alignment metrics from a SAM or BAM file.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectArraysVariantCallingMetrics Collects summary and per-sample from the provided arrays VCF file  CollectArraysVariantCallingMetrics Collects summary and per-sample from the provided arrays VCF file Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectBaseDistributionByCycle Chart the nucleotide distribution per cycle in a SAM or BAM file  CollectBaseDistributionByCycle Chart the nucleotide distribution per cycle in a SAM or BAM file Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectGcBiasMetrics Collect metrics regarding GC bias.   CollectGcBiasMetrics Collect metrics regarding GC bias.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectHiSeqXPfFailMetrics Classify PF-Failing reads in a HiSeqX Illumina Basecalling directory into various categories.  CollectHiSeqXPfFailMetrics Classify PF-Failing reads in a HiSeqX Illumina Basecalling directory into various categories. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectHsMetrics Collects hybrid-selection (HS) metrics for a SAM or BAM file.   CollectHsMetrics Collects hybrid-selection (HS) metrics for a SAM or BAM file.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectIndependentReplicateMetrics **EXPERIMENTAL - USE AT YOUR OWN RISK** Estimates the rate of independent replication rate of reads within a bam.  CollectIndependentReplicateMetrics **EXPERIMENTAL - USE AT YOUR OWN RISK** Estimates the rate of independent replication rate of reads within a bam. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:   Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectInsertSizeMetrics Collect metrics about the insert size distribution of a paired-end library.   CollectInsertSizeMetrics Collect metrics about the insert size distribution of a paired-end library.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectJumpingLibraryMetrics Collect jumping library metrics.   CollectJumpingLibraryMetrics Collect jumping library metrics.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectMultipleMetrics Collect multiple classes of metrics.   CollectMultipleMetrics Collect multiple classes of metrics.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectOxoGMetrics Collect metrics to assess oxidative artifacts.  CollectOxoGMetrics Collect metrics to assess oxidative artifacts. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectQualityYieldMetrics Collect metrics about reads that pass quality thresholds and Illumina-specific filters.   CollectQualityYieldMetrics Collect metrics about reads that pass quality thresholds and Illumina-specific filters.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectRawWgsMetrics Collect whole genome sequencing-related metrics.   CollectRawWgsMetrics Collect whole genome sequencing-related metrics.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectRnaSeqMetrics Produces RNA alignment metrics for a SAM or BAM file.   CollectRnaSeqMetrics Produces RNA alignment metrics for a SAM or BAM file.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectRrbsMetrics Collects metrics from reduced representation bisulfite sequencing (Rrbs) data.   CollectRrbsMetrics Collects metrics from reduced representation bisulfite sequencing (Rrbs) data.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectSamErrorMetrics Program to collect error metrics on bases stratified in various ways.  CollectSamErrorMetrics Program to collect error metrics on bases stratified in various ways. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectSequencingArtifactMetrics Collect metrics to quantify single-base sequencing artifacts.   CollectSequencingArtifactMetrics Collect metrics to quantify single-base sequencing artifacts.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectTargetedPcrMetrics Calculate PCR-related metrics from targeted sequencing data.   CollectTargetedPcrMetrics Calculate PCR-related metrics from targeted sequencing data.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectVariantCallingMetrics Collects per-sample and aggregate (spanning all samples) metrics from the provided VCF file  CollectVariantCallingMetrics Collects per-sample and aggregate (spanning all samples) metrics from the provided VCF file Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectWgsMetrics Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.  CollectWgsMetrics Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectWgsMetricsWithNonZeroCoverage **EXPERIMENTAL - USE AT YOUR OWN RISK** Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.   CollectWgsMetricsWithNonZeroCoverage **EXPERIMENTAL - USE AT YOUR OWN RISK** Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CompareMetrics Compare two metrics files.  CompareMetrics Compare two metrics files. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CompareSAMs Compare two input ".sam" or ".bam" files.   CompareSAMs Compare two input ".sam" or ".bam" files.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  ConvertSequencingArtifactToOxoG Extract OxoG metrics from generalized artifacts metrics.   ConvertSequencingArtifactToOxoG Extract OxoG metrics from generalized artifacts metrics.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CrosscheckFingerprints Checks that all data in the input files appear to have come from the same individual  CrosscheckFingerprints Checks that all data in the input files appear to have come from the same individual Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CrosscheckReadGroupFingerprints DEPRECATED: USE CrosscheckFingerprints.   CrosscheckReadGroupFingerprints DEPRECATED: USE CrosscheckFingerprints.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  EstimateLibraryComplexity Estimates the numbers of unique molecules in a sequencing library.   EstimateLibraryComplexity Estimates the numbers of unique molecules in a sequencing library.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  ExtractFingerprint Computes a fingerprint from the input file.  ExtractFingerprint Computes a fingerprint from the input file. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  IdentifyContaminant Computes a fingerprint from the supplied SAM/BAM file, given a contamination estimate.  IdentifyContaminant Computes a fingerprint from the supplied SAM/BAM file, given a contamination estimate. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  LiftOverHaplotypeMap Lifts over a haplotype database from one reference to another  LiftOverHaplotypeMap Lifts over a haplotype database from one reference to another Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  MeanQualityByCycle Collect mean quality by cycle.  MeanQualityByCycle Collect mean quality by cycle. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  QualityScoreDistribution Chart the distribution of quality scores.   QualityScoreDistribution Chart the distribution of quality scores.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  ValidateSamFile Validates a SAM or BAM file.  ValidateSamFile Validates a SAM or BAM file. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  ViewSam Prints a SAM or BAM file to the screen  ViewSam Prints a SAM or BAM file to the screen Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: -------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------- Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: Genotyping Arrays Manipulation: Tools that manipulate data generated by Genotyping arrays Genotyping Arrays Manipulation: Tools that manipulate data generated by Genotyping arrays Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  BpmToNormalizationManifestCsv Program to convert an Illumina bpm file into a bpm.csv file.  BpmToNormalizationManifestCsv Program to convert an Illumina bpm file into a bpm.csv file. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CombineGenotypingArrayVcfs Program to combine multiple genotyping array VCF files into one VCF.  CombineGenotypingArrayVcfs Program to combine multiple genotyping array VCF files into one VCF. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CompareGtcFiles Compares two GTC files.  CompareGtcFiles Compares two GTC files. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CreateVerifyIDIntensityContaminationMetricsFile Program to generate a picard metrics file from the output of the VerifyIDIntensity tool.  CreateVerifyIDIntensityContaminationMetricsFile Program to generate a picard metrics file from the output of the VerifyIDIntensity tool. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  GtcToVcf Program to convert an Illumina GTC file to a VCF  GtcToVcf Program to convert an Illumina GTC file to a VCF Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  MergePedIntoVcf Program to merge a single-sample ped file from zCall into a single-sample VCF.  MergePedIntoVcf Program to merge a single-sample ped file from zCall into a single-sample VCF. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  VcfToAdpc Program to convert an Arrays VCF to an ADPC file.  VcfToAdpc Program to convert an Arrays VCF to an ADPC file. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: -------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------- Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: Intervals Manipulation: Tools that process genomic intervals in various formats Intervals Manipulation: Tools that process genomic intervals in various formats Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  BedToIntervalList Converts a BED file to a Picard Interval List.   BedToIntervalList Converts a BED file to a Picard Interval List.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  IntervalListToBed Converts an Picard IntervalList file to a BED file.  IntervalListToBed Converts an Picard IntervalList file to a BED file. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  IntervalListTools A tool for performing various IntervalList manipulations  IntervalListTools A tool for performing various IntervalList manipulations Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  LiftOverIntervalList Lifts over an interval list from one reference build to another.   LiftOverIntervalList Lifts over an interval list from one reference build to another.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: -------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------- Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: Other: Miscellaneous tools, e.g. those that aid in data streaming Other: Miscellaneous tools, e.g. those that aid in data streaming Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  FifoBuffer Provides a large, FIFO buffer that can be used to buffer input and output streams between programs.  FifoBuffer Provides a large, FIFO buffer that can be used to buffer input and output streams between programs. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: -------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------- Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: Read Data Manipulation: Tools that manipulate read data in SAM, BAM or CRAM format Read Data Manipulation: Tools that manipulate read data in SAM, BAM or CRAM format Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  AddCommentsToBam Adds comments to the header of a BAM file.  AddCommentsToBam Adds comments to the header of a BAM file. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  AddOATag Record current alignment information to OA tag.  AddOATag Record current alignment information to OA tag. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  AddOrReplaceReadGroups Assigns all the reads in a file to a single new read-group.  AddOrReplaceReadGroups Assigns all the reads in a file to a single new read-group. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  BamToBfq Converts a BAM file into a BFQ (binary fastq formatted) file  BamToBfq Converts a BAM file into a BFQ (binary fastq formatted) file Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  BuildBamIndex Generates a BAM index ".bai" file.   BuildBamIndex Generates a BAM index ".bai" file.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CleanSam Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads  CleanSam Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CollectDuplicateMetrics Collect Duplicate metrics from marked file.  CollectDuplicateMetrics Collect Duplicate metrics from marked file. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  DownsampleSam Downsample a SAM or BAM file.  DownsampleSam Downsample a SAM or BAM file. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  FastqToSam Converts a FASTQ file to an unaligned BAM or SAM file  FastqToSam Converts a FASTQ file to an unaligned BAM or SAM file Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  FilterSamReads Subsets reads from a SAM or BAM file by applying one of several filters.  FilterSamReads Subsets reads from a SAM or BAM file by applying one of several filters. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  FixMateInformation Verify mate-pair information between mates and fix if needed.  FixMateInformation Verify mate-pair information between mates and fix if needed. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  GatherBamFiles Concatenate efficiently BAM files that resulted from a scattered parallel analysis  GatherBamFiles Concatenate efficiently BAM files that resulted from a scattered parallel analysis Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  MarkDuplicates Identifies duplicate reads.   MarkDuplicates Identifies duplicate reads.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  MarkDuplicatesWithMateCigar Identifies duplicate reads, accounting for mate CIGAR.   MarkDuplicatesWithMateCigar Identifies duplicate reads, accounting for mate CIGAR.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  MergeBamAlignment Merge alignment data from a SAM or BAM with data in an unmapped BAM file.   MergeBamAlignment Merge alignment data from a SAM or BAM with data in an unmapped BAM file.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  MergeSamFiles Merges multiple SAM and/or BAM files into a single file.   MergeSamFiles Merges multiple SAM and/or BAM files into a single file.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  PositionBasedDownsampleSam Downsample a SAM or BAM file to retain a subset of the reads based on the reads location in each tile in the flowcell.  PositionBasedDownsampleSam Downsample a SAM or BAM file to retain a subset of the reads based on the reads location in each tile in the flowcell. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  ReorderSam Reorders reads in a SAM or BAM file to match ordering in a second reference file.  ReorderSam Reorders reads in a SAM or BAM file to match ordering in a second reference file. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  ReplaceSamHeader Replaces the SAMFileHeader in a SAM or BAM file.   ReplaceSamHeader Replaces the SAMFileHeader in a SAM or BAM file.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  RevertOriginalBaseQualitiesAndAddMateCigar Reverts the original base qualities and adds the mate cigar tag to read-group BAMs  RevertOriginalBaseQualitiesAndAddMateCigar Reverts the original base qualities and adds the mate cigar tag to read-group BAMs Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  RevertSam Reverts SAM or BAM files to a previous state.   RevertSam Reverts SAM or BAM files to a previous state.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  SamFormatConverter Convert a BAM file to a SAM file, or a SAM to a BAM  SamFormatConverter Convert a BAM file to a SAM file, or a SAM to a BAM Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  SamToFastq Converts a SAM or BAM file to FASTQ.  SamToFastq Converts a SAM or BAM file to FASTQ. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  SamToFastqWithTags Converts a SAM or BAM file to FASTQ alongside FASTQs created from tags.  SamToFastqWithTags Converts a SAM or BAM file to FASTQ alongside FASTQs created from tags. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  SetNmAndUqTags DEPRECATED: Use SetNmMdAndUqTags instead.  SetNmAndUqTags DEPRECATED: Use SetNmMdAndUqTags instead. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  SetNmMdAndUqTags Fixes the NM, MD, and UQ tags in a SAM file   SetNmMdAndUqTags Fixes the NM, MD, and UQ tags in a SAM file  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  SimpleMarkDuplicatesWithMateCigar **EXPERIMENTAL - USE AT YOUR OWN RISK** Examines aligned records in the supplied SAM or BAM file to locate duplicate molecules.  SimpleMarkDuplicatesWithMateCigar **EXPERIMENTAL - USE AT YOUR OWN RISK** Examines aligned records in the supplied SAM or BAM file to locate duplicate molecules. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  SortSam Sorts a SAM or BAM file  SortSam Sorts a SAM or BAM file Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  SplitSamByLibrary Splits a SAM or BAM file into individual files by library  SplitSamByLibrary Splits a SAM or BAM file into individual files by library Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  SplitSamByNumberOfReads Splits a SAM or BAM file to multiple BAMs.  SplitSamByNumberOfReads Splits a SAM or BAM file to multiple BAMs. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  UmiAwareMarkDuplicatesWithMateCigar **EXPERIMENTAL - USE AT YOUR OWN RISK** Identifies duplicate reads using information from read positions and UMIs.   UmiAwareMarkDuplicatesWithMateCigar **EXPERIMENTAL - USE AT YOUR OWN RISK** Identifies duplicate reads using information from read positions and UMIs.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: -------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------- Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: Reference: Tools that analyze and manipulate FASTA format references Reference: Tools that analyze and manipulate FASTA format references Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  BaitDesigner Designs oligonucleotide baits for hybrid selection reactions.  BaitDesigner Designs oligonucleotide baits for hybrid selection reactions. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  CreateSequenceDictionary Creates a sequence dictionary for a reference sequence.   CreateSequenceDictionary Creates a sequence dictionary for a reference sequence.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  ExtractSequences Subsets intervals from a reference sequence to a new FASTA file.  ExtractSequences Subsets intervals from a reference sequence to a new FASTA file. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  NonNFastaSize Counts the number of non-N bases in a fasta file.  NonNFastaSize Counts the number of non-N bases in a fasta file. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  NormalizeFasta Normalizes lines of sequence in a FASTA file to be of the same length.  NormalizeFasta Normalizes lines of sequence in a FASTA file to be of the same length. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  ScatterIntervalsByNs Writes an interval list created by splitting a reference at Ns.  ScatterIntervalsByNs Writes an interval list created by splitting a reference at Ns. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: -------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------- Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: Test Tools: Tools for internal test purposes  Test Tools: Tools for internal test purposes  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  MockCLP No-op CLP for testing initialization behavior.  MockCLP No-op CLP for testing initialization behavior. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: -------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------- Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: Variant Evaluation and Refinement: Tools that evaluate and refine variant calls, e.g. with annotations not offered by the engine Variant Evaluation and Refinement: Tools that evaluate and refine variant calls, e.g. with annotations not offered by the engine Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  FindMendelianViolations Finds mendelian violations of all types within a VCF  FindMendelianViolations Finds mendelian violations of all types within a VCF Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  GenotypeConcordance Calculates the concordance between genotype data of one sample in each of two VCFs - truth (or reference) vs. calls.  GenotypeConcordance Calculates the concordance between genotype data of one sample in each of two VCFs - truth (or reference) vs. calls. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: -------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------- Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: Variant Filtering: Tools that filter variants by annotating the FILTER column Variant Filtering: Tools that filter variants by annotating the FILTER column Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  FilterVcf Hard filters a VCF.  FilterVcf Hard filters a VCF. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: -------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------- Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: Variant Manipulation: Tools that manipulate variant call format (VCF) data Variant Manipulation: Tools that manipulate variant call format (VCF) data Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  FixVcfHeader Replaces or fixes a VCF header.  FixVcfHeader Replaces or fixes a VCF header. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  GatherVcfs Gathers multiple VCF files from a scatter operation into a single VCF file  GatherVcfs Gathers multiple VCF files from a scatter operation into a single VCF file Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  LiftoverVcf Lifts over a VCF file from one reference build to another.   LiftoverVcf Lifts over a VCF file from one reference build to another.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  MakeSitesOnlyVcf Creates a VCF that contains all the site-level information for all records in the input VCF but no genotype information.  MakeSitesOnlyVcf Creates a VCF that contains all the site-level information for all records in the input VCF but no genotype information. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  MakeVcfSampleNameMap Creates a TSV from sample name to VCF/GVCF path, with one line per input.  MakeVcfSampleNameMap Creates a TSV from sample name to VCF/GVCF path, with one line per input. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  MergeVcfs Combines multiple variant files into a single variant file  MergeVcfs Combines multiple variant files into a single variant file Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  RenameSampleInVcf Renames a sample within a VCF or BCF.  RenameSampleInVcf Renames a sample within a VCF or BCF. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  SortVcf Sorts one or more VCF files.   SortVcf Sorts one or more VCF files.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  SplitVcfs Splits SNPs and INDELs into separate files.   SplitVcfs Splits SNPs and INDELs into separate files.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  UpdateVcfSequenceDictionary Takes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary.  UpdateVcfSequenceDictionary Takes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary. Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  VcfFormatConverter Converts VCF to BCF or BCF to VCF.   VcfFormatConverter Converts VCF to BCF or BCF to VCF.  Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:  VcfToIntervalList Converts a VCF or BCF file to a Picard Interval List  VcfToIntervalList Converts a VCF or BCF file to a Picard Interval List Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: -------------------------------------------------------------------------------------- -------------------------------------------------------------------------------------- Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err: Test: Test method testPrintUsage(picard.cmdline.PicardCommandLineTest) produced standard out/err:   Running Test: Test method testProcessCommandLinePrograms(picard.cmdline.PicardCommandLineTest) Running Test: Test method failingDataPosFileTest[0](testdata/picard/illumina/readerTests/s_1_1101_pos.txt)(picard.illumina.parser.readers.PosFileReaderTest) Running Test: Test method failingDataPosFileTest[1](testdata/picard/illumina/readerTests/s_1_1102_pos.txt)(picard.illumina.parser.readers.PosFileReaderTest) Running Test: Test method failingDataPosFileTest[2](testdata/picard/illumina/readerTests/s_1_1103_pos.txt)(picard.illumina.parser.readers.PosFileReaderTest) Running Test: Test method failingNamePosFileTest(picard.illumina.parser.readers.PosFileReaderTest) Running Test: Test method validPosFileTest(picard.illumina.parser.readers.PosFileReaderTest) Running Test: Test method zeroLengthFileTest(picard.illumina.parser.readers.PosFileReaderTest) Running Test: Test method multiTileDataTest[0]([1, 2, 3], null, [testdata/picard/illumina/parserTests/posParser/s_1_1_pos.txt, testdata/picard/illumina/parserTests/posParser/s_1_2_pos.txt, testdata/picard/illumina/parserTests/posParser/s_1_3_pos.txt])(picard.illumina.parser.PosParserTest) Running Test: Test method multiTileDataTest[1]([1, 2, 3], 1, [testdata/picard/illumina/parserTests/posParser/s_1_1_pos.txt, testdata/picard/illumina/parserTests/posParser/s_1_2_pos.txt, testdata/picard/illumina/parserTests/posParser/s_1_3_pos.txt])(picard.illumina.parser.PosParserTest) Running Test: Test method multiTileDataTest[2]([1, 3], 0, [testdata/picard/illumina/parserTests/posParser/s_1_1_pos.txt, testdata/picard/illumina/parserTests/posParser/s_1_3_pos.txt])(picard.illumina.parser.PosParserTest) Running Test: Test method multiTileDataTest[3]([3201, 3202], null, [testdata/picard/illumina/parserTests/posParser/s_9_3201_pos.txt, testdata/picard/illumina/parserTests/posParser/s_9_3202_pos.txt])(picard.illumina.parser.PosParserTest) Running Test: Test method multiTileDataTest[4]([3201, 3202], 1, [testdata/picard/illumina/parserTests/posParser/s_9_3201_pos.txt, testdata/picard/illumina/parserTests/posParser/s_9_3202_pos.txt])(picard.illumina.parser.PosParserTest) Running Test: Test method singleTileDataTest[0](1, 1, testdata/picard/illumina/parserTests/posParser/s_1_1_pos.txt)(picard.illumina.parser.PosParserTest) Running Test: Test method singleTileDataTest[1](1, null, testdata/picard/illumina/parserTests/posParser/s_1_1_pos.txt)(picard.illumina.parser.PosParserTest) Running Test: Test method singleTileDataTest[2](3202, 3202, testdata/picard/illumina/parserTests/posParser/s_9_3202_pos.txt)(picard.illumina.parser.PosParserTest) Running Test: Test method singleTileDataTest[3](3202, null, testdata/picard/illumina/parserTests/posParser/s_9_3202_pos.txt)(picard.illumina.parser.PosParserTest) Running Test: Test method TestBuilder(picard.sam.PositionBasedDownsampleSamTest) Test: Test method TestBuilder(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: WARNING 2024-07-02 12:01:38 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.TestBuilder STANDARD_ERROR WARNING 2024-07-02 12:01:38 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestBuilder(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.TestBuilder STANDARD_OUT No errors found Running Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:39 PositionBasedDownsampleSam Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.TestInvalidArguments[0](-1.0) STANDARD_ERROR INFO 2024-07-02 12:01:39 PositionBasedDownsampleSam Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam12627574574049539623.bam -FRACTION -1.0 ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam12627574574049539623.bam -FRACTION -1.0 Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:39.521 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 12:01:39.521 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: USAGE: PositionBasedDownsampleSam [options] USAGE: PositionBasedDownsampleSam [options] Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Summary Summary Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Class to downsample a SAM/BAM file based on the position of the read in a flowcell. As with DownsampleSam, all the reads Class to downsample a SAM/BAM file based on the position of the read in a flowcell. As with DownsampleSam, all the reads Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: with the same queryname are either kept or dropped as a unit. with the same queryname are either kept or dropped as a unit. Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Details Details Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: The downsampling is _not_ random (and there is no random seed). It is deterministically determined by the position of The downsampling is _not_ random (and there is no random seed). It is deterministically determined by the position of Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: each read within its tile. Specifically, it draws an ellipse that covers a FRACTION of the total tile's area and of all each read within its tile. Specifically, it draws an ellipse that covers a FRACTION of the total tile's area and of all Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: the edges of the tile. It uses this area to determine whether to keep or drop the record. Since reads with the same name the edges of the tile. It uses this area to determine whether to keep or drop the record. Since reads with the same name Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: have the same position (mates, secondary and supplemental alignments), the decision will be the same for all of them. have the same position (mates, secondary and supplemental alignments), the decision will be the same for all of them. Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: The main concern of this downsampling method is that due to "optical duplicates" downsampling randomly can create a The main concern of this downsampling method is that due to "optical duplicates" downsampling randomly can create a Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: result that has a different optical duplicate rate, and therefore a different estimated library size (when running result that has a different optical duplicate rate, and therefore a different estimated library size (when running Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: MarkDuplicates). This method keeps (physically) close read together, so that (except for reads near the boundary of the MarkDuplicates). This method keeps (physically) close read together, so that (except for reads near the boundary of the Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: circle) optical duplicates are kept or dropped as a group. By default the program expects the read names to have 5 or 7 circle) optical duplicates are kept or dropped as a group. By default the program expects the read names to have 5 or 7 Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: fields separated by colons (:) and it takes the last two to indicate the x and y coordinates of the reads within the fields separated by colons (:) and it takes the last two to indicate the x and y coordinates of the reads within the Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: tile whence it was sequenced. See DEFAULT_READ_NAME_REGEX for more detail. The program traverses the INPUT twice: first tile whence it was sequenced. See DEFAULT_READ_NAME_REGEX for more detail. The program traverses the INPUT twice: first Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: to find out the size of each of the tiles, and next to perform the downsampling. Downsampling invalidates the duplicate to find out the size of each of the tiles, and next to perform the downsampling. Downsampling invalidates the duplicate Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: flag because duplicate reads before downsampling may not all remain duplicated after downsampling. Thus, the default flag because duplicate reads before downsampling may not all remain duplicated after downsampling. Thus, the default Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: setting also removes the duplicate information. setting also removes the duplicate information. Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Example Example Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: java -jar picard.jar PositionBasedDownsampleSam \ java -jar picard.jar PositionBasedDownsampleSam \ Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: O=downsampled.bam \ O=downsampled.bam \ Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION=0.1 FRACTION=0.1 Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Caveats Caveats Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 1: This method is technology and read-name dependent. If the read-names do not have coordinate information Note 1: This method is technology and read-name dependent. If the read-names do not have coordinate information Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: embedded in them, or if your BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this embedded in them, or if your BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: will not work properly. It has been designed to work with Illumina technology and reads-names. Consider modifying {@link will not work properly. It has been designed to work with Illumina technology and reads-names. Consider modifying {@link Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: #READ_NAME_REGEX} in other cases. #READ_NAME_REGEX} in other cases. Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 2: The code has been designed to simulate, as accurately as possible, sequencing less, not for getting an exact Note 2: The code has been designed to simulate, as accurately as possible, sequencing less, not for getting an exact Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: downsampled fraction (Use {@link DownsampleSam} for that.) In particular, since the reads may be distributed non-evenly downsampled fraction (Use {@link DownsampleSam} for that.) In particular, since the reads may be distributed non-evenly Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: within the lanes/tiles, the resulting downsampling percentage will not be accurately determined by the input argument within the lanes/tiles, the resulting downsampling percentage will not be accurately determined by the input argument Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION. FRACTION. Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 3:Consider running {@link MarkDuplicates} after downsampling in order to "expose" the duplicates whose Note 3:Consider running {@link MarkDuplicates} after downsampling in order to "expose" the duplicates whose Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: representative has been downsampled away. representative has been downsampled away. Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 4:The downsampling assumes a uniform distribution of reads in the flowcell. Input already downsampled with Note 4:The downsampling assumes a uniform distribution of reads in the flowcell. Input already downsampled with Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: PositionBasedDownsampleSam violates this assumption. To guard against such input, PositionBasedDownsampleSam always PositionBasedDownsampleSam violates this assumption. To guard against such input, PositionBasedDownsampleSam always Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: places a PG record in the header of its output, and aborts whenever it finds such a PG record in its input. places a PG record in the header of its output, and aborts whenever it finds such a PG record in its input. Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Version: null Version: null Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Options: Options: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: --help --help Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: --stdhelp --stdhelp Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: tools. tools. Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INPUT=File INPUT=File Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: I=File The input SAM or BAM file to downsample. Required. I=File The input SAM or BAM file to downsample. Required. Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: O=File The output, downsampled, SAM or BAM file. Required. O=File The output, downsampled, SAM or BAM file. Required. Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION=Double FRACTION=Double Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: F=Double The (approximate) fraction of reads to be kept, between 0 and 1. Required. F=Double The (approximate) fraction of reads to be kept, between 0 and 1. Required. Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: REMOVE_DUPLICATE_INFORMATION=Boolean REMOVE_DUPLICATE_INFORMATION=Boolean Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Determines whether the duplicate tag should be reset since the downsampling requires Determines whether the duplicate tag should be reset since the downsampling requires Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: re-marking duplicates. Default value: true. This option can be set to 'null' to clear the re-marking duplicates. Default value: true. This option can be set to 'null' to clear the Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: default value. Possible values: {true, false} default value. Possible values: {true, false} Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: READ_NAME_REGEX=String Use these regular expressions to parse read names in the input SAM file. Read names are READ_NAME_REGEX=String Use these regular expressions to parse read names in the input SAM file. Read names are Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: parsed to extract three variables: tile/region, x coordinate and y coordinate. The x and y parsed to extract three variables: tile/region, x coordinate and y coordinate. The x and y Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: coordinates are used to determine the downsample decision. Set this option to null to coordinates are used to determine the downsample decision. Set this option to null to Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: disable optical duplicate detection, e.g. for RNA-seq The regular expression should disable optical duplicate detection, e.g. for RNA-seq The regular expression should Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: contain three capture groups for the three variables, in order. It must match the entire contain three capture groups for the three variables, in order. It must match the entire Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: read name. Note that if the default regex is specified, a regex match is not actually read name. Note that if the default regex is specified, a regex match is not actually Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: done, but instead the read name is split on colons (:). For 5 element names, the 3rd, 4th done, but instead the read name is split on colons (:). For 5 element names, the 3rd, 4th Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: the 5th, 6th, and 7th elements are assumed to be tile, x and y values. Default value: the 5th, 6th, and 7th elements are assumed to be tile, x and y values. Default value: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: . This option can . This option can Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: be set to 'null' to clear the default value. be set to 'null' to clear the default value. Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: null. STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: null. Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Allow downsampling again despite this being a bad idea with possibly unexpected results. Allow downsampling again despite this being a bad idea with possibly unexpected results. Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Default value: false. This option can be set to 'null' to clear the default value. Default value: false. This option can be set to 'null' to clear the default value. Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Possible values: {true, false} Possible values: {true, false} Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[0](-1.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION must be a value between 0 and 1, found: -1.0 FRACTION must be a value between 0 and 1, found: -1.0 Running Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:39 PositionBasedDownsampleSam Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.TestInvalidArguments[1](-1.0E-5) STANDARD_ERROR INFO 2024-07-02 12:01:39 PositionBasedDownsampleSam Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam5431698702480393943.bam -FRACTION -1.0E-5 ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam5431698702480393943.bam -FRACTION -1.0E-5 Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:39.842 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 12:01:39.842 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: USAGE: PositionBasedDownsampleSam [options] USAGE: PositionBasedDownsampleSam [options] Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Summary Summary Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Class to downsample a SAM/BAM file based on the position of the read in a flowcell. As with DownsampleSam, all the reads Class to downsample a SAM/BAM file based on the position of the read in a flowcell. As with DownsampleSam, all the reads Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: with the same queryname are either kept or dropped as a unit. with the same queryname are either kept or dropped as a unit. Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Details Details Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: The downsampling is _not_ random (and there is no random seed). It is deterministically determined by the position of The downsampling is _not_ random (and there is no random seed). It is deterministically determined by the position of Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: each read within its tile. Specifically, it draws an ellipse that covers a FRACTION of the total tile's area and of all each read within its tile. Specifically, it draws an ellipse that covers a FRACTION of the total tile's area and of all Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: the edges of the tile. It uses this area to determine whether to keep or drop the record. Since reads with the same name the edges of the tile. It uses this area to determine whether to keep or drop the record. Since reads with the same name Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: have the same position (mates, secondary and supplemental alignments), the decision will be the same for all of them. have the same position (mates, secondary and supplemental alignments), the decision will be the same for all of them. Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: The main concern of this downsampling method is that due to "optical duplicates" downsampling randomly can create a The main concern of this downsampling method is that due to "optical duplicates" downsampling randomly can create a Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: result that has a different optical duplicate rate, and therefore a different estimated library size (when running result that has a different optical duplicate rate, and therefore a different estimated library size (when running Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: MarkDuplicates). This method keeps (physically) close read together, so that (except for reads near the boundary of the MarkDuplicates). This method keeps (physically) close read together, so that (except for reads near the boundary of the Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: circle) optical duplicates are kept or dropped as a group. By default the program expects the read names to have 5 or 7 circle) optical duplicates are kept or dropped as a group. By default the program expects the read names to have 5 or 7 Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: fields separated by colons (:) and it takes the last two to indicate the x and y coordinates of the reads within the fields separated by colons (:) and it takes the last two to indicate the x and y coordinates of the reads within the Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: tile whence it was sequenced. See DEFAULT_READ_NAME_REGEX for more detail. The program traverses the INPUT twice: first tile whence it was sequenced. See DEFAULT_READ_NAME_REGEX for more detail. The program traverses the INPUT twice: first Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: to find out the size of each of the tiles, and next to perform the downsampling. Downsampling invalidates the duplicate to find out the size of each of the tiles, and next to perform the downsampling. Downsampling invalidates the duplicate Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: flag because duplicate reads before downsampling may not all remain duplicated after downsampling. Thus, the default flag because duplicate reads before downsampling may not all remain duplicated after downsampling. Thus, the default Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: setting also removes the duplicate information. setting also removes the duplicate information. Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Example Example Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: java -jar picard.jar PositionBasedDownsampleSam \ java -jar picard.jar PositionBasedDownsampleSam \ Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: O=downsampled.bam \ O=downsampled.bam \ Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION=0.1 FRACTION=0.1 Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Caveats Caveats Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 1: This method is technology and read-name dependent. If the read-names do not have coordinate information Note 1: This method is technology and read-name dependent. If the read-names do not have coordinate information Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: embedded in them, or if your BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this embedded in them, or if your BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: will not work properly. It has been designed to work with Illumina technology and reads-names. Consider modifying {@link will not work properly. It has been designed to work with Illumina technology and reads-names. Consider modifying {@link Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: #READ_NAME_REGEX} in other cases. #READ_NAME_REGEX} in other cases. Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 2: The code has been designed to simulate, as accurately as possible, sequencing less, not for getting an exact Note 2: The code has been designed to simulate, as accurately as possible, sequencing less, not for getting an exact Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: downsampled fraction (Use {@link DownsampleSam} for that.) In particular, since the reads may be distributed non-evenly downsampled fraction (Use {@link DownsampleSam} for that.) In particular, since the reads may be distributed non-evenly Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: within the lanes/tiles, the resulting downsampling percentage will not be accurately determined by the input argument within the lanes/tiles, the resulting downsampling percentage will not be accurately determined by the input argument Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION. FRACTION. Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 3:Consider running {@link MarkDuplicates} after downsampling in order to "expose" the duplicates whose Note 3:Consider running {@link MarkDuplicates} after downsampling in order to "expose" the duplicates whose Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: representative has been downsampled away. representative has been downsampled away. Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 4:The downsampling assumes a uniform distribution of reads in the flowcell. Input already downsampled with Note 4:The downsampling assumes a uniform distribution of reads in the flowcell. Input already downsampled with Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: PositionBasedDownsampleSam violates this assumption. To guard against such input, PositionBasedDownsampleSam always PositionBasedDownsampleSam violates this assumption. To guard against such input, PositionBasedDownsampleSam always Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: places a PG record in the header of its output, and aborts whenever it finds such a PG record in its input. places a PG record in the header of its output, and aborts whenever it finds such a PG record in its input. Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Version: null Version: null Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Options: Options: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: --help --help Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: --stdhelp --stdhelp Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: tools. tools. Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INPUT=File INPUT=File Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: I=File The input SAM or BAM file to downsample. Required. I=File The input SAM or BAM file to downsample. Required. Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: O=File The output, downsampled, SAM or BAM file. Required. O=File The output, downsampled, SAM or BAM file. Required. Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION=Double FRACTION=Double Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: F=Double The (approximate) fraction of reads to be kept, between 0 and 1. Required. F=Double The (approximate) fraction of reads to be kept, between 0 and 1. Required. Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: REMOVE_DUPLICATE_INFORMATION=Boolean REMOVE_DUPLICATE_INFORMATION=Boolean Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Determines whether the duplicate tag should be reset since the downsampling requires Determines whether the duplicate tag should be reset since the downsampling requires Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: re-marking duplicates. Default value: true. This option can be set to 'null' to clear the re-marking duplicates. Default value: true. This option can be set to 'null' to clear the Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: default value. Possible values: {true, false} default value. Possible values: {true, false} Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: READ_NAME_REGEX=String Use these regular expressions to parse read names in the input SAM file. Read names are READ_NAME_REGEX=String Use these regular expressions to parse read names in the input SAM file. Read names are Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: parsed to extract three variables: tile/region, x coordinate and y coordinate. The x and y parsed to extract three variables: tile/region, x coordinate and y coordinate. The x and y Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: coordinates are used to determine the downsample decision. Set this option to null to coordinates are used to determine the downsample decision. Set this option to null to Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: disable optical duplicate detection, e.g. for RNA-seq The regular expression should disable optical duplicate detection, e.g. for RNA-seq The regular expression should Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: contain three capture groups for the three variables, in order. It must match the entire contain three capture groups for the three variables, in order. It must match the entire Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: read name. Note that if the default regex is specified, a regex match is not actually read name. Note that if the default regex is specified, a regex match is not actually Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: done, but instead the read name is split on colons (:). For 5 element names, the 3rd, 4th done, but instead the read name is split on colons (:). For 5 element names, the 3rd, 4th Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: the 5th, 6th, and 7th elements are assumed to be tile, x and y values. Default value: the 5th, 6th, and 7th elements are assumed to be tile, x and y values. Default value: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: . This option can . This option can Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: be set to 'null' to clear the default value. be set to 'null' to clear the default value. Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: null. STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: null. Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Allow downsampling again despite this being a bad idea with possibly unexpected results. Allow downsampling again despite this being a bad idea with possibly unexpected results. Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Default value: false. This option can be set to 'null' to clear the default value. Default value: false. This option can be set to 'null' to clear the default value. Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Possible values: {true, false} Possible values: {true, false} Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[1](-1.0E-5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION must be a value between 0 and 1, found: -1.0E-5 FRACTION must be a value between 0 and 1, found: -1.0E-5 Running Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:40 PositionBasedDownsampleSam Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.TestInvalidArguments[2](-5.0) STANDARD_ERROR INFO 2024-07-02 12:01:40 PositionBasedDownsampleSam Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam652429689838558744.bam -FRACTION -5.0 ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam652429689838558744.bam -FRACTION -5.0 Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:40.110 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 12:01:40.110 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: USAGE: PositionBasedDownsampleSam [options] USAGE: PositionBasedDownsampleSam [options] Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Summary Summary Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Class to downsample a SAM/BAM file based on the position of the read in a flowcell. As with DownsampleSam, all the reads Class to downsample a SAM/BAM file based on the position of the read in a flowcell. As with DownsampleSam, all the reads Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: with the same queryname are either kept or dropped as a unit. with the same queryname are either kept or dropped as a unit. Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Details Details Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: The downsampling is _not_ random (and there is no random seed). It is deterministically determined by the position of The downsampling is _not_ random (and there is no random seed). It is deterministically determined by the position of Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: each read within its tile. Specifically, it draws an ellipse that covers a FRACTION of the total tile's area and of all each read within its tile. Specifically, it draws an ellipse that covers a FRACTION of the total tile's area and of all Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: the edges of the tile. It uses this area to determine whether to keep or drop the record. Since reads with the same name the edges of the tile. It uses this area to determine whether to keep or drop the record. Since reads with the same name Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: have the same position (mates, secondary and supplemental alignments), the decision will be the same for all of them. have the same position (mates, secondary and supplemental alignments), the decision will be the same for all of them. Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: The main concern of this downsampling method is that due to "optical duplicates" downsampling randomly can create a The main concern of this downsampling method is that due to "optical duplicates" downsampling randomly can create a Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: result that has a different optical duplicate rate, and therefore a different estimated library size (when running result that has a different optical duplicate rate, and therefore a different estimated library size (when running Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: MarkDuplicates). This method keeps (physically) close read together, so that (except for reads near the boundary of the MarkDuplicates). This method keeps (physically) close read together, so that (except for reads near the boundary of the Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: circle) optical duplicates are kept or dropped as a group. By default the program expects the read names to have 5 or 7 circle) optical duplicates are kept or dropped as a group. By default the program expects the read names to have 5 or 7 Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: fields separated by colons (:) and it takes the last two to indicate the x and y coordinates of the reads within the fields separated by colons (:) and it takes the last two to indicate the x and y coordinates of the reads within the Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: tile whence it was sequenced. See DEFAULT_READ_NAME_REGEX for more detail. The program traverses the INPUT twice: first tile whence it was sequenced. See DEFAULT_READ_NAME_REGEX for more detail. The program traverses the INPUT twice: first Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: to find out the size of each of the tiles, and next to perform the downsampling. Downsampling invalidates the duplicate to find out the size of each of the tiles, and next to perform the downsampling. Downsampling invalidates the duplicate Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: flag because duplicate reads before downsampling may not all remain duplicated after downsampling. Thus, the default flag because duplicate reads before downsampling may not all remain duplicated after downsampling. Thus, the default Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: setting also removes the duplicate information. setting also removes the duplicate information. Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Example Example Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: java -jar picard.jar PositionBasedDownsampleSam \ java -jar picard.jar PositionBasedDownsampleSam \ Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: O=downsampled.bam \ O=downsampled.bam \ Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION=0.1 FRACTION=0.1 Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Caveats Caveats Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 1: This method is technology and read-name dependent. If the read-names do not have coordinate information Note 1: This method is technology and read-name dependent. If the read-names do not have coordinate information Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: embedded in them, or if your BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this embedded in them, or if your BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: will not work properly. It has been designed to work with Illumina technology and reads-names. Consider modifying {@link will not work properly. It has been designed to work with Illumina technology and reads-names. Consider modifying {@link Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: #READ_NAME_REGEX} in other cases. #READ_NAME_REGEX} in other cases. Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 2: The code has been designed to simulate, as accurately as possible, sequencing less, not for getting an exact Note 2: The code has been designed to simulate, as accurately as possible, sequencing less, not for getting an exact Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: downsampled fraction (Use {@link DownsampleSam} for that.) In particular, since the reads may be distributed non-evenly downsampled fraction (Use {@link DownsampleSam} for that.) In particular, since the reads may be distributed non-evenly Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: within the lanes/tiles, the resulting downsampling percentage will not be accurately determined by the input argument within the lanes/tiles, the resulting downsampling percentage will not be accurately determined by the input argument Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION. FRACTION. Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 3:Consider running {@link MarkDuplicates} after downsampling in order to "expose" the duplicates whose Note 3:Consider running {@link MarkDuplicates} after downsampling in order to "expose" the duplicates whose Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: representative has been downsampled away. representative has been downsampled away. Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 4:The downsampling assumes a uniform distribution of reads in the flowcell. Input already downsampled with Note 4:The downsampling assumes a uniform distribution of reads in the flowcell. Input already downsampled with Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: PositionBasedDownsampleSam violates this assumption. To guard against such input, PositionBasedDownsampleSam always PositionBasedDownsampleSam violates this assumption. To guard against such input, PositionBasedDownsampleSam always Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: places a PG record in the header of its output, and aborts whenever it finds such a PG record in its input. places a PG record in the header of its output, and aborts whenever it finds such a PG record in its input. Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Version: null Version: null Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Options: Options: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: --help --help Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: --stdhelp --stdhelp Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: tools. tools. Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INPUT=File INPUT=File Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: I=File The input SAM or BAM file to downsample. Required. I=File The input SAM or BAM file to downsample. Required. Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: O=File The output, downsampled, SAM or BAM file. Required. O=File The output, downsampled, SAM or BAM file. Required. Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION=Double FRACTION=Double Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: F=Double The (approximate) fraction of reads to be kept, between 0 and 1. Required. F=Double The (approximate) fraction of reads to be kept, between 0 and 1. Required. Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: REMOVE_DUPLICATE_INFORMATION=Boolean REMOVE_DUPLICATE_INFORMATION=Boolean Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Determines whether the duplicate tag should be reset since the downsampling requires Determines whether the duplicate tag should be reset since the downsampling requires Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: re-marking duplicates. Default value: true. This option can be set to 'null' to clear the re-marking duplicates. Default value: true. This option can be set to 'null' to clear the Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: default value. Possible values: {true, false} default value. Possible values: {true, false} Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: READ_NAME_REGEX=String Use these regular expressions to parse read names in the input SAM file. Read names are READ_NAME_REGEX=String Use these regular expressions to parse read names in the input SAM file. Read names are Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: parsed to extract three variables: tile/region, x coordinate and y coordinate. The x and y parsed to extract three variables: tile/region, x coordinate and y coordinate. The x and y Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: coordinates are used to determine the downsample decision. Set this option to null to coordinates are used to determine the downsample decision. Set this option to null to Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: disable optical duplicate detection, e.g. for RNA-seq The regular expression should disable optical duplicate detection, e.g. for RNA-seq The regular expression should Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: contain three capture groups for the three variables, in order. It must match the entire contain three capture groups for the three variables, in order. It must match the entire Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: read name. Note that if the default regex is specified, a regex match is not actually read name. Note that if the default regex is specified, a regex match is not actually Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: done, but instead the read name is split on colons (:). For 5 element names, the 3rd, 4th done, but instead the read name is split on colons (:). For 5 element names, the 3rd, 4th Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: the 5th, 6th, and 7th elements are assumed to be tile, x and y values. Default value: the 5th, 6th, and 7th elements are assumed to be tile, x and y values. Default value: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: . This option can . This option can Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: be set to 'null' to clear the default value. be set to 'null' to clear the default value. Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: null. STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: null. Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Allow downsampling again despite this being a bad idea with possibly unexpected results. Allow downsampling again despite this being a bad idea with possibly unexpected results. Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Default value: false. This option can be set to 'null' to clear the default value. Default value: false. This option can be set to 'null' to clear the default value. Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Possible values: {true, false} Possible values: {true, false} Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[2](-5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION must be a value between 0 and 1, found: -5.0 FRACTION must be a value between 0 and 1, found: -5.0 Running Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:40 PositionBasedDownsampleSam Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.TestInvalidArguments[3](1.00001) STANDARD_ERROR INFO 2024-07-02 12:01:40 PositionBasedDownsampleSam Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam5527505180210855168.bam -FRACTION 1.00001 ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam5527505180210855168.bam -FRACTION 1.00001 Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:40.344 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 12:01:40.344 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: USAGE: PositionBasedDownsampleSam [options] USAGE: PositionBasedDownsampleSam [options] Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Summary Summary Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Class to downsample a SAM/BAM file based on the position of the read in a flowcell. As with DownsampleSam, all the reads Class to downsample a SAM/BAM file based on the position of the read in a flowcell. As with DownsampleSam, all the reads Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: with the same queryname are either kept or dropped as a unit. with the same queryname are either kept or dropped as a unit. Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Details Details Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: The downsampling is _not_ random (and there is no random seed). It is deterministically determined by the position of The downsampling is _not_ random (and there is no random seed). It is deterministically determined by the position of Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: each read within its tile. Specifically, it draws an ellipse that covers a FRACTION of the total tile's area and of all each read within its tile. Specifically, it draws an ellipse that covers a FRACTION of the total tile's area and of all Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: the edges of the tile. It uses this area to determine whether to keep or drop the record. Since reads with the same name the edges of the tile. It uses this area to determine whether to keep or drop the record. Since reads with the same name Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: have the same position (mates, secondary and supplemental alignments), the decision will be the same for all of them. have the same position (mates, secondary and supplemental alignments), the decision will be the same for all of them. Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: The main concern of this downsampling method is that due to "optical duplicates" downsampling randomly can create a The main concern of this downsampling method is that due to "optical duplicates" downsampling randomly can create a Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: result that has a different optical duplicate rate, and therefore a different estimated library size (when running result that has a different optical duplicate rate, and therefore a different estimated library size (when running Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: MarkDuplicates). This method keeps (physically) close read together, so that (except for reads near the boundary of the MarkDuplicates). This method keeps (physically) close read together, so that (except for reads near the boundary of the Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: circle) optical duplicates are kept or dropped as a group. By default the program expects the read names to have 5 or 7 circle) optical duplicates are kept or dropped as a group. By default the program expects the read names to have 5 or 7 Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: fields separated by colons (:) and it takes the last two to indicate the x and y coordinates of the reads within the fields separated by colons (:) and it takes the last two to indicate the x and y coordinates of the reads within the Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: tile whence it was sequenced. See DEFAULT_READ_NAME_REGEX for more detail. The program traverses the INPUT twice: first tile whence it was sequenced. See DEFAULT_READ_NAME_REGEX for more detail. The program traverses the INPUT twice: first Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: to find out the size of each of the tiles, and next to perform the downsampling. Downsampling invalidates the duplicate to find out the size of each of the tiles, and next to perform the downsampling. Downsampling invalidates the duplicate Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: flag because duplicate reads before downsampling may not all remain duplicated after downsampling. Thus, the default flag because duplicate reads before downsampling may not all remain duplicated after downsampling. Thus, the default Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: setting also removes the duplicate information. setting also removes the duplicate information. Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Example Example Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: java -jar picard.jar PositionBasedDownsampleSam \ java -jar picard.jar PositionBasedDownsampleSam \ Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: O=downsampled.bam \ O=downsampled.bam \ Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION=0.1 FRACTION=0.1 Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Caveats Caveats Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 1: This method is technology and read-name dependent. If the read-names do not have coordinate information Note 1: This method is technology and read-name dependent. If the read-names do not have coordinate information Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: embedded in them, or if your BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this embedded in them, or if your BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: will not work properly. It has been designed to work with Illumina technology and reads-names. Consider modifying {@link will not work properly. It has been designed to work with Illumina technology and reads-names. Consider modifying {@link Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: #READ_NAME_REGEX} in other cases. #READ_NAME_REGEX} in other cases. Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 2: The code has been designed to simulate, as accurately as possible, sequencing less, not for getting an exact Note 2: The code has been designed to simulate, as accurately as possible, sequencing less, not for getting an exact Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: downsampled fraction (Use {@link DownsampleSam} for that.) In particular, since the reads may be distributed non-evenly downsampled fraction (Use {@link DownsampleSam} for that.) In particular, since the reads may be distributed non-evenly Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: within the lanes/tiles, the resulting downsampling percentage will not be accurately determined by the input argument within the lanes/tiles, the resulting downsampling percentage will not be accurately determined by the input argument Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION. FRACTION. Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 3:Consider running {@link MarkDuplicates} after downsampling in order to "expose" the duplicates whose Note 3:Consider running {@link MarkDuplicates} after downsampling in order to "expose" the duplicates whose Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: representative has been downsampled away. representative has been downsampled away. Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 4:The downsampling assumes a uniform distribution of reads in the flowcell. Input already downsampled with Note 4:The downsampling assumes a uniform distribution of reads in the flowcell. Input already downsampled with Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: PositionBasedDownsampleSam violates this assumption. To guard against such input, PositionBasedDownsampleSam always PositionBasedDownsampleSam violates this assumption. To guard against such input, PositionBasedDownsampleSam always Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: places a PG record in the header of its output, and aborts whenever it finds such a PG record in its input. places a PG record in the header of its output, and aborts whenever it finds such a PG record in its input. Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Version: null Version: null Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Options: Options: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: --help --help Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: --stdhelp --stdhelp Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: tools. tools. Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INPUT=File INPUT=File Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: I=File The input SAM or BAM file to downsample. Required. I=File The input SAM or BAM file to downsample. Required. Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: O=File The output, downsampled, SAM or BAM file. Required. O=File The output, downsampled, SAM or BAM file. Required. Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION=Double FRACTION=Double Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: F=Double The (approximate) fraction of reads to be kept, between 0 and 1. Required. F=Double The (approximate) fraction of reads to be kept, between 0 and 1. Required. Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: REMOVE_DUPLICATE_INFORMATION=Boolean REMOVE_DUPLICATE_INFORMATION=Boolean Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Determines whether the duplicate tag should be reset since the downsampling requires Determines whether the duplicate tag should be reset since the downsampling requires Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: re-marking duplicates. Default value: true. This option can be set to 'null' to clear the re-marking duplicates. Default value: true. This option can be set to 'null' to clear the Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: default value. Possible values: {true, false} default value. Possible values: {true, false} Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: READ_NAME_REGEX=String Use these regular expressions to parse read names in the input SAM file. Read names are READ_NAME_REGEX=String Use these regular expressions to parse read names in the input SAM file. Read names are Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: parsed to extract three variables: tile/region, x coordinate and y coordinate. The x and y parsed to extract three variables: tile/region, x coordinate and y coordinate. The x and y Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: coordinates are used to determine the downsample decision. Set this option to null to coordinates are used to determine the downsample decision. Set this option to null to Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: disable optical duplicate detection, e.g. for RNA-seq The regular expression should disable optical duplicate detection, e.g. for RNA-seq The regular expression should Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: contain three capture groups for the three variables, in order. It must match the entire contain three capture groups for the three variables, in order. It must match the entire Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: read name. Note that if the default regex is specified, a regex match is not actually read name. Note that if the default regex is specified, a regex match is not actually Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: done, but instead the read name is split on colons (:). For 5 element names, the 3rd, 4th done, but instead the read name is split on colons (:). For 5 element names, the 3rd, 4th Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: the 5th, 6th, and 7th elements are assumed to be tile, x and y values. Default value: the 5th, 6th, and 7th elements are assumed to be tile, x and y values. Default value: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: . This option can . This option can Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: be set to 'null' to clear the default value. be set to 'null' to clear the default value. Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: null. STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: null. Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Allow downsampling again despite this being a bad idea with possibly unexpected results. Allow downsampling again despite this being a bad idea with possibly unexpected results. Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Default value: false. This option can be set to 'null' to clear the default value. Default value: false. This option can be set to 'null' to clear the default value. Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Possible values: {true, false} Possible values: {true, false} Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[3](1.00001)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION must be a value between 0 and 1, found: 1.00001 FRACTION must be a value between 0 and 1, found: 1.00001 Running Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:40 PositionBasedDownsampleSam Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.TestInvalidArguments[4](5.0) STANDARD_ERROR INFO 2024-07-02 12:01:40 PositionBasedDownsampleSam Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam2800284413399182728.bam -FRACTION 5.0 ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam2800284413399182728.bam -FRACTION 5.0 Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:40.607 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 12:01:40.607 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: USAGE: PositionBasedDownsampleSam [options] USAGE: PositionBasedDownsampleSam [options] Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Summary Summary Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Class to downsample a SAM/BAM file based on the position of the read in a flowcell. As with DownsampleSam, all the reads Class to downsample a SAM/BAM file based on the position of the read in a flowcell. As with DownsampleSam, all the reads Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: with the same queryname are either kept or dropped as a unit. with the same queryname are either kept or dropped as a unit. Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Details Details Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: The downsampling is _not_ random (and there is no random seed). It is deterministically determined by the position of The downsampling is _not_ random (and there is no random seed). It is deterministically determined by the position of Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: each read within its tile. Specifically, it draws an ellipse that covers a FRACTION of the total tile's area and of all each read within its tile. Specifically, it draws an ellipse that covers a FRACTION of the total tile's area and of all Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: the edges of the tile. It uses this area to determine whether to keep or drop the record. Since reads with the same name the edges of the tile. It uses this area to determine whether to keep or drop the record. Since reads with the same name Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: have the same position (mates, secondary and supplemental alignments), the decision will be the same for all of them. have the same position (mates, secondary and supplemental alignments), the decision will be the same for all of them. Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: The main concern of this downsampling method is that due to "optical duplicates" downsampling randomly can create a The main concern of this downsampling method is that due to "optical duplicates" downsampling randomly can create a Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: result that has a different optical duplicate rate, and therefore a different estimated library size (when running result that has a different optical duplicate rate, and therefore a different estimated library size (when running Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: MarkDuplicates). This method keeps (physically) close read together, so that (except for reads near the boundary of the MarkDuplicates). This method keeps (physically) close read together, so that (except for reads near the boundary of the Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: circle) optical duplicates are kept or dropped as a group. By default the program expects the read names to have 5 or 7 circle) optical duplicates are kept or dropped as a group. By default the program expects the read names to have 5 or 7 Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: fields separated by colons (:) and it takes the last two to indicate the x and y coordinates of the reads within the fields separated by colons (:) and it takes the last two to indicate the x and y coordinates of the reads within the Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: tile whence it was sequenced. See DEFAULT_READ_NAME_REGEX for more detail. The program traverses the INPUT twice: first tile whence it was sequenced. See DEFAULT_READ_NAME_REGEX for more detail. The program traverses the INPUT twice: first Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: to find out the size of each of the tiles, and next to perform the downsampling. Downsampling invalidates the duplicate to find out the size of each of the tiles, and next to perform the downsampling. Downsampling invalidates the duplicate Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: flag because duplicate reads before downsampling may not all remain duplicated after downsampling. Thus, the default flag because duplicate reads before downsampling may not all remain duplicated after downsampling. Thus, the default Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: setting also removes the duplicate information. setting also removes the duplicate information. Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Example Example Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: java -jar picard.jar PositionBasedDownsampleSam \ java -jar picard.jar PositionBasedDownsampleSam \ Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: O=downsampled.bam \ O=downsampled.bam \ Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION=0.1 FRACTION=0.1 Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Caveats Caveats Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 1: This method is technology and read-name dependent. If the read-names do not have coordinate information Note 1: This method is technology and read-name dependent. If the read-names do not have coordinate information Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: embedded in them, or if your BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this embedded in them, or if your BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: will not work properly. It has been designed to work with Illumina technology and reads-names. Consider modifying {@link will not work properly. It has been designed to work with Illumina technology and reads-names. Consider modifying {@link Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: #READ_NAME_REGEX} in other cases. #READ_NAME_REGEX} in other cases. Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 2: The code has been designed to simulate, as accurately as possible, sequencing less, not for getting an exact Note 2: The code has been designed to simulate, as accurately as possible, sequencing less, not for getting an exact Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: downsampled fraction (Use {@link DownsampleSam} for that.) In particular, since the reads may be distributed non-evenly downsampled fraction (Use {@link DownsampleSam} for that.) In particular, since the reads may be distributed non-evenly Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: within the lanes/tiles, the resulting downsampling percentage will not be accurately determined by the input argument within the lanes/tiles, the resulting downsampling percentage will not be accurately determined by the input argument Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION. FRACTION. Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 3:Consider running {@link MarkDuplicates} after downsampling in order to "expose" the duplicates whose Note 3:Consider running {@link MarkDuplicates} after downsampling in order to "expose" the duplicates whose Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: representative has been downsampled away. representative has been downsampled away. Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 4:The downsampling assumes a uniform distribution of reads in the flowcell. Input already downsampled with Note 4:The downsampling assumes a uniform distribution of reads in the flowcell. Input already downsampled with Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: PositionBasedDownsampleSam violates this assumption. To guard against such input, PositionBasedDownsampleSam always PositionBasedDownsampleSam violates this assumption. To guard against such input, PositionBasedDownsampleSam always Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: places a PG record in the header of its output, and aborts whenever it finds such a PG record in its input. places a PG record in the header of its output, and aborts whenever it finds such a PG record in its input. Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Version: null Version: null Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Options: Options: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: --help --help Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: --stdhelp --stdhelp Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: tools. tools. Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INPUT=File INPUT=File Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: I=File The input SAM or BAM file to downsample. Required. I=File The input SAM or BAM file to downsample. Required. Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: O=File The output, downsampled, SAM or BAM file. Required. O=File The output, downsampled, SAM or BAM file. Required. Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION=Double FRACTION=Double Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: F=Double The (approximate) fraction of reads to be kept, between 0 and 1. Required. F=Double The (approximate) fraction of reads to be kept, between 0 and 1. Required. Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: REMOVE_DUPLICATE_INFORMATION=Boolean REMOVE_DUPLICATE_INFORMATION=Boolean Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Determines whether the duplicate tag should be reset since the downsampling requires Determines whether the duplicate tag should be reset since the downsampling requires Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: re-marking duplicates. Default value: true. This option can be set to 'null' to clear the re-marking duplicates. Default value: true. This option can be set to 'null' to clear the Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: default value. Possible values: {true, false} default value. Possible values: {true, false} Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: READ_NAME_REGEX=String Use these regular expressions to parse read names in the input SAM file. Read names are READ_NAME_REGEX=String Use these regular expressions to parse read names in the input SAM file. Read names are Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: parsed to extract three variables: tile/region, x coordinate and y coordinate. The x and y parsed to extract three variables: tile/region, x coordinate and y coordinate. The x and y Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: coordinates are used to determine the downsample decision. Set this option to null to coordinates are used to determine the downsample decision. Set this option to null to Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: disable optical duplicate detection, e.g. for RNA-seq The regular expression should disable optical duplicate detection, e.g. for RNA-seq The regular expression should Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: contain three capture groups for the three variables, in order. It must match the entire contain three capture groups for the three variables, in order. It must match the entire Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: read name. Note that if the default regex is specified, a regex match is not actually read name. Note that if the default regex is specified, a regex match is not actually Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: done, but instead the read name is split on colons (:). For 5 element names, the 3rd, 4th done, but instead the read name is split on colons (:). For 5 element names, the 3rd, 4th Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: the 5th, 6th, and 7th elements are assumed to be tile, x and y values. Default value: the 5th, 6th, and 7th elements are assumed to be tile, x and y values. Default value: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: . This option can . This option can Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: be set to 'null' to clear the default value. be set to 'null' to clear the default value. Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: null. STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: null. Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Allow downsampling again despite this being a bad idea with possibly unexpected results. Allow downsampling again despite this being a bad idea with possibly unexpected results. Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Default value: false. This option can be set to 'null' to clear the default value. Default value: false. This option can be set to 'null' to clear the default value. Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Possible values: {true, false} Possible values: {true, false} Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[4](5.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION must be a value between 0 and 1, found: 5.0 FRACTION must be a value between 0 and 1, found: 5.0 Running Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:40 PositionBasedDownsampleSam Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.TestInvalidArguments[5](50.0) STANDARD_ERROR INFO 2024-07-02 12:01:40 PositionBasedDownsampleSam Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam3881933877868962350.bam -FRACTION 50.0 ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam3881933877868962350.bam -FRACTION 50.0 Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:40.838 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 12:01:40.838 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: USAGE: PositionBasedDownsampleSam [options] USAGE: PositionBasedDownsampleSam [options] Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Summary Summary Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Class to downsample a SAM/BAM file based on the position of the read in a flowcell. As with DownsampleSam, all the reads Class to downsample a SAM/BAM file based on the position of the read in a flowcell. As with DownsampleSam, all the reads Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: with the same queryname are either kept or dropped as a unit. with the same queryname are either kept or dropped as a unit. Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Details Details Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: The downsampling is _not_ random (and there is no random seed). It is deterministically determined by the position of The downsampling is _not_ random (and there is no random seed). It is deterministically determined by the position of Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: each read within its tile. Specifically, it draws an ellipse that covers a FRACTION of the total tile's area and of all each read within its tile. Specifically, it draws an ellipse that covers a FRACTION of the total tile's area and of all Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: the edges of the tile. It uses this area to determine whether to keep or drop the record. Since reads with the same name the edges of the tile. It uses this area to determine whether to keep or drop the record. Since reads with the same name Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: have the same position (mates, secondary and supplemental alignments), the decision will be the same for all of them. have the same position (mates, secondary and supplemental alignments), the decision will be the same for all of them. Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: The main concern of this downsampling method is that due to "optical duplicates" downsampling randomly can create a The main concern of this downsampling method is that due to "optical duplicates" downsampling randomly can create a Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: result that has a different optical duplicate rate, and therefore a different estimated library size (when running result that has a different optical duplicate rate, and therefore a different estimated library size (when running Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: MarkDuplicates). This method keeps (physically) close read together, so that (except for reads near the boundary of the MarkDuplicates). This method keeps (physically) close read together, so that (except for reads near the boundary of the Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: circle) optical duplicates are kept or dropped as a group. By default the program expects the read names to have 5 or 7 circle) optical duplicates are kept or dropped as a group. By default the program expects the read names to have 5 or 7 Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: fields separated by colons (:) and it takes the last two to indicate the x and y coordinates of the reads within the fields separated by colons (:) and it takes the last two to indicate the x and y coordinates of the reads within the Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: tile whence it was sequenced. See DEFAULT_READ_NAME_REGEX for more detail. The program traverses the INPUT twice: first tile whence it was sequenced. See DEFAULT_READ_NAME_REGEX for more detail. The program traverses the INPUT twice: first Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: to find out the size of each of the tiles, and next to perform the downsampling. Downsampling invalidates the duplicate to find out the size of each of the tiles, and next to perform the downsampling. Downsampling invalidates the duplicate Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: flag because duplicate reads before downsampling may not all remain duplicated after downsampling. Thus, the default flag because duplicate reads before downsampling may not all remain duplicated after downsampling. Thus, the default Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: setting also removes the duplicate information. setting also removes the duplicate information. Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Example Example Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: java -jar picard.jar PositionBasedDownsampleSam \ java -jar picard.jar PositionBasedDownsampleSam \ Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: O=downsampled.bam \ O=downsampled.bam \ Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION=0.1 FRACTION=0.1 Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Caveats Caveats Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 1: This method is technology and read-name dependent. If the read-names do not have coordinate information Note 1: This method is technology and read-name dependent. If the read-names do not have coordinate information Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: embedded in them, or if your BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this embedded in them, or if your BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: will not work properly. It has been designed to work with Illumina technology and reads-names. Consider modifying {@link will not work properly. It has been designed to work with Illumina technology and reads-names. Consider modifying {@link Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: #READ_NAME_REGEX} in other cases. #READ_NAME_REGEX} in other cases. Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 2: The code has been designed to simulate, as accurately as possible, sequencing less, not for getting an exact Note 2: The code has been designed to simulate, as accurately as possible, sequencing less, not for getting an exact Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: downsampled fraction (Use {@link DownsampleSam} for that.) In particular, since the reads may be distributed non-evenly downsampled fraction (Use {@link DownsampleSam} for that.) In particular, since the reads may be distributed non-evenly Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: within the lanes/tiles, the resulting downsampling percentage will not be accurately determined by the input argument within the lanes/tiles, the resulting downsampling percentage will not be accurately determined by the input argument Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION. FRACTION. Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 3:Consider running {@link MarkDuplicates} after downsampling in order to "expose" the duplicates whose Note 3:Consider running {@link MarkDuplicates} after downsampling in order to "expose" the duplicates whose Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: representative has been downsampled away. representative has been downsampled away. Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 4:The downsampling assumes a uniform distribution of reads in the flowcell. Input already downsampled with Note 4:The downsampling assumes a uniform distribution of reads in the flowcell. Input already downsampled with Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: PositionBasedDownsampleSam violates this assumption. To guard against such input, PositionBasedDownsampleSam always PositionBasedDownsampleSam violates this assumption. To guard against such input, PositionBasedDownsampleSam always Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: places a PG record in the header of its output, and aborts whenever it finds such a PG record in its input. places a PG record in the header of its output, and aborts whenever it finds such a PG record in its input. Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Version: null Version: null Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Options: Options: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: --help --help Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: --stdhelp --stdhelp Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: tools. tools. Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INPUT=File INPUT=File Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: I=File The input SAM or BAM file to downsample. Required. I=File The input SAM or BAM file to downsample. Required. Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: O=File The output, downsampled, SAM or BAM file. Required. O=File The output, downsampled, SAM or BAM file. Required. Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION=Double FRACTION=Double Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: F=Double The (approximate) fraction of reads to be kept, between 0 and 1. Required. F=Double The (approximate) fraction of reads to be kept, between 0 and 1. Required. Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: REMOVE_DUPLICATE_INFORMATION=Boolean REMOVE_DUPLICATE_INFORMATION=Boolean Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Determines whether the duplicate tag should be reset since the downsampling requires Determines whether the duplicate tag should be reset since the downsampling requires Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: re-marking duplicates. Default value: true. This option can be set to 'null' to clear the re-marking duplicates. Default value: true. This option can be set to 'null' to clear the Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: default value. Possible values: {true, false} default value. Possible values: {true, false} Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: READ_NAME_REGEX=String Use these regular expressions to parse read names in the input SAM file. Read names are READ_NAME_REGEX=String Use these regular expressions to parse read names in the input SAM file. Read names are Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: parsed to extract three variables: tile/region, x coordinate and y coordinate. The x and y parsed to extract three variables: tile/region, x coordinate and y coordinate. The x and y Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: coordinates are used to determine the downsample decision. Set this option to null to coordinates are used to determine the downsample decision. Set this option to null to Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: disable optical duplicate detection, e.g. for RNA-seq The regular expression should disable optical duplicate detection, e.g. for RNA-seq The regular expression should Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: contain three capture groups for the three variables, in order. It must match the entire contain three capture groups for the three variables, in order. It must match the entire Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: read name. Note that if the default regex is specified, a regex match is not actually read name. Note that if the default regex is specified, a regex match is not actually Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: done, but instead the read name is split on colons (:). For 5 element names, the 3rd, 4th done, but instead the read name is split on colons (:). For 5 element names, the 3rd, 4th Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: the 5th, 6th, and 7th elements are assumed to be tile, x and y values. Default value: the 5th, 6th, and 7th elements are assumed to be tile, x and y values. Default value: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: . This option can . This option can Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: be set to 'null' to clear the default value. be set to 'null' to clear the default value. Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: null. STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: null. Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Allow downsampling again despite this being a bad idea with possibly unexpected results. Allow downsampling again despite this being a bad idea with possibly unexpected results. Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Default value: false. This option can be set to 'null' to clear the default value. Default value: false. This option can be set to 'null' to clear the default value. Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Possible values: {true, false} Possible values: {true, false} Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[5](50.0)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION must be a value between 0 and 1, found: 50.0 FRACTION must be a value between 0 and 1, found: 50.0 Running Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:41 PositionBasedDownsampleSam Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.TestInvalidArguments[6](1.7976931348623157E308) STANDARD_ERROR INFO 2024-07-02 12:01:41 PositionBasedDownsampleSam Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam1404860128967621061.bam -FRACTION 1.7976931348623157E308 ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam1404860128967621061.bam -FRACTION 1.7976931348623157E308 Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:41.165 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 12:01:41.165 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: USAGE: PositionBasedDownsampleSam [options] USAGE: PositionBasedDownsampleSam [options] Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Summary Summary Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Class to downsample a SAM/BAM file based on the position of the read in a flowcell. As with DownsampleSam, all the reads Class to downsample a SAM/BAM file based on the position of the read in a flowcell. As with DownsampleSam, all the reads Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: with the same queryname are either kept or dropped as a unit. with the same queryname are either kept or dropped as a unit. Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Details Details Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: The downsampling is _not_ random (and there is no random seed). It is deterministically determined by the position of The downsampling is _not_ random (and there is no random seed). It is deterministically determined by the position of Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: each read within its tile. Specifically, it draws an ellipse that covers a FRACTION of the total tile's area and of all each read within its tile. Specifically, it draws an ellipse that covers a FRACTION of the total tile's area and of all Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: the edges of the tile. It uses this area to determine whether to keep or drop the record. Since reads with the same name the edges of the tile. It uses this area to determine whether to keep or drop the record. Since reads with the same name Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: have the same position (mates, secondary and supplemental alignments), the decision will be the same for all of them. have the same position (mates, secondary and supplemental alignments), the decision will be the same for all of them. Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: The main concern of this downsampling method is that due to "optical duplicates" downsampling randomly can create a The main concern of this downsampling method is that due to "optical duplicates" downsampling randomly can create a Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: result that has a different optical duplicate rate, and therefore a different estimated library size (when running result that has a different optical duplicate rate, and therefore a different estimated library size (when running Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: MarkDuplicates). This method keeps (physically) close read together, so that (except for reads near the boundary of the MarkDuplicates). This method keeps (physically) close read together, so that (except for reads near the boundary of the Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: circle) optical duplicates are kept or dropped as a group. By default the program expects the read names to have 5 or 7 circle) optical duplicates are kept or dropped as a group. By default the program expects the read names to have 5 or 7 Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: fields separated by colons (:) and it takes the last two to indicate the x and y coordinates of the reads within the fields separated by colons (:) and it takes the last two to indicate the x and y coordinates of the reads within the Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: tile whence it was sequenced. See DEFAULT_READ_NAME_REGEX for more detail. The program traverses the INPUT twice: first tile whence it was sequenced. See DEFAULT_READ_NAME_REGEX for more detail. The program traverses the INPUT twice: first Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: to find out the size of each of the tiles, and next to perform the downsampling. Downsampling invalidates the duplicate to find out the size of each of the tiles, and next to perform the downsampling. Downsampling invalidates the duplicate Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: flag because duplicate reads before downsampling may not all remain duplicated after downsampling. Thus, the default flag because duplicate reads before downsampling may not all remain duplicated after downsampling. Thus, the default Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: setting also removes the duplicate information. setting also removes the duplicate information. Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Example Example Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: java -jar picard.jar PositionBasedDownsampleSam \ java -jar picard.jar PositionBasedDownsampleSam \ Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: O=downsampled.bam \ O=downsampled.bam \ Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION=0.1 FRACTION=0.1 Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Caveats Caveats Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 1: This method is technology and read-name dependent. If the read-names do not have coordinate information Note 1: This method is technology and read-name dependent. If the read-names do not have coordinate information Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: embedded in them, or if your BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this embedded in them, or if your BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: will not work properly. It has been designed to work with Illumina technology and reads-names. Consider modifying {@link will not work properly. It has been designed to work with Illumina technology and reads-names. Consider modifying {@link Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: #READ_NAME_REGEX} in other cases. #READ_NAME_REGEX} in other cases. Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 2: The code has been designed to simulate, as accurately as possible, sequencing less, not for getting an exact Note 2: The code has been designed to simulate, as accurately as possible, sequencing less, not for getting an exact Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: downsampled fraction (Use {@link DownsampleSam} for that.) In particular, since the reads may be distributed non-evenly downsampled fraction (Use {@link DownsampleSam} for that.) In particular, since the reads may be distributed non-evenly Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: within the lanes/tiles, the resulting downsampling percentage will not be accurately determined by the input argument within the lanes/tiles, the resulting downsampling percentage will not be accurately determined by the input argument Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION. FRACTION. Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 3:Consider running {@link MarkDuplicates} after downsampling in order to "expose" the duplicates whose Note 3:Consider running {@link MarkDuplicates} after downsampling in order to "expose" the duplicates whose Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: representative has been downsampled away. representative has been downsampled away. Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 4:The downsampling assumes a uniform distribution of reads in the flowcell. Input already downsampled with Note 4:The downsampling assumes a uniform distribution of reads in the flowcell. Input already downsampled with Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: PositionBasedDownsampleSam violates this assumption. To guard against such input, PositionBasedDownsampleSam always PositionBasedDownsampleSam violates this assumption. To guard against such input, PositionBasedDownsampleSam always Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: places a PG record in the header of its output, and aborts whenever it finds such a PG record in its input. places a PG record in the header of its output, and aborts whenever it finds such a PG record in its input. Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Version: null Version: null Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Options: Options: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: --help --help Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: --stdhelp --stdhelp Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: tools. tools. Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INPUT=File INPUT=File Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: I=File The input SAM or BAM file to downsample. Required. I=File The input SAM or BAM file to downsample. Required. Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: O=File The output, downsampled, SAM or BAM file. Required. O=File The output, downsampled, SAM or BAM file. Required. Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION=Double FRACTION=Double Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: F=Double The (approximate) fraction of reads to be kept, between 0 and 1. Required. F=Double The (approximate) fraction of reads to be kept, between 0 and 1. Required. Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: REMOVE_DUPLICATE_INFORMATION=Boolean REMOVE_DUPLICATE_INFORMATION=Boolean Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Determines whether the duplicate tag should be reset since the downsampling requires Determines whether the duplicate tag should be reset since the downsampling requires Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: re-marking duplicates. Default value: true. This option can be set to 'null' to clear the re-marking duplicates. Default value: true. This option can be set to 'null' to clear the Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: default value. Possible values: {true, false} default value. Possible values: {true, false} Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: READ_NAME_REGEX=String Use these regular expressions to parse read names in the input SAM file. Read names are READ_NAME_REGEX=String Use these regular expressions to parse read names in the input SAM file. Read names are Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: parsed to extract three variables: tile/region, x coordinate and y coordinate. The x and y parsed to extract three variables: tile/region, x coordinate and y coordinate. The x and y Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: coordinates are used to determine the downsample decision. Set this option to null to coordinates are used to determine the downsample decision. Set this option to null to Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: disable optical duplicate detection, e.g. for RNA-seq The regular expression should disable optical duplicate detection, e.g. for RNA-seq The regular expression should Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: contain three capture groups for the three variables, in order. It must match the entire contain three capture groups for the three variables, in order. It must match the entire Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: read name. Note that if the default regex is specified, a regex match is not actually read name. Note that if the default regex is specified, a regex match is not actually Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: done, but instead the read name is split on colons (:). For 5 element names, the 3rd, 4th done, but instead the read name is split on colons (:). For 5 element names, the 3rd, 4th Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: the 5th, 6th, and 7th elements are assumed to be tile, x and y values. Default value: the 5th, 6th, and 7th elements are assumed to be tile, x and y values. Default value: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: . This option can . This option can Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: be set to 'null' to clear the default value. be set to 'null' to clear the default value. Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: null. STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: null. Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Allow downsampling again despite this being a bad idea with possibly unexpected results. Allow downsampling again despite this being a bad idea with possibly unexpected results. Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Default value: false. This option can be set to 'null' to clear the default value. Default value: false. This option can be set to 'null' to clear the default value. Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Possible values: {true, false} Possible values: {true, false} Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[6](1.7976931348623157E308)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION must be a value between 0 and 1, found: 1.7976931348623157E308 FRACTION must be a value between 0 and 1, found: 1.7976931348623157E308 Running Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:41 PositionBasedDownsampleSam Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.TestInvalidArguments[7](Infinity) STANDARD_ERROR INFO 2024-07-02 12:01:41 PositionBasedDownsampleSam Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam6083666772943160754.bam -FRACTION Infinity ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam6083666772943160754.bam -FRACTION Infinity Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:41.391 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 12:01:41.391 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: USAGE: PositionBasedDownsampleSam [options] USAGE: PositionBasedDownsampleSam [options] Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Summary Summary Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Class to downsample a SAM/BAM file based on the position of the read in a flowcell. As with DownsampleSam, all the reads Class to downsample a SAM/BAM file based on the position of the read in a flowcell. As with DownsampleSam, all the reads Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: with the same queryname are either kept or dropped as a unit. with the same queryname are either kept or dropped as a unit. Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Details Details Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: The downsampling is _not_ random (and there is no random seed). It is deterministically determined by the position of The downsampling is _not_ random (and there is no random seed). It is deterministically determined by the position of Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: each read within its tile. Specifically, it draws an ellipse that covers a FRACTION of the total tile's area and of all each read within its tile. Specifically, it draws an ellipse that covers a FRACTION of the total tile's area and of all Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: the edges of the tile. It uses this area to determine whether to keep or drop the record. Since reads with the same name the edges of the tile. It uses this area to determine whether to keep or drop the record. Since reads with the same name Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: have the same position (mates, secondary and supplemental alignments), the decision will be the same for all of them. have the same position (mates, secondary and supplemental alignments), the decision will be the same for all of them. Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: The main concern of this downsampling method is that due to "optical duplicates" downsampling randomly can create a The main concern of this downsampling method is that due to "optical duplicates" downsampling randomly can create a Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: result that has a different optical duplicate rate, and therefore a different estimated library size (when running result that has a different optical duplicate rate, and therefore a different estimated library size (when running Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: MarkDuplicates). This method keeps (physically) close read together, so that (except for reads near the boundary of the MarkDuplicates). This method keeps (physically) close read together, so that (except for reads near the boundary of the Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: circle) optical duplicates are kept or dropped as a group. By default the program expects the read names to have 5 or 7 circle) optical duplicates are kept or dropped as a group. By default the program expects the read names to have 5 or 7 Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: fields separated by colons (:) and it takes the last two to indicate the x and y coordinates of the reads within the fields separated by colons (:) and it takes the last two to indicate the x and y coordinates of the reads within the Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: tile whence it was sequenced. See DEFAULT_READ_NAME_REGEX for more detail. The program traverses the INPUT twice: first tile whence it was sequenced. See DEFAULT_READ_NAME_REGEX for more detail. The program traverses the INPUT twice: first Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: to find out the size of each of the tiles, and next to perform the downsampling. Downsampling invalidates the duplicate to find out the size of each of the tiles, and next to perform the downsampling. Downsampling invalidates the duplicate Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: flag because duplicate reads before downsampling may not all remain duplicated after downsampling. Thus, the default flag because duplicate reads before downsampling may not all remain duplicated after downsampling. Thus, the default Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: setting also removes the duplicate information. setting also removes the duplicate information. Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Example Example Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: java -jar picard.jar PositionBasedDownsampleSam \ java -jar picard.jar PositionBasedDownsampleSam \ Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: O=downsampled.bam \ O=downsampled.bam \ Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION=0.1 FRACTION=0.1 Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Caveats Caveats Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 1: This method is technology and read-name dependent. If the read-names do not have coordinate information Note 1: This method is technology and read-name dependent. If the read-names do not have coordinate information Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: embedded in them, or if your BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this embedded in them, or if your BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: will not work properly. It has been designed to work with Illumina technology and reads-names. Consider modifying {@link will not work properly. It has been designed to work with Illumina technology and reads-names. Consider modifying {@link Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: #READ_NAME_REGEX} in other cases. #READ_NAME_REGEX} in other cases. Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 2: The code has been designed to simulate, as accurately as possible, sequencing less, not for getting an exact Note 2: The code has been designed to simulate, as accurately as possible, sequencing less, not for getting an exact Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: downsampled fraction (Use {@link DownsampleSam} for that.) In particular, since the reads may be distributed non-evenly downsampled fraction (Use {@link DownsampleSam} for that.) In particular, since the reads may be distributed non-evenly Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: within the lanes/tiles, the resulting downsampling percentage will not be accurately determined by the input argument within the lanes/tiles, the resulting downsampling percentage will not be accurately determined by the input argument Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION. FRACTION. Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 3:Consider running {@link MarkDuplicates} after downsampling in order to "expose" the duplicates whose Note 3:Consider running {@link MarkDuplicates} after downsampling in order to "expose" the duplicates whose Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: representative has been downsampled away. representative has been downsampled away. Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 4:The downsampling assumes a uniform distribution of reads in the flowcell. Input already downsampled with Note 4:The downsampling assumes a uniform distribution of reads in the flowcell. Input already downsampled with Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: PositionBasedDownsampleSam violates this assumption. To guard against such input, PositionBasedDownsampleSam always PositionBasedDownsampleSam violates this assumption. To guard against such input, PositionBasedDownsampleSam always Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: places a PG record in the header of its output, and aborts whenever it finds such a PG record in its input. places a PG record in the header of its output, and aborts whenever it finds such a PG record in its input. Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Version: null Version: null Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Options: Options: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: --help --help Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: --stdhelp --stdhelp Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: tools. tools. Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INPUT=File INPUT=File Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: I=File The input SAM or BAM file to downsample. Required. I=File The input SAM or BAM file to downsample. Required. Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: O=File The output, downsampled, SAM or BAM file. Required. O=File The output, downsampled, SAM or BAM file. Required. Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION=Double FRACTION=Double Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: F=Double The (approximate) fraction of reads to be kept, between 0 and 1. Required. F=Double The (approximate) fraction of reads to be kept, between 0 and 1. Required. Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: REMOVE_DUPLICATE_INFORMATION=Boolean REMOVE_DUPLICATE_INFORMATION=Boolean Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Determines whether the duplicate tag should be reset since the downsampling requires Determines whether the duplicate tag should be reset since the downsampling requires Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: re-marking duplicates. Default value: true. This option can be set to 'null' to clear the re-marking duplicates. Default value: true. This option can be set to 'null' to clear the Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: default value. Possible values: {true, false} default value. Possible values: {true, false} Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: READ_NAME_REGEX=String Use these regular expressions to parse read names in the input SAM file. Read names are READ_NAME_REGEX=String Use these regular expressions to parse read names in the input SAM file. Read names are Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: parsed to extract three variables: tile/region, x coordinate and y coordinate. The x and y parsed to extract three variables: tile/region, x coordinate and y coordinate. The x and y Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: coordinates are used to determine the downsample decision. Set this option to null to coordinates are used to determine the downsample decision. Set this option to null to Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: disable optical duplicate detection, e.g. for RNA-seq The regular expression should disable optical duplicate detection, e.g. for RNA-seq The regular expression should Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: contain three capture groups for the three variables, in order. It must match the entire contain three capture groups for the three variables, in order. It must match the entire Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: read name. Note that if the default regex is specified, a regex match is not actually read name. Note that if the default regex is specified, a regex match is not actually Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: done, but instead the read name is split on colons (:). For 5 element names, the 3rd, 4th done, but instead the read name is split on colons (:). For 5 element names, the 3rd, 4th Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: the 5th, 6th, and 7th elements are assumed to be tile, x and y values. Default value: the 5th, 6th, and 7th elements are assumed to be tile, x and y values. Default value: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: . This option can . This option can Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: be set to 'null' to clear the default value. be set to 'null' to clear the default value. Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: null. STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: null. Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Allow downsampling again despite this being a bad idea with possibly unexpected results. Allow downsampling again despite this being a bad idea with possibly unexpected results. Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Default value: false. This option can be set to 'null' to clear the default value. Default value: false. This option can be set to 'null' to clear the default value. Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Possible values: {true, false} Possible values: {true, false} Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[7](Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION must be a value between 0 and 1, found: Infinity FRACTION must be a value between 0 and 1, found: Infinity Running Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:41 PositionBasedDownsampleSam Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.TestInvalidArguments[8](-Infinity) STANDARD_ERROR INFO 2024-07-02 12:01:41 PositionBasedDownsampleSam Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam1860403039618700652.bam -FRACTION -Infinity ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam1860403039618700652.bam -FRACTION -Infinity Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:41.626 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 12:01:41.626 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: USAGE: PositionBasedDownsampleSam [options] USAGE: PositionBasedDownsampleSam [options] Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#PositionBasedDownsampleSam Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Summary Summary Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Class to downsample a SAM/BAM file based on the position of the read in a flowcell. As with DownsampleSam, all the reads Class to downsample a SAM/BAM file based on the position of the read in a flowcell. As with DownsampleSam, all the reads Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: with the same queryname are either kept or dropped as a unit. with the same queryname are either kept or dropped as a unit. Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Details Details Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: The downsampling is _not_ random (and there is no random seed). It is deterministically determined by the position of The downsampling is _not_ random (and there is no random seed). It is deterministically determined by the position of Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: each read within its tile. Specifically, it draws an ellipse that covers a FRACTION of the total tile's area and of all each read within its tile. Specifically, it draws an ellipse that covers a FRACTION of the total tile's area and of all Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: the edges of the tile. It uses this area to determine whether to keep or drop the record. Since reads with the same name the edges of the tile. It uses this area to determine whether to keep or drop the record. Since reads with the same name Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: have the same position (mates, secondary and supplemental alignments), the decision will be the same for all of them. have the same position (mates, secondary and supplemental alignments), the decision will be the same for all of them. Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: The main concern of this downsampling method is that due to "optical duplicates" downsampling randomly can create a The main concern of this downsampling method is that due to "optical duplicates" downsampling randomly can create a Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: result that has a different optical duplicate rate, and therefore a different estimated library size (when running result that has a different optical duplicate rate, and therefore a different estimated library size (when running Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: MarkDuplicates). This method keeps (physically) close read together, so that (except for reads near the boundary of the MarkDuplicates). This method keeps (physically) close read together, so that (except for reads near the boundary of the Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: circle) optical duplicates are kept or dropped as a group. By default the program expects the read names to have 5 or 7 circle) optical duplicates are kept or dropped as a group. By default the program expects the read names to have 5 or 7 Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: fields separated by colons (:) and it takes the last two to indicate the x and y coordinates of the reads within the fields separated by colons (:) and it takes the last two to indicate the x and y coordinates of the reads within the Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: tile whence it was sequenced. See DEFAULT_READ_NAME_REGEX for more detail. The program traverses the INPUT twice: first tile whence it was sequenced. See DEFAULT_READ_NAME_REGEX for more detail. The program traverses the INPUT twice: first Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: to find out the size of each of the tiles, and next to perform the downsampling. Downsampling invalidates the duplicate to find out the size of each of the tiles, and next to perform the downsampling. Downsampling invalidates the duplicate Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: flag because duplicate reads before downsampling may not all remain duplicated after downsampling. Thus, the default flag because duplicate reads before downsampling may not all remain duplicated after downsampling. Thus, the default Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: setting also removes the duplicate information. setting also removes the duplicate information. Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Example Example Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: java -jar picard.jar PositionBasedDownsampleSam \ java -jar picard.jar PositionBasedDownsampleSam \ Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: O=downsampled.bam \ O=downsampled.bam \ Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION=0.1 FRACTION=0.1 Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Caveats Caveats Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 1: This method is technology and read-name dependent. If the read-names do not have coordinate information Note 1: This method is technology and read-name dependent. If the read-names do not have coordinate information Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: embedded in them, or if your BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this embedded in them, or if your BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: will not work properly. It has been designed to work with Illumina technology and reads-names. Consider modifying {@link will not work properly. It has been designed to work with Illumina technology and reads-names. Consider modifying {@link Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: #READ_NAME_REGEX} in other cases. #READ_NAME_REGEX} in other cases. Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 2: The code has been designed to simulate, as accurately as possible, sequencing less, not for getting an exact Note 2: The code has been designed to simulate, as accurately as possible, sequencing less, not for getting an exact Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: downsampled fraction (Use {@link DownsampleSam} for that.) In particular, since the reads may be distributed non-evenly downsampled fraction (Use {@link DownsampleSam} for that.) In particular, since the reads may be distributed non-evenly Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: within the lanes/tiles, the resulting downsampling percentage will not be accurately determined by the input argument within the lanes/tiles, the resulting downsampling percentage will not be accurately determined by the input argument Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION. FRACTION. Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 3:Consider running {@link MarkDuplicates} after downsampling in order to "expose" the duplicates whose Note 3:Consider running {@link MarkDuplicates} after downsampling in order to "expose" the duplicates whose Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: representative has been downsampled away. representative has been downsampled away. Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Note 4:The downsampling assumes a uniform distribution of reads in the flowcell. Input already downsampled with Note 4:The downsampling assumes a uniform distribution of reads in the flowcell. Input already downsampled with Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: PositionBasedDownsampleSam violates this assumption. To guard against such input, PositionBasedDownsampleSam always PositionBasedDownsampleSam violates this assumption. To guard against such input, PositionBasedDownsampleSam always Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: places a PG record in the header of its output, and aborts whenever it finds such a PG record in its input. places a PG record in the header of its output, and aborts whenever it finds such a PG record in its input. Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Version: null Version: null Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Options: Options: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: --help --help Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: --stdhelp --stdhelp Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: tools. tools. Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INPUT=File INPUT=File Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: I=File The input SAM or BAM file to downsample. Required. I=File The input SAM or BAM file to downsample. Required. Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: O=File The output, downsampled, SAM or BAM file. Required. O=File The output, downsampled, SAM or BAM file. Required. Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION=Double FRACTION=Double Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: F=Double The (approximate) fraction of reads to be kept, between 0 and 1. Required. F=Double The (approximate) fraction of reads to be kept, between 0 and 1. Required. Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: REMOVE_DUPLICATE_INFORMATION=Boolean REMOVE_DUPLICATE_INFORMATION=Boolean Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Determines whether the duplicate tag should be reset since the downsampling requires Determines whether the duplicate tag should be reset since the downsampling requires Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: re-marking duplicates. Default value: true. This option can be set to 'null' to clear the re-marking duplicates. Default value: true. This option can be set to 'null' to clear the Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: default value. Possible values: {true, false} default value. Possible values: {true, false} Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: READ_NAME_REGEX=String Use these regular expressions to parse read names in the input SAM file. Read names are READ_NAME_REGEX=String Use these regular expressions to parse read names in the input SAM file. Read names are Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: parsed to extract three variables: tile/region, x coordinate and y coordinate. The x and y parsed to extract three variables: tile/region, x coordinate and y coordinate. The x and y Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: coordinates are used to determine the downsample decision. Set this option to null to coordinates are used to determine the downsample decision. Set this option to null to Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: disable optical duplicate detection, e.g. for RNA-seq The regular expression should disable optical duplicate detection, e.g. for RNA-seq The regular expression should Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: contain three capture groups for the three variables, in order. It must match the entire contain three capture groups for the three variables, in order. It must match the entire Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: read name. Note that if the default regex is specified, a regex match is not actually read name. Note that if the default regex is specified, a regex match is not actually Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: done, but instead the read name is split on colons (:). For 5 element names, the 3rd, 4th done, but instead the read name is split on colons (:). For 5 element names, the 3rd, 4th Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: the 5th, 6th, and 7th elements are assumed to be tile, x and y values. Default value: the 5th, 6th, and 7th elements are assumed to be tile, x and y values. Default value: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: . This option can . This option can Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: be set to 'null' to clear the default value. be set to 'null' to clear the default value. Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: null. STOP_AFTER=Long Stop after processing N reads, mainly for debugging. Default value: null. Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=Boolean Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Allow downsampling again despite this being a bad idea with possibly unexpected results. Allow downsampling again despite this being a bad idea with possibly unexpected results. Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Default value: false. This option can be set to 'null' to clear the default value. Default value: false. This option can be set to 'null' to clear the default value. Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Possible values: {true, false} Possible values: {true, false} Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidArguments[8](-Infinity)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: FRACTION must be a value between 0 and 1, found: -Infinity FRACTION must be a value between 0 and 1, found: -Infinity Running Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:41 PositionBasedDownsampleSam Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.TestInvalidTwice[0](true) STANDARD_ERROR INFO 2024-07-02 12:01:41 PositionBasedDownsampleSam Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam4754131930490854558.bam -FRACTION 0.1 ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam4754131930490854558.bam -FRACTION 0.1 Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:41.854 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:41.854 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:41.854 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:41.854 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:41.854 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:41.854 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:41.854 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:41.854 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:41 GMT+14:00 2024] PositionBasedDownsampleSam INPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam OUTPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam4754131930490854558.bam FRACTION=0.1 REMOVE_DUPLICATE_INFORMATION=true READ_NAME_REGEX= ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:41 GMT+14:00 2024] PositionBasedDownsampleSam INPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam OUTPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam4754131930490854558.bam FRACTION=0.1 REMOVE_DUPLICATE_INFORMATION=true READ_NAME_REGEX= ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:41 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before. INFO 2024-07-02 12:01:41 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before. Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:41 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles. INFO 2024-07-02 12:01:41 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles. Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam First pass done. INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam First pass done. Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Starting second pass. Outputting reads. INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Starting second pass. Outputting reads. Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Second pass done. INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Second pass done. Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: WARNING 2024-07-02 12:01:42 PositionBasedDownsampleSam You've requested FRACTION=0.100000, the resulting downsampling resulted in a rate of 0.069400. WARNING 2024-07-02 12:01:42 PositionBasedDownsampleSam You've requested FRACTION=0.100000, the resulting downsampling resulted in a rate of 0.069400. Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Finished! Kept 1388 out of 20000 reads (P=0.0694000). INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Finished! Kept 1388 out of 20000 reads (P=0.0694000). Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:42 GMT+14:00 2024] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 12:01:42 GMT+14:00 2024] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam4754131930490854558.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam4705168899814155524.bam -FRACTION 0.1 -ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS true ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam4754131930490854558.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam4705168899814155524.bam -FRACTION 0.1 -ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS true Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:42.261 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:42.261 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:42.262 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:42.262 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:42.262 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:42.262 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:42.262 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:42.262 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:42 GMT+14:00 2024] PositionBasedDownsampleSam INPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam4754131930490854558.bam OUTPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam4705168899814155524.bam FRACTION=0.1 ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=true REMOVE_DUPLICATE_INFORMATION=true READ_NAME_REGEX= VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:42 GMT+14:00 2024] PositionBasedDownsampleSam INPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam4754131930490854558.bam OUTPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam4705168899814155524.bam FRACTION=0.1 ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=true REMOVE_DUPLICATE_INFORMATION=true READ_NAME_REGEX= VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before. INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before. Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: WARNING 2024-07-02 12:01:42 PositionBasedDownsampleSam Found previous Program Record that indicates that this BAM has been downsampled already with this program. Operation not supported! Previous PG: SAMProgramRecord{PN=PositionBasedDownsampleSam, CL=PositionBasedDownsampleSam INPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam OUTPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam4754131930490854558.bam FRACTION=0.1 REMOVE_DUPLICATE_INFORMATION=true READ_NAME_REGEX= ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false} WARNING 2024-07-02 12:01:42 PositionBasedDownsampleSam Found previous Program Record that indicates that this BAM has been downsampled already with this program. Operation not supported! Previous PG: SAMProgramRecord{PN=PositionBasedDownsampleSam, CL=PositionBasedDownsampleSam INPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam OUTPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam4754131930490854558.bam FRACTION=0.1 REMOVE_DUPLICATE_INFORMATION=true READ_NAME_REGEX= ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false} Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles. INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles. Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam First pass done. INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam First pass done. Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Starting second pass. Outputting reads. INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Starting second pass. Outputting reads. Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Second pass done. INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Second pass done. Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: WARNING 2024-07-02 12:01:42 PositionBasedDownsampleSam You've requested FRACTION=0.100000, the resulting downsampling resulted in a rate of 0.998559. WARNING 2024-07-02 12:01:42 PositionBasedDownsampleSam You've requested FRACTION=0.100000, the resulting downsampling resulted in a rate of 0.998559. Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Finished! Kept 1386 out of 1388 reads (P=0.998559). INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Finished! Kept 1386 out of 1388 reads (P=0.998559). Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:42 GMT+14:00 2024] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:42 GMT+14:00 2024] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method TestInvalidTwice[0](true)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.TestInvalidTwice[1](false) STANDARD_ERROR INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam2416406314030057170.bam -FRACTION 0.1 ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam2416406314030057170.bam -FRACTION 0.1 Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:42.331 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:42.331 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:42.331 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:42.331 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:42.331 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:42.331 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:42.331 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:42.331 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:42 GMT+14:00 2024] PositionBasedDownsampleSam INPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam OUTPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam2416406314030057170.bam FRACTION=0.1 REMOVE_DUPLICATE_INFORMATION=true READ_NAME_REGEX= ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:42 GMT+14:00 2024] PositionBasedDownsampleSam INPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam OUTPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam2416406314030057170.bam FRACTION=0.1 REMOVE_DUPLICATE_INFORMATION=true READ_NAME_REGEX= ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before. INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before. Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles. INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles. Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam First pass done. INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam First pass done. Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Starting second pass. Outputting reads. INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Starting second pass. Outputting reads. Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Second pass done. INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Second pass done. Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: WARNING 2024-07-02 12:01:42 PositionBasedDownsampleSam You've requested FRACTION=0.100000, the resulting downsampling resulted in a rate of 0.069400. WARNING 2024-07-02 12:01:42 PositionBasedDownsampleSam You've requested FRACTION=0.100000, the resulting downsampling resulted in a rate of 0.069400. Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Finished! Kept 1388 out of 20000 reads (P=0.0694000). INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Finished! Kept 1388 out of 20000 reads (P=0.0694000). Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:42 GMT+14:00 2024] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:42 GMT+14:00 2024] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam2416406314030057170.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam6600430939012920339.bam -FRACTION 0.1 ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam2416406314030057170.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam6600430939012920339.bam -FRACTION 0.1 Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:42.635 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:42.635 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:42.635 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:42.635 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:42.635 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:42.635 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:42.635 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:42.635 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:42 GMT+14:00 2024] PositionBasedDownsampleSam INPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam2416406314030057170.bam OUTPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam6600430939012920339.bam FRACTION=0.1 REMOVE_DUPLICATE_INFORMATION=true READ_NAME_REGEX= ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:42 GMT+14:00 2024] PositionBasedDownsampleSam INPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam2416406314030057170.bam OUTPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam6600430939012920339.bam FRACTION=0.1 REMOVE_DUPLICATE_INFORMATION=true READ_NAME_REGEX= ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before. INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before. Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ERROR 2024-07-02 12:01:42 PositionBasedDownsampleSam Found previous Program Record that indicates that this BAM has been downsampled already with this program. Operation not supported! Previous PG: SAMProgramRecord{PN=PositionBasedDownsampleSam, CL=PositionBasedDownsampleSam INPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam OUTPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam2416406314030057170.bam FRACTION=0.1 REMOVE_DUPLICATE_INFORMATION=true READ_NAME_REGEX= ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false} ERROR 2024-07-02 12:01:42 PositionBasedDownsampleSam Found previous Program Record that indicates that this BAM has been downsampled already with this program. Operation not supported! Previous PG: SAMProgramRecord{PN=PositionBasedDownsampleSam, CL=PositionBasedDownsampleSam INPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam OUTPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam2416406314030057170.bam FRACTION=0.1 REMOVE_DUPLICATE_INFORMATION=true READ_NAME_REGEX= ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false} Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:42 GMT+14:00 2024] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:42 GMT+14:00 2024] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.00 minutes. Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestInvalidTwice[1](false)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.testDownsampleSingleTile[0](0.3) STANDARD_ERROR INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam7229331474677468410.bam -FRACTION 0.3 -CREATE_INDEX true ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam7229331474677468410.bam -FRACTION 0.3 -CREATE_INDEX true Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:42.683 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:42.683 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:42.683 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:42.683 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:42.683 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:42.683 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:42.683 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:42.683 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:42 GMT+14:00 2024] PositionBasedDownsampleSam INPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam OUTPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam7229331474677468410.bam FRACTION=0.3 CREATE_INDEX=true REMOVE_DUPLICATE_INFORMATION=true READ_NAME_REGEX= ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:42 GMT+14:00 2024] PositionBasedDownsampleSam INPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam OUTPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam7229331474677468410.bam FRACTION=0.3 CREATE_INDEX=true REMOVE_DUPLICATE_INFORMATION=true READ_NAME_REGEX= ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before. INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before. Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles. INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles. Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam First pass done. INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam First pass done. Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Starting second pass. Outputting reads. INFO 2024-07-02 12:01:42 PositionBasedDownsampleSam Starting second pass. Outputting reads. Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:43 PositionBasedDownsampleSam Second pass done. INFO 2024-07-02 12:01:43 PositionBasedDownsampleSam Second pass done. Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:43 PositionBasedDownsampleSam Finished! Kept 5544 out of 20000 reads (P=0.277200). INFO 2024-07-02 12:01:43 PositionBasedDownsampleSam Finished! Kept 5544 out of 20000 reads (P=0.277200). Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:43 GMT+14:00 2024] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 12:01:43 GMT+14:00 2024] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: WARNING 2024-07-02 12:01:43 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:43 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleSingleTile[0](0.3)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.testDownsampleSingleTile[0](0.3) STANDARD_OUT No errors found Running Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:43 PositionBasedDownsampleSam Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.testDownsampleSingleTile[1](0.4) STANDARD_ERROR INFO 2024-07-02 12:01:43 PositionBasedDownsampleSam Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam17950324328980840214.bam -FRACTION 0.4 -CREATE_INDEX true ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam17950324328980840214.bam -FRACTION 0.4 -CREATE_INDEX true Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:43.582 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:43.582 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:43.582 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:43.582 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:43.583 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:43.583 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:43.583 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:43.583 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:43 GMT+14:00 2024] PositionBasedDownsampleSam INPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam OUTPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam17950324328980840214.bam FRACTION=0.4 CREATE_INDEX=true REMOVE_DUPLICATE_INFORMATION=true READ_NAME_REGEX= ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:43 GMT+14:00 2024] PositionBasedDownsampleSam INPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam OUTPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam17950324328980840214.bam FRACTION=0.4 CREATE_INDEX=true REMOVE_DUPLICATE_INFORMATION=true READ_NAME_REGEX= ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:43 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:43 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before. INFO 2024-07-02 12:01:43 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before. Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:43 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles. INFO 2024-07-02 12:01:43 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles. Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:43 PositionBasedDownsampleSam First pass done. INFO 2024-07-02 12:01:43 PositionBasedDownsampleSam First pass done. Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:43 PositionBasedDownsampleSam Starting second pass. Outputting reads. INFO 2024-07-02 12:01:43 PositionBasedDownsampleSam Starting second pass. Outputting reads. Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:44 PositionBasedDownsampleSam Second pass done. INFO 2024-07-02 12:01:44 PositionBasedDownsampleSam Second pass done. Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:44 PositionBasedDownsampleSam Finished! Kept 7652 out of 20000 reads (P=0.382600). INFO 2024-07-02 12:01:44 PositionBasedDownsampleSam Finished! Kept 7652 out of 20000 reads (P=0.382600). Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:44 GMT+14:00 2024] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 12:01:44 GMT+14:00 2024] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: WARNING 2024-07-02 12:01:44 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:44 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleSingleTile[1](0.4)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.testDownsampleSingleTile[1](0.4) STANDARD_OUT No errors found Running Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:44 PositionBasedDownsampleSam Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.testDownsampleSingleTile[2](0.5) STANDARD_ERROR INFO 2024-07-02 12:01:44 PositionBasedDownsampleSam Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam7758055086544208846.bam -FRACTION 0.5 -CREATE_INDEX true ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam7758055086544208846.bam -FRACTION 0.5 -CREATE_INDEX true Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:44.502 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:44.502 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:44.502 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:44.502 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:44.503 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:44.503 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:44.503 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:44.503 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:44 GMT+14:00 2024] PositionBasedDownsampleSam INPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam OUTPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam7758055086544208846.bam FRACTION=0.5 CREATE_INDEX=true REMOVE_DUPLICATE_INFORMATION=true READ_NAME_REGEX= ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:44 GMT+14:00 2024] PositionBasedDownsampleSam INPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam OUTPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam7758055086544208846.bam FRACTION=0.5 CREATE_INDEX=true REMOVE_DUPLICATE_INFORMATION=true READ_NAME_REGEX= ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:44 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:44 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before. INFO 2024-07-02 12:01:44 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before. Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:44 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles. INFO 2024-07-02 12:01:44 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles. Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:44 PositionBasedDownsampleSam First pass done. INFO 2024-07-02 12:01:44 PositionBasedDownsampleSam First pass done. Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:44 PositionBasedDownsampleSam Starting second pass. Outputting reads. INFO 2024-07-02 12:01:44 PositionBasedDownsampleSam Starting second pass. Outputting reads. Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:45 PositionBasedDownsampleSam Second pass done. INFO 2024-07-02 12:01:45 PositionBasedDownsampleSam Second pass done. Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:45 PositionBasedDownsampleSam Finished! Kept 9688 out of 20000 reads (P=0.484400). INFO 2024-07-02 12:01:45 PositionBasedDownsampleSam Finished! Kept 9688 out of 20000 reads (P=0.484400). Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:45 GMT+14:00 2024] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 12:01:45 GMT+14:00 2024] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: WARNING 2024-07-02 12:01:45 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:45 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleSingleTile[2](0.5)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.testDownsampleSingleTile[2](0.5) STANDARD_OUT No errors found Running Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:45 PositionBasedDownsampleSam Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.testDownsampleSingleTile[3](0.6) STANDARD_ERROR INFO 2024-07-02 12:01:45 PositionBasedDownsampleSam Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam2274483898512971865.bam -FRACTION 0.6 -CREATE_INDEX true ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam2274483898512971865.bam -FRACTION 0.6 -CREATE_INDEX true Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:45.543 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:45.543 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:45.543 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:45.543 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:45.543 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:45.543 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:45.543 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:45.543 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:45 GMT+14:00 2024] PositionBasedDownsampleSam INPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam OUTPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam2274483898512971865.bam FRACTION=0.6 CREATE_INDEX=true REMOVE_DUPLICATE_INFORMATION=true READ_NAME_REGEX= ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:45 GMT+14:00 2024] PositionBasedDownsampleSam INPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam OUTPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam2274483898512971865.bam FRACTION=0.6 CREATE_INDEX=true REMOVE_DUPLICATE_INFORMATION=true READ_NAME_REGEX= ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:45 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:45 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before. INFO 2024-07-02 12:01:45 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before. Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:45 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles. INFO 2024-07-02 12:01:45 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles. Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:45 PositionBasedDownsampleSam First pass done. INFO 2024-07-02 12:01:45 PositionBasedDownsampleSam First pass done. Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:45 PositionBasedDownsampleSam Starting second pass. Outputting reads. INFO 2024-07-02 12:01:45 PositionBasedDownsampleSam Starting second pass. Outputting reads. Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:46 PositionBasedDownsampleSam Second pass done. INFO 2024-07-02 12:01:46 PositionBasedDownsampleSam Second pass done. Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:46 PositionBasedDownsampleSam Finished! Kept 12348 out of 20000 reads (P=0.617400). INFO 2024-07-02 12:01:46 PositionBasedDownsampleSam Finished! Kept 12348 out of 20000 reads (P=0.617400). Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:46 GMT+14:00 2024] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 12:01:46 GMT+14:00 2024] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: WARNING 2024-07-02 12:01:46 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:46 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleSingleTile[3](0.6)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.testDownsampleSingleTile[3](0.6) STANDARD_OUT No errors found Running Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:46 PositionBasedDownsampleSam Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.testDownsampleSingleTile[4](0.7) STANDARD_ERROR INFO 2024-07-02 12:01:46 PositionBasedDownsampleSam Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam15062661509462098099.bam -FRACTION 0.7 -CREATE_INDEX true ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam15062661509462098099.bam -FRACTION 0.7 -CREATE_INDEX true Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:46.656 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:46.656 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:46.656 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:46.656 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:46.656 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:46.656 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:46.656 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:46.656 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:46 GMT+14:00 2024] PositionBasedDownsampleSam INPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam OUTPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam15062661509462098099.bam FRACTION=0.7 CREATE_INDEX=true REMOVE_DUPLICATE_INFORMATION=true READ_NAME_REGEX= ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:46 GMT+14:00 2024] PositionBasedDownsampleSam INPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam OUTPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam15062661509462098099.bam FRACTION=0.7 CREATE_INDEX=true REMOVE_DUPLICATE_INFORMATION=true READ_NAME_REGEX= ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:46 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:46 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before. INFO 2024-07-02 12:01:46 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before. Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:46 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles. INFO 2024-07-02 12:01:46 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles. Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:46 PositionBasedDownsampleSam First pass done. INFO 2024-07-02 12:01:46 PositionBasedDownsampleSam First pass done. Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:46 PositionBasedDownsampleSam Starting second pass. Outputting reads. INFO 2024-07-02 12:01:46 PositionBasedDownsampleSam Starting second pass. Outputting reads. Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:47 PositionBasedDownsampleSam Second pass done. INFO 2024-07-02 12:01:47 PositionBasedDownsampleSam Second pass done. Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:47 PositionBasedDownsampleSam Finished! Kept 14456 out of 20000 reads (P=0.722800). INFO 2024-07-02 12:01:47 PositionBasedDownsampleSam Finished! Kept 14456 out of 20000 reads (P=0.722800). Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:47 GMT+14:00 2024] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 12:01:47 GMT+14:00 2024] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: WARNING 2024-07-02 12:01:47 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:47 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleSingleTile[4](0.7)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.testDownsampleSingleTile[4](0.7) STANDARD_OUT No errors found Running Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:47 PositionBasedDownsampleSam Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.testDownsampleSingleTile[5](0.7999999999999999) STANDARD_ERROR INFO 2024-07-02 12:01:47 PositionBasedDownsampleSam Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam15382847969380661204.bam -FRACTION 0.7999999999999999 -CREATE_INDEX true ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam15382847969380661204.bam -FRACTION 0.7999999999999999 -CREATE_INDEX true Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:47.955 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:47.955 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:47.955 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:47.955 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:47.955 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:47.955 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:47.955 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:47.955 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:47 GMT+14:00 2024] PositionBasedDownsampleSam INPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam OUTPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam15382847969380661204.bam FRACTION=0.7999999999999999 CREATE_INDEX=true REMOVE_DUPLICATE_INFORMATION=true READ_NAME_REGEX= ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:47 GMT+14:00 2024] PositionBasedDownsampleSam INPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam OUTPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam15382847969380661204.bam FRACTION=0.7999999999999999 CREATE_INDEX=true REMOVE_DUPLICATE_INFORMATION=true READ_NAME_REGEX= ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:47 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:47 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before. INFO 2024-07-02 12:01:47 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before. Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:47 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles. INFO 2024-07-02 12:01:47 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles. Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:48 PositionBasedDownsampleSam First pass done. INFO 2024-07-02 12:01:48 PositionBasedDownsampleSam First pass done. Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:48 PositionBasedDownsampleSam Starting second pass. Outputting reads. INFO 2024-07-02 12:01:48 PositionBasedDownsampleSam Starting second pass. Outputting reads. Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:48 PositionBasedDownsampleSam Second pass done. INFO 2024-07-02 12:01:48 PositionBasedDownsampleSam Second pass done. Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:48 PositionBasedDownsampleSam Finished! Kept 16642 out of 20000 reads (P=0.832100). INFO 2024-07-02 12:01:48 PositionBasedDownsampleSam Finished! Kept 16642 out of 20000 reads (P=0.832100). Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:48 GMT+14:00 2024] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 12:01:48 GMT+14:00 2024] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: WARNING 2024-07-02 12:01:48 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:48 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleSingleTile[5](0.7999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.testDownsampleSingleTile[5](0.7999999999999999) STANDARD_OUT No errors found Running Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:48 PositionBasedDownsampleSam Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.testDownsampleSingleTile[6](0.8999999999999999) STANDARD_ERROR INFO 2024-07-02 12:01:48 PositionBasedDownsampleSam Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam2360904772293382047.bam -FRACTION 0.8999999999999999 -CREATE_INDEX true ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam2360904772293382047.bam -FRACTION 0.8999999999999999 -CREATE_INDEX true Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:48.430 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:48.430 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:48.431 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:48.431 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:48.431 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:48.431 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:48.431 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:48.431 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:48 GMT+14:00 2024] PositionBasedDownsampleSam INPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam OUTPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam2360904772293382047.bam FRACTION=0.8999999999999999 CREATE_INDEX=true REMOVE_DUPLICATE_INFORMATION=true READ_NAME_REGEX= ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:48 GMT+14:00 2024] PositionBasedDownsampleSam INPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam OUTPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam2360904772293382047.bam FRACTION=0.8999999999999999 CREATE_INDEX=true REMOVE_DUPLICATE_INFORMATION=true READ_NAME_REGEX= ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:48 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:48 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before. INFO 2024-07-02 12:01:48 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before. Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:48 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles. INFO 2024-07-02 12:01:48 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles. Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:48 PositionBasedDownsampleSam First pass done. INFO 2024-07-02 12:01:48 PositionBasedDownsampleSam First pass done. Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:48 PositionBasedDownsampleSam Starting second pass. Outputting reads. INFO 2024-07-02 12:01:48 PositionBasedDownsampleSam Starting second pass. Outputting reads. Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:48 PositionBasedDownsampleSam Second pass done. INFO 2024-07-02 12:01:48 PositionBasedDownsampleSam Second pass done. Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:48 PositionBasedDownsampleSam Finished! Kept 18612 out of 20000 reads (P=0.930600). INFO 2024-07-02 12:01:48 PositionBasedDownsampleSam Finished! Kept 18612 out of 20000 reads (P=0.930600). Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:48 GMT+14:00 2024] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 12:01:48 GMT+14:00 2024] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: WARNING 2024-07-02 12:01:48 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:48 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleSingleTile[6](0.8999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.testDownsampleSingleTile[6](0.8999999999999999) STANDARD_OUT No errors found Running Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:49 PositionBasedDownsampleSam Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.testDownsampleSingleTile[7](0.9999999999999999) STANDARD_ERROR INFO 2024-07-02 12:01:49 PositionBasedDownsampleSam Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam16186479405085866851.bam -FRACTION 0.9999999999999999 -CREATE_INDEX true ********** PositionBasedDownsampleSam -INPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam -OUTPUT /tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam16186479405085866851.bam -FRACTION 0.9999999999999999 -CREATE_INDEX true Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: ********** ********** Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:49.398 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:49.398 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:49.398 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:49.398 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:49.398 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:49.398 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: 12:01:49.398 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:49.398 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:49 GMT+14:00 2024] PositionBasedDownsampleSam INPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam OUTPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam16186479405085866851.bam FRACTION=0.9999999999999999 CREATE_INDEX=true REMOVE_DUPLICATE_INFORMATION=true READ_NAME_REGEX= ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:49 GMT+14:00 2024] PositionBasedDownsampleSam INPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam11835122495711712491.bam OUTPUT=/tmp/pds_test12539628239057506412PositionalDownsampling/PositionalDownsampleSam16186479405085866851.bam FRACTION=0.9999999999999999 CREATE_INDEX=true REMOVE_DUPLICATE_INFORMATION=true READ_NAME_REGEX= ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:49 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:49 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before. INFO 2024-07-02 12:01:49 PositionBasedDownsampleSam Checking to see if input file has been downsampled with this program before. Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:49 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles. INFO 2024-07-02 12:01:49 PositionBasedDownsampleSam Starting first pass. Examining read distribution in tiles. Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:49 PositionBasedDownsampleSam First pass done. INFO 2024-07-02 12:01:49 PositionBasedDownsampleSam First pass done. Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:49 PositionBasedDownsampleSam Starting second pass. Outputting reads. INFO 2024-07-02 12:01:49 PositionBasedDownsampleSam Starting second pass. Outputting reads. Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:49 PositionBasedDownsampleSam Second pass done. INFO 2024-07-02 12:01:49 PositionBasedDownsampleSam Second pass done. Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: INFO 2024-07-02 12:01:49 PositionBasedDownsampleSam Finished! Kept 20000 out of 20000 reads (P=1.00000). INFO 2024-07-02 12:01:49 PositionBasedDownsampleSam Finished! Kept 20000 out of 20000 reads (P=1.00000). Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: [Tue Jul 02 12:01:49 GMT+14:00 2024] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.01 minutes. [Tue Jul 02 12:01:49 GMT+14:00 2024] picard.sam.PositionBasedDownsampleSam done. Elapsed time: 0.01 minutes. Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: WARNING 2024-07-02 12:01:49 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:49 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testDownsampleSingleTile[7](0.9999999999999999)(picard.sam.PositionBasedDownsampleSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.PositionBasedDownsampleSamTest.testDownsampleSingleTile[7](0.9999999999999999) STANDARD_OUT No errors found Running Test: Test method testPrimaryAlignmentKeyCompare[0]([r1 0b aligned to *:0--1., r1 1/2 0b aligned to *:0--1.], -1)(picard.sam.util.PrimaryAlignmentKeyTest) Running Test: Test method testPrimaryAlignmentKeyCompare[1]([r1 0b aligned to *:0--1., r1 2/2 0b aligned to *:0--1.], -2)(picard.sam.util.PrimaryAlignmentKeyTest) Running Test: Test method testPrimaryAlignmentKeyCompare[2]([r1 1/2 0b aligned to *:0--1., r1 2/2 0b aligned to *:0--1.], -1)(picard.sam.util.PrimaryAlignmentKeyTest) Running Test: Test method testPrimaryAlignmentKeyCompare[3]([r1 1/2 0b aligned to *:0--1., r1 0b aligned to *:0--1.], 1)(picard.sam.util.PrimaryAlignmentKeyTest) Running Test: Test method testPrimaryAlignmentKeyCompare[4]([r1 2/2 0b aligned to *:0--1., r1 0b aligned to *:0--1.], 2)(picard.sam.util.PrimaryAlignmentKeyTest) Running Test: Test method testPrimaryAlignmentKeyCompare[5]([r1 2/2 0b aligned to *:0--1., r1 1/2 0b aligned to *:0--1.], 1)(picard.sam.util.PrimaryAlignmentKeyTest) Running Test: Test method testPrimaryAlignmentKeyCompare[6]([r1 0b aligned to *:0--1., r1 0b aligned to *:0--1.], 0)(picard.sam.util.PrimaryAlignmentKeyTest) Running Test: Test method testPrimaryAlignmentKeyCompare[7]([r1 1/2 0b aligned to *:0--1., r1 1/2 0b aligned to *:0--1.], 0)(picard.sam.util.PrimaryAlignmentKeyTest) Running Test: Test method testPrimaryAlignmentKeyCompare[8]([r1 2/2 0b aligned to *:0--1., r1 2/2 0b aligned to *:0--1.], 0)(picard.sam.util.PrimaryAlignmentKeyTest) Running Test: Test method testPrimaryAlignmentKeyCompare[9]([r1 0b aligned to *:0--1., r2 0b aligned to *:0--1.], -1)(picard.sam.util.PrimaryAlignmentKeyTest) Running Test: Test method testRejectNonPrimary[0](r1 0b aligned to *:0--1.)(picard.sam.util.PrimaryAlignmentKeyTest) Running Test: Test method testRejectNonPrimary[1](r1 0b aligned to *:0--1.)(picard.sam.util.PrimaryAlignmentKeyTest) Running Test: Test method testBasicHalfmappedReadPair(picard.util.QuerySortedReadPairIteratorUtilTest) Running Test: Test method testBasicPairedRead(picard.util.QuerySortedReadPairIteratorUtilTest) Running Test: Test method testBasicUnmappedReadPair(picard.util.QuerySortedReadPairIteratorUtilTest) Running Test: Test method testFragmentNoReadPair(picard.util.QuerySortedReadPairIteratorUtilTest) Running Test: Test method testFailingRScript(picard.util.RExecutorTest) Test: Test method testFailingRScript(picard.util.RExecutorTest) produced standard out/err: INFO 2024-07-02 12:01:50 RExecutor Executing R script via command: Rscript /tmp/script6951133872321077042.R Gradle suite > Gradle test > picard.util.RExecutorTest.testFailingRScript STANDARD_ERROR INFO 2024-07-02 12:01:50 RExecutor Executing R script via command: Rscript /tmp/script6951133872321077042.R Test: Test method testFailingRScript(picard.util.RExecutorTest) produced standard out/err: ERROR 2024-07-02 12:01:51 ProcessExecutor Error: object 'alsdfj' not found ERROR 2024-07-02 12:01:51 ProcessExecutor Error: object 'alsdfj' not found Test: Test method testFailingRScript(picard.util.RExecutorTest) produced standard out/err: ERROR 2024-07-02 12:01:51 ProcessExecutor Execution halted ERROR 2024-07-02 12:01:51 ProcessExecutor Execution halted Running Test: Test method testPassingRScript(picard.util.RExecutorTest) Test: Test method testPassingRScript(picard.util.RExecutorTest) produced standard out/err: INFO 2024-07-02 12:01:51 RExecutor Executing R script via command: Rscript /tmp/script16315405336197999386.R Gradle suite > Gradle test > picard.util.RExecutorTest.testPassingRScript STANDARD_ERROR INFO 2024-07-02 12:01:51 RExecutor Executing R script via command: Rscript /tmp/script16315405336197999386.R Test: Test method testPassingRScript(picard.util.RExecutorTest) produced standard out/err: INFO 2024-07-02 12:01:53 ProcessExecutor [1] "Tue Jul 2 12:01:53 2024" INFO 2024-07-02 12:01:53 ProcessExecutor [1] "Tue Jul 2 12:01:53 2024" Running Test: Test method testRScriptNotFound(picard.util.RExecutorTest) Running Test: Test method testChimericStratifier[0](CHIMERIC_3 2/2 36b aligned to chr1:100-120., CHIMERIC)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[1](CHIMERIC_4 1/2 36b aligned to chr1:100-119., CHIMERIC)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[2](IMPROPER_3 1/2 36b aligned to chr1:100-135., IMPROPER)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[3](PROPER_1 1/2 36b aligned to chr1:100-135., PROPER)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[4](PROPER_3 1/2 36b aligned to chr1:100-135., PROPER)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[5](UNKNOWN_1 2/2 36b unmapped read., UNKNOWN)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[6](CHIMERIC_1 1/2 36b aligned to chr1:100-119., CHIMERIC)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[7](CHIMERIC_2 2/2 36b aligned to chr1:100-120., CHIMERIC)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[8](DISCORDANT_1 1/2 36b aligned to chr1:100-135., DISCORDANT)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[9](DISCORDANT_2 2/2 36b aligned to chr1:100-135., DISCORDANT)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[10](IMPROPER_1 1/2 36b aligned to chr1:100-135., IMPROPER)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[11](UNKNOWN_1 1/2 36b aligned to chr1:100-135., UNKNOWN)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[12](CHIMERIC_1 2/2 36b aligned to chr1:200-220., CHIMERIC)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[13](CHIMERIC_2 1/2 36b aligned to chr1:300-319., CHIMERIC)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[14](IMPROPER_1 2/2 36b aligned to chr1:400-435., IMPROPER)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[15](IMPROPER_4 2/2 36b aligned to chr1:400-435., IMPROPER)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[16](IMPROPER_3 2/2 36b aligned to chr1:400-435., IMPROPER)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[17](PROPER_1 2/2 36b aligned to chr1:400-435., PROPER)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[18](PROPER_3 2/2 36b aligned to chr1:400-435., PROPER)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[19](PROPER_4 2/2 36b aligned to chr1:400-435., PROPER)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[20](CHIMERIC_3 1/2 36b aligned to chr1:500-519., CHIMERIC)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[21](IMPROPER_4 1/2 36b aligned to chr1:600-635., IMPROPER)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[22](PROPER_4 1/2 36b aligned to chr1:600-635., PROPER)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[23](CHIMERIC_4 2/2 36b aligned to chr1:700-720., CHIMERIC)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[24](DISCORDANT_3 1/2 36b aligned to chr1:2000-2035., DISCORDANT)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[25](DISCORDANT_1 2/2 36b aligned to chr2:100-135., DISCORDANT)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[26](IMPROPER_2 2/2 36b aligned to chr2:400-435., IMPROPER)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[27](PROPER_2 1/2 36b aligned to chr2:400-435., PROPER)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[28](PROPER_2 2/2 36b aligned to chr2:600-635., PROPER)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[29](IMPROPER_2 1/2 36b aligned to chr2:600-635., IMPROPER)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[30](DISCORDANT_2 1/2 36b aligned to chr2:1000-1035., DISCORDANT)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[31](UNKNOWN_2 1/2 36b aligned to chr2:1000-1035., UNKNOWN)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[32](UNKNOWN_2 2/2 36b unmapped read., UNKNOWN)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[33](DISCORDANT_4 2/2 36b aligned to chr3:100-135., DISCORDANT)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[34](UNKNOWN_4 1/2 36b unmapped read., UNKNOWN)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[35](UNKNOWN_4 2/2 36b aligned to chr3:100-135., UNKNOWN)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[36](DISCORDANT_4 1/2 36b aligned to chr6:10000-10035., DISCORDANT)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[37](DISCORDANT_3 2/2 36b aligned to chr7:100-135., DISCORDANT)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[38](UNKNOWN_3 1/2 36b unmapped read., UNKNOWN)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testChimericStratifier[39](UNKNOWN_3 2/2 36b aligned to chr7:100-135., UNKNOWN)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testGetIndelElement[0](, 0, Insertion, null)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testGetIndelElement[1](1M1I, 1, Insertion, I)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testGetIndelElement[2](1I, 0, Insertion, I)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testGetIndelElement[3](1I1M, 0, Insertion, I)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testGetIndelElement[4](1D1M, -1, Deletion, D)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testGetIndelElement[5](1S1I1D, 1, Insertion, I)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testGetIndelElement[6](1S1D1M1I, 0, Deletion, D)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testGetIndelElement[7](2D2I1M, 0, Insertion, I)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testGetIndelElement[8](2I2D1M, 1, Deletion, D)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[0](-1, true, 71, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[1](0, true, 71, 0, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[2](1, true, 71, 1, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[3](2, true, 71, 1, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[4](3, true, 71, 1, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[5](4, true, 71, 1, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[6](5, true, 71, 2, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[7](6, true, 71, 3, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[8](7, true, 71, 4, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[9](8, true, 71, 1, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[10](-1, false, 71, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[11](0, false, 71, 1, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[12](1, false, 71, 1, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[13](2, false, 71, 4, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[14](3, false, 71, 3, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[15](4, false, 71, 2, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[16](5, false, 71, 1, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[17](6, false, 71, 9, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[18](7, false, 71, 8, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[19](8, false, 71, 7, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[20](9, false, 71, 6, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[21](10, false, 71, 5, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[22](11, false, 71, 4, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[23](12, false, 71, 3, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[24](13, false, 71, 2, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[25](14, false, 71, 1, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[26](15, false, 71, 0, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[27](16, false, 71, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[28](7, true, 65, SHORT_HOMOPOLYMER,G,A, picard.sam.SamErrorMetric.ReadBaseStratification$3@69b2acc7)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[29](8, true, 65, SHORT_HOMOPOLYMER,A,A, picard.sam.SamErrorMetric.ReadBaseStratification$3@69b2acc7)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[30](9, true, 65, SHORT_HOMOPOLYMER,A,A, picard.sam.SamErrorMetric.ReadBaseStratification$3@69b2acc7)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[31](10, true, 65, SHORT_HOMOPOLYMER,A,A, picard.sam.SamErrorMetric.ReadBaseStratification$3@69b2acc7)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[32](11, true, 65, SHORT_HOMOPOLYMER,A,A, picard.sam.SamErrorMetric.ReadBaseStratification$3@69b2acc7)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[33](12, true, 65, SHORT_HOMOPOLYMER,A,A, picard.sam.SamErrorMetric.ReadBaseStratification$3@69b2acc7)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[34](13, true, 65, LONG_HOMOPOLYMER,A,A, picard.sam.SamErrorMetric.ReadBaseStratification$3@69b2acc7)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[35](14, true, 65, LONG_HOMOPOLYMER,A,A, picard.sam.SamErrorMetric.ReadBaseStratification$3@69b2acc7)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[36](15, true, 65, LONG_HOMOPOLYMER,A,A, picard.sam.SamErrorMetric.ReadBaseStratification$3@69b2acc7)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength[37](16, true, 65, null, picard.sam.SamErrorMetric.ReadBaseStratification$3@69b2acc7)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testHomopolymerLength2(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[0](-1, true, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@263b6847)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[1](0, true, C, picard.sam.SamErrorMetric.ReadBaseStratification$1@263b6847)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[2](1, true, A, picard.sam.SamErrorMetric.ReadBaseStratification$1@263b6847)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[3](2, true, T, picard.sam.SamErrorMetric.ReadBaseStratification$1@263b6847)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[4](3, true, G, picard.sam.SamErrorMetric.ReadBaseStratification$1@263b6847)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[5](4, true, G, picard.sam.SamErrorMetric.ReadBaseStratification$1@263b6847)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[6](5, true, G, picard.sam.SamErrorMetric.ReadBaseStratification$1@263b6847)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[7](6, true, G, picard.sam.SamErrorMetric.ReadBaseStratification$1@263b6847)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[8](7, true, A, picard.sam.SamErrorMetric.ReadBaseStratification$1@263b6847)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[9](8, true, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@263b6847)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[10](-1, false, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@263b6847)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[11](0, false, G, picard.sam.SamErrorMetric.ReadBaseStratification$1@263b6847)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[12](1, false, T, picard.sam.SamErrorMetric.ReadBaseStratification$1@263b6847)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[13](2, false, A, picard.sam.SamErrorMetric.ReadBaseStratification$1@263b6847)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[14](3, false, C, picard.sam.SamErrorMetric.ReadBaseStratification$1@263b6847)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[15](4, false, C, picard.sam.SamErrorMetric.ReadBaseStratification$1@263b6847)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[16](5, false, C, picard.sam.SamErrorMetric.ReadBaseStratification$1@263b6847)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[17](6, false, C, picard.sam.SamErrorMetric.ReadBaseStratification$1@263b6847)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[18](7, false, T, picard.sam.SamErrorMetric.ReadBaseStratification$1@263b6847)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[19](8, false, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@263b6847)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[20](0, true, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@8df04bb)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[21](1, true, C, picard.sam.SamErrorMetric.ReadBaseStratification$1@8df04bb)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[22](2, true, A, picard.sam.SamErrorMetric.ReadBaseStratification$1@8df04bb)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[23](3, true, T, picard.sam.SamErrorMetric.ReadBaseStratification$1@8df04bb)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[24](4, true, G, picard.sam.SamErrorMetric.ReadBaseStratification$1@8df04bb)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[25](5, true, G, picard.sam.SamErrorMetric.ReadBaseStratification$1@8df04bb)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[26](6, true, G, picard.sam.SamErrorMetric.ReadBaseStratification$1@8df04bb)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[27](7, true, G, picard.sam.SamErrorMetric.ReadBaseStratification$1@8df04bb)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[28](8, true, A, picard.sam.SamErrorMetric.ReadBaseStratification$1@8df04bb)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[29](9, true, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@8df04bb)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[30](-2, false, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@8df04bb)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[31](-1, false, G, picard.sam.SamErrorMetric.ReadBaseStratification$1@8df04bb)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[32](0, false, T, picard.sam.SamErrorMetric.ReadBaseStratification$1@8df04bb)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[33](1, false, A, picard.sam.SamErrorMetric.ReadBaseStratification$1@8df04bb)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[34](2, false, C, picard.sam.SamErrorMetric.ReadBaseStratification$1@8df04bb)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[35](3, false, C, picard.sam.SamErrorMetric.ReadBaseStratification$1@8df04bb)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[36](4, false, C, picard.sam.SamErrorMetric.ReadBaseStratification$1@8df04bb)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[37](5, false, C, picard.sam.SamErrorMetric.ReadBaseStratification$1@8df04bb)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[38](6, false, T, picard.sam.SamErrorMetric.ReadBaseStratification$1@8df04bb)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[39](7, false, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@8df04bb)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[40](-2, true, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@5c0396af)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[41](-1, true, C, picard.sam.SamErrorMetric.ReadBaseStratification$1@5c0396af)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[42](0, true, A, picard.sam.SamErrorMetric.ReadBaseStratification$1@5c0396af)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[43](1, true, T, picard.sam.SamErrorMetric.ReadBaseStratification$1@5c0396af)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[44](2, true, G, picard.sam.SamErrorMetric.ReadBaseStratification$1@5c0396af)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[45](3, true, G, picard.sam.SamErrorMetric.ReadBaseStratification$1@5c0396af)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[46](4, true, G, picard.sam.SamErrorMetric.ReadBaseStratification$1@5c0396af)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[47](5, true, G, picard.sam.SamErrorMetric.ReadBaseStratification$1@5c0396af)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[48](6, true, A, picard.sam.SamErrorMetric.ReadBaseStratification$1@5c0396af)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[49](7, true, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@5c0396af)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[50](0, false, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@5c0396af)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[51](1, false, G, picard.sam.SamErrorMetric.ReadBaseStratification$1@5c0396af)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[52](2, false, T, picard.sam.SamErrorMetric.ReadBaseStratification$1@5c0396af)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[53](3, false, A, picard.sam.SamErrorMetric.ReadBaseStratification$1@5c0396af)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[54](4, false, C, picard.sam.SamErrorMetric.ReadBaseStratification$1@5c0396af)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[55](5, false, C, picard.sam.SamErrorMetric.ReadBaseStratification$1@5c0396af)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[56](6, false, C, picard.sam.SamErrorMetric.ReadBaseStratification$1@5c0396af)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[57](7, false, C, picard.sam.SamErrorMetric.ReadBaseStratification$1@5c0396af)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[58](8, false, T, picard.sam.SamErrorMetric.ReadBaseStratification$1@5c0396af)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[59](9, false, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@5c0396af)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[60](-1, true, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@58f3ea70)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[61](0, true, C, picard.sam.SamErrorMetric.ReadBaseStratification$1@58f3ea70)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[62](1, true, A, picard.sam.SamErrorMetric.ReadBaseStratification$1@58f3ea70)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[63](2, true, T, picard.sam.SamErrorMetric.ReadBaseStratification$1@58f3ea70)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[64](3, true, G, picard.sam.SamErrorMetric.ReadBaseStratification$1@58f3ea70)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[65](4, true, G, picard.sam.SamErrorMetric.ReadBaseStratification$1@58f3ea70)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[66](5, true, G, picard.sam.SamErrorMetric.ReadBaseStratification$1@58f3ea70)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[67](6, true, G, picard.sam.SamErrorMetric.ReadBaseStratification$1@58f3ea70)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[68](7, true, A, picard.sam.SamErrorMetric.ReadBaseStratification$1@58f3ea70)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[69](8, true, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@58f3ea70)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[70](-1, false, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@58f3ea70)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[71](0, false, G, picard.sam.SamErrorMetric.ReadBaseStratification$1@58f3ea70)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[72](1, false, T, picard.sam.SamErrorMetric.ReadBaseStratification$1@58f3ea70)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[73](2, false, A, picard.sam.SamErrorMetric.ReadBaseStratification$1@58f3ea70)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[74](3, false, C, picard.sam.SamErrorMetric.ReadBaseStratification$1@58f3ea70)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[75](4, false, C, picard.sam.SamErrorMetric.ReadBaseStratification$1@58f3ea70)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[76](5, false, C, picard.sam.SamErrorMetric.ReadBaseStratification$1@58f3ea70)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[77](6, false, C, picard.sam.SamErrorMetric.ReadBaseStratification$1@58f3ea70)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[78](7, false, T, picard.sam.SamErrorMetric.ReadBaseStratification$1@58f3ea70)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[79](8, false, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@58f3ea70)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[80](-1, true, null, picard.sam.SamErrorMetric.ReadBaseStratification$3@4d01371f)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[81](0, true, C,A, picard.sam.SamErrorMetric.ReadBaseStratification$3@4d01371f)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[82](1, true, A,T, picard.sam.SamErrorMetric.ReadBaseStratification$3@4d01371f)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[83](2, true, T,G, picard.sam.SamErrorMetric.ReadBaseStratification$3@4d01371f)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[84](3, true, G,G, picard.sam.SamErrorMetric.ReadBaseStratification$3@4d01371f)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[85](4, true, G,G, picard.sam.SamErrorMetric.ReadBaseStratification$3@4d01371f)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[86](5, true, G,G, picard.sam.SamErrorMetric.ReadBaseStratification$3@4d01371f)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[87](6, true, G,A, picard.sam.SamErrorMetric.ReadBaseStratification$3@4d01371f)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[88](7, true, null, picard.sam.SamErrorMetric.ReadBaseStratification$3@4d01371f)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[89](0, false, null, picard.sam.SamErrorMetric.ReadBaseStratification$3@4d01371f)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[90](1, false, T,G, picard.sam.SamErrorMetric.ReadBaseStratification$3@4d01371f)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[91](2, false, A,T, picard.sam.SamErrorMetric.ReadBaseStratification$3@4d01371f)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[92](3, false, C,A, picard.sam.SamErrorMetric.ReadBaseStratification$3@4d01371f)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[93](4, false, C,C, picard.sam.SamErrorMetric.ReadBaseStratification$3@4d01371f)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[94](5, false, C,C, picard.sam.SamErrorMetric.ReadBaseStratification$3@4d01371f)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[95](6, false, C,C, picard.sam.SamErrorMetric.ReadBaseStratification$3@4d01371f)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[96](7, false, T,C, picard.sam.SamErrorMetric.ReadBaseStratification$3@4d01371f)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[97](8, false, null, picard.sam.SamErrorMetric.ReadBaseStratification$3@4d01371f)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[98](0, true, null, picard.sam.SamErrorMetric.ReadBaseStratification$3@3bf6830)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[99](1, true, C,A, picard.sam.SamErrorMetric.ReadBaseStratification$3@3bf6830)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[100](2, true, A,T, picard.sam.SamErrorMetric.ReadBaseStratification$3@3bf6830)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[101](3, true, T,G, picard.sam.SamErrorMetric.ReadBaseStratification$3@3bf6830)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[102](4, true, G,G, picard.sam.SamErrorMetric.ReadBaseStratification$3@3bf6830)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[103](5, true, G,G, picard.sam.SamErrorMetric.ReadBaseStratification$3@3bf6830)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[104](6, true, G,G, picard.sam.SamErrorMetric.ReadBaseStratification$3@3bf6830)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[105](7, true, G,A, picard.sam.SamErrorMetric.ReadBaseStratification$3@3bf6830)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[106](8, true, null, picard.sam.SamErrorMetric.ReadBaseStratification$3@3bf6830)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[107](-1, false, null, picard.sam.SamErrorMetric.ReadBaseStratification$3@3bf6830)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[108](0, false, T,G, picard.sam.SamErrorMetric.ReadBaseStratification$3@3bf6830)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[109](1, false, A,T, picard.sam.SamErrorMetric.ReadBaseStratification$3@3bf6830)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[110](2, false, C,A, picard.sam.SamErrorMetric.ReadBaseStratification$3@3bf6830)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[111](3, false, C,C, picard.sam.SamErrorMetric.ReadBaseStratification$3@3bf6830)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[112](4, false, C,C, picard.sam.SamErrorMetric.ReadBaseStratification$3@3bf6830)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[113](5, false, C,C, picard.sam.SamErrorMetric.ReadBaseStratification$3@3bf6830)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[114](6, false, T,C, picard.sam.SamErrorMetric.ReadBaseStratification$3@3bf6830)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[115](7, false, null, picard.sam.SamErrorMetric.ReadBaseStratification$3@3bf6830)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[116](-1, true, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[117](0, true, 0, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[118](1, true, 1, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[119](2, true, 1, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[120](3, true, 1, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[121](4, true, 1, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[122](5, true, 2, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[123](6, true, 3, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[124](7, true, 4, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[125](8, true, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[126](-1, false, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[127](0, false, 1, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[128](1, false, 1, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[129](2, false, 4, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[130](3, false, 3, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[131](4, false, 2, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[132](5, false, 1, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[133](6, false, 1, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[134](7, false, 0, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[135](8, false, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@56d368e9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[136](0, true, null, picard.sam.SamErrorMetric.ReadBaseStratification$3@11b4a829)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[137](1, true, 1,C,A, picard.sam.SamErrorMetric.ReadBaseStratification$3@11b4a829)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[138](2, true, 1,A,T, picard.sam.SamErrorMetric.ReadBaseStratification$3@11b4a829)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[139](3, true, 1,T,G, picard.sam.SamErrorMetric.ReadBaseStratification$3@11b4a829)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[140](4, true, 1,G,G, picard.sam.SamErrorMetric.ReadBaseStratification$3@11b4a829)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[141](5, true, 2,G,G, picard.sam.SamErrorMetric.ReadBaseStratification$3@11b4a829)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[142](6, true, 3,G,G, picard.sam.SamErrorMetric.ReadBaseStratification$3@11b4a829)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[143](7, true, 4,G,A, picard.sam.SamErrorMetric.ReadBaseStratification$3@11b4a829)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[144](8, true, null, picard.sam.SamErrorMetric.ReadBaseStratification$3@11b4a829)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[145](-1, false, null, picard.sam.SamErrorMetric.ReadBaseStratification$3@11b4a829)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[146](0, false, 1,T,G, picard.sam.SamErrorMetric.ReadBaseStratification$3@11b4a829)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[147](1, false, 1,A,T, picard.sam.SamErrorMetric.ReadBaseStratification$3@11b4a829)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[148](2, false, 4,C,A, picard.sam.SamErrorMetric.ReadBaseStratification$3@11b4a829)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[149](3, false, 3,C,C, picard.sam.SamErrorMetric.ReadBaseStratification$3@11b4a829)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[150](4, false, 2,C,C, picard.sam.SamErrorMetric.ReadBaseStratification$3@11b4a829)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[151](5, false, 1,C,C, picard.sam.SamErrorMetric.ReadBaseStratification$3@11b4a829)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[152](6, false, 1,T,C, picard.sam.SamErrorMetric.ReadBaseStratification$3@11b4a829)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[153](7, false, null, picard.sam.SamErrorMetric.ReadBaseStratification$3@11b4a829)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[154](0, true, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@d2b79c9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[155](1, true, CAT, picard.sam.SamErrorMetric.ReadBaseStratification$1@d2b79c9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[156](2, true, ATG, picard.sam.SamErrorMetric.ReadBaseStratification$1@d2b79c9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[157](3, true, TGG, picard.sam.SamErrorMetric.ReadBaseStratification$1@d2b79c9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[158](4, true, GGG, picard.sam.SamErrorMetric.ReadBaseStratification$1@d2b79c9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[159](5, true, GGG, picard.sam.SamErrorMetric.ReadBaseStratification$1@d2b79c9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[160](6, true, GGA, picard.sam.SamErrorMetric.ReadBaseStratification$1@d2b79c9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[161](7, true, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@d2b79c9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[162](0, false, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@d2b79c9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[163](1, false, ATG, picard.sam.SamErrorMetric.ReadBaseStratification$1@d2b79c9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[164](2, false, CAT, picard.sam.SamErrorMetric.ReadBaseStratification$1@d2b79c9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[165](3, false, CCA, picard.sam.SamErrorMetric.ReadBaseStratification$1@d2b79c9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[166](4, false, CCC, picard.sam.SamErrorMetric.ReadBaseStratification$1@d2b79c9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[167](5, false, CCC, picard.sam.SamErrorMetric.ReadBaseStratification$1@d2b79c9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[168](6, false, TCC, picard.sam.SamErrorMetric.ReadBaseStratification$1@d2b79c9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[169](7, false, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@d2b79c9)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[170](0, true, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@39439de6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[171](1, true, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@39439de6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[172](2, true, CATGG, picard.sam.SamErrorMetric.ReadBaseStratification$1@39439de6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[173](3, true, ATGGG, picard.sam.SamErrorMetric.ReadBaseStratification$1@39439de6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[174](4, true, TGGGG, picard.sam.SamErrorMetric.ReadBaseStratification$1@39439de6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[175](5, true, GGGGA, picard.sam.SamErrorMetric.ReadBaseStratification$1@39439de6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[176](6, true, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@39439de6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[177](7, true, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@39439de6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[178](0, false, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@39439de6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[179](1, false, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@39439de6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[180](2, false, CCATG, picard.sam.SamErrorMetric.ReadBaseStratification$1@39439de6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[181](3, false, CCCAT, picard.sam.SamErrorMetric.ReadBaseStratification$1@39439de6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[182](4, false, CCCCA, picard.sam.SamErrorMetric.ReadBaseStratification$1@39439de6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[183](5, false, TCCCC, picard.sam.SamErrorMetric.ReadBaseStratification$1@39439de6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[184](6, false, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@39439de6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[185](7, false, null, picard.sam.SamErrorMetric.ReadBaseStratification$1@39439de6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[186](0, true, all, picard.sam.SamErrorMetric.ReadBaseStratification$2@6d239119)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[187](1, true, all, picard.sam.SamErrorMetric.ReadBaseStratification$2@6d239119)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[188](2, true, all, picard.sam.SamErrorMetric.ReadBaseStratification$2@6d239119)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[189](3, true, all, picard.sam.SamErrorMetric.ReadBaseStratification$2@6d239119)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[190](4, true, all, picard.sam.SamErrorMetric.ReadBaseStratification$2@6d239119)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[191](5, true, all, picard.sam.SamErrorMetric.ReadBaseStratification$2@6d239119)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[192](6, true, all, picard.sam.SamErrorMetric.ReadBaseStratification$2@6d239119)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[193](7, true, all, picard.sam.SamErrorMetric.ReadBaseStratification$2@6d239119)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[194](0, false, all, picard.sam.SamErrorMetric.ReadBaseStratification$2@6d239119)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[195](1, false, all, picard.sam.SamErrorMetric.ReadBaseStratification$2@6d239119)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[196](2, false, all, picard.sam.SamErrorMetric.ReadBaseStratification$2@6d239119)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[197](3, false, all, picard.sam.SamErrorMetric.ReadBaseStratification$2@6d239119)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[198](4, false, all, picard.sam.SamErrorMetric.ReadBaseStratification$2@6d239119)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[199](5, false, all, picard.sam.SamErrorMetric.ReadBaseStratification$2@6d239119)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[200](6, false, all, picard.sam.SamErrorMetric.ReadBaseStratification$2@6d239119)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[201](7, false, all, picard.sam.SamErrorMetric.ReadBaseStratification$2@6d239119)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[202](7, false, -, picard.sam.SamErrorMetric.ReadBaseStratification$2@57e19ec0)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[203](7, true, +, picard.sam.SamErrorMetric.ReadBaseStratification$2@57e19ec0)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[204](1, false, 0.63, picard.sam.SamErrorMetric.ReadBaseStratification$GCContentStratifier@3a6b7487)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[205](1, false, 93, picard.sam.SamErrorMetric.ReadBaseStratification$FlowCellTileStratifier@2d4fd721)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[206](1, false, 3, picard.sam.SamErrorMetric.ReadBaseStratification$FlowCellXStratifier@54d76f8a)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[207](1, false, 7, picard.sam.SamErrorMetric.ReadBaseStratification$FlowCellYStratifier@60166641)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[208](1, false, rgID, picard.sam.SamErrorMetric.ReadBaseStratification$2@28ff3543)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[209](1, false, FIRST, picard.sam.SamErrorMetric.ReadBaseStratification$2@2e47bd9a)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[210](1, true, +, picard.sam.SamErrorMetric.ReadBaseStratification$2@57e19ec0)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[211](1, false, -, picard.sam.SamErrorMetric.ReadBaseStratification$2@57e19ec0)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[212](1, true, F1R2, picard.sam.SamErrorMetric.ReadBaseStratification$2@364f17f7)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[213](1, false, F2R1, picard.sam.SamErrorMetric.ReadBaseStratification$2@364f17f7)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[214](0, true, QUINTILE_1, picard.sam.SamErrorMetric.ReadBaseStratification$BinnedReadCycleStratifier@282d5ce6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[215](1, true, QUINTILE_2, picard.sam.SamErrorMetric.ReadBaseStratification$BinnedReadCycleStratifier@282d5ce6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[216](2, true, QUINTILE_2, picard.sam.SamErrorMetric.ReadBaseStratification$BinnedReadCycleStratifier@282d5ce6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[217](3, true, QUINTILE_3, picard.sam.SamErrorMetric.ReadBaseStratification$BinnedReadCycleStratifier@282d5ce6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[218](4, true, QUINTILE_4, picard.sam.SamErrorMetric.ReadBaseStratification$BinnedReadCycleStratifier@282d5ce6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[219](5, true, QUINTILE_4, picard.sam.SamErrorMetric.ReadBaseStratification$BinnedReadCycleStratifier@282d5ce6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[220](6, true, QUINTILE_5, picard.sam.SamErrorMetric.ReadBaseStratification$BinnedReadCycleStratifier@282d5ce6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[221](7, true, QUINTILE_5, picard.sam.SamErrorMetric.ReadBaseStratification$BinnedReadCycleStratifier@282d5ce6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[222](7, false, QUINTILE_1, picard.sam.SamErrorMetric.ReadBaseStratification$BinnedReadCycleStratifier@282d5ce6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[223](6, false, QUINTILE_2, picard.sam.SamErrorMetric.ReadBaseStratification$BinnedReadCycleStratifier@282d5ce6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[224](5, false, QUINTILE_2, picard.sam.SamErrorMetric.ReadBaseStratification$BinnedReadCycleStratifier@282d5ce6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[225](4, false, QUINTILE_3, picard.sam.SamErrorMetric.ReadBaseStratification$BinnedReadCycleStratifier@282d5ce6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[226](3, false, QUINTILE_4, picard.sam.SamErrorMetric.ReadBaseStratification$BinnedReadCycleStratifier@282d5ce6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[227](2, false, QUINTILE_4, picard.sam.SamErrorMetric.ReadBaseStratification$BinnedReadCycleStratifier@282d5ce6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[228](1, false, QUINTILE_5, picard.sam.SamErrorMetric.ReadBaseStratification$BinnedReadCycleStratifier@282d5ce6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[229](0, false, QUINTILE_5, picard.sam.SamErrorMetric.ReadBaseStratification$BinnedReadCycleStratifier@282d5ce6)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[230](0, true, 1, picard.sam.SamErrorMetric.ReadBaseStratification$1@7b5a19a2)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[231](1, true, 2, picard.sam.SamErrorMetric.ReadBaseStratification$1@7b5a19a2)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[232](2, true, 3, picard.sam.SamErrorMetric.ReadBaseStratification$1@7b5a19a2)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[233](3, true, 4, picard.sam.SamErrorMetric.ReadBaseStratification$1@7b5a19a2)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[234](4, true, 5, picard.sam.SamErrorMetric.ReadBaseStratification$1@7b5a19a2)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[235](5, true, 6, picard.sam.SamErrorMetric.ReadBaseStratification$1@7b5a19a2)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[236](6, true, 7, picard.sam.SamErrorMetric.ReadBaseStratification$1@7b5a19a2)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[237](7, true, 8, picard.sam.SamErrorMetric.ReadBaseStratification$1@7b5a19a2)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[238](7, false, 1, picard.sam.SamErrorMetric.ReadBaseStratification$1@7b5a19a2)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[239](6, false, 2, picard.sam.SamErrorMetric.ReadBaseStratification$1@7b5a19a2)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[240](5, false, 3, picard.sam.SamErrorMetric.ReadBaseStratification$1@7b5a19a2)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[241](4, false, 4, picard.sam.SamErrorMetric.ReadBaseStratification$1@7b5a19a2)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[242](3, false, 5, picard.sam.SamErrorMetric.ReadBaseStratification$1@7b5a19a2)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[243](2, false, 6, picard.sam.SamErrorMetric.ReadBaseStratification$1@7b5a19a2)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[244](1, false, 7, picard.sam.SamErrorMetric.ReadBaseStratification$1@7b5a19a2)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[245](0, false, 8, picard.sam.SamErrorMetric.ReadBaseStratification$1@7b5a19a2)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[246](0, true, 80, picard.sam.SamErrorMetric.ReadBaseStratification$2@166dbdc5)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[247](0, true, 65, picard.sam.SamErrorMetric.ReadBaseStratification$1@3d5131a3)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[248](1, true, 66, picard.sam.SamErrorMetric.ReadBaseStratification$1@3d5131a3)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[249](2, true, 67, picard.sam.SamErrorMetric.ReadBaseStratification$1@3d5131a3)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[250](3, true, 68, picard.sam.SamErrorMetric.ReadBaseStratification$1@3d5131a3)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[251](4, true, 69, picard.sam.SamErrorMetric.ReadBaseStratification$1@3d5131a3)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[252](5, true, 70, picard.sam.SamErrorMetric.ReadBaseStratification$1@3d5131a3)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[253](6, true, 71, picard.sam.SamErrorMetric.ReadBaseStratification$1@3d5131a3)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[254](7, true, 72, picard.sam.SamErrorMetric.ReadBaseStratification$1@3d5131a3)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testReadBaseStratifier[255](0, true, 40, picard.sam.SamErrorMetric.ReadBaseStratification$2@7fd99083)(picard.sam.SamErrorMetric.ReadBaseStratificationTest) Running Test: Test method testGetRapidDefaultReadNameRegexSplit(picard.sam.util.ReadNameParserTests) Running Test: Test method testParseReadNameOK[0](RUNID:7:1203:2886:82292, 1203, 2886, 82292)(picard.sam.util.ReadNameParserTests) Running Test: Test method testParseReadNameOK[1](RUNID:7:1203:2884:16834, 1203, 2884, 16834)(picard.sam.util.ReadNameParserTests) Running Test: Test method testParseReadNameOverflow[0](RUNID:7:1203:2886:82292, 1203, 2886, 82292)(picard.sam.util.ReadNameParserTests) Running Test: Test method testParseReadNameOverflow[1](RUNID:7:1203:2884:16834, 1203, 2884, 16834)(picard.sam.util.ReadNameParserTests) Running Test: Test method testRapidParseInt(picard.sam.util.ReadNameParserTests) Running Test: Test method testRapidParseIntFails(picard.sam.util.ReadNameParserTests) Running Test: Test method testReadNameParsing[0]((?:.*:)?([0-9]+)[^:]*:([0-9]+)[^:]*:([0-9]+)[^:]*$, RUNID:123:000000000-ZZZZZ:1:1105:17981:23325, 1105, 17981, 23325, true)(picard.sam.util.ReadNameParserTests) Running Test: Test method testReadNameParsing[1]((?:.*:)?([0-9]+)[^:]*:([0-9]+)[^:]*:([0-9]+)[^:]*$, RUNID:123:000000000-ZZZZZ:1:1109:22981:17995, 1109, 22981, 17995, true)(picard.sam.util.ReadNameParserTests) Running Test: Test method testReadNameParsing[2]((?:.*:)?([0-9]+)[^:]*:([0-9]+)[^:]*:([0-9]+)[^:]*$, 1109:22981:17995, 1109, 22981, 17995, true)(picard.sam.util.ReadNameParserTests) Running Test: Test method testReadNameParsing[3]((?:.*:)?([0-9]+)[^:]*:([0-9]+)[^:]*:([0-9]+)[^:]*$, RUNID:7:1203:2886:82292, 1203, 2886, 82292, true)(picard.sam.util.ReadNameParserTests) Running Test: Test method testReadNameParsing[4]((?:.*:)?([0-9]+)[^:]*:([0-9]+)[^:]*:([0-9]+)[^:]*$, RUNID:7:1203:2884:16834, 1203, 2884, 16834, true)(picard.sam.util.ReadNameParserTests) Running Test: Test method testReadNameParsing[5]((?:.*:)?([0-9]+)[^:]*:([0-9]+)[^:]*:([0-9]+)[^:]*$, 1109ABC:22981DEF:17995GHI, 1109, 22981, 17995, true)(picard.sam.util.ReadNameParserTests) Running Test: Test method testReadNameParsing[6](, RUNID:123:000000000-ZZZZZ:1:1105:17981:23325, 1105, 17981, 23325, true)(picard.sam.util.ReadNameParserTests) Running Test: Test method testReadNameParsing[7](, RUNID:123:000000000-ZZZZZ:1:1109:22981:17995, 1109, 22981, 17995, true)(picard.sam.util.ReadNameParserTests) Running Test: Test method testReadNameParsing[8](, 1109:22981:17995, 1109, 22981, 17995, false)(picard.sam.util.ReadNameParserTests) Running Test: Test method testReadNameParsing[9](, RUNID:7:1203:2886:82292, 1203, 2886, 82292, true)(picard.sam.util.ReadNameParserTests) Running Test: Test method testReadNameParsing[10](, RUNID:7:1203:2884:16834, 1203, 2884, 16834, true)(picard.sam.util.ReadNameParserTests) Running Test: Test method testSerializedReadNameParser(picard.sam.util.ReadNameParserTests) Running Test: Test method testInvalidReadStructureFromList[0](, [])(picard.illumina.ReadStructureTest) Running Test: Test method testInvalidReadStructureFromList[1](0T, [0T])(picard.illumina.ReadStructureTest) Running Test: Test method testInvalidReadStructureFromList[2](-1T, [-1T])(picard.illumina.ReadStructureTest) Running Test: Test method testInvalidReadStructureFromList[3](0S, [0S])(picard.illumina.ReadStructureTest) Running Test: Test method testInvalidReadStructureFromList[4](0M, [0M])(picard.illumina.ReadStructureTest) Running Test: Test method testInvalidReadStructureFromList[5](-1B, [-1B])(picard.illumina.ReadStructureTest) Running Test: Test method testInvalidReadStructureFromList[6](-1M, [-1M])(picard.illumina.ReadStructureTest) Running Test: Test method testInvalidReadStructureFromList[7](-66S1B, [-66S, 1B])(picard.illumina.ReadStructureTest) Running Test: Test method testInvalidReadStructureFromList[8](77T82B0S, [77T, 82B, 0S])(picard.illumina.ReadStructureTest) Running Test: Test method testInvalidReadStructureFromString[0](, [])(picard.illumina.ReadStructureTest) Running Test: Test method testInvalidReadStructureFromString[1](0T, [0T])(picard.illumina.ReadStructureTest) Running Test: Test method testInvalidReadStructureFromString[2](-1T, [-1T])(picard.illumina.ReadStructureTest) Running Test: Test method testInvalidReadStructureFromString[3](0S, [0S])(picard.illumina.ReadStructureTest) Running Test: Test method testInvalidReadStructureFromString[4](0M, [0M])(picard.illumina.ReadStructureTest) Running Test: Test method testInvalidReadStructureFromString[5](-1B, [-1B])(picard.illumina.ReadStructureTest) Running Test: Test method testInvalidReadStructureFromString[6](-1M, [-1M])(picard.illumina.ReadStructureTest) Running Test: Test method testInvalidReadStructureFromString[7](8C, null)(picard.illumina.ReadStructureTest) Running Test: Test method testInvalidReadStructureFromString[8](B5, null)(picard.illumina.ReadStructureTest) Running Test: Test method testInvalidReadStructureFromString[9](SS, null)(picard.illumina.ReadStructureTest) Running Test: Test method testInvalidReadStructureFromString[10](SM, null)(picard.illumina.ReadStructureTest) Running Test: Test method testInvalidReadStructureFromString[11](75TS, null)(picard.illumina.ReadStructureTest) Running Test: Test method testInvalidReadStructureFromString[12](8*T, null)(picard.illumina.ReadStructureTest) Running Test: Test method testInvalidReadStructureFromString[13](-66S1B, [-66S, 1B])(picard.illumina.ReadStructureTest) Running Test: Test method testInvalidReadStructureFromString[14](-0T5B8C, null)(picard.illumina.ReadStructureTest) Running Test: Test method testInvalidReadStructureFromString[15](77T82B0S, [77T, 82B, 0S])(picard.illumina.ReadStructureTest) Running Test: Test method testSubstructureToReadStructure[0](picard.illumina.parser.ReadStructure$Substructure@4e680701)(picard.illumina.ReadStructureTest) Running Test: Test method testSubstructureToReadStructure[1](picard.illumina.parser.ReadStructure$Substructure@2be3b1d1)(picard.illumina.ReadStructureTest) Running Test: Test method testSubstructureToReadStructure[2](picard.illumina.parser.ReadStructure$Substructure@769010ee)(picard.illumina.ReadStructureTest) Running Test: Test method testSubstructureToReadStructure[3](picard.illumina.parser.ReadStructure$Substructure@602c8477)(picard.illumina.ReadStructureTest) Running Test: Test method testSubstructureToReadStructure[4](picard.illumina.parser.ReadStructure$Substructure@1c8e33c0)(picard.illumina.ReadStructureTest) Running Test: Test method testSubstructureToReadStructure[5](picard.illumina.parser.ReadStructure$Substructure@70c8ea01)(picard.illumina.ReadStructureTest) Running Test: Test method testSubstructureToReadStructure[6](picard.illumina.parser.ReadStructure$Substructure@d02bd26)(picard.illumina.ReadStructureTest) Running Test: Test method testSubstructureToReadStructure[0](picard.illumina.parser.ReadStructure$Substructure@503a7082, 10T10T)(picard.illumina.ReadStructureTest) Running Test: Test method testSubstructureToReadStructure[1](picard.illumina.parser.ReadStructure$Substructure@54bcae3f, 10T10T)(picard.illumina.ReadStructureTest) Running Test: Test method testSubstructureToReadStructure[2](picard.illumina.parser.ReadStructure$Substructure@186fd62d, 10T8B10T)(picard.illumina.ReadStructureTest) Running Test: Test method testSubstructureToReadStructure[3](picard.illumina.parser.ReadStructure$Substructure@1b66253e, 10T8B5M10T)(picard.illumina.ReadStructureTest) Running Test: Test method testSubstructureToReadStructure[4](picard.illumina.parser.ReadStructure$Substructure@76da78db, 10T8B10T)(picard.illumina.ReadStructureTest) Running Test: Test method testSubstructureToReadStructure[5](picard.illumina.parser.ReadStructure$Substructure@230224d8, 8S8S)(picard.illumina.ReadStructureTest) Running Test: Test method testSubstructureToReadStructure[6](picard.illumina.parser.ReadStructure$Substructure@60b12cb, 8S8S)(picard.illumina.ReadStructureTest) Running Test: Test method testSubstructureToReadStructure[7](picard.illumina.parser.ReadStructure$Substructure@368caa, 8B)(picard.illumina.ReadStructureTest) Running Test: Test method testSubstructureToReadStructure[8](picard.illumina.parser.ReadStructure$Substructure@682733bd, 8M)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromList[0](2T, [2T], 1, 0, 0, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromList[1](1234B, [1234B], 0, 1, 0, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromList[2](2147483647S, [2147483647S], 0, 0, 1, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromList[3](2147483647M, [2147483647M], 0, 0, 0, 1)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromList[4](76T76T, [76T, 76T], 2, 0, 0, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromList[5](76T1B, [76T, 1B], 1, 1, 0, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromList[6](76B1T, [76B, 1T], 1, 1, 0, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromList[7](1S1B, [1S, 1B], 0, 1, 1, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromList[8](1S1B1M, [1S, 1B, 1M], 0, 1, 1, 1)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromList[9](1T999S, [1T, 999S], 1, 0, 1, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromList[10](100T20T100T, [100T, 20T, 100T], 3, 0, 0, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromList[11](2S50S10S, [2S, 50S, 10S], 0, 0, 3, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromList[12](10T1B11T, [10T, 1B, 11T], 2, 1, 0, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromList[13](201T13T111B, [201T, 13T, 111B], 2, 1, 0, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromList[14](15B1T1T, [15B, 1T, 1T], 2, 1, 0, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromList[15](99B7T6B, [99B, 7T, 6B], 1, 2, 0, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromList[16](631B776S638T, [631B, 776S, 638T], 1, 1, 1, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromList[17](631M776S638T, [631M, 776S, 638T], 1, 0, 1, 1)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromList[18](3T7B60S2T, [3T, 7B, 60S, 2T], 2, 1, 1, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromList[19](20B9S100T1T, [20B, 9S, 100T, 1T], 2, 1, 1, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromList[20](33T42B9T81B, [33T, 42B, 9T, 81B], 2, 2, 0, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromList[21](28B56B13T123S, [28B, 56B, 13T, 123S], 1, 2, 1, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromList[22](92S8B8B32B, [92S, 8B, 8B, 32B], 0, 3, 1, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromList[23](92S8M8M32M, [92S, 8M, 8M, 32M], 0, 0, 1, 3)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromList[24](2S88B7T8S9T9T84B100S2S4B3B, [2S, 88B, 7T, 8S, 9T, 9T, 84B, 100S, 2S, 4B, 3B], 3, 4, 4, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromList[25](2S88B7T8S9T9T84B3M100S2S4B3M3B, [2S, 88B, 7T, 8S, 9T, 9T, 84B, 3M, 100S, 2S, 4B, 3M, 3B], 3, 4, 4, 2)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromString[0](2T, [2T], 1, 0, 0, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromString[1](1234B, [1234B], 0, 1, 0, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromString[2](2147483647S, [2147483647S], 0, 0, 1, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromString[3](2147483647M, [2147483647M], 0, 0, 0, 1)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromString[4](76T76T, [76T, 76T], 2, 0, 0, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromString[5](76T1B, [76T, 1B], 1, 1, 0, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromString[6](76B1T, [76B, 1T], 1, 1, 0, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromString[7](1S1B, [1S, 1B], 0, 1, 1, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromString[8](1S1B1M, [1S, 1B, 1M], 0, 1, 1, 1)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromString[9](1T999S, [1T, 999S], 1, 0, 1, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromString[10](100T20T100T, [100T, 20T, 100T], 3, 0, 0, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromString[11](2S50S10S, [2S, 50S, 10S], 0, 0, 3, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromString[12](10T1B11T, [10T, 1B, 11T], 2, 1, 0, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromString[13](201T13T111B, [201T, 13T, 111B], 2, 1, 0, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromString[14](15B1T1T, [15B, 1T, 1T], 2, 1, 0, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromString[15](99B7T6B, [99B, 7T, 6B], 1, 2, 0, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromString[16](631B776S638T, [631B, 776S, 638T], 1, 1, 1, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromString[17](631M776S638T, [631M, 776S, 638T], 1, 0, 1, 1)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromString[18](3T7B60S2T, [3T, 7B, 60S, 2T], 2, 1, 1, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromString[19](20B9S100T1T, [20B, 9S, 100T, 1T], 2, 1, 1, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromString[20](33T42B9T81B, [33T, 42B, 9T, 81B], 2, 2, 0, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromString[21](28B56B13T123S, [28B, 56B, 13T, 123S], 1, 2, 1, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromString[22](92S8B8B32B, [92S, 8B, 8B, 32B], 0, 3, 1, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromString[23](92S8M8M32M, [92S, 8M, 8M, 32M], 0, 0, 1, 3)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromString[24](2S88B7T8S9T9T84B100S2S4B3B, [2S, 88B, 7T, 8S, 9T, 9T, 84B, 100S, 2S, 4B, 3B], 3, 4, 4, 0)(picard.illumina.ReadStructureTest) Running Test: Test method testValidStructuresFromString[25](2S88B7T8S9T9T84B3M100S2S4B3M3B, [2S, 88B, 7T, 8S, 9T, 9T, 84B, 3M, 100S, 2S, 4B, 3M, 3B], 3, 4, 4, 2)(picard.illumina.ReadStructureTest) Running Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ValidateSamFile Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0) STANDARD_ERROR INFO 2024-07-02 12:01:53 ValidateSamFile Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorderIN11666211656780847505.bam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorderIN11666211656780847505.bam -IGNORE MISSING_TAG_NM Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:53.537 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:53.537 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:53.537 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:53.537 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:53.537 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:53.537 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:53.537 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:53.537 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:53 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderIN11666211656780847505.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:53 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderIN11666211656780847505.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:53 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:53 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0) STANDARD_OUT No errors found Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:53 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0) STANDARD_ERROR [Tue Jul 02 12:01:53 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam INFO 2024-07-02 12:01:53 ReorderSam Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ReorderSam -INPUT /tmp/reorderIN11666211656780847505.bam -OUTPUT /tmp/reorderOUT7981036151584350776.bam -SEQUENCE_DICTIONARY /tmp/reorder4762006348346863556.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE true ********** ReorderSam -INPUT /tmp/reorderIN11666211656780847505.bam -OUTPUT /tmp/reorderOUT7981036151584350776.bam -SEQUENCE_DICTIONARY /tmp/reorder4762006348346863556.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE true Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:53.604 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:53.604 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:53.604 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:53.604 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:53.604 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:53.604 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:53.604 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:53.604 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:53 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorderIN11666211656780847505.bam OUTPUT=/tmp/reorderOUT7981036151584350776.bam SEQUENCE_DICTIONARY=/tmp/reorder4762006348346863556.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:53 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorderIN11666211656780847505.bam OUTPUT=/tmp/reorderOUT7981036151584350776.bam SEQUENCE_DICTIONARY=/tmp/reorder4762006348346863556.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SAM/BAM file INFO 2024-07-02 12:01:53 ReorderSam SAM/BAM file Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Reference INFO 2024-07-02 12:01:53 ReorderSam Reference Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:53 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Reordering SAM/BAM file: INFO 2024-07-02 12:01:53 ReorderSam Reordering SAM/BAM file: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=0] INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=0] Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=1] INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=1] Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=2] INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=2] Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=3] INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=3] Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr8 [index=7] to => ref contig chr8 [index=4] INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr8 [index=7] to => ref contig chr8 [index=4] Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=5] INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=5] Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=6] INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=6] Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=7] INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=7] Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=8] INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=8] Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=9] INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=9] Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=10] INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=10] Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=11] INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=11] Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr9 [index=8] to => ref contig chr9 [index=12] INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr9 [index=8] to => ref contig chr9 [index=12] Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=13] INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=13] Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=14] INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=14] Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=15] INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=15] Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=16] INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=16] Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=17] INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=17] Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr7 [index=6] to => ref contig chr7 [index=18] INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr7 [index=6] to => ref contig chr7 [index=18] Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=19] INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=19] Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=20] INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=20] Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=21] INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=21] Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=22] INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=22] Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=23] INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=23] Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=24] INFO 2024-07-02 12:01:53 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=24] Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Writing reads... INFO 2024-07-02 12:01:53 ReorderSam Writing reads... Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr1 INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr1 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Processing chr1 INFO 2024-07-02 12:01:53 ReorderSam Processing chr1 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Wrote 5 reads INFO 2024-07-02 12:01:53 ReorderSam Wrote 5 reads Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr2 INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr2 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Processing chr2 INFO 2024-07-02 12:01:53 ReorderSam Processing chr2 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Wrote 2 reads INFO 2024-07-02 12:01:53 ReorderSam Wrote 2 reads Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr3 INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr3 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Processing chr3 INFO 2024-07-02 12:01:53 ReorderSam Processing chr3 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Wrote 2 reads INFO 2024-07-02 12:01:53 ReorderSam Wrote 2 reads Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr4 INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr4 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Processing chr4 INFO 2024-07-02 12:01:53 ReorderSam Processing chr4 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Wrote 2 reads INFO 2024-07-02 12:01:53 ReorderSam Wrote 2 reads Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr5 INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr5 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Processing chr5 INFO 2024-07-02 12:01:53 ReorderSam Processing chr5 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Wrote 2 reads INFO 2024-07-02 12:01:53 ReorderSam Wrote 2 reads Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr6 INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr6 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Processing chr6 INFO 2024-07-02 12:01:53 ReorderSam Processing chr6 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Wrote 1 reads INFO 2024-07-02 12:01:53 ReorderSam Wrote 1 reads Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr7 INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr7 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Processing chr7 INFO 2024-07-02 12:01:53 ReorderSam Processing chr7 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr8 INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr8 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Processing chr8 INFO 2024-07-02 12:01:53 ReorderSam Processing chr8 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr9 INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr9 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Processing chr9 INFO 2024-07-02 12:01:53 ReorderSam Processing chr9 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr10 INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr10 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Processing chr10 INFO 2024-07-02 12:01:53 ReorderSam Processing chr10 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr11 INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr11 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Processing chr11 INFO 2024-07-02 12:01:53 ReorderSam Processing chr11 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr12 INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr12 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Processing chr12 INFO 2024-07-02 12:01:53 ReorderSam Processing chr12 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr13 INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr13 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Processing chr13 INFO 2024-07-02 12:01:53 ReorderSam Processing chr13 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr14 INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr14 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Processing chr14 INFO 2024-07-02 12:01:53 ReorderSam Processing chr14 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr15 INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr15 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Processing chr15 INFO 2024-07-02 12:01:53 ReorderSam Processing chr15 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr16 INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr16 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Processing chr16 INFO 2024-07-02 12:01:53 ReorderSam Processing chr16 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr17 INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr17 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Processing chr17 INFO 2024-07-02 12:01:53 ReorderSam Processing chr17 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr18 INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr18 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Processing chr18 INFO 2024-07-02 12:01:53 ReorderSam Processing chr18 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr19 INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr19 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Processing chr19 INFO 2024-07-02 12:01:53 ReorderSam Processing chr19 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr20 INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr20 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Processing chr20 INFO 2024-07-02 12:01:53 ReorderSam Processing chr20 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr21 INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr21 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Processing chr21 INFO 2024-07-02 12:01:53 ReorderSam Processing chr21 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr22 INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chr22 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Processing chr22 INFO 2024-07-02 12:01:53 ReorderSam Processing chr22 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chrX INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chrX Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Processing chrX INFO 2024-07-02 12:01:53 ReorderSam Processing chrX Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chrY INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chrY Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Processing chrY INFO 2024-07-02 12:01:53 ReorderSam Processing chrY Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chrM INFO 2024-07-02 12:01:53 ReorderSam writing the reads from chrM Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Processing chrM INFO 2024-07-02 12:01:53 ReorderSam Processing chrM Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:53 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Processing unmapped INFO 2024-07-02 12:01:53 ReorderSam Processing unmapped Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ReorderSam Wrote 3 reads INFO 2024-07-02 12:01:53 ReorderSam Wrote 3 reads Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:53 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:53 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:53 ValidateSamFile INFO 2024-07-02 12:01:53 ValidateSamFile Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorderOUT7981036151584350776.bam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorderOUT7981036151584350776.bam -IGNORE MISSING_TAG_NM Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:53.888 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:53.888 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:53.888 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:53.888 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:53.888 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:53.888 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:53.888 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:53.888 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:53 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderOUT7981036151584350776.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:53 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderOUT7981036151584350776.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:53 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:53 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:53 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0) STANDARD_OUT No errors found Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:53 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0) STANDARD_ERROR [Tue Jul 02 12:01:53 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ValidateSamFile Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0) STANDARD_ERROR INFO 2024-07-02 12:01:54 ValidateSamFile Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorderIN5283478637420601075.bam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorderIN5283478637420601075.bam -IGNORE MISSING_TAG_NM Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.140 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:54.140 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.140 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:54.140 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.141 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:54.141 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.153 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:54.153 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:54 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderIN5283478637420601075.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:54 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderIN5283478637420601075.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:54 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:54 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0) STANDARD_OUT No errors found Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:54 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0) STANDARD_ERROR [Tue Jul 02 12:01:54 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam INFO 2024-07-02 12:01:54 ReorderSam Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ReorderSam -INPUT /tmp/reorderIN5283478637420601075.bam -OUTPUT /tmp/reorderOUT17705556605668268931.bam -SEQUENCE_DICTIONARY /tmp/reorder1179736487288524925.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE false ********** ReorderSam -INPUT /tmp/reorderIN5283478637420601075.bam -OUTPUT /tmp/reorderOUT17705556605668268931.bam -SEQUENCE_DICTIONARY /tmp/reorder1179736487288524925.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE false Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.246 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:54.246 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.246 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:54.246 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.246 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:54.246 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.246 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:54.246 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:54 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorderIN5283478637420601075.bam OUTPUT=/tmp/reorderOUT17705556605668268931.bam SEQUENCE_DICTIONARY=/tmp/reorder1179736487288524925.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:54 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorderIN5283478637420601075.bam OUTPUT=/tmp/reorderOUT17705556605668268931.bam SEQUENCE_DICTIONARY=/tmp/reorder1179736487288524925.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SAM/BAM file INFO 2024-07-02 12:01:54 ReorderSam SAM/BAM file Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reference INFO 2024-07-02 12:01:54 ReorderSam Reference Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering SAM/BAM file: INFO 2024-07-02 12:01:54 ReorderSam Reordering SAM/BAM file: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=0] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=0] Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=1] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=1] Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=2] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=2] Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=3] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=3] Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr8 [index=7] to => ref contig chr8 [index=4] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr8 [index=7] to => ref contig chr8 [index=4] Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=5] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=5] Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=6] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=6] Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=7] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=7] Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=8] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=8] Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=9] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=9] Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=10] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=10] Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=11] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=11] Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr9 [index=8] to => ref contig chr9 [index=12] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr9 [index=8] to => ref contig chr9 [index=12] Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=13] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=13] Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=14] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=14] Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=15] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=15] Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=16] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=16] Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=17] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=17] Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr7 [index=6] to => ref contig chr7 [index=18] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr7 [index=6] to => ref contig chr7 [index=18] Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=19] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=19] Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=20] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=20] Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=21] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=21] Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=22] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=22] Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=23] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=23] Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=24] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=24] Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Writing reads... INFO 2024-07-02 12:01:54 ReorderSam Writing reads... Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr1 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr1 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr1 INFO 2024-07-02 12:01:54 ReorderSam Processing chr1 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 5 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 5 reads Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr2 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr2 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr2 INFO 2024-07-02 12:01:54 ReorderSam Processing chr2 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 2 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 2 reads Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr3 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr3 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr3 INFO 2024-07-02 12:01:54 ReorderSam Processing chr3 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 2 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 2 reads Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr4 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr4 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr4 INFO 2024-07-02 12:01:54 ReorderSam Processing chr4 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 2 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 2 reads Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr5 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr5 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr5 INFO 2024-07-02 12:01:54 ReorderSam Processing chr5 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 2 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 2 reads Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr6 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr6 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr6 INFO 2024-07-02 12:01:54 ReorderSam Processing chr6 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 1 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 1 reads Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr7 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr7 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr7 INFO 2024-07-02 12:01:54 ReorderSam Processing chr7 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr8 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr8 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr8 INFO 2024-07-02 12:01:54 ReorderSam Processing chr8 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr9 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr9 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr9 INFO 2024-07-02 12:01:54 ReorderSam Processing chr9 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr10 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr10 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr10 INFO 2024-07-02 12:01:54 ReorderSam Processing chr10 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr11 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr11 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr11 INFO 2024-07-02 12:01:54 ReorderSam Processing chr11 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr12 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr12 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr12 INFO 2024-07-02 12:01:54 ReorderSam Processing chr12 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr13 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr13 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr13 INFO 2024-07-02 12:01:54 ReorderSam Processing chr13 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr14 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr14 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr14 INFO 2024-07-02 12:01:54 ReorderSam Processing chr14 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr15 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr15 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr15 INFO 2024-07-02 12:01:54 ReorderSam Processing chr15 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr16 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr16 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr16 INFO 2024-07-02 12:01:54 ReorderSam Processing chr16 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr17 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr17 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr17 INFO 2024-07-02 12:01:54 ReorderSam Processing chr17 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr18 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr18 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr18 INFO 2024-07-02 12:01:54 ReorderSam Processing chr18 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr19 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr19 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr19 INFO 2024-07-02 12:01:54 ReorderSam Processing chr19 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr20 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr20 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr20 INFO 2024-07-02 12:01:54 ReorderSam Processing chr20 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr21 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr21 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr21 INFO 2024-07-02 12:01:54 ReorderSam Processing chr21 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr22 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr22 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr22 INFO 2024-07-02 12:01:54 ReorderSam Processing chr22 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chrX INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chrX Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chrX INFO 2024-07-02 12:01:54 ReorderSam Processing chrX Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chrY INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chrY Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chrY INFO 2024-07-02 12:01:54 ReorderSam Processing chrY Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chrM INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chrM Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chrM INFO 2024-07-02 12:01:54 ReorderSam Processing chrM Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing unmapped INFO 2024-07-02 12:01:54 ReorderSam Processing unmapped Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 3 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 3 reads Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:54 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:54 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ValidateSamFile INFO 2024-07-02 12:01:54 ValidateSamFile Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorderOUT17705556605668268931.bam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorderOUT17705556605668268931.bam -IGNORE MISSING_TAG_NM Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.374 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:54.374 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.374 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:54.374 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.375 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:54.375 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.375 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:54.375 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:54 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderOUT17705556605668268931.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:54 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderOUT17705556605668268931.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:54 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:54 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0) STANDARD_OUT No errors found Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:54 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0) STANDARD_ERROR [Tue Jul 02 12:01:54 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ValidateSamFile Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1) STANDARD_ERROR INFO 2024-07-02 12:01:54 ValidateSamFile Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorderIN7366040458018211345.bam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorderIN7366040458018211345.bam -IGNORE MISSING_TAG_NM Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.473 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:54.473 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.473 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:54.473 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.473 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:54.473 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.473 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:54.473 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:54 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderIN7366040458018211345.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:54 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderIN7366040458018211345.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:54 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:54 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1) STANDARD_OUT No errors found Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:54 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1) STANDARD_ERROR [Tue Jul 02 12:01:54 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam INFO 2024-07-02 12:01:54 ReorderSam Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ReorderSam -INPUT /tmp/reorderIN7366040458018211345.bam -OUTPUT /tmp/reorderOUT2516498592341848231.bam -SEQUENCE_DICTIONARY /tmp/reorder17270551808244151670.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE false ********** ReorderSam -INPUT /tmp/reorderIN7366040458018211345.bam -OUTPUT /tmp/reorderOUT2516498592341848231.bam -SEQUENCE_DICTIONARY /tmp/reorder17270551808244151670.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE false Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.547 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:54.547 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.547 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:54.547 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.547 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:54.547 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.547 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:54.547 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:54 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorderIN7366040458018211345.bam OUTPUT=/tmp/reorderOUT2516498592341848231.bam SEQUENCE_DICTIONARY=/tmp/reorder17270551808244151670.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:54 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorderIN7366040458018211345.bam OUTPUT=/tmp/reorderOUT2516498592341848231.bam SEQUENCE_DICTIONARY=/tmp/reorder17270551808244151670.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SAM/BAM file INFO 2024-07-02 12:01:54 ReorderSam SAM/BAM file Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reference INFO 2024-07-02 12:01:54 ReorderSam Reference Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr1 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr1 LN=200000001 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr2 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr2 LN=200000001 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr3 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr3 LN=200000001 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr4 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr4 LN=200000001 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr5 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr5 LN=200000001 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr6 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr6 LN=200000001 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr7 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr7 LN=200000001 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr8 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr8 LN=200000001 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr9 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr9 LN=200000001 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr10 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr10 LN=200000001 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr11 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr11 LN=200000001 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr12 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr12 LN=200000001 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr13 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr13 LN=200000001 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr14 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr14 LN=200000001 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr15 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr15 LN=200000001 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr16 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr16 LN=200000001 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr17 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr17 LN=200000001 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr18 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr18 LN=200000001 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr19 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr19 LN=200000001 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr20 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr20 LN=200000001 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr21 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr21 LN=200000001 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr22 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr22 LN=200000001 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chrX LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chrX LN=200000001 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chrY LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chrY LN=200000001 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chrM LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chrM LN=200000001 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering SAM/BAM file: INFO 2024-07-02 12:01:54 ReorderSam Reordering SAM/BAM file: Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ERROR 2024-07-02 12:01:54 ReorderSam ERROR 2024-07-02 12:01:54 ReorderSam Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: picard.PicardException: Discordant contig lengths: read chr1 LN=200000000, ref chr1 LN=200000001 picard.PicardException: Discordant contig lengths: read chr1 LN=200000000, ref chr1 LN=200000001 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:257) at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:257) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSam.doWork(ReorderSam.java:137) at picard.sam.ReorderSam.doWork(ReorderSam.java:137) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183) at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSamTest.TestsWithIndex(ReorderSamTest.java:142) at picard.sam.ReorderSamTest.TestsWithIndex(ReorderSamTest.java:142) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:54 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:54 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ValidateSamFile Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1) STANDARD_ERROR INFO 2024-07-02 12:01:54 ValidateSamFile Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorderIN3747294028526474158.bam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorderIN3747294028526474158.bam -IGNORE MISSING_TAG_NM Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.648 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:54.648 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.648 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:54.648 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.648 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:54.648 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.648 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:54.648 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:54 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderIN3747294028526474158.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:54 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderIN3747294028526474158.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:54 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:54 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1) STANDARD_OUT No errors found Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:54 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1) STANDARD_ERROR [Tue Jul 02 12:01:54 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam INFO 2024-07-02 12:01:54 ReorderSam Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ReorderSam -INPUT /tmp/reorderIN3747294028526474158.bam -OUTPUT /tmp/reorderOUT5504668060871008683.bam -SEQUENCE_DICTIONARY /tmp/reorder5986899221834815501.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE true ********** ReorderSam -INPUT /tmp/reorderIN3747294028526474158.bam -OUTPUT /tmp/reorderOUT5504668060871008683.bam -SEQUENCE_DICTIONARY /tmp/reorder5986899221834815501.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE true Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.732 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:54.732 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.732 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:54.732 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.732 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:54.732 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.732 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:54.732 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:54 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorderIN3747294028526474158.bam OUTPUT=/tmp/reorderOUT5504668060871008683.bam SEQUENCE_DICTIONARY=/tmp/reorder5986899221834815501.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:54 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorderIN3747294028526474158.bam OUTPUT=/tmp/reorderOUT5504668060871008683.bam SEQUENCE_DICTIONARY=/tmp/reorder5986899221834815501.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SAM/BAM file INFO 2024-07-02 12:01:54 ReorderSam SAM/BAM file Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reference INFO 2024-07-02 12:01:54 ReorderSam Reference Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr1 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr1 LN=200000001 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr2 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr2 LN=200000001 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr3 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr3 LN=200000001 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr4 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr4 LN=200000001 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr5 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr5 LN=200000001 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr6 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr6 LN=200000001 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr7 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr7 LN=200000001 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr8 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr8 LN=200000001 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr9 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr9 LN=200000001 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr10 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr10 LN=200000001 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr11 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr11 LN=200000001 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr12 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr12 LN=200000001 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr13 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr13 LN=200000001 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr14 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr14 LN=200000001 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr15 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr15 LN=200000001 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr16 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr16 LN=200000001 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr17 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr17 LN=200000001 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr18 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr18 LN=200000001 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr19 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr19 LN=200000001 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr20 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr20 LN=200000001 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr21 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr21 LN=200000001 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr22 LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chr22 LN=200000001 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chrX LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chrX LN=200000001 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chrY LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chrY LN=200000001 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chrM LN=200000001 INFO 2024-07-02 12:01:54 ReorderSam SN=chrM LN=200000001 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering SAM/BAM file: INFO 2024-07-02 12:01:54 ReorderSam Reordering SAM/BAM file: Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ERROR 2024-07-02 12:01:54 ReorderSam ERROR 2024-07-02 12:01:54 ReorderSam Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: picard.PicardException: Discordant contig lengths: read chr1 LN=200000000, ref chr1 LN=200000001 picard.PicardException: Discordant contig lengths: read chr1 LN=200000000, ref chr1 LN=200000001 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:257) at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:257) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSam.doWork(ReorderSam.java:137) at picard.sam.ReorderSam.doWork(ReorderSam.java:137) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183) at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSamTest.TestsWithIndex(ReorderSamTest.java:142) at picard.sam.ReorderSamTest.TestsWithIndex(ReorderSamTest.java:142) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:54 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:54 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ValidateSamFile Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0) STANDARD_ERROR INFO 2024-07-02 12:01:54 ValidateSamFile Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorderIN2507577072849245370.bam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorderIN2507577072849245370.bam -IGNORE MISSING_TAG_NM Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.833 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:54.833 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.833 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:54.833 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.833 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:54.833 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.833 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:54.833 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:54 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderIN2507577072849245370.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:54 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderIN2507577072849245370.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:54 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:54 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0) STANDARD_OUT No errors found Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:54 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0) STANDARD_ERROR [Tue Jul 02 12:01:54 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam INFO 2024-07-02 12:01:54 ReorderSam Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ReorderSam -INPUT /tmp/reorderIN2507577072849245370.bam -OUTPUT /tmp/reorderOUT7101590177124899352.bam -SEQUENCE_DICTIONARY /tmp/reorder10303653702408857550.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE true ********** ReorderSam -INPUT /tmp/reorderIN2507577072849245370.bam -OUTPUT /tmp/reorderOUT7101590177124899352.bam -SEQUENCE_DICTIONARY /tmp/reorder10303653702408857550.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE true Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.925 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:54.925 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.925 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:54.925 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.925 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:54.925 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:54.925 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:54.925 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:54 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorderIN2507577072849245370.bam OUTPUT=/tmp/reorderOUT7101590177124899352.bam SEQUENCE_DICTIONARY=/tmp/reorder10303653702408857550.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:54 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorderIN2507577072849245370.bam OUTPUT=/tmp/reorderOUT7101590177124899352.bam SEQUENCE_DICTIONARY=/tmp/reorder10303653702408857550.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:54 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SAM/BAM file INFO 2024-07-02 12:01:54 ReorderSam SAM/BAM file Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reference INFO 2024-07-02 12:01:54 ReorderSam Reference Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:54 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering SAM/BAM file: INFO 2024-07-02 12:01:54 ReorderSam Reordering SAM/BAM file: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=0] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=0] Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=1] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=1] Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=2] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=2] Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=3] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=3] Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=4] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=4] Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=5] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=5] Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=6] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=6] Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=7] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=7] Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=8] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=8] Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=9] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=9] Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=10] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=10] Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=11] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=11] Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=12] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=12] Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=13] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=13] Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=14] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=14] Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=15] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=15] Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=16] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=16] Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=17] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=17] Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=18] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=18] Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=19] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=19] Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=20] INFO 2024-07-02 12:01:54 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=20] Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Writing reads... INFO 2024-07-02 12:01:54 ReorderSam Writing reads... Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr1 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr1 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr1 INFO 2024-07-02 12:01:54 ReorderSam Processing chr1 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 5 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 5 reads Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr2 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr2 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr2 INFO 2024-07-02 12:01:54 ReorderSam Processing chr2 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 2 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 2 reads Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr3 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr3 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr3 INFO 2024-07-02 12:01:54 ReorderSam Processing chr3 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 2 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 2 reads Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr4 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr4 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr4 INFO 2024-07-02 12:01:54 ReorderSam Processing chr4 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 2 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 2 reads Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr5 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr5 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr5 INFO 2024-07-02 12:01:54 ReorderSam Processing chr5 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 2 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 2 reads Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr6 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr6 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr6 INFO 2024-07-02 12:01:54 ReorderSam Processing chr6 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 1 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 1 reads Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr7 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr7 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr7 INFO 2024-07-02 12:01:54 ReorderSam Processing chr7 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr8 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr8 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr8 INFO 2024-07-02 12:01:54 ReorderSam Processing chr8 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr9 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr9 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr9 INFO 2024-07-02 12:01:54 ReorderSam Processing chr9 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr10 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr10 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr10 INFO 2024-07-02 12:01:54 ReorderSam Processing chr10 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr11 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr11 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr11 INFO 2024-07-02 12:01:54 ReorderSam Processing chr11 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr12 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr12 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr12 INFO 2024-07-02 12:01:54 ReorderSam Processing chr12 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr13 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr13 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr13 INFO 2024-07-02 12:01:54 ReorderSam Processing chr13 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr14 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr14 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr14 INFO 2024-07-02 12:01:54 ReorderSam Processing chr14 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr15 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr15 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr15 INFO 2024-07-02 12:01:54 ReorderSam Processing chr15 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr16 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr16 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr16 INFO 2024-07-02 12:01:54 ReorderSam Processing chr16 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr17 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr17 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr17 INFO 2024-07-02 12:01:54 ReorderSam Processing chr17 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr18 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr18 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr18 INFO 2024-07-02 12:01:54 ReorderSam Processing chr18 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr19 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr19 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr19 INFO 2024-07-02 12:01:54 ReorderSam Processing chr19 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr20 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr20 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr20 INFO 2024-07-02 12:01:54 ReorderSam Processing chr20 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr21 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr21 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr21 INFO 2024-07-02 12:01:54 ReorderSam Processing chr21 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr22 INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chr22 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chr22 INFO 2024-07-02 12:01:54 ReorderSam Processing chr22 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chrX INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chrX Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chrX INFO 2024-07-02 12:01:54 ReorderSam Processing chrX Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chrY INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chrY Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chrY INFO 2024-07-02 12:01:54 ReorderSam Processing chrY Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chrM INFO 2024-07-02 12:01:54 ReorderSam writing the reads from chrM Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing chrM INFO 2024-07-02 12:01:54 ReorderSam Processing chrM Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Processing unmapped INFO 2024-07-02 12:01:54 ReorderSam Processing unmapped Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:54 ReorderSam Wrote 3 reads INFO 2024-07-02 12:01:54 ReorderSam Wrote 3 reads Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:54 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:54 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ValidateSamFile INFO 2024-07-02 12:01:55 ValidateSamFile Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorderOUT7101590177124899352.bam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorderOUT7101590177124899352.bam -IGNORE MISSING_TAG_NM Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.040 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:55.040 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.040 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:55.040 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.041 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:55.041 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.049 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:55.049 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderOUT7101590177124899352.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:55 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderOUT7101590177124899352.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:55 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:55 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0) STANDARD_OUT No errors found Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0) STANDARD_ERROR [Tue Jul 02 12:01:55 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ValidateSamFile Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1) STANDARD_ERROR INFO 2024-07-02 12:01:55 ValidateSamFile Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorderIN14884960598360025803.bam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorderIN14884960598360025803.bam -IGNORE MISSING_TAG_NM Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.160 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:55.160 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.160 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:55.160 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.161 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:55.161 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.161 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:55.161 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderIN14884960598360025803.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:55 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderIN14884960598360025803.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:55 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:55 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1) STANDARD_OUT No errors found Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1) STANDARD_ERROR [Tue Jul 02 12:01:55 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam INFO 2024-07-02 12:01:55 ReorderSam Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ReorderSam -INPUT /tmp/reorderIN14884960598360025803.bam -OUTPUT /tmp/reorderOUT8097479411707688554.bam -SEQUENCE_DICTIONARY /tmp/reorder1526828452816582381.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE false ********** ReorderSam -INPUT /tmp/reorderIN14884960598360025803.bam -OUTPUT /tmp/reorderOUT8097479411707688554.bam -SEQUENCE_DICTIONARY /tmp/reorder1526828452816582381.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE false Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.239 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:55.239 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.239 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:55.239 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.240 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:55.240 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.240 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:55.240 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorderIN14884960598360025803.bam OUTPUT=/tmp/reorderOUT8097479411707688554.bam SEQUENCE_DICTIONARY=/tmp/reorder1526828452816582381.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:55 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorderIN14884960598360025803.bam OUTPUT=/tmp/reorderOUT8097479411707688554.bam SEQUENCE_DICTIONARY=/tmp/reorder1526828452816582381.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SAM/BAM file INFO 2024-07-02 12:01:55 ReorderSam SAM/BAM file Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reference INFO 2024-07-02 12:01:55 ReorderSam Reference Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering SAM/BAM file: INFO 2024-07-02 12:01:55 ReorderSam Reordering SAM/BAM file: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=0] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=0] Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=1] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=1] Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=2] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=2] Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=3] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=3] Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=4] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=4] Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=5] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=5] Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=6] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=6] Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=7] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=7] Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=8] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=8] Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=9] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=9] Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=10] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=10] Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=11] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=11] Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=12] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=12] Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=13] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=13] Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=14] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=14] Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=15] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=15] Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=16] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=16] Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=17] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=17] Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=18] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=18] Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=19] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=19] Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=20] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=20] Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ERROR 2024-07-02 12:01:55 ReorderSam ERROR 2024-07-02 12:01:55 ReorderSam Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: picard.PicardException: New reference sequence does not contain a matching contig for chr6 picard.PicardException: New reference sequence does not contain a matching contig for chr6 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:273) at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:273) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSam.doWork(ReorderSam.java:137) at picard.sam.ReorderSam.doWork(ReorderSam.java:137) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183) at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSamTest.TestsWithIndex(ReorderSamTest.java:142) at picard.sam.ReorderSamTest.TestsWithIndex(ReorderSamTest.java:142) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:55 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ValidateSamFile Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0) STANDARD_ERROR INFO 2024-07-02 12:01:55 ValidateSamFile Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorderIN9709389282015701875.bam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorderIN9709389282015701875.bam -IGNORE MISSING_TAG_NM Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.361 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:55.361 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.361 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:55.361 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.362 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:55.362 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.362 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:55.362 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderIN9709389282015701875.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:55 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderIN9709389282015701875.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:55 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:55 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0) STANDARD_OUT No errors found Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0) STANDARD_ERROR [Tue Jul 02 12:01:55 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam INFO 2024-07-02 12:01:55 ReorderSam Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ReorderSam -INPUT /tmp/reorderIN9709389282015701875.bam -OUTPUT /tmp/reorderOUT14642033153507246648.bam -SEQUENCE_DICTIONARY /tmp/reorder6187438851779247558.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE true ********** ReorderSam -INPUT /tmp/reorderIN9709389282015701875.bam -OUTPUT /tmp/reorderOUT14642033153507246648.bam -SEQUENCE_DICTIONARY /tmp/reorder6187438851779247558.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE true Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.436 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:55.436 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.436 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:55.436 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.436 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:55.436 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.436 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:55.436 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorderIN9709389282015701875.bam OUTPUT=/tmp/reorderOUT14642033153507246648.bam SEQUENCE_DICTIONARY=/tmp/reorder6187438851779247558.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:55 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorderIN9709389282015701875.bam OUTPUT=/tmp/reorderOUT14642033153507246648.bam SEQUENCE_DICTIONARY=/tmp/reorder6187438851779247558.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SAM/BAM file INFO 2024-07-02 12:01:55 ReorderSam SAM/BAM file Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reference INFO 2024-07-02 12:01:55 ReorderSam Reference Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering SAM/BAM file: INFO 2024-07-02 12:01:55 ReorderSam Reordering SAM/BAM file: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=0] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=0] Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=1] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=1] Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=2] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=2] Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=3] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=3] Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=4] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=4] Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=5] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=5] Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=6] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=6] Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=7] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=7] Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=8] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=8] Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=9] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=9] Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=10] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=10] Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=11] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=11] Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=12] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=12] Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=13] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=13] Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=14] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=14] Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=15] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=15] Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=16] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=16] Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=17] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=17] Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=18] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=18] Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=19] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=19] Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=20] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=20] Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=21] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=21] Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Writing reads... INFO 2024-07-02 12:01:55 ReorderSam Writing reads... Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr1 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr1 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr1 INFO 2024-07-02 12:01:55 ReorderSam Processing chr1 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 5 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 5 reads Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr2 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr2 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr2 INFO 2024-07-02 12:01:55 ReorderSam Processing chr2 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 2 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 2 reads Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr3 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr3 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr3 INFO 2024-07-02 12:01:55 ReorderSam Processing chr3 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 2 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 2 reads Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr4 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr4 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr4 INFO 2024-07-02 12:01:55 ReorderSam Processing chr4 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 2 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 2 reads Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr5 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr5 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr5 INFO 2024-07-02 12:01:55 ReorderSam Processing chr5 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 2 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 2 reads Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr6 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr6 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr6 INFO 2024-07-02 12:01:55 ReorderSam Processing chr6 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 1 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 1 reads Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr7 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr7 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr7 INFO 2024-07-02 12:01:55 ReorderSam Processing chr7 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr8 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr8 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr8 INFO 2024-07-02 12:01:55 ReorderSam Processing chr8 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr9 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr9 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr9 INFO 2024-07-02 12:01:55 ReorderSam Processing chr9 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr10 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr10 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr10 INFO 2024-07-02 12:01:55 ReorderSam Processing chr10 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr11 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr11 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr11 INFO 2024-07-02 12:01:55 ReorderSam Processing chr11 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr12 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr12 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr12 INFO 2024-07-02 12:01:55 ReorderSam Processing chr12 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr13 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr13 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr13 INFO 2024-07-02 12:01:55 ReorderSam Processing chr13 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr14 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr14 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr14 INFO 2024-07-02 12:01:55 ReorderSam Processing chr14 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr15 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr15 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr15 INFO 2024-07-02 12:01:55 ReorderSam Processing chr15 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr16 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr16 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr16 INFO 2024-07-02 12:01:55 ReorderSam Processing chr16 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr17 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr17 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr17 INFO 2024-07-02 12:01:55 ReorderSam Processing chr17 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr18 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr18 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr18 INFO 2024-07-02 12:01:55 ReorderSam Processing chr18 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr19 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr19 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr19 INFO 2024-07-02 12:01:55 ReorderSam Processing chr19 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr20 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr20 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr20 INFO 2024-07-02 12:01:55 ReorderSam Processing chr20 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr21 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr21 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr21 INFO 2024-07-02 12:01:55 ReorderSam Processing chr21 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr22 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr22 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr22 INFO 2024-07-02 12:01:55 ReorderSam Processing chr22 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chrX INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chrX Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chrX INFO 2024-07-02 12:01:55 ReorderSam Processing chrX Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chrY INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chrY Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chrY INFO 2024-07-02 12:01:55 ReorderSam Processing chrY Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chrM INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chrM Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chrM INFO 2024-07-02 12:01:55 ReorderSam Processing chrM Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing unmapped INFO 2024-07-02 12:01:55 ReorderSam Processing unmapped Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 3 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 3 reads Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:55 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ValidateSamFile INFO 2024-07-02 12:01:55 ValidateSamFile Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorderOUT14642033153507246648.bam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorderOUT14642033153507246648.bam -IGNORE MISSING_TAG_NM Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.558 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:55.558 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.558 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:55.558 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.559 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:55.559 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.559 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:55.559 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderOUT14642033153507246648.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:55 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderOUT14642033153507246648.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:55 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:55 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0) STANDARD_OUT No errors found Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0) STANDARD_ERROR [Tue Jul 02 12:01:55 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ValidateSamFile Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1) STANDARD_ERROR INFO 2024-07-02 12:01:55 ValidateSamFile Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorderIN4276075472403754091.bam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorderIN4276075472403754091.bam -IGNORE MISSING_TAG_NM Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.659 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:55.659 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.659 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:55.659 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.659 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:55.659 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.659 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:55.659 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderIN4276075472403754091.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:55 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderIN4276075472403754091.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:55 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:55 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1) STANDARD_OUT No errors found Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1) STANDARD_ERROR [Tue Jul 02 12:01:55 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam INFO 2024-07-02 12:01:55 ReorderSam Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ReorderSam -INPUT /tmp/reorderIN4276075472403754091.bam -OUTPUT /tmp/reorderOUT12424862604648187030.bam -SEQUENCE_DICTIONARY /tmp/reorder8719419783487189870.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE false ********** ReorderSam -INPUT /tmp/reorderIN4276075472403754091.bam -OUTPUT /tmp/reorderOUT12424862604648187030.bam -SEQUENCE_DICTIONARY /tmp/reorder8719419783487189870.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE false Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.741 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:55.741 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.741 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:55.741 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.741 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:55.741 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.741 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:55.741 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorderIN4276075472403754091.bam OUTPUT=/tmp/reorderOUT12424862604648187030.bam SEQUENCE_DICTIONARY=/tmp/reorder8719419783487189870.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:55 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorderIN4276075472403754091.bam OUTPUT=/tmp/reorderOUT12424862604648187030.bam SEQUENCE_DICTIONARY=/tmp/reorder8719419783487189870.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SAM/BAM file INFO 2024-07-02 12:01:55 ReorderSam SAM/BAM file Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reference INFO 2024-07-02 12:01:55 ReorderSam Reference Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering SAM/BAM file: INFO 2024-07-02 12:01:55 ReorderSam Reordering SAM/BAM file: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=0] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=0] Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=1] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=1] Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=2] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=2] Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=3] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=3] Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=4] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=4] Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=5] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=5] Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=6] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=6] Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=7] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=7] Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=8] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=8] Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=9] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=9] Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=10] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=10] Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=11] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=11] Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=12] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=12] Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=13] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=13] Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=14] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=14] Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=15] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=15] Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=16] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=16] Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=17] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=17] Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=18] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=18] Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=19] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=19] Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=20] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=20] Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=21] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=21] Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ERROR 2024-07-02 12:01:55 ReorderSam ERROR 2024-07-02 12:01:55 ReorderSam Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: picard.PicardException: New reference sequence does not contain a matching contig for chr7 picard.PicardException: New reference sequence does not contain a matching contig for chr7 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:273) at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:273) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSam.doWork(ReorderSam.java:137) at picard.sam.ReorderSam.doWork(ReorderSam.java:137) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183) at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSamTest.TestsWithIndex(ReorderSamTest.java:142) at picard.sam.ReorderSamTest.TestsWithIndex(ReorderSamTest.java:142) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:55 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ValidateSamFile Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0) STANDARD_ERROR INFO 2024-07-02 12:01:55 ValidateSamFile Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorderIN11047449689714350077.bam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorderIN11047449689714350077.bam -IGNORE MISSING_TAG_NM Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.850 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:55.850 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.850 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:55.850 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.850 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:55.850 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.850 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:55.850 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderIN11047449689714350077.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:55 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderIN11047449689714350077.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:55 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:55 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0) STANDARD_OUT No errors found Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0) STANDARD_ERROR [Tue Jul 02 12:01:55 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam INFO 2024-07-02 12:01:55 ReorderSam Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ReorderSam -INPUT /tmp/reorderIN11047449689714350077.bam -OUTPUT /tmp/reorderOUT7074328198248044418.bam -SEQUENCE_DICTIONARY /tmp/reorder3060269507646519029.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE true ********** ReorderSam -INPUT /tmp/reorderIN11047449689714350077.bam -OUTPUT /tmp/reorderOUT7074328198248044418.bam -SEQUENCE_DICTIONARY /tmp/reorder3060269507646519029.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE true Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.924 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:55.924 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.924 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:55.924 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.933 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:55.933 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:55.933 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:55.933 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorderIN11047449689714350077.bam OUTPUT=/tmp/reorderOUT7074328198248044418.bam SEQUENCE_DICTIONARY=/tmp/reorder3060269507646519029.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:55 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorderIN11047449689714350077.bam OUTPUT=/tmp/reorderOUT7074328198248044418.bam SEQUENCE_DICTIONARY=/tmp/reorder3060269507646519029.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:55 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SAM/BAM file INFO 2024-07-02 12:01:55 ReorderSam SAM/BAM file Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reference INFO 2024-07-02 12:01:55 ReorderSam Reference Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=test3 LN=100 INFO 2024-07-02 12:01:55 ReorderSam SN=test3 LN=100 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=test1 LN=100 INFO 2024-07-02 12:01:55 ReorderSam SN=test1 LN=100 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=test4 LN=100 INFO 2024-07-02 12:01:55 ReorderSam SN=test4 LN=100 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=test2 LN=100 INFO 2024-07-02 12:01:55 ReorderSam SN=test2 LN=100 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:55 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering SAM/BAM file: INFO 2024-07-02 12:01:55 ReorderSam Reordering SAM/BAM file: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=1] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=1] Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=2] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=2] Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=3] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=3] Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=4] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=4] Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=5] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=5] Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr8 [index=7] to => ref contig chr8 [index=6] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr8 [index=7] to => ref contig chr8 [index=6] Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=7] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=7] Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=8] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=8] Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=10] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=10] Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=13] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=13] Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=14] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=14] Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr7 [index=6] to => ref contig chr7 [index=15] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr7 [index=6] to => ref contig chr7 [index=15] Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=16] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=16] Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr9 [index=8] to => ref contig chr9 [index=17] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr9 [index=8] to => ref contig chr9 [index=17] Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=18] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=18] Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=19] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=19] Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=20] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=20] Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=21] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=21] Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=22] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=22] Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=23] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=23] Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=24] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=24] Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=25] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=25] Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=26] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=26] Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=27] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=27] Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=28] INFO 2024-07-02 12:01:55 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=28] Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Writing reads... INFO 2024-07-02 12:01:55 ReorderSam Writing reads... Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr1 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr1 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr1 INFO 2024-07-02 12:01:55 ReorderSam Processing chr1 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 5 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 5 reads Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr2 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr2 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr2 INFO 2024-07-02 12:01:55 ReorderSam Processing chr2 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 2 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 2 reads Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr3 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr3 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr3 INFO 2024-07-02 12:01:55 ReorderSam Processing chr3 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 2 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 2 reads Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr4 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr4 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr4 INFO 2024-07-02 12:01:55 ReorderSam Processing chr4 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 2 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 2 reads Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr5 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr5 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr5 INFO 2024-07-02 12:01:55 ReorderSam Processing chr5 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 2 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 2 reads Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr6 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr6 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr6 INFO 2024-07-02 12:01:55 ReorderSam Processing chr6 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 1 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 1 reads Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr7 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr7 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr7 INFO 2024-07-02 12:01:55 ReorderSam Processing chr7 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr8 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr8 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr8 INFO 2024-07-02 12:01:55 ReorderSam Processing chr8 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr9 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr9 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr9 INFO 2024-07-02 12:01:55 ReorderSam Processing chr9 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr10 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr10 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr10 INFO 2024-07-02 12:01:55 ReorderSam Processing chr10 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr11 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr11 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr11 INFO 2024-07-02 12:01:55 ReorderSam Processing chr11 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr12 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr12 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr12 INFO 2024-07-02 12:01:55 ReorderSam Processing chr12 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr13 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr13 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr13 INFO 2024-07-02 12:01:55 ReorderSam Processing chr13 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr14 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr14 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr14 INFO 2024-07-02 12:01:55 ReorderSam Processing chr14 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr15 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr15 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr15 INFO 2024-07-02 12:01:55 ReorderSam Processing chr15 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr16 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr16 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr16 INFO 2024-07-02 12:01:55 ReorderSam Processing chr16 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr17 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr17 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr17 INFO 2024-07-02 12:01:55 ReorderSam Processing chr17 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr18 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr18 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr18 INFO 2024-07-02 12:01:55 ReorderSam Processing chr18 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr19 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr19 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr19 INFO 2024-07-02 12:01:55 ReorderSam Processing chr19 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr20 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr20 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr20 INFO 2024-07-02 12:01:55 ReorderSam Processing chr20 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr21 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr21 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr21 INFO 2024-07-02 12:01:55 ReorderSam Processing chr21 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr22 INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chr22 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chr22 INFO 2024-07-02 12:01:55 ReorderSam Processing chr22 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chrX INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chrX Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chrX INFO 2024-07-02 12:01:55 ReorderSam Processing chrX Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chrY INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chrY Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chrY INFO 2024-07-02 12:01:55 ReorderSam Processing chrY Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chrM INFO 2024-07-02 12:01:55 ReorderSam writing the reads from chrM Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing chrM INFO 2024-07-02 12:01:55 ReorderSam Processing chrM Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Processing unmapped INFO 2024-07-02 12:01:55 ReorderSam Processing unmapped Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:55 ReorderSam Wrote 3 reads INFO 2024-07-02 12:01:55 ReorderSam Wrote 3 reads Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:55 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:55 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ValidateSamFile INFO 2024-07-02 12:01:56 ValidateSamFile Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorderOUT7074328198248044418.bam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorderOUT7074328198248044418.bam -IGNORE MISSING_TAG_NM Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.050 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:56.050 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.050 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:56.050 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.051 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:56.051 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.051 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:56.051 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:56 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderOUT7074328198248044418.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:56 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderOUT7074328198248044418.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0) STANDARD_OUT No errors found Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:56 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0) STANDARD_ERROR [Tue Jul 02 12:01:56 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ValidateSamFile Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0) STANDARD_ERROR INFO 2024-07-02 12:01:56 ValidateSamFile Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorderIN7887312327603063272.bam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorderIN7887312327603063272.bam -IGNORE MISSING_TAG_NM Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.174 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:56.174 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.175 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:56.175 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.175 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:56.175 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.175 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:56.175 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:56 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderIN7887312327603063272.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:56 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderIN7887312327603063272.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0) STANDARD_OUT No errors found Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:56 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0) STANDARD_ERROR [Tue Jul 02 12:01:56 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam INFO 2024-07-02 12:01:56 ReorderSam Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ReorderSam -INPUT /tmp/reorderIN7887312327603063272.bam -OUTPUT /tmp/reorderOUT5366387231114982047.bam -SEQUENCE_DICTIONARY /tmp/reorder14219800759186980978.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE false ********** ReorderSam -INPUT /tmp/reorderIN7887312327603063272.bam -OUTPUT /tmp/reorderOUT5366387231114982047.bam -SEQUENCE_DICTIONARY /tmp/reorder14219800759186980978.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE false Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.248 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:56.248 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.248 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:56.248 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.257 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:56.257 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.257 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:56.257 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:56 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorderIN7887312327603063272.bam OUTPUT=/tmp/reorderOUT5366387231114982047.bam SEQUENCE_DICTIONARY=/tmp/reorder14219800759186980978.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:56 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorderIN7887312327603063272.bam OUTPUT=/tmp/reorderOUT5366387231114982047.bam SEQUENCE_DICTIONARY=/tmp/reorder14219800759186980978.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SAM/BAM file INFO 2024-07-02 12:01:56 ReorderSam SAM/BAM file Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reference INFO 2024-07-02 12:01:56 ReorderSam Reference Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=test3 LN=100 INFO 2024-07-02 12:01:56 ReorderSam SN=test3 LN=100 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=test1 LN=100 INFO 2024-07-02 12:01:56 ReorderSam SN=test1 LN=100 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=test4 LN=100 INFO 2024-07-02 12:01:56 ReorderSam SN=test4 LN=100 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=test2 LN=100 INFO 2024-07-02 12:01:56 ReorderSam SN=test2 LN=100 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering SAM/BAM file: INFO 2024-07-02 12:01:56 ReorderSam Reordering SAM/BAM file: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=1] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=1] Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=2] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=2] Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=3] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=3] Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=4] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=4] Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=5] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=5] Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr8 [index=7] to => ref contig chr8 [index=6] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr8 [index=7] to => ref contig chr8 [index=6] Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=7] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=7] Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=8] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=8] Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=10] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=10] Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=13] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=13] Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=14] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=14] Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr7 [index=6] to => ref contig chr7 [index=15] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr7 [index=6] to => ref contig chr7 [index=15] Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=16] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=16] Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr9 [index=8] to => ref contig chr9 [index=17] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr9 [index=8] to => ref contig chr9 [index=17] Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=18] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=18] Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=19] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=19] Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=20] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=20] Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=21] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=21] Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=22] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=22] Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=23] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=23] Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=24] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=24] Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=25] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=25] Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=26] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=26] Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=27] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=27] Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=28] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=28] Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Writing reads... INFO 2024-07-02 12:01:56 ReorderSam Writing reads... Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr1 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr1 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr1 INFO 2024-07-02 12:01:56 ReorderSam Processing chr1 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 5 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 5 reads Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr2 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr2 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr2 INFO 2024-07-02 12:01:56 ReorderSam Processing chr2 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 2 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 2 reads Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr3 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr3 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr3 INFO 2024-07-02 12:01:56 ReorderSam Processing chr3 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 2 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 2 reads Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr4 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr4 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr4 INFO 2024-07-02 12:01:56 ReorderSam Processing chr4 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 2 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 2 reads Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr5 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr5 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr5 INFO 2024-07-02 12:01:56 ReorderSam Processing chr5 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 2 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 2 reads Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr6 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr6 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr6 INFO 2024-07-02 12:01:56 ReorderSam Processing chr6 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 1 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 1 reads Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr7 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr7 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr7 INFO 2024-07-02 12:01:56 ReorderSam Processing chr7 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr8 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr8 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr8 INFO 2024-07-02 12:01:56 ReorderSam Processing chr8 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr9 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr9 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr9 INFO 2024-07-02 12:01:56 ReorderSam Processing chr9 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr10 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr10 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr10 INFO 2024-07-02 12:01:56 ReorderSam Processing chr10 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr11 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr11 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr11 INFO 2024-07-02 12:01:56 ReorderSam Processing chr11 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr12 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr12 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr12 INFO 2024-07-02 12:01:56 ReorderSam Processing chr12 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr13 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr13 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr13 INFO 2024-07-02 12:01:56 ReorderSam Processing chr13 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr14 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr14 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr14 INFO 2024-07-02 12:01:56 ReorderSam Processing chr14 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr15 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr15 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr15 INFO 2024-07-02 12:01:56 ReorderSam Processing chr15 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr16 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr16 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr16 INFO 2024-07-02 12:01:56 ReorderSam Processing chr16 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr17 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr17 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr17 INFO 2024-07-02 12:01:56 ReorderSam Processing chr17 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr18 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr18 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr18 INFO 2024-07-02 12:01:56 ReorderSam Processing chr18 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr19 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr19 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr19 INFO 2024-07-02 12:01:56 ReorderSam Processing chr19 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr20 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr20 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr20 INFO 2024-07-02 12:01:56 ReorderSam Processing chr20 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr21 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr21 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr21 INFO 2024-07-02 12:01:56 ReorderSam Processing chr21 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr22 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr22 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr22 INFO 2024-07-02 12:01:56 ReorderSam Processing chr22 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chrX INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chrX Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chrX INFO 2024-07-02 12:01:56 ReorderSam Processing chrX Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chrY INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chrY Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chrY INFO 2024-07-02 12:01:56 ReorderSam Processing chrY Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chrM INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chrM Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chrM INFO 2024-07-02 12:01:56 ReorderSam Processing chrM Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing unmapped INFO 2024-07-02 12:01:56 ReorderSam Processing unmapped Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 3 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 3 reads Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:56 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:56 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ValidateSamFile INFO 2024-07-02 12:01:56 ValidateSamFile Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorderOUT5366387231114982047.bam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorderOUT5366387231114982047.bam -IGNORE MISSING_TAG_NM Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.366 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:56.366 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.367 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:56.367 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.367 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:56.367 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.367 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:56.367 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:56 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderOUT5366387231114982047.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:56 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderOUT5366387231114982047.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0) STANDARD_OUT No errors found Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:56 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0) STANDARD_ERROR [Tue Jul 02 12:01:56 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ValidateSamFile Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0) STANDARD_ERROR INFO 2024-07-02 12:01:56 ValidateSamFile Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorderIN9294679783940775644.bam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorderIN9294679783940775644.bam -IGNORE MISSING_TAG_NM Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.447 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:56.447 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.447 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:56.447 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.447 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:56.447 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.447 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:56.447 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:56 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderIN9294679783940775644.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:56 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderIN9294679783940775644.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0) STANDARD_OUT No errors found Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:56 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0) STANDARD_ERROR [Tue Jul 02 12:01:56 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam INFO 2024-07-02 12:01:56 ReorderSam Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ReorderSam -INPUT /tmp/reorderIN9294679783940775644.bam -OUTPUT /tmp/reorderOUT6495170754142147972.bam -SEQUENCE_DICTIONARY /tmp/reorder16412398034846029952.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE true ********** ReorderSam -INPUT /tmp/reorderIN9294679783940775644.bam -OUTPUT /tmp/reorderOUT6495170754142147972.bam -SEQUENCE_DICTIONARY /tmp/reorder16412398034846029952.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE true Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.504 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:56.504 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:56.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.504 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:56.504 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:56.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:56 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorderIN9294679783940775644.bam OUTPUT=/tmp/reorderOUT6495170754142147972.bam SEQUENCE_DICTIONARY=/tmp/reorder16412398034846029952.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:56 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorderIN9294679783940775644.bam OUTPUT=/tmp/reorderOUT6495170754142147972.bam SEQUENCE_DICTIONARY=/tmp/reorder16412398034846029952.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SAM/BAM file INFO 2024-07-02 12:01:56 ReorderSam SAM/BAM file Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reference INFO 2024-07-02 12:01:56 ReorderSam Reference Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:56 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering SAM/BAM file: INFO 2024-07-02 12:01:56 ReorderSam Reordering SAM/BAM file: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=0] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=0] Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=1] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=1] Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=2] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=2] Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=3] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=3] Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr7 [index=6] to => ref contig chr7 [index=4] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr7 [index=6] to => ref contig chr7 [index=4] Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr8 [index=7] to => ref contig chr8 [index=5] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr8 [index=7] to => ref contig chr8 [index=5] Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr9 [index=8] to => ref contig chr9 [index=6] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr9 [index=8] to => ref contig chr9 [index=6] Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=7] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=7] Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=8] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=8] Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=9] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=9] Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=10] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=10] Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=11] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=11] Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=12] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=12] Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=13] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=13] Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=14] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=14] Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=15] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=15] Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=16] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=16] Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=17] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=17] Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=18] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=18] Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=19] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=19] Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=20] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=20] Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=21] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=21] Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=22] INFO 2024-07-02 12:01:56 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=22] Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Writing reads... INFO 2024-07-02 12:01:56 ReorderSam Writing reads... Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr1 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr1 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr1 INFO 2024-07-02 12:01:56 ReorderSam Processing chr1 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 5 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 5 reads Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr2 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr2 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr2 INFO 2024-07-02 12:01:56 ReorderSam Processing chr2 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 2 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 2 reads Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr3 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr3 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr3 INFO 2024-07-02 12:01:56 ReorderSam Processing chr3 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 2 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 2 reads Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr4 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr4 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr4 INFO 2024-07-02 12:01:56 ReorderSam Processing chr4 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 2 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 2 reads Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr5 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr5 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr5 INFO 2024-07-02 12:01:56 ReorderSam Processing chr5 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 2 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 2 reads Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr6 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr6 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr6 INFO 2024-07-02 12:01:56 ReorderSam Processing chr6 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 1 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 1 reads Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr7 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr7 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr7 INFO 2024-07-02 12:01:56 ReorderSam Processing chr7 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr8 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr8 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr8 INFO 2024-07-02 12:01:56 ReorderSam Processing chr8 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr9 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr9 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr9 INFO 2024-07-02 12:01:56 ReorderSam Processing chr9 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr10 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr10 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr10 INFO 2024-07-02 12:01:56 ReorderSam Processing chr10 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr11 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr11 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr11 INFO 2024-07-02 12:01:56 ReorderSam Processing chr11 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr12 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr12 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr12 INFO 2024-07-02 12:01:56 ReorderSam Processing chr12 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr13 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr13 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr13 INFO 2024-07-02 12:01:56 ReorderSam Processing chr13 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr14 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr14 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr14 INFO 2024-07-02 12:01:56 ReorderSam Processing chr14 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr15 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr15 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr15 INFO 2024-07-02 12:01:56 ReorderSam Processing chr15 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr16 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr16 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr16 INFO 2024-07-02 12:01:56 ReorderSam Processing chr16 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr17 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr17 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr17 INFO 2024-07-02 12:01:56 ReorderSam Processing chr17 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr18 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr18 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr18 INFO 2024-07-02 12:01:56 ReorderSam Processing chr18 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr19 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr19 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr19 INFO 2024-07-02 12:01:56 ReorderSam Processing chr19 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr20 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr20 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr20 INFO 2024-07-02 12:01:56 ReorderSam Processing chr20 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr21 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr21 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr21 INFO 2024-07-02 12:01:56 ReorderSam Processing chr21 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr22 INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chr22 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chr22 INFO 2024-07-02 12:01:56 ReorderSam Processing chr22 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chrX INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chrX Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chrX INFO 2024-07-02 12:01:56 ReorderSam Processing chrX Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chrY INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chrY Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chrY INFO 2024-07-02 12:01:56 ReorderSam Processing chrY Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chrM INFO 2024-07-02 12:01:56 ReorderSam writing the reads from chrM Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing chrM INFO 2024-07-02 12:01:56 ReorderSam Processing chrM Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 0 reads Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Processing unmapped INFO 2024-07-02 12:01:56 ReorderSam Processing unmapped Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ReorderSam Wrote 3 reads INFO 2024-07-02 12:01:56 ReorderSam Wrote 3 reads Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:56 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:56 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ValidateSamFile INFO 2024-07-02 12:01:56 ValidateSamFile Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorderOUT6495170754142147972.bam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorderOUT6495170754142147972.bam -IGNORE MISSING_TAG_NM Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.664 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:56.664 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.664 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:56.664 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.664 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:56.664 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.664 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:56.664 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:56 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderOUT6495170754142147972.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:56 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderOUT6495170754142147972.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0) STANDARD_OUT No errors found Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:56 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0) STANDARD_ERROR [Tue Jul 02 12:01:56 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:56 ValidateSamFile Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1) STANDARD_ERROR INFO 2024-07-02 12:01:56 ValidateSamFile Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorderIN15753696878201428956.bam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorderIN15753696878201428956.bam -IGNORE MISSING_TAG_NM Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.995 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:56.995 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.995 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:56.995 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.995 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:56.995 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:56.995 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:56.995 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:56 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderIN15753696878201428956.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:56 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorderIN15753696878201428956.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:56 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:56 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1) STANDARD_OUT No errors found Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:57 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1) STANDARD_ERROR [Tue Jul 02 12:01:57 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam INFO 2024-07-02 12:01:57 ReorderSam Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ReorderSam -INPUT /tmp/reorderIN15753696878201428956.bam -OUTPUT /tmp/reorderOUT12675765539336051302.bam -SEQUENCE_DICTIONARY /tmp/reorder13624110312000116192.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE false ********** ReorderSam -INPUT /tmp/reorderIN15753696878201428956.bam -OUTPUT /tmp/reorderOUT12675765539336051302.bam -SEQUENCE_DICTIONARY /tmp/reorder13624110312000116192.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE false Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:57.231 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:57.231 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:57.231 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:57.231 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:57.232 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:57.232 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:57.232 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:57.232 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:57 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorderIN15753696878201428956.bam OUTPUT=/tmp/reorderOUT12675765539336051302.bam SEQUENCE_DICTIONARY=/tmp/reorder13624110312000116192.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:57 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorderIN15753696878201428956.bam OUTPUT=/tmp/reorderOUT12675765539336051302.bam SEQUENCE_DICTIONARY=/tmp/reorder13624110312000116192.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SAM/BAM file INFO 2024-07-02 12:01:57 ReorderSam SAM/BAM file Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reference INFO 2024-07-02 12:01:57 ReorderSam Reference Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering SAM/BAM file: INFO 2024-07-02 12:01:57 ReorderSam Reordering SAM/BAM file: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=0] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=0] Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=1] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=1] Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=2] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=2] Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=3] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=3] Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr7 [index=6] to => ref contig chr7 [index=4] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr7 [index=6] to => ref contig chr7 [index=4] Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr8 [index=7] to => ref contig chr8 [index=5] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr8 [index=7] to => ref contig chr8 [index=5] Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr9 [index=8] to => ref contig chr9 [index=6] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr9 [index=8] to => ref contig chr9 [index=6] Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=7] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=7] Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=8] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=8] Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=9] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=9] Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=10] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=10] Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=11] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=11] Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=12] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=12] Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=13] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=13] Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=14] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=14] Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=15] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=15] Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=16] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=16] Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=17] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=17] Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=18] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=18] Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=19] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=19] Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=20] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=20] Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=21] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=21] Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=22] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=22] Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ERROR 2024-07-02 12:01:57 ReorderSam ERROR 2024-07-02 12:01:57 ReorderSam Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: picard.PicardException: New reference sequence does not contain a matching contig for chr1 picard.PicardException: New reference sequence does not contain a matching contig for chr1 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:273) at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:273) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSam.doWork(ReorderSam.java:137) at picard.sam.ReorderSam.doWork(ReorderSam.java:137) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183) at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSamTest.TestsWithIndex(ReorderSamTest.java:142) at picard.sam.ReorderSamTest.TestsWithIndex(ReorderSamTest.java:142) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:57 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:57 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@3ab24a51, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ValidateSamFile Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0) STANDARD_ERROR INFO 2024-07-02 12:01:57 ValidateSamFile Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorder13683787532257625339.sam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorder13683787532257625339.sam -IGNORE MISSING_TAG_NM Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:57.406 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:57.406 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:57.406 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:57.406 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:57.407 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:57.407 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:57.407 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:57.407 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:57 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder13683787532257625339.sam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:57 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder13683787532257625339.sam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:57 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:57 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0) STANDARD_OUT No errors found Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:57 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0) STANDARD_ERROR [Tue Jul 02 12:01:57 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam INFO 2024-07-02 12:01:57 ReorderSam Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ReorderSam -INPUT /tmp/reorder13683787532257625339.sam -OUTPUT /tmp/reorder15905476874616786059.bam -SEQUENCE_DICTIONARY /tmp/reorder2400140980809369938.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE true ********** ReorderSam -INPUT /tmp/reorder13683787532257625339.sam -OUTPUT /tmp/reorder15905476874616786059.bam -SEQUENCE_DICTIONARY /tmp/reorder2400140980809369938.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE true Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:57.544 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:57.544 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:57.544 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:57.544 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:57.544 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:57.544 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:57.544 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:57.544 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:57 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorder13683787532257625339.sam OUTPUT=/tmp/reorder15905476874616786059.bam SEQUENCE_DICTIONARY=/tmp/reorder2400140980809369938.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:57 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorder13683787532257625339.sam OUTPUT=/tmp/reorder15905476874616786059.bam SEQUENCE_DICTIONARY=/tmp/reorder2400140980809369938.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SAM/BAM file INFO 2024-07-02 12:01:57 ReorderSam SAM/BAM file Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reference INFO 2024-07-02 12:01:57 ReorderSam Reference Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering SAM/BAM file: INFO 2024-07-02 12:01:57 ReorderSam Reordering SAM/BAM file: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=0] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=0] Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=1] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=1] Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=2] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=2] Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=3] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=3] Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr8 [index=7] to => ref contig chr8 [index=4] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr8 [index=7] to => ref contig chr8 [index=4] Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=5] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=5] Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=6] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=6] Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=7] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=7] Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=8] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=8] Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=9] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=9] Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=10] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=10] Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=11] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=11] Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr9 [index=8] to => ref contig chr9 [index=12] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr9 [index=8] to => ref contig chr9 [index=12] Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=13] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=13] Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=14] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=14] Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=15] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=15] Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=16] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=16] Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=17] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=17] Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr7 [index=6] to => ref contig chr7 [index=18] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr7 [index=6] to => ref contig chr7 [index=18] Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=19] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=19] Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=20] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=20] Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=21] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=21] Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=22] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=22] Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=23] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=23] Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=24] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=24] Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Writing reads... INFO 2024-07-02 12:01:57 ReorderSam Writing reads... Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Processing All reads INFO 2024-07-02 12:01:57 ReorderSam Processing All reads Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Wrote 17 reads INFO 2024-07-02 12:01:57 ReorderSam Wrote 17 reads Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:57 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:57 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ValidateSamFile INFO 2024-07-02 12:01:57 ValidateSamFile Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorder15905476874616786059.bam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorder15905476874616786059.bam -IGNORE MISSING_TAG_NM Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:57.692 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:57.692 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:57.692 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:57.692 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:57.692 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:57.692 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:57.692 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:57.692 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:57 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder15905476874616786059.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:57 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder15905476874616786059.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:57 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:57 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0) STANDARD_OUT No errors found Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:57 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0) STANDARD_ERROR [Tue Jul 02 12:01:57 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ValidateSamFile Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0) STANDARD_ERROR INFO 2024-07-02 12:01:57 ValidateSamFile Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorder16783572829916719966.sam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorder16783572829916719966.sam -IGNORE MISSING_TAG_NM Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:57.838 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:57.838 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:57.838 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:57.838 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:57.839 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:57.839 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:57.839 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:57.839 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:57 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder16783572829916719966.sam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:57 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder16783572829916719966.sam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:57 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:57 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0) STANDARD_OUT No errors found Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:57 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0) STANDARD_ERROR [Tue Jul 02 12:01:57 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam INFO 2024-07-02 12:01:57 ReorderSam Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ReorderSam -INPUT /tmp/reorder16783572829916719966.sam -OUTPUT /tmp/reorder17740448203286423665.bam -SEQUENCE_DICTIONARY /tmp/reorder1856022718303457060.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE false ********** ReorderSam -INPUT /tmp/reorder16783572829916719966.sam -OUTPUT /tmp/reorder17740448203286423665.bam -SEQUENCE_DICTIONARY /tmp/reorder1856022718303457060.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE false Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:57.943 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:57.943 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:57.943 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:57.943 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:57.943 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:57.943 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:57.943 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:57.943 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:57 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorder16783572829916719966.sam OUTPUT=/tmp/reorder17740448203286423665.bam SEQUENCE_DICTIONARY=/tmp/reorder1856022718303457060.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:57 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorder16783572829916719966.sam OUTPUT=/tmp/reorder17740448203286423665.bam SEQUENCE_DICTIONARY=/tmp/reorder1856022718303457060.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:57 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SAM/BAM file INFO 2024-07-02 12:01:57 ReorderSam SAM/BAM file Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reference INFO 2024-07-02 12:01:57 ReorderSam Reference Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:57 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering SAM/BAM file: INFO 2024-07-02 12:01:57 ReorderSam Reordering SAM/BAM file: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=0] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=0] Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=1] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=1] Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=2] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=2] Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=3] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=3] Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr8 [index=7] to => ref contig chr8 [index=4] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr8 [index=7] to => ref contig chr8 [index=4] Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=5] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=5] Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=6] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=6] Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=7] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=7] Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=8] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=8] Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=9] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=9] Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=10] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=10] Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=11] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=11] Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr9 [index=8] to => ref contig chr9 [index=12] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr9 [index=8] to => ref contig chr9 [index=12] Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=13] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=13] Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=14] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=14] Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=15] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=15] Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=16] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=16] Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=17] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=17] Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr7 [index=6] to => ref contig chr7 [index=18] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr7 [index=6] to => ref contig chr7 [index=18] Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=19] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=19] Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=20] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=20] Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=21] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=21] Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=22] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=22] Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=23] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=23] Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=24] INFO 2024-07-02 12:01:57 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=24] Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Writing reads... INFO 2024-07-02 12:01:57 ReorderSam Writing reads... Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Processing All reads INFO 2024-07-02 12:01:57 ReorderSam Processing All reads Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:57 ReorderSam Wrote 17 reads INFO 2024-07-02 12:01:57 ReorderSam Wrote 17 reads Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:57 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:57 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ValidateSamFile INFO 2024-07-02 12:01:58 ValidateSamFile Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorder17740448203286423665.bam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorder17740448203286423665.bam -IGNORE MISSING_TAG_NM Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:58.110 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:58.110 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:58.110 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:58.110 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:58.110 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:58.110 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:58.110 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:58.110 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:58 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder17740448203286423665.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:58 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder17740448203286423665.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:58 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:58 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0) STANDARD_OUT No errors found Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:58 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0) STANDARD_ERROR [Tue Jul 02 12:01:58 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ValidateSamFile Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1) STANDARD_ERROR INFO 2024-07-02 12:01:58 ValidateSamFile Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorder4770184499093819011.sam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorder4770184499093819011.sam -IGNORE MISSING_TAG_NM Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:58.244 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:58.244 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:58.244 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:58.244 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:58.244 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:58.244 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:58.244 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:58.244 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:58 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder4770184499093819011.sam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:58 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder4770184499093819011.sam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:58 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:58 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1) STANDARD_OUT No errors found Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:58 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1) STANDARD_ERROR [Tue Jul 02 12:01:58 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam INFO 2024-07-02 12:01:58 ReorderSam Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ReorderSam -INPUT /tmp/reorder4770184499093819011.sam -OUTPUT /tmp/reorder10961553850315794677.bam -SEQUENCE_DICTIONARY /tmp/reorder16983398992511208569.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE false ********** ReorderSam -INPUT /tmp/reorder4770184499093819011.sam -OUTPUT /tmp/reorder10961553850315794677.bam -SEQUENCE_DICTIONARY /tmp/reorder16983398992511208569.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE false Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:58.351 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:58.351 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:58.351 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:58.351 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:58.352 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:58.352 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:58.352 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:58.352 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:58 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorder4770184499093819011.sam OUTPUT=/tmp/reorder10961553850315794677.bam SEQUENCE_DICTIONARY=/tmp/reorder16983398992511208569.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:58 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorder4770184499093819011.sam OUTPUT=/tmp/reorder10961553850315794677.bam SEQUENCE_DICTIONARY=/tmp/reorder16983398992511208569.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SAM/BAM file INFO 2024-07-02 12:01:58 ReorderSam SAM/BAM file Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Reference INFO 2024-07-02 12:01:58 ReorderSam Reference Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr1 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr1 LN=200000001 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr2 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr2 LN=200000001 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr3 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr3 LN=200000001 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr4 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr4 LN=200000001 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr5 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr5 LN=200000001 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr6 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr6 LN=200000001 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr7 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr7 LN=200000001 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr8 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr8 LN=200000001 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr9 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr9 LN=200000001 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr10 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr10 LN=200000001 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr11 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr11 LN=200000001 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr12 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr12 LN=200000001 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr13 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr13 LN=200000001 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr14 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr14 LN=200000001 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr15 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr15 LN=200000001 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr16 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr16 LN=200000001 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr17 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr17 LN=200000001 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr18 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr18 LN=200000001 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr19 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr19 LN=200000001 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr20 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr20 LN=200000001 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr21 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr21 LN=200000001 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr22 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr22 LN=200000001 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chrX LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chrX LN=200000001 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chrY LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chrY LN=200000001 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chrM LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chrM LN=200000001 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Reordering SAM/BAM file: INFO 2024-07-02 12:01:58 ReorderSam Reordering SAM/BAM file: Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ERROR 2024-07-02 12:01:58 ReorderSam ERROR 2024-07-02 12:01:58 ReorderSam Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: picard.PicardException: Discordant contig lengths: read chr1 LN=200000000, ref chr1 LN=200000001 picard.PicardException: Discordant contig lengths: read chr1 LN=200000000, ref chr1 LN=200000001 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:257) at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:257) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSam.doWork(ReorderSam.java:137) at picard.sam.ReorderSam.doWork(ReorderSam.java:137) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183) at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSamTest.TestsWithoutIndex(ReorderSamTest.java:159) at picard.sam.ReorderSamTest.TestsWithoutIndex(ReorderSamTest.java:159) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:58 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:58 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ValidateSamFile Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1) STANDARD_ERROR INFO 2024-07-02 12:01:58 ValidateSamFile Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorder17335248647910909975.sam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorder17335248647910909975.sam -IGNORE MISSING_TAG_NM Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:58.514 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:58.514 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:58.514 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:58.514 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:58.514 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:58.514 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:58.514 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:58.514 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:58 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder17335248647910909975.sam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:58 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder17335248647910909975.sam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:58 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:58 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1) STANDARD_OUT No errors found Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:58 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1) STANDARD_ERROR [Tue Jul 02 12:01:58 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam INFO 2024-07-02 12:01:58 ReorderSam Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ReorderSam -INPUT /tmp/reorder17335248647910909975.sam -OUTPUT /tmp/reorder5311223459978950067.bam -SEQUENCE_DICTIONARY /tmp/reorder16423155639933372610.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE true ********** ReorderSam -INPUT /tmp/reorder17335248647910909975.sam -OUTPUT /tmp/reorder5311223459978950067.bam -SEQUENCE_DICTIONARY /tmp/reorder16423155639933372610.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE true Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:58.621 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:58.621 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:58.621 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:58.621 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:58.621 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:58.621 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:58.621 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:58.621 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:58 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorder17335248647910909975.sam OUTPUT=/tmp/reorder5311223459978950067.bam SEQUENCE_DICTIONARY=/tmp/reorder16423155639933372610.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:58 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorder17335248647910909975.sam OUTPUT=/tmp/reorder5311223459978950067.bam SEQUENCE_DICTIONARY=/tmp/reorder16423155639933372610.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SAM/BAM file INFO 2024-07-02 12:01:58 ReorderSam SAM/BAM file Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Reference INFO 2024-07-02 12:01:58 ReorderSam Reference Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr1 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr1 LN=200000001 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr2 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr2 LN=200000001 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr3 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr3 LN=200000001 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr4 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr4 LN=200000001 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr5 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr5 LN=200000001 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr6 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr6 LN=200000001 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr7 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr7 LN=200000001 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr8 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr8 LN=200000001 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr9 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr9 LN=200000001 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr10 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr10 LN=200000001 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr11 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr11 LN=200000001 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr12 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr12 LN=200000001 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr13 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr13 LN=200000001 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr14 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr14 LN=200000001 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr15 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr15 LN=200000001 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr16 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr16 LN=200000001 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr17 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr17 LN=200000001 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr18 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr18 LN=200000001 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr19 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr19 LN=200000001 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr20 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr20 LN=200000001 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr21 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr21 LN=200000001 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr22 LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chr22 LN=200000001 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chrX LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chrX LN=200000001 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chrY LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chrY LN=200000001 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chrM LN=200000001 INFO 2024-07-02 12:01:58 ReorderSam SN=chrM LN=200000001 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Reordering SAM/BAM file: INFO 2024-07-02 12:01:58 ReorderSam Reordering SAM/BAM file: Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: ERROR 2024-07-02 12:01:58 ReorderSam ERROR 2024-07-02 12:01:58 ReorderSam Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: picard.PicardException: Discordant contig lengths: read chr1 LN=200000000, ref chr1 LN=200000001 picard.PicardException: Discordant contig lengths: read chr1 LN=200000000, ref chr1 LN=200000001 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:257) at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:257) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSam.doWork(ReorderSam.java:137) at picard.sam.ReorderSam.doWork(ReorderSam.java:137) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183) at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSamTest.TestsWithoutIndex(ReorderSamTest.java:159) at picard.sam.ReorderSamTest.TestsWithoutIndex(ReorderSamTest.java:159) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:58 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:58 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null)], true, 1)(picard.sam.ReorderSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ValidateSamFile Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0) STANDARD_ERROR INFO 2024-07-02 12:01:58 ValidateSamFile Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorder5027256001095821416.sam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorder5027256001095821416.sam -IGNORE MISSING_TAG_NM Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:58.785 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:58.785 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:58.785 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:58.785 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:58.786 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:58.786 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:58.786 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:58.786 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:58 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder5027256001095821416.sam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:58 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder5027256001095821416.sam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:58 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:58 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0) STANDARD_OUT No errors found Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:58 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0) STANDARD_ERROR [Tue Jul 02 12:01:58 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam INFO 2024-07-02 12:01:58 ReorderSam Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ReorderSam -INPUT /tmp/reorder5027256001095821416.sam -OUTPUT /tmp/reorder8734740495339144189.bam -SEQUENCE_DICTIONARY /tmp/reorder10093082045576575818.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE true ********** ReorderSam -INPUT /tmp/reorder5027256001095821416.sam -OUTPUT /tmp/reorder8734740495339144189.bam -SEQUENCE_DICTIONARY /tmp/reorder10093082045576575818.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE true Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:58.876 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:58.876 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:58.876 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:58.876 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:58.889 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:58.889 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:58.889 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:58.889 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:58 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorder5027256001095821416.sam OUTPUT=/tmp/reorder8734740495339144189.bam SEQUENCE_DICTIONARY=/tmp/reorder10093082045576575818.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:58 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorder5027256001095821416.sam OUTPUT=/tmp/reorder8734740495339144189.bam SEQUENCE_DICTIONARY=/tmp/reorder10093082045576575818.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:58 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SAM/BAM file INFO 2024-07-02 12:01:58 ReorderSam SAM/BAM file Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Reference INFO 2024-07-02 12:01:58 ReorderSam Reference Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:58 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Reordering SAM/BAM file: INFO 2024-07-02 12:01:58 ReorderSam Reordering SAM/BAM file: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=0] INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=0] Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=1] INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=1] Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=2] INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=2] Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=3] INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=3] Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=4] INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=4] Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=5] INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=5] Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=6] INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=6] Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=7] INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=7] Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=8] INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=8] Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=9] INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=9] Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=10] INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=10] Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=11] INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=11] Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=12] INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=12] Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=13] INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=13] Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=14] INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=14] Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=15] INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=15] Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=16] INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=16] Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=17] INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=17] Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=18] INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=18] Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=19] INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=19] Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=20] INFO 2024-07-02 12:01:58 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=20] Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Writing reads... INFO 2024-07-02 12:01:58 ReorderSam Writing reads... Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Processing All reads INFO 2024-07-02 12:01:58 ReorderSam Processing All reads Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:58 ReorderSam Wrote 17 reads INFO 2024-07-02 12:01:58 ReorderSam Wrote 17 reads Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:58 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:58 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ValidateSamFile INFO 2024-07-02 12:01:59 ValidateSamFile Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorder8734740495339144189.bam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorder8734740495339144189.bam -IGNORE MISSING_TAG_NM Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.050 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:59.050 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.050 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:59.050 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.051 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:59.051 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.051 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:59.051 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder8734740495339144189.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:59 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder8734740495339144189.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0) STANDARD_OUT No errors found Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0) STANDARD_ERROR [Tue Jul 02 12:01:59 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ValidateSamFile Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1) STANDARD_ERROR INFO 2024-07-02 12:01:59 ValidateSamFile Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorder8874496714388364673.sam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorder8874496714388364673.sam -IGNORE MISSING_TAG_NM Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.135 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:59.135 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.135 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:59.135 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.135 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:59.135 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.135 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:59.135 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder8874496714388364673.sam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:59 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder8874496714388364673.sam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1) STANDARD_OUT No errors found Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1) STANDARD_ERROR [Tue Jul 02 12:01:59 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam INFO 2024-07-02 12:01:59 ReorderSam Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ReorderSam -INPUT /tmp/reorder8874496714388364673.sam -OUTPUT /tmp/reorder2887824803422244566.bam -SEQUENCE_DICTIONARY /tmp/reorder15149099616361034435.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE false ********** ReorderSam -INPUT /tmp/reorder8874496714388364673.sam -OUTPUT /tmp/reorder2887824803422244566.bam -SEQUENCE_DICTIONARY /tmp/reorder15149099616361034435.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE false Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.208 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:59.208 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.208 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:59.208 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.208 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:59.208 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.208 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:59.208 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorder8874496714388364673.sam OUTPUT=/tmp/reorder2887824803422244566.bam SEQUENCE_DICTIONARY=/tmp/reorder15149099616361034435.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:59 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorder8874496714388364673.sam OUTPUT=/tmp/reorder2887824803422244566.bam SEQUENCE_DICTIONARY=/tmp/reorder15149099616361034435.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SAM/BAM file INFO 2024-07-02 12:01:59 ReorderSam SAM/BAM file Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reference INFO 2024-07-02 12:01:59 ReorderSam Reference Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering SAM/BAM file: INFO 2024-07-02 12:01:59 ReorderSam Reordering SAM/BAM file: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=0] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=0] Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=1] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=1] Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=2] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=2] Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=3] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=3] Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=4] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=4] Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=5] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=5] Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=6] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=6] Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=7] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=7] Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=8] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=8] Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=9] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=9] Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=10] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=10] Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=11] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=11] Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=12] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=12] Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=13] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=13] Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=14] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=14] Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=15] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=15] Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=16] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=16] Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=17] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=17] Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=18] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=18] Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=19] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=19] Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=20] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=20] Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ERROR 2024-07-02 12:01:59 ReorderSam ERROR 2024-07-02 12:01:59 ReorderSam Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: picard.PicardException: New reference sequence does not contain a matching contig for chr6 picard.PicardException: New reference sequence does not contain a matching contig for chr6 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:273) at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:273) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSam.doWork(ReorderSam.java:137) at picard.sam.ReorderSam.doWork(ReorderSam.java:137) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183) at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSamTest.TestsWithoutIndex(ReorderSamTest.java:159) at picard.sam.ReorderSamTest.TestsWithoutIndex(ReorderSamTest.java:159) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:59 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ValidateSamFile Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0) STANDARD_ERROR INFO 2024-07-02 12:01:59 ValidateSamFile Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorder13040155744039281468.sam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorder13040155744039281468.sam -IGNORE MISSING_TAG_NM Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.300 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:59.300 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.300 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:59.300 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.300 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:59.300 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.300 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:59.300 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder13040155744039281468.sam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:59 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder13040155744039281468.sam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0) STANDARD_OUT No errors found Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0) STANDARD_ERROR [Tue Jul 02 12:01:59 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam INFO 2024-07-02 12:01:59 ReorderSam Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ReorderSam -INPUT /tmp/reorder13040155744039281468.sam -OUTPUT /tmp/reorder8864300693070056818.bam -SEQUENCE_DICTIONARY /tmp/reorder13485990569517657844.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE true ********** ReorderSam -INPUT /tmp/reorder13040155744039281468.sam -OUTPUT /tmp/reorder8864300693070056818.bam -SEQUENCE_DICTIONARY /tmp/reorder13485990569517657844.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE true Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.406 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:59.406 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.406 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:59.406 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.406 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:59.406 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.406 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:59.406 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorder13040155744039281468.sam OUTPUT=/tmp/reorder8864300693070056818.bam SEQUENCE_DICTIONARY=/tmp/reorder13485990569517657844.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:59 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorder13040155744039281468.sam OUTPUT=/tmp/reorder8864300693070056818.bam SEQUENCE_DICTIONARY=/tmp/reorder13485990569517657844.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SAM/BAM file INFO 2024-07-02 12:01:59 ReorderSam SAM/BAM file Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reference INFO 2024-07-02 12:01:59 ReorderSam Reference Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering SAM/BAM file: INFO 2024-07-02 12:01:59 ReorderSam Reordering SAM/BAM file: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=0] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=0] Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=1] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=1] Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=2] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=2] Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=3] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=3] Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=4] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=4] Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=5] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=5] Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=6] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=6] Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=7] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=7] Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=8] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=8] Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=9] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=9] Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=10] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=10] Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=11] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=11] Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=12] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=12] Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=13] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=13] Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=14] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=14] Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=15] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=15] Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=16] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=16] Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=17] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=17] Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=18] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=18] Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=19] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=19] Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=20] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=20] Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=21] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=21] Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Writing reads... INFO 2024-07-02 12:01:59 ReorderSam Writing reads... Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Processing All reads INFO 2024-07-02 12:01:59 ReorderSam Processing All reads Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Wrote 17 reads INFO 2024-07-02 12:01:59 ReorderSam Wrote 17 reads Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:59 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ValidateSamFile INFO 2024-07-02 12:01:59 ValidateSamFile Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorder8864300693070056818.bam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorder8864300693070056818.bam -IGNORE MISSING_TAG_NM Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.545 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:59.545 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.545 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:59.545 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.546 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:59.546 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.546 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:59.546 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder8864300693070056818.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:59 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder8864300693070056818.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0) STANDARD_OUT No errors found Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0) STANDARD_ERROR [Tue Jul 02 12:01:59 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ValidateSamFile Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1) STANDARD_ERROR INFO 2024-07-02 12:01:59 ValidateSamFile Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorder13391295189488841634.sam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorder13391295189488841634.sam -IGNORE MISSING_TAG_NM Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.683 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:59.683 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.683 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:59.683 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.683 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:59.683 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.683 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:59.683 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder13391295189488841634.sam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:59 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder13391295189488841634.sam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1) STANDARD_OUT No errors found Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1) STANDARD_ERROR [Tue Jul 02 12:01:59 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam INFO 2024-07-02 12:01:59 ReorderSam Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ReorderSam -INPUT /tmp/reorder13391295189488841634.sam -OUTPUT /tmp/reorder5593496422227048405.bam -SEQUENCE_DICTIONARY /tmp/reorder11932262429041535910.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE false ********** ReorderSam -INPUT /tmp/reorder13391295189488841634.sam -OUTPUT /tmp/reorder5593496422227048405.bam -SEQUENCE_DICTIONARY /tmp/reorder11932262429041535910.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE false Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.771 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:59.771 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.771 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:59.771 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.771 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:59.771 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.771 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:59.771 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorder13391295189488841634.sam OUTPUT=/tmp/reorder5593496422227048405.bam SEQUENCE_DICTIONARY=/tmp/reorder11932262429041535910.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:59 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorder13391295189488841634.sam OUTPUT=/tmp/reorder5593496422227048405.bam SEQUENCE_DICTIONARY=/tmp/reorder11932262429041535910.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SAM/BAM file INFO 2024-07-02 12:01:59 ReorderSam SAM/BAM file Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reference INFO 2024-07-02 12:01:59 ReorderSam Reference Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering SAM/BAM file: INFO 2024-07-02 12:01:59 ReorderSam Reordering SAM/BAM file: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=0] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=0] Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=1] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=1] Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=2] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=2] Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=3] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=3] Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=4] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=4] Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=5] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=5] Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=6] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=6] Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=7] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=7] Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=8] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=8] Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=9] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=9] Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=10] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=10] Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=11] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=11] Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=12] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=12] Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=13] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=13] Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=14] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=14] Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=15] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=15] Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=16] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=16] Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=17] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=17] Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=18] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=18] Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=19] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=19] Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=20] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=20] Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=21] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=21] Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ERROR 2024-07-02 12:01:59 ReorderSam ERROR 2024-07-02 12:01:59 ReorderSam Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: picard.PicardException: New reference sequence does not contain a matching contig for chr7 picard.PicardException: New reference sequence does not contain a matching contig for chr7 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:273) at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:273) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSam.doWork(ReorderSam.java:137) at picard.sam.ReorderSam.doWork(ReorderSam.java:137) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183) at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSamTest.TestsWithoutIndex(ReorderSamTest.java:159) at picard.sam.ReorderSamTest.TestsWithoutIndex(ReorderSamTest.java:159) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:59 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ValidateSamFile Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0) STANDARD_ERROR INFO 2024-07-02 12:01:59 ValidateSamFile Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorder14471642224540673750.sam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorder14471642224540673750.sam -IGNORE MISSING_TAG_NM Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.878 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:59.878 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.878 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:59.878 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.878 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:59.878 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.878 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:59.878 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder14471642224540673750.sam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:59 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder14471642224540673750.sam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:01:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:01:59 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0) STANDARD_OUT No errors found Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0) STANDARD_ERROR [Tue Jul 02 12:01:59 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam INFO 2024-07-02 12:01:59 ReorderSam Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ReorderSam -INPUT /tmp/reorder14471642224540673750.sam -OUTPUT /tmp/reorder3901178015115893799.bam -SEQUENCE_DICTIONARY /tmp/reorder1955348726342431290.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE true ********** ReorderSam -INPUT /tmp/reorder14471642224540673750.sam -OUTPUT /tmp/reorder3901178015115893799.bam -SEQUENCE_DICTIONARY /tmp/reorder1955348726342431290.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE true Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.947 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:59.947 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.947 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:59.947 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.947 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:01:59.947 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:01:59.947 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:01:59.947 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorder14471642224540673750.sam OUTPUT=/tmp/reorder3901178015115893799.bam SEQUENCE_DICTIONARY=/tmp/reorder1955348726342431290.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:01:59 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorder14471642224540673750.sam OUTPUT=/tmp/reorder3901178015115893799.bam SEQUENCE_DICTIONARY=/tmp/reorder1955348726342431290.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:01:59 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SAM/BAM file INFO 2024-07-02 12:01:59 ReorderSam SAM/BAM file Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reference INFO 2024-07-02 12:01:59 ReorderSam Reference Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=test3 LN=100 INFO 2024-07-02 12:01:59 ReorderSam SN=test3 LN=100 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=test1 LN=100 INFO 2024-07-02 12:01:59 ReorderSam SN=test1 LN=100 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=test4 LN=100 INFO 2024-07-02 12:01:59 ReorderSam SN=test4 LN=100 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=test2 LN=100 INFO 2024-07-02 12:01:59 ReorderSam SN=test2 LN=100 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:01:59 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering SAM/BAM file: INFO 2024-07-02 12:01:59 ReorderSam Reordering SAM/BAM file: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=1] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=1] Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=2] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=2] Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=3] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=3] Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=4] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=4] Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=5] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=5] Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr8 [index=7] to => ref contig chr8 [index=6] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr8 [index=7] to => ref contig chr8 [index=6] Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=7] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=7] Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=8] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=8] Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=10] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=10] Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=13] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=13] Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=14] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=14] Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr7 [index=6] to => ref contig chr7 [index=15] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr7 [index=6] to => ref contig chr7 [index=15] Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=16] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=16] Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr9 [index=8] to => ref contig chr9 [index=17] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr9 [index=8] to => ref contig chr9 [index=17] Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=18] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=18] Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=19] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=19] Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=20] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=20] Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=21] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=21] Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=22] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=22] Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=23] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=23] Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=24] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=24] Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=25] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=25] Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=26] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=26] Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=27] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=27] Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=28] INFO 2024-07-02 12:01:59 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=28] Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Writing reads... INFO 2024-07-02 12:01:59 ReorderSam Writing reads... Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Processing All reads INFO 2024-07-02 12:01:59 ReorderSam Processing All reads Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:01:59 ReorderSam Wrote 17 reads INFO 2024-07-02 12:01:59 ReorderSam Wrote 17 reads Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:01:59 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:01:59 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ValidateSamFile INFO 2024-07-02 12:02:00 ValidateSamFile Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorder3901178015115893799.bam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorder3901178015115893799.bam -IGNORE MISSING_TAG_NM Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:00.039 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:00.039 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:00.039 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:00.039 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:00.039 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:00.039 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:00.039 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:00.039 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:02:00 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder3901178015115893799.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:00 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder3901178015115893799.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:02:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:02:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:02:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0) STANDARD_OUT No errors found Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:02:00 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0) STANDARD_ERROR [Tue Jul 02 12:02:00 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ValidateSamFile Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0) STANDARD_ERROR INFO 2024-07-02 12:02:00 ValidateSamFile Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorder15076148715666378213.sam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorder15076148715666378213.sam -IGNORE MISSING_TAG_NM Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:00.138 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:00.138 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:00.138 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:00.138 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:00.138 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:00.138 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:00.138 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:00.138 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:02:00 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder15076148715666378213.sam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:00 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder15076148715666378213.sam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:02:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:02:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:02:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0) STANDARD_OUT No errors found Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:02:00 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0) STANDARD_ERROR [Tue Jul 02 12:02:00 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam INFO 2024-07-02 12:02:00 ReorderSam Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ReorderSam -INPUT /tmp/reorder15076148715666378213.sam -OUTPUT /tmp/reorder5240261381670413420.bam -SEQUENCE_DICTIONARY /tmp/reorder211171059834880084.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE false ********** ReorderSam -INPUT /tmp/reorder15076148715666378213.sam -OUTPUT /tmp/reorder5240261381670413420.bam -SEQUENCE_DICTIONARY /tmp/reorder211171059834880084.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE false Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:00.192 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:00.192 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:00.192 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:00.192 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:00.193 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:00.193 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:00.193 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:00.193 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:02:00 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorder15076148715666378213.sam OUTPUT=/tmp/reorder5240261381670413420.bam SEQUENCE_DICTIONARY=/tmp/reorder211171059834880084.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:00 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorder15076148715666378213.sam OUTPUT=/tmp/reorder5240261381670413420.bam SEQUENCE_DICTIONARY=/tmp/reorder211171059834880084.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:02:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SAM/BAM file INFO 2024-07-02 12:02:00 ReorderSam SAM/BAM file Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reference INFO 2024-07-02 12:02:00 ReorderSam Reference Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=test3 LN=100 INFO 2024-07-02 12:02:00 ReorderSam SN=test3 LN=100 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=test1 LN=100 INFO 2024-07-02 12:02:00 ReorderSam SN=test1 LN=100 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=test4 LN=100 INFO 2024-07-02 12:02:00 ReorderSam SN=test4 LN=100 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=test2 LN=100 INFO 2024-07-02 12:02:00 ReorderSam SN=test2 LN=100 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering SAM/BAM file: INFO 2024-07-02 12:02:00 ReorderSam Reordering SAM/BAM file: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=1] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=1] Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=2] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=2] Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=3] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=3] Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=4] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=4] Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=5] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=5] Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr8 [index=7] to => ref contig chr8 [index=6] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr8 [index=7] to => ref contig chr8 [index=6] Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=7] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr2 [index=1] to => ref contig chr2 [index=7] Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=8] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=8] Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=10] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr1 [index=0] to => ref contig chr1 [index=10] Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=13] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=13] Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=14] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=14] Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr7 [index=6] to => ref contig chr7 [index=15] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr7 [index=6] to => ref contig chr7 [index=15] Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=16] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=16] Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr9 [index=8] to => ref contig chr9 [index=17] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr9 [index=8] to => ref contig chr9 [index=17] Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=18] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=18] Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=19] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=19] Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=20] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=20] Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=21] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=21] Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=22] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=22] Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=23] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=23] Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=24] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=24] Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=25] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=25] Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=26] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=26] Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=27] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=27] Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=28] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=28] Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Writing reads... INFO 2024-07-02 12:02:00 ReorderSam Writing reads... Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Processing All reads INFO 2024-07-02 12:02:00 ReorderSam Processing All reads Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Wrote 17 reads INFO 2024-07-02 12:02:00 ReorderSam Wrote 17 reads Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:02:00 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:00 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ValidateSamFile INFO 2024-07-02 12:02:00 ValidateSamFile Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorder5240261381670413420.bam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorder5240261381670413420.bam -IGNORE MISSING_TAG_NM Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:00.297 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:00.297 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:00.297 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:00.297 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:00.297 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:00.297 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:00.297 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:00.297 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:02:00 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder5240261381670413420.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:00 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder5240261381670413420.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:02:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:02:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:02:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0) STANDARD_OUT No errors found Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:02:00 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0) STANDARD_ERROR [Tue Jul 02 12:02:00 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null)], false, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ValidateSamFile Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0) STANDARD_ERROR INFO 2024-07-02 12:02:00 ValidateSamFile Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorder10563965939615985982.sam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorder10563965939615985982.sam -IGNORE MISSING_TAG_NM Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:00.424 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:00.424 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:00.424 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:00.424 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:00.437 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:00.437 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:00.437 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:00.437 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:02:00 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder10563965939615985982.sam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:00 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder10563965939615985982.sam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:02:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:02:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:02:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0) STANDARD_OUT No errors found Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:02:00 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0) STANDARD_ERROR [Tue Jul 02 12:02:00 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam INFO 2024-07-02 12:02:00 ReorderSam Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ReorderSam -INPUT /tmp/reorder10563965939615985982.sam -OUTPUT /tmp/reorder15868072159751309559.bam -SEQUENCE_DICTIONARY /tmp/reorder9787217056369445118.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE true ********** ReorderSam -INPUT /tmp/reorder10563965939615985982.sam -OUTPUT /tmp/reorder15868072159751309559.bam -SEQUENCE_DICTIONARY /tmp/reorder9787217056369445118.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE true Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:00.538 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:00.538 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:00.538 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:00.538 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:00.538 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:00.538 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:00.538 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:00.538 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:02:00 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorder10563965939615985982.sam OUTPUT=/tmp/reorder15868072159751309559.bam SEQUENCE_DICTIONARY=/tmp/reorder9787217056369445118.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:00 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorder10563965939615985982.sam OUTPUT=/tmp/reorder15868072159751309559.bam SEQUENCE_DICTIONARY=/tmp/reorder9787217056369445118.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=true ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:02:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SAM/BAM file INFO 2024-07-02 12:02:00 ReorderSam SAM/BAM file Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reference INFO 2024-07-02 12:02:00 ReorderSam Reference Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:02:00 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering SAM/BAM file: INFO 2024-07-02 12:02:00 ReorderSam Reordering SAM/BAM file: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=0] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=0] Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=1] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=1] Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=2] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=2] Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=3] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=3] Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr7 [index=6] to => ref contig chr7 [index=4] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr7 [index=6] to => ref contig chr7 [index=4] Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr8 [index=7] to => ref contig chr8 [index=5] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr8 [index=7] to => ref contig chr8 [index=5] Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr9 [index=8] to => ref contig chr9 [index=6] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr9 [index=8] to => ref contig chr9 [index=6] Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=7] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=7] Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=8] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=8] Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=9] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=9] Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=10] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=10] Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=11] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=11] Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=12] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=12] Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=13] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=13] Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=14] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=14] Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=15] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=15] Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=16] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=16] Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=17] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=17] Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=18] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=18] Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=19] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=19] Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=20] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=20] Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=21] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=21] Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=22] INFO 2024-07-02 12:02:00 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=22] Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Writing reads... INFO 2024-07-02 12:02:00 ReorderSam Writing reads... Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Processing All reads INFO 2024-07-02 12:02:00 ReorderSam Processing All reads Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ReorderSam Wrote 17 reads INFO 2024-07-02 12:02:00 ReorderSam Wrote 17 reads Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:02:00 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:00 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:00 ValidateSamFile INFO 2024-07-02 12:02:00 ValidateSamFile Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorder15868072159751309559.bam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorder15868072159751309559.bam -IGNORE MISSING_TAG_NM Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:00.860 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:00.860 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:00.860 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:00.860 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:00.860 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:00.860 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:00.860 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:00.860 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:02:00 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder15868072159751309559.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:00 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder15868072159751309559.bam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:02:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:00 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:02:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:02:00 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0) STANDARD_OUT No errors found Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:02:00 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0) STANDARD_ERROR [Tue Jul 02 12:02:00 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], true, 0)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ValidateSamFile Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1) STANDARD_ERROR INFO 2024-07-02 12:02:01 ValidateSamFile Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ValidateSamFile -I /tmp/reorder14146867347722495797.sam -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /tmp/reorder14146867347722495797.sam -IGNORE MISSING_TAG_NM Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:01.028 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:01.028 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:01.028 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:01.028 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:01.028 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:01.028 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:01.028 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:01.028 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:02:01 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder14146867347722495797.sam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:01 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/reorder14146867347722495797.sam IGNORE=[MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:02:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: WARNING 2024-07-02 12:02:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:02:01 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1) STANDARD_OUT No errors found Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:02:01 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ReorderSamTest.TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1) STANDARD_ERROR [Tue Jul 02 12:02:01 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam INFO 2024-07-02 12:02:01 ReorderSam Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ReorderSam -INPUT /tmp/reorder14146867347722495797.sam -OUTPUT /tmp/reorder9003108202091048960.bam -SEQUENCE_DICTIONARY /tmp/reorder2845101447906927981.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE false ********** ReorderSam -INPUT /tmp/reorder14146867347722495797.sam -OUTPUT /tmp/reorder9003108202091048960.bam -SEQUENCE_DICTIONARY /tmp/reorder2845101447906927981.dict -ALLOW_INCOMPLETE_DICT_CONCORDANCE false Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ********** ********** Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:01.298 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:01.298 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:01.299 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:01.299 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:01.299 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:01.299 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: 12:02:01.299 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:01.299 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:02:01 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorder14146867347722495797.sam OUTPUT=/tmp/reorder9003108202091048960.bam SEQUENCE_DICTIONARY=/tmp/reorder2845101447906927981.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:01 GMT+14:00 2024] ReorderSam INPUT=/tmp/reorder14146867347722495797.sam OUTPUT=/tmp/reorder9003108202091048960.bam SEQUENCE_DICTIONARY=/tmp/reorder2845101447906927981.dict ALLOW_INCOMPLETE_DICT_CONCORDANCE=false ALLOW_CONTIG_LENGTH_DISCORDANCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:02:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SAM/BAM file INFO 2024-07-02 12:02:01 ReorderSam SAM/BAM file Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr1 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr1 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr2 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr2 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam Reference INFO 2024-07-02 12:02:01 ReorderSam Reference Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr3 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr3 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr4 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr4 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr5 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr5 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr6 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr6 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr7 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr7 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr8 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr8 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr9 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr9 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr10 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr10 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr11 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr11 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr12 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr12 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr13 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr13 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr14 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr14 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr15 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr15 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr16 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr16 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr17 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr17 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr18 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr18 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr19 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr19 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr20 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr20 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr21 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr21 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chr22 LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chr22 LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chrX LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chrX LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chrY LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chrY LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam SN=chrM LN=200000000 INFO 2024-07-02 12:02:01 ReorderSam SN=chrM LN=200000000 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam Reordering SAM/BAM file: INFO 2024-07-02 12:02:01 ReorderSam Reordering SAM/BAM file: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=0] INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr3 [index=2] to => ref contig chr3 [index=0] Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=1] INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr4 [index=3] to => ref contig chr4 [index=1] Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=2] INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr5 [index=4] to => ref contig chr5 [index=2] Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=3] INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr6 [index=5] to => ref contig chr6 [index=3] Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr7 [index=6] to => ref contig chr7 [index=4] INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr7 [index=6] to => ref contig chr7 [index=4] Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr8 [index=7] to => ref contig chr8 [index=5] INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr8 [index=7] to => ref contig chr8 [index=5] Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr9 [index=8] to => ref contig chr9 [index=6] INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr9 [index=8] to => ref contig chr9 [index=6] Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=7] INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr10 [index=9] to => ref contig chr10 [index=7] Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=8] INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr11 [index=10] to => ref contig chr11 [index=8] Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=9] INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr12 [index=11] to => ref contig chr12 [index=9] Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=10] INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr13 [index=12] to => ref contig chr13 [index=10] Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=11] INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr14 [index=13] to => ref contig chr14 [index=11] Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=12] INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr15 [index=14] to => ref contig chr15 [index=12] Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=13] INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr16 [index=15] to => ref contig chr16 [index=13] Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=14] INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr17 [index=16] to => ref contig chr17 [index=14] Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=15] INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr18 [index=17] to => ref contig chr18 [index=15] Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=16] INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr19 [index=18] to => ref contig chr19 [index=16] Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=17] INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr20 [index=19] to => ref contig chr20 [index=17] Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=18] INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr21 [index=20] to => ref contig chr21 [index=18] Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=19] INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chr22 [index=21] to => ref contig chr22 [index=19] Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=20] INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chrX [index=22] to => ref contig chrX [index=20] Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=21] INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chrY [index=23] to => ref contig chrY [index=21] Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=22] INFO 2024-07-02 12:02:01 ReorderSam Reordering read contig chrM [index=24] to => ref contig chrM [index=22] Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: ERROR 2024-07-02 12:02:01 ReorderSam ERROR 2024-07-02 12:02:01 ReorderSam Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: picard.PicardException: New reference sequence does not contain a matching contig for chr1 picard.PicardException: New reference sequence does not contain a matching contig for chr1 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:273) at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:273) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSam.doWork(ReorderSam.java:137) at picard.sam.ReorderSam.doWork(ReorderSam.java:137) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:108) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:100) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183) at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at picard.sam.ReorderSamTest.TestsWithoutIndex(ReorderSamTest.java:159) at picard.sam.ReorderSamTest.TestsWithoutIndex(ReorderSamTest.java:159) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: [Tue Jul 02 12:02:01 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:01 GMT+14:00 2024] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes. Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5a78b911, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null)], false, 1)(picard.sam.ReorderSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method basicPositiveTests[0](null, true, true, true, true, true, null, null, [])(picard.sam.RevertSamTest) Test: Test method basicPositiveTests[0](null, true, true, true, true, true, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 RevertSam Gradle suite > Gradle test > picard.sam.RevertSamTest.basicPositiveTests[0](null, true, true, true, true, true, null, null, []) STANDARD_ERROR INFO 2024-07-02 12:02:01 RevertSam Test: Test method basicPositiveTests[0](null, true, true, true, true, true, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: Test: Test method basicPositiveTests[0](null, true, true, true, true, true, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method basicPositiveTests[0](null, true, true, true, true, true, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method basicPositiveTests[0](null, true, true, true, true, true, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method basicPositiveTests[0](null, true, true, true, true, true, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method basicPositiveTests[0](null, true, true, true, true, true, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method basicPositiveTests[0](null, true, true, true, true, true, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method basicPositiveTests[0](null, true, true, true, true, true, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method basicPositiveTests[0](null, true, true, true, true, true, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: ********** RevertSam -INPUT testdata/picard/sam/revert_sam_basic.sam -OUTPUT /tmp/pbuilder2/picardRevertSamTest10791024027621749570 -OUTPUT_BY_READGROUP true -REMOVE_DUPLICATE_INFORMATION true -REMOVE_ALIGNMENT_INFORMATION true -RESTORE_ORIGINAL_QUALITIES true ********** RevertSam -INPUT testdata/picard/sam/revert_sam_basic.sam -OUTPUT /tmp/pbuilder2/picardRevertSamTest10791024027621749570 -OUTPUT_BY_READGROUP true -REMOVE_DUPLICATE_INFORMATION true -REMOVE_ALIGNMENT_INFORMATION true -RESTORE_ORIGINAL_QUALITIES true Test: Test method basicPositiveTests[0](null, true, true, true, true, true, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method basicPositiveTests[0](null, true, true, true, true, true, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: Test: Test method basicPositiveTests[0](null, true, true, true, true, true, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: Test: Test method basicPositiveTests[0](null, true, true, true, true, true, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: 12:02:01.461 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:01.461 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method basicPositiveTests[0](null, true, true, true, true, true, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: 12:02:01.461 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:01.461 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method basicPositiveTests[0](null, true, true, true, true, true, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: 12:02:01.461 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:01.461 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method basicPositiveTests[0](null, true, true, true, true, true, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: 12:02:01.461 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:01.461 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method basicPositiveTests[0](null, true, true, true, true, true, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:01 GMT+14:00 2024] RevertSam INPUT=testdata/picard/sam/revert_sam_basic.sam OUTPUT=/tmp/pbuilder2/picardRevertSamTest10791024027621749570 OUTPUT_BY_READGROUP=true RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true RESTORE_HARDCLIPS=true OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic SORT_ORDER=queryname ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS] SANITIZE=false MAX_DISCARD_FRACTION=0.01 KEEP_FIRST_DUPLICATE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:01 GMT+14:00 2024] RevertSam INPUT=testdata/picard/sam/revert_sam_basic.sam OUTPUT=/tmp/pbuilder2/picardRevertSamTest10791024027621749570 OUTPUT_BY_READGROUP=true RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true RESTORE_HARDCLIPS=true OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic SORT_ORDER=queryname ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS] SANITIZE=false MAX_DISCARD_FRACTION=0.01 KEEP_FIRST_DUPLICATE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method basicPositiveTests[0](null, true, true, true, true, true, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method basicPositiveTests[0](null, true, true, true, true, true, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:01 GMT+14:00 2024] picard.sam.RevertSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:01 GMT+14:00 2024] picard.sam.RevertSam done. Elapsed time: 0.00 minutes. Test: Test method basicPositiveTests[0](null, true, true, true, true, true, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method basicPositiveTests[1](queryname, true, true, true, true, false, Hey,Dad!, null, [XT])(picard.sam.RevertSamTest) Test: Test method basicPositiveTests[1](queryname, true, true, true, true, false, Hey,Dad!, null, [XT])(picard.sam.RevertSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 RevertSam Gradle suite > Gradle test > picard.sam.RevertSamTest.basicPositiveTests[1](queryname, true, true, true, true, false, Hey,Dad!, null, [XT]) STANDARD_ERROR INFO 2024-07-02 12:02:01 RevertSam Test: Test method basicPositiveTests[1](queryname, true, true, true, true, false, Hey,Dad!, null, [XT])(picard.sam.RevertSamTest) produced standard out/err: Test: Test method basicPositiveTests[1](queryname, true, true, true, true, false, Hey,Dad!, null, [XT])(picard.sam.RevertSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method basicPositiveTests[1](queryname, true, true, true, true, false, Hey,Dad!, null, [XT])(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method basicPositiveTests[1](queryname, true, true, true, true, false, Hey,Dad!, null, [XT])(picard.sam.RevertSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method basicPositiveTests[1](queryname, true, true, true, true, false, Hey,Dad!, null, [XT])(picard.sam.RevertSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method basicPositiveTests[1](queryname, true, true, true, true, false, Hey,Dad!, null, [XT])(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method basicPositiveTests[1](queryname, true, true, true, true, false, Hey,Dad!, null, [XT])(picard.sam.RevertSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method basicPositiveTests[1](queryname, true, true, true, true, false, Hey,Dad!, null, [XT])(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method basicPositiveTests[1](queryname, true, true, true, true, false, Hey,Dad!, null, [XT])(picard.sam.RevertSamTest) produced standard out/err: ********** RevertSam -INPUT testdata/picard/sam/revert_sam_basic.sam -OUTPUT /tmp/reverted10657553099763301274.sam -SORT_ORDER queryname -REMOVE_DUPLICATE_INFORMATION true -REMOVE_ALIGNMENT_INFORMATION true -RESTORE_ORIGINAL_QUALITIES true -SAMPLE_ALIAS Hey,Dad! -ATTRIBUTE_TO_CLEAR XT ********** RevertSam -INPUT testdata/picard/sam/revert_sam_basic.sam -OUTPUT /tmp/reverted10657553099763301274.sam -SORT_ORDER queryname -REMOVE_DUPLICATE_INFORMATION true -REMOVE_ALIGNMENT_INFORMATION true -RESTORE_ORIGINAL_QUALITIES true -SAMPLE_ALIAS Hey,Dad! -ATTRIBUTE_TO_CLEAR XT Test: Test method basicPositiveTests[1](queryname, true, true, true, true, false, Hey,Dad!, null, [XT])(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method basicPositiveTests[1](queryname, true, true, true, true, false, Hey,Dad!, null, [XT])(picard.sam.RevertSamTest) produced standard out/err: Test: Test method basicPositiveTests[1](queryname, true, true, true, true, false, Hey,Dad!, null, [XT])(picard.sam.RevertSamTest) produced standard out/err: Test: Test method basicPositiveTests[1](queryname, true, true, true, true, false, Hey,Dad!, null, [XT])(picard.sam.RevertSamTest) produced standard out/err: 12:02:01.646 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:01.646 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method basicPositiveTests[1](queryname, true, true, true, true, false, Hey,Dad!, null, [XT])(picard.sam.RevertSamTest) produced standard out/err: 12:02:01.647 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:01.647 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method basicPositiveTests[1](queryname, true, true, true, true, false, Hey,Dad!, null, [XT])(picard.sam.RevertSamTest) produced standard out/err: 12:02:01.647 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:01.647 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method basicPositiveTests[1](queryname, true, true, true, true, false, Hey,Dad!, null, [XT])(picard.sam.RevertSamTest) produced standard out/err: 12:02:01.647 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:01.647 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method basicPositiveTests[1](queryname, true, true, true, true, false, Hey,Dad!, null, [XT])(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:01 GMT+14:00 2024] RevertSam INPUT=testdata/picard/sam/revert_sam_basic.sam OUTPUT=/tmp/reverted10657553099763301274.sam SORT_ORDER=queryname RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS, XT] SAMPLE_ALIAS=Hey,Dad! OUTPUT_BY_READGROUP=false RESTORE_HARDCLIPS=true OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic SANITIZE=false MAX_DISCARD_FRACTION=0.01 KEEP_FIRST_DUPLICATE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:01 GMT+14:00 2024] RevertSam INPUT=testdata/picard/sam/revert_sam_basic.sam OUTPUT=/tmp/reverted10657553099763301274.sam SORT_ORDER=queryname RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS, XT] SAMPLE_ALIAS=Hey,Dad! OUTPUT_BY_READGROUP=false RESTORE_HARDCLIPS=true OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic SANITIZE=false MAX_DISCARD_FRACTION=0.01 KEEP_FIRST_DUPLICATE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method basicPositiveTests[1](queryname, true, true, true, true, false, Hey,Dad!, null, [XT])(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method basicPositiveTests[1](queryname, true, true, true, true, false, Hey,Dad!, null, [XT])(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:01 GMT+14:00 2024] picard.sam.RevertSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:01 GMT+14:00 2024] picard.sam.RevertSam done. Elapsed time: 0.00 minutes. Test: Test method basicPositiveTests[1](queryname, true, true, true, true, false, Hey,Dad!, null, [XT])(picard.sam.RevertSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method basicPositiveTests[2](null, false, true, true, false, false, Hey,Dad!, NewLibraryName, [XT])(picard.sam.RevertSamTest) Test: Test method basicPositiveTests[2](null, false, true, true, false, false, Hey,Dad!, NewLibraryName, [XT])(picard.sam.RevertSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 RevertSam Gradle suite > Gradle test > picard.sam.RevertSamTest.basicPositiveTests[2](null, false, true, true, false, false, Hey,Dad!, NewLibraryName, [XT]) STANDARD_ERROR INFO 2024-07-02 12:02:01 RevertSam Test: Test method basicPositiveTests[2](null, false, true, true, false, false, Hey,Dad!, NewLibraryName, [XT])(picard.sam.RevertSamTest) produced standard out/err: Test: Test method basicPositiveTests[2](null, false, true, true, false, false, Hey,Dad!, NewLibraryName, [XT])(picard.sam.RevertSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method basicPositiveTests[2](null, false, true, true, false, false, Hey,Dad!, NewLibraryName, [XT])(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method basicPositiveTests[2](null, false, true, true, false, false, Hey,Dad!, NewLibraryName, [XT])(picard.sam.RevertSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method basicPositiveTests[2](null, false, true, true, false, false, Hey,Dad!, NewLibraryName, [XT])(picard.sam.RevertSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method basicPositiveTests[2](null, false, true, true, false, false, Hey,Dad!, NewLibraryName, [XT])(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method basicPositiveTests[2](null, false, true, true, false, false, Hey,Dad!, NewLibraryName, [XT])(picard.sam.RevertSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method basicPositiveTests[2](null, false, true, true, false, false, Hey,Dad!, NewLibraryName, [XT])(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method basicPositiveTests[2](null, false, true, true, false, false, Hey,Dad!, NewLibraryName, [XT])(picard.sam.RevertSamTest) produced standard out/err: ********** RevertSam -INPUT testdata/picard/sam/revert_sam_basic.sam -OUTPUT /tmp/reverted18072594307119073293.sam -REMOVE_DUPLICATE_INFORMATION false -REMOVE_ALIGNMENT_INFORMATION true -RESTORE_ORIGINAL_QUALITIES false -SAMPLE_ALIAS Hey,Dad! -LIBRARY_NAME NewLibraryName -ATTRIBUTE_TO_CLEAR XT ********** RevertSam -INPUT testdata/picard/sam/revert_sam_basic.sam -OUTPUT /tmp/reverted18072594307119073293.sam -REMOVE_DUPLICATE_INFORMATION false -REMOVE_ALIGNMENT_INFORMATION true -RESTORE_ORIGINAL_QUALITIES false -SAMPLE_ALIAS Hey,Dad! -LIBRARY_NAME NewLibraryName -ATTRIBUTE_TO_CLEAR XT Test: Test method basicPositiveTests[2](null, false, true, true, false, false, Hey,Dad!, NewLibraryName, [XT])(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method basicPositiveTests[2](null, false, true, true, false, false, Hey,Dad!, NewLibraryName, [XT])(picard.sam.RevertSamTest) produced standard out/err: Test: Test method basicPositiveTests[2](null, false, true, true, false, false, Hey,Dad!, NewLibraryName, [XT])(picard.sam.RevertSamTest) produced standard out/err: Test: Test method basicPositiveTests[2](null, false, true, true, false, false, Hey,Dad!, NewLibraryName, [XT])(picard.sam.RevertSamTest) produced standard out/err: 12:02:01.791 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:01.791 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method basicPositiveTests[2](null, false, true, true, false, false, Hey,Dad!, NewLibraryName, [XT])(picard.sam.RevertSamTest) produced standard out/err: 12:02:01.791 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:01.791 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method basicPositiveTests[2](null, false, true, true, false, false, Hey,Dad!, NewLibraryName, [XT])(picard.sam.RevertSamTest) produced standard out/err: 12:02:01.791 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:01.791 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method basicPositiveTests[2](null, false, true, true, false, false, Hey,Dad!, NewLibraryName, [XT])(picard.sam.RevertSamTest) produced standard out/err: 12:02:01.791 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:01.791 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method basicPositiveTests[2](null, false, true, true, false, false, Hey,Dad!, NewLibraryName, [XT])(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:01 GMT+14:00 2024] RevertSam INPUT=testdata/picard/sam/revert_sam_basic.sam OUTPUT=/tmp/reverted18072594307119073293.sam RESTORE_ORIGINAL_QUALITIES=false REMOVE_DUPLICATE_INFORMATION=false REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS, XT] SAMPLE_ALIAS=Hey,Dad! LIBRARY_NAME=NewLibraryName OUTPUT_BY_READGROUP=false RESTORE_HARDCLIPS=true OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic SORT_ORDER=queryname SANITIZE=false MAX_DISCARD_FRACTION=0.01 KEEP_FIRST_DUPLICATE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:01 GMT+14:00 2024] RevertSam INPUT=testdata/picard/sam/revert_sam_basic.sam OUTPUT=/tmp/reverted18072594307119073293.sam RESTORE_ORIGINAL_QUALITIES=false REMOVE_DUPLICATE_INFORMATION=false REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS, XT] SAMPLE_ALIAS=Hey,Dad! LIBRARY_NAME=NewLibraryName OUTPUT_BY_READGROUP=false RESTORE_HARDCLIPS=true OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic SORT_ORDER=queryname SANITIZE=false MAX_DISCARD_FRACTION=0.01 KEEP_FIRST_DUPLICATE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method basicPositiveTests[2](null, false, true, true, false, false, Hey,Dad!, NewLibraryName, [XT])(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method basicPositiveTests[2](null, false, true, true, false, false, Hey,Dad!, NewLibraryName, [XT])(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:01 GMT+14:00 2024] picard.sam.RevertSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:01 GMT+14:00 2024] picard.sam.RevertSam done. Elapsed time: 0.00 minutes. Test: Test method basicPositiveTests[2](null, false, true, true, false, false, Hey,Dad!, NewLibraryName, [XT])(picard.sam.RevertSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method basicPositiveTests[3](null, false, false, false, false, false, null, null, [])(picard.sam.RevertSamTest) Test: Test method basicPositiveTests[3](null, false, false, false, false, false, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: INFO 2024-07-02 12:02:01 RevertSam Gradle suite > Gradle test > picard.sam.RevertSamTest.basicPositiveTests[3](null, false, false, false, false, false, null, null, []) STANDARD_ERROR INFO 2024-07-02 12:02:01 RevertSam Test: Test method basicPositiveTests[3](null, false, false, false, false, false, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: Test: Test method basicPositiveTests[3](null, false, false, false, false, false, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method basicPositiveTests[3](null, false, false, false, false, false, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method basicPositiveTests[3](null, false, false, false, false, false, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method basicPositiveTests[3](null, false, false, false, false, false, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method basicPositiveTests[3](null, false, false, false, false, false, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method basicPositiveTests[3](null, false, false, false, false, false, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method basicPositiveTests[3](null, false, false, false, false, false, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method basicPositiveTests[3](null, false, false, false, false, false, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: ********** RevertSam -INPUT testdata/picard/sam/revert_sam_basic.sam -OUTPUT /tmp/reverted13697282281850516784.sam -REMOVE_DUPLICATE_INFORMATION false -REMOVE_ALIGNMENT_INFORMATION false -RESTORE_HARDCLIPS false -RESTORE_ORIGINAL_QUALITIES false ********** RevertSam -INPUT testdata/picard/sam/revert_sam_basic.sam -OUTPUT /tmp/reverted13697282281850516784.sam -REMOVE_DUPLICATE_INFORMATION false -REMOVE_ALIGNMENT_INFORMATION false -RESTORE_HARDCLIPS false -RESTORE_ORIGINAL_QUALITIES false Test: Test method basicPositiveTests[3](null, false, false, false, false, false, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method basicPositiveTests[3](null, false, false, false, false, false, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: Test: Test method basicPositiveTests[3](null, false, false, false, false, false, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: Test: Test method basicPositiveTests[3](null, false, false, false, false, false, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: 12:02:01.926 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:01.926 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method basicPositiveTests[3](null, false, false, false, false, false, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: 12:02:01.926 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:01.926 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method basicPositiveTests[3](null, false, false, false, false, false, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: 12:02:01.926 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:01.926 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method basicPositiveTests[3](null, false, false, false, false, false, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: 12:02:01.926 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:01.926 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method basicPositiveTests[3](null, false, false, false, false, false, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:01 GMT+14:00 2024] RevertSam INPUT=testdata/picard/sam/revert_sam_basic.sam OUTPUT=/tmp/reverted13697282281850516784.sam RESTORE_HARDCLIPS=false RESTORE_ORIGINAL_QUALITIES=false REMOVE_DUPLICATE_INFORMATION=false REMOVE_ALIGNMENT_INFORMATION=false OUTPUT_BY_READGROUP=false OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic SORT_ORDER=queryname ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS] SANITIZE=false MAX_DISCARD_FRACTION=0.01 KEEP_FIRST_DUPLICATE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:01 GMT+14:00 2024] RevertSam INPUT=testdata/picard/sam/revert_sam_basic.sam OUTPUT=/tmp/reverted13697282281850516784.sam RESTORE_HARDCLIPS=false RESTORE_ORIGINAL_QUALITIES=false REMOVE_DUPLICATE_INFORMATION=false REMOVE_ALIGNMENT_INFORMATION=false OUTPUT_BY_READGROUP=false OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic SORT_ORDER=queryname ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS] SANITIZE=false MAX_DISCARD_FRACTION=0.01 KEEP_FIRST_DUPLICATE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method basicPositiveTests[3](null, false, false, false, false, false, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:01 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method basicPositiveTests[3](null, false, false, false, false, false, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:01 GMT+14:00 2024] picard.sam.RevertSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:01 GMT+14:00 2024] picard.sam.RevertSam done. Elapsed time: 0.00 minutes. Test: Test method basicPositiveTests[3](null, false, false, false, false, false, null, null, [])(picard.sam.RevertSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testAssertAllReadGroupsMappedFailure(picard.sam.RevertSamTest) Running Test: Test method testAssertAllReadGroupsMappedSuccess(picard.sam.RevertSamTest) Running Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: USAGE: RevertSam [options] Gradle suite > Gradle test > picard.sam.RevertSamTest.testCommandLineHelp STANDARD_ERROR USAGE: RevertSam [options] Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#RevertSam Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#RevertSam Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Reverts SAM or BAM files to a previous state. This tool removes or restores certain properties of the SAM records, Reverts SAM or BAM files to a previous state. This tool removes or restores certain properties of the SAM records, Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: including alignment information, which can be used to produce an unmapped BAM (uBAM) from a previously aligned BAM. It including alignment information, which can be used to produce an unmapped BAM (uBAM) from a previously aligned BAM. It Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: is also capable of restoring the original quality scores of a BAM file that has already undergone base quality score is also capable of restoring the original quality scores of a BAM file that has already undergone base quality score Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: recalibration (BQSR) if theoriginal qualities were retained. recalibration (BQSR) if theoriginal qualities were retained. Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Examples Examples Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Example with single output: Example with single output: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: java -jar picard.jar RevertSam \ java -jar picard.jar RevertSam \ Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: O=reverted.bam O=reverted.bam Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Example outputting by read group with output map: Example outputting by read group with output map: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: java -jar picard.jar RevertSam \ java -jar picard.jar RevertSam \ Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: OUTPUT_BY_READGROUP=true \ OUTPUT_BY_READGROUP=true \ Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: OUTPUT_MAP=reverted_bam_paths.tsv OUTPUT_MAP=reverted_bam_paths.tsv Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Will output a BAM/SAM file per read group. Will output a BAM/SAM file per read group. Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Example outputting by read group without output map: Example outputting by read group without output map: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: java -jar picard.jar RevertSam \ java -jar picard.jar RevertSam \ Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: OUTPUT_BY_READGROUP=true \ OUTPUT_BY_READGROUP=true \ Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: O=/write/reverted/read/group/bams/in/this/dir O=/write/reverted/read/group/bams/in/this/dir Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Will output a BAM file per read group. Output format can be overridden with the OUTPUT_BY_READGROUP_FILE_FORMAT option. Will output a BAM file per read group. Output format can be overridden with the OUTPUT_BY_READGROUP_FILE_FORMAT option. Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Note: If the program fails due to a SAM validation error, consider setting the VALIDATION_STRINGENCY option to LENIENT Note: If the program fails due to a SAM validation error, consider setting the VALIDATION_STRINGENCY option to LENIENT Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: or SILENT if the failures are expected to be obviated by the reversion process (e.g. invalid alignment information will or SILENT if the failures are expected to be obviated by the reversion process (e.g. invalid alignment information will Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: be obviated when the REMOVE_ALIGNMENT_INFORMATION option is used). be obviated when the REMOVE_ALIGNMENT_INFORMATION option is used). Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Version: null Version: null Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Options: Options: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: --help --help Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: tools. tools. Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: I=File The input SAM/BAM file to revert the state of. Required. I=File The input SAM/BAM file to revert the state of. Required. Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: O=File The output SAM/BAM file to create, or an output directory if OUTPUT_BY_READGROUP is true. O=File The output SAM/BAM file to create, or an output directory if OUTPUT_BY_READGROUP is true. Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Required. Cannot be used in conjuction with option(s) OUTPUT_MAP (OM) Required. Cannot be used in conjuction with option(s) OUTPUT_MAP (OM) Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: OUTPUT_MAP=File OUTPUT_MAP=File Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: OM=File Tab separated file with two columns, READ_GROUP_ID and OUTPUT, providing file mapping only OM=File Tab separated file with two columns, READ_GROUP_ID and OUTPUT, providing file mapping only Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: used if OUTPUT_BY_READGROUP is true. Required. Cannot be used in conjuction with used if OUTPUT_BY_READGROUP is true. Required. Cannot be used in conjuction with Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: option(s) OUTPUT (O) option(s) OUTPUT (O) Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: OUTPUT_BY_READGROUP=Boolean OUTPUT_BY_READGROUP=Boolean Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: OBR=Boolean When true, outputs each read group in a separate file. Default value: false. This option OBR=Boolean When true, outputs each read group in a separate file. Default value: false. This option Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: can be set to 'null' to clear the default value. Possible values: {true, false} can be set to 'null' to clear the default value. Possible values: {true, false} Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: RESTORE_HARDCLIPS=Boolean RESTORE_HARDCLIPS=Boolean Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: RHC=Boolean When true, restores reads and qualities of records with hard-clips containing XB and XQ RHC=Boolean When true, restores reads and qualities of records with hard-clips containing XB and XQ Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: tags. Default value: true. This option can be set to 'null' to clear the default value. tags. Default value: true. This option can be set to 'null' to clear the default value. Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Possible values: {true, false} Possible values: {true, false} Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: OUTPUT_BY_READGROUP_FILE_FORMAT=FileType OUTPUT_BY_READGROUP_FILE_FORMAT=FileType Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: OBRFF=FileType When using OUTPUT_BY_READGROUP, the output file format can be set to a certain format. OBRFF=FileType When using OUTPUT_BY_READGROUP, the output file format can be set to a certain format. Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Default value: dynamic. This option can be set to 'null' to clear the default value. Default value: dynamic. This option can be set to 'null' to clear the default value. Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Possible values: { Possible values: { Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: sam (Generate SAM files.) sam (Generate SAM files.) Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: bam (Generate BAM files.) bam (Generate BAM files.) Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: cram (Generate CRAM files.) cram (Generate CRAM files.) Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: dynamic (Generate files based on the extention of INPUT.) dynamic (Generate files based on the extention of INPUT.) Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: } } Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: SO=SortOrder The sort order to create the reverted output file with. Default value: queryname. This SO=SortOrder The sort order to create the reverted output file with. Default value: queryname. This Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: option can be set to 'null' to clear the default value. Possible values: {unsorted, option can be set to 'null' to clear the default value. Possible values: {unsorted, Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: queryname, coordinate, duplicate, unknown} queryname, coordinate, duplicate, unknown} Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: RESTORE_ORIGINAL_QUALITIES=Boolean RESTORE_ORIGINAL_QUALITIES=Boolean Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: OQ=Boolean True to restore original qualities from the OQ field to the QUAL field if available. OQ=Boolean True to restore original qualities from the OQ field to the QUAL field if available. Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Default value: true. This option can be set to 'null' to clear the default value. Possible Default value: true. This option can be set to 'null' to clear the default value. Possible Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: values: {true, false} values: {true, false} Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: REMOVE_DUPLICATE_INFORMATION=Boolean REMOVE_DUPLICATE_INFORMATION=Boolean Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Remove duplicate read flags from all reads. Note that if this is false and Remove duplicate read flags from all reads. Note that if this is false and Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: REMOVE_ALIGNMENT_INFORMATION==true, the output may have the unusual but sometimes REMOVE_ALIGNMENT_INFORMATION==true, the output may have the unusual but sometimes Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: desirable trait of having unmapped reads that are marked as duplicates. Default value: desirable trait of having unmapped reads that are marked as duplicates. Default value: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: true. This option can be set to 'null' to clear the default value. Possible values: {true, true. This option can be set to 'null' to clear the default value. Possible values: {true, Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: false} false} Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: REMOVE_ALIGNMENT_INFORMATION=Boolean REMOVE_ALIGNMENT_INFORMATION=Boolean Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Remove all alignment information from the file. Default value: true. This option can be Remove all alignment information from the file. Default value: true. This option can be Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: set to 'null' to clear the default value. Possible values: {true, false} set to 'null' to clear the default value. Possible values: {true, false} Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: ATTRIBUTE_TO_CLEAR=String When removing alignment information, the set of optional tags to remove. Default value: ATTRIBUTE_TO_CLEAR=String When removing alignment information, the set of optional tags to remove. Default value: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: [NM, UQ, PG, MD, MQ, SA, MC, AS]. This option can be set to 'null' to clear the default [NM, UQ, PG, MD, MQ, SA, MC, AS]. This option can be set to 'null' to clear the default Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: value. This option may be specified 0 or more times. This option can be set to 'null' to value. This option may be specified 0 or more times. This option can be set to 'null' to Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: clear the default list. clear the default list. Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: SANITIZE=Boolean WARNING: This option is potentially destructive. If enabled will discard reads in order to SANITIZE=Boolean WARNING: This option is potentially destructive. If enabled will discard reads in order to Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: produce a consistent output BAM. Reads discarded include (but are not limited to) paired produce a consistent output BAM. Reads discarded include (but are not limited to) paired Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: reads with missing mates, duplicated records, records with mismatches in length of bases reads with missing mates, duplicated records, records with mismatches in length of bases Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: and qualities. This option can only be enabled if the output sort order is queryname and and qualities. This option can only be enabled if the output sort order is queryname and Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: will always cause sorting to occur. Default value: false. This option can be set to will always cause sorting to occur. Default value: false. This option can be set to Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: 'null' to clear the default value. Possible values: {true, false} 'null' to clear the default value. Possible values: {true, false} Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: MAX_DISCARD_FRACTION=Double If SANITIZE=true and higher than MAX_DISCARD_FRACTION reads are discarded due to MAX_DISCARD_FRACTION=Double If SANITIZE=true and higher than MAX_DISCARD_FRACTION reads are discarded due to Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: sanitization thenthe program will exit with an Exception instead of exiting cleanly. sanitization thenthe program will exit with an Exception instead of exiting cleanly. Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Output BAM will still be valid. Default value: 0.01. This option can be set to 'null' to Output BAM will still be valid. Default value: 0.01. This option can be set to 'null' to Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: clear the default value. clear the default value. Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: KEEP_FIRST_DUPLICATE=Boolean If SANITIZE=true keep the first record when we find more than one record with the same KEEP_FIRST_DUPLICATE=Boolean If SANITIZE=true keep the first record when we find more than one record with the same Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: name for R1/R2/unpaired reads respectively. For paired end reads, keeps only the first R1 name for R1/R2/unpaired reads respectively. For paired end reads, keeps only the first R1 Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: and R2 found respectively, and discards all unpaired reads. Duplicates do not refer to the and R2 found respectively, and discards all unpaired reads. Duplicates do not refer to the Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: duplicate flag in the FLAG field, but instead reads with the same name. Default value: duplicate flag in the FLAG field, but instead reads with the same name. Default value: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: false. This option can be set to 'null' to clear the default value. Possible values: false. This option can be set to 'null' to clear the default value. Possible values: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: {true, false} {true, false} Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: SAMPLE_ALIAS=String SAMPLE_ALIAS=String Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: ALIAS=String The sample alias to use in the reverted output file. This will override the existing ALIAS=String The sample alias to use in the reverted output file. This will override the existing Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: sample alias in the file and is used only if all the read groups in the input file have sample alias in the file and is used only if all the read groups in the input file have Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: the same sample alias. Default value: null. the same sample alias. Default value: null. Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: LIBRARY_NAME=String LIBRARY_NAME=String Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: LIB=String The library name to use in the reverted output file. This will override the existing LIB=String The library name to use in the reverted output file. This will override the existing Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: sample alias in the file and is used only if all the read groups in the input file have sample alias in the file and is used only if all the read groups in the input file have Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: the same library name. Default value: null. the same library name. Default value: null. Test: Test method testCommandLineHelp(picard.sam.RevertSamTest) produced standard out/err: Running Test: Test method testFilePathsWithMapFile(picard.sam.RevertSamTest) Running Test: Test method testFilePathsWithoutMapFile(picard.sam.RevertSamTest) Running Test: Test method testGetDefaultExtension(picard.sam.RevertSamTest) Running Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: INFO 2024-07-02 12:02:02 MergeBamAlignment Gradle suite > Gradle test > picard.sam.RevertSamTest.testHardClipRoundTrip STANDARD_ERROR INFO 2024-07-02 12:02:02 MergeBamAlignment Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/hardclip.unmapped.sam -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/hardclip.aligned.sam -OUTPUT /tmp/test-output-hard-clipped-round-trip-mba8109347594766918896.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta -HARD_CLIP_OVERLAPPING_READS true ********** MergeBamAlignment -UNMAPPED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/hardclip.unmapped.sam -ALIGNED_BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/hardclip.aligned.sam -OUTPUT /tmp/test-output-hard-clipped-round-trip-mba8109347594766918896.sam -REFERENCE_SEQUENCE /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta -HARD_CLIP_OVERLAPPING_READS true Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: 12:02:02.258 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:02.258 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: 12:02:02.259 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:02.259 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: 12:02:02.259 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:02.259 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: 12:02:02.259 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:02.259 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:02 GMT+14:00 2024] MergeBamAlignment UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/hardclip.unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/hardclip.aligned.sam] OUTPUT=/tmp/test-output-hard-clipped-round-trip-mba8109347594766918896.sam HARD_CLIP_OVERLAPPING_READS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta ADD_PG_TAG_TO_READS=true PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ] READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:02 GMT+14:00 2024] MergeBamAlignment UNMAPPED_BAM=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/hardclip.unmapped.sam ALIGNED_BAM=[/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/hardclip.aligned.sam] OUTPUT=/tmp/test-output-hard-clipped-round-trip-mba8109347594766918896.sam HARD_CLIP_OVERLAPPING_READS=true REFERENCE_SEQUENCE=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/cliptest.fasta ADD_PG_TAG_TO_READS=true PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_REVERSE=[OQ, U2] ATTRIBUTES_TO_REVERSE_COMPLEMENT=[E2, SQ] READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 MATCHING_DICTIONARY_TAGS=[M5, LN] UNMAPPED_READ_STRATEGY=DO_NOT_CHANGE VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: INFO 2024-07-02 12:02:02 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/hardclip.aligned.sam] INFO 2024-07-02 12:02:02 SamAlignmentMerger Processing SAM file(s): [/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/MergeBamAlignment/hardclip.aligned.sam] Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: INFO 2024-07-02 12:02:02 AbstractAlignmentMerger Wrote 10 alignment records and 0 unmapped reads. INFO 2024-07-02 12:02:02 AbstractAlignmentMerger Wrote 10 alignment records and 0 unmapped reads. Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:02 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:02 GMT+14:00 2024] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: INFO 2024-07-02 12:02:02 RevertSam INFO 2024-07-02 12:02:02 RevertSam Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: ********** RevertSam -I /tmp/test-output-hard-clipped-round-trip-mba8109347594766918896.sam -RESTORE_HARDCLIPS true -O /tmp/test-output-hard-clipped-round-trip-reverted9468939547388534343.sam ********** RevertSam -I /tmp/test-output-hard-clipped-round-trip-mba8109347594766918896.sam -RESTORE_HARDCLIPS true -O /tmp/test-output-hard-clipped-round-trip-reverted9468939547388534343.sam Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: 12:02:02.472 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:02.472 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: 12:02:02.472 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:02.472 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: 12:02:02.472 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:02.472 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: 12:02:02.472 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:02.472 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:02 GMT+14:00 2024] RevertSam INPUT=/tmp/test-output-hard-clipped-round-trip-mba8109347594766918896.sam OUTPUT=/tmp/test-output-hard-clipped-round-trip-reverted9468939547388534343.sam RESTORE_HARDCLIPS=true OUTPUT_BY_READGROUP=false OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic SORT_ORDER=queryname RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS] SANITIZE=false MAX_DISCARD_FRACTION=0.01 KEEP_FIRST_DUPLICATE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:02 GMT+14:00 2024] RevertSam INPUT=/tmp/test-output-hard-clipped-round-trip-mba8109347594766918896.sam OUTPUT=/tmp/test-output-hard-clipped-round-trip-reverted9468939547388534343.sam RESTORE_HARDCLIPS=true OUTPUT_BY_READGROUP=false OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic SORT_ORDER=queryname RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS] SANITIZE=false MAX_DISCARD_FRACTION=0.01 KEEP_FIRST_DUPLICATE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:02 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:02 GMT+14:00 2024] picard.sam.RevertSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:02 GMT+14:00 2024] picard.sam.RevertSam done. Elapsed time: 0.00 minutes. Test: Test method testHardClipRoundTrip(picard.sam.RevertSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testIsOutputMapHeaderValid(picard.sam.RevertSamTest) Running Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: INFO 2024-07-02 12:02:02 RevertSam Gradle suite > Gradle test > picard.sam.RevertSamTest.testMutexOutputMapVsOutput STANDARD_ERROR INFO 2024-07-02 12:02:02 RevertSam Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: ********** RevertSam -INPUT testdata/picard/sam/revert_sam_basic.sam -OUTPUT_BY_READGROUP true -OUTPUT /tmp/pbuilder2/picardRevertSamTest18254346263622724220 -OUTPUT_MAP testdata/picard/sam/revert_sam_valid_output_map.txt ********** RevertSam -INPUT testdata/picard/sam/revert_sam_basic.sam -OUTPUT_BY_READGROUP true -OUTPUT /tmp/pbuilder2/picardRevertSamTest18254346263622724220 -OUTPUT_MAP testdata/picard/sam/revert_sam_valid_output_map.txt Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: ERROR: Option 'OUTPUT' cannot be used in conjunction with option(s) OUTPUT_MAP ERROR: Option 'OUTPUT' cannot be used in conjunction with option(s) OUTPUT_MAP Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: USAGE: RevertSam [options] USAGE: RevertSam [options] Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#RevertSam Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#RevertSam Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Reverts SAM or BAM files to a previous state. This tool removes or restores certain properties of the SAM records, Reverts SAM or BAM files to a previous state. This tool removes or restores certain properties of the SAM records, Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: including alignment information, which can be used to produce an unmapped BAM (uBAM) from a previously aligned BAM. It including alignment information, which can be used to produce an unmapped BAM (uBAM) from a previously aligned BAM. It Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: is also capable of restoring the original quality scores of a BAM file that has already undergone base quality score is also capable of restoring the original quality scores of a BAM file that has already undergone base quality score Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: recalibration (BQSR) if theoriginal qualities were retained. recalibration (BQSR) if theoriginal qualities were retained. Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Examples Examples Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Example with single output: Example with single output: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: java -jar picard.jar RevertSam \ java -jar picard.jar RevertSam \ Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: O=reverted.bam O=reverted.bam Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Example outputting by read group with output map: Example outputting by read group with output map: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: java -jar picard.jar RevertSam \ java -jar picard.jar RevertSam \ Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: OUTPUT_BY_READGROUP=true \ OUTPUT_BY_READGROUP=true \ Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: OUTPUT_MAP=reverted_bam_paths.tsv OUTPUT_MAP=reverted_bam_paths.tsv Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Will output a BAM/SAM file per read group. Will output a BAM/SAM file per read group. Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Example outputting by read group without output map: Example outputting by read group without output map: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: java -jar picard.jar RevertSam \ java -jar picard.jar RevertSam \ Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: OUTPUT_BY_READGROUP=true \ OUTPUT_BY_READGROUP=true \ Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: O=/write/reverted/read/group/bams/in/this/dir O=/write/reverted/read/group/bams/in/this/dir Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Will output a BAM file per read group. Output format can be overridden with the OUTPUT_BY_READGROUP_FILE_FORMAT option. Will output a BAM file per read group. Output format can be overridden with the OUTPUT_BY_READGROUP_FILE_FORMAT option. Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Note: If the program fails due to a SAM validation error, consider setting the VALIDATION_STRINGENCY option to LENIENT Note: If the program fails due to a SAM validation error, consider setting the VALIDATION_STRINGENCY option to LENIENT Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: or SILENT if the failures are expected to be obviated by the reversion process (e.g. invalid alignment information will or SILENT if the failures are expected to be obviated by the reversion process (e.g. invalid alignment information will Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: be obviated when the REMOVE_ALIGNMENT_INFORMATION option is used). be obviated when the REMOVE_ALIGNMENT_INFORMATION option is used). Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Version: null Version: null Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Options: Options: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: --help --help Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: tools. tools. Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: I=File The input SAM/BAM file to revert the state of. Required. I=File The input SAM/BAM file to revert the state of. Required. Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: O=File The output SAM/BAM file to create, or an output directory if OUTPUT_BY_READGROUP is true. O=File The output SAM/BAM file to create, or an output directory if OUTPUT_BY_READGROUP is true. Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Required. Cannot be used in conjuction with option(s) OUTPUT_MAP (OM) Required. Cannot be used in conjuction with option(s) OUTPUT_MAP (OM) Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: OUTPUT_MAP=File OUTPUT_MAP=File Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: OM=File Tab separated file with two columns, READ_GROUP_ID and OUTPUT, providing file mapping only OM=File Tab separated file with two columns, READ_GROUP_ID and OUTPUT, providing file mapping only Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: used if OUTPUT_BY_READGROUP is true. Required. Cannot be used in conjuction with used if OUTPUT_BY_READGROUP is true. Required. Cannot be used in conjuction with Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: option(s) OUTPUT (O) option(s) OUTPUT (O) Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: OUTPUT_BY_READGROUP=Boolean OUTPUT_BY_READGROUP=Boolean Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: OBR=Boolean When true, outputs each read group in a separate file. Default value: false. This option OBR=Boolean When true, outputs each read group in a separate file. Default value: false. This option Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: can be set to 'null' to clear the default value. Possible values: {true, false} can be set to 'null' to clear the default value. Possible values: {true, false} Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: RESTORE_HARDCLIPS=Boolean RESTORE_HARDCLIPS=Boolean Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: RHC=Boolean When true, restores reads and qualities of records with hard-clips containing XB and XQ RHC=Boolean When true, restores reads and qualities of records with hard-clips containing XB and XQ Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: tags. Default value: true. This option can be set to 'null' to clear the default value. tags. Default value: true. This option can be set to 'null' to clear the default value. Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Possible values: {true, false} Possible values: {true, false} Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: OUTPUT_BY_READGROUP_FILE_FORMAT=FileType OUTPUT_BY_READGROUP_FILE_FORMAT=FileType Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: OBRFF=FileType When using OUTPUT_BY_READGROUP, the output file format can be set to a certain format. OBRFF=FileType When using OUTPUT_BY_READGROUP, the output file format can be set to a certain format. Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Default value: dynamic. This option can be set to 'null' to clear the default value. Default value: dynamic. This option can be set to 'null' to clear the default value. Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Possible values: { Possible values: { Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: sam (Generate SAM files.) sam (Generate SAM files.) Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: bam (Generate BAM files.) bam (Generate BAM files.) Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: cram (Generate CRAM files.) cram (Generate CRAM files.) Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: dynamic (Generate files based on the extention of INPUT.) dynamic (Generate files based on the extention of INPUT.) Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: } } Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: SO=SortOrder The sort order to create the reverted output file with. Default value: queryname. This SO=SortOrder The sort order to create the reverted output file with. Default value: queryname. This Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: option can be set to 'null' to clear the default value. Possible values: {unsorted, option can be set to 'null' to clear the default value. Possible values: {unsorted, Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: queryname, coordinate, duplicate, unknown} queryname, coordinate, duplicate, unknown} Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: RESTORE_ORIGINAL_QUALITIES=Boolean RESTORE_ORIGINAL_QUALITIES=Boolean Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: OQ=Boolean True to restore original qualities from the OQ field to the QUAL field if available. OQ=Boolean True to restore original qualities from the OQ field to the QUAL field if available. Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Default value: true. This option can be set to 'null' to clear the default value. Possible Default value: true. This option can be set to 'null' to clear the default value. Possible Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: values: {true, false} values: {true, false} Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: REMOVE_DUPLICATE_INFORMATION=Boolean REMOVE_DUPLICATE_INFORMATION=Boolean Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Remove duplicate read flags from all reads. Note that if this is false and Remove duplicate read flags from all reads. Note that if this is false and Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: REMOVE_ALIGNMENT_INFORMATION==true, the output may have the unusual but sometimes REMOVE_ALIGNMENT_INFORMATION==true, the output may have the unusual but sometimes Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: desirable trait of having unmapped reads that are marked as duplicates. Default value: desirable trait of having unmapped reads that are marked as duplicates. Default value: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: true. This option can be set to 'null' to clear the default value. Possible values: {true, true. This option can be set to 'null' to clear the default value. Possible values: {true, Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: false} false} Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: REMOVE_ALIGNMENT_INFORMATION=Boolean REMOVE_ALIGNMENT_INFORMATION=Boolean Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Remove all alignment information from the file. Default value: true. This option can be Remove all alignment information from the file. Default value: true. This option can be Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: set to 'null' to clear the default value. Possible values: {true, false} set to 'null' to clear the default value. Possible values: {true, false} Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: ATTRIBUTE_TO_CLEAR=String When removing alignment information, the set of optional tags to remove. Default value: ATTRIBUTE_TO_CLEAR=String When removing alignment information, the set of optional tags to remove. Default value: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: [NM, UQ, PG, MD, MQ, SA, MC, AS]. This option can be set to 'null' to clear the default [NM, UQ, PG, MD, MQ, SA, MC, AS]. This option can be set to 'null' to clear the default Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: value. This option may be specified 0 or more times. This option can be set to 'null' to value. This option may be specified 0 or more times. This option can be set to 'null' to Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: clear the default list. clear the default list. Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: SANITIZE=Boolean WARNING: This option is potentially destructive. If enabled will discard reads in order to SANITIZE=Boolean WARNING: This option is potentially destructive. If enabled will discard reads in order to Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: produce a consistent output BAM. Reads discarded include (but are not limited to) paired produce a consistent output BAM. Reads discarded include (but are not limited to) paired Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: reads with missing mates, duplicated records, records with mismatches in length of bases reads with missing mates, duplicated records, records with mismatches in length of bases Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: and qualities. This option can only be enabled if the output sort order is queryname and and qualities. This option can only be enabled if the output sort order is queryname and Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: will always cause sorting to occur. Default value: false. This option can be set to will always cause sorting to occur. Default value: false. This option can be set to Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: 'null' to clear the default value. Possible values: {true, false} 'null' to clear the default value. Possible values: {true, false} Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: MAX_DISCARD_FRACTION=Double If SANITIZE=true and higher than MAX_DISCARD_FRACTION reads are discarded due to MAX_DISCARD_FRACTION=Double If SANITIZE=true and higher than MAX_DISCARD_FRACTION reads are discarded due to Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: sanitization thenthe program will exit with an Exception instead of exiting cleanly. sanitization thenthe program will exit with an Exception instead of exiting cleanly. Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Output BAM will still be valid. Default value: 0.01. This option can be set to 'null' to Output BAM will still be valid. Default value: 0.01. This option can be set to 'null' to Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: clear the default value. clear the default value. Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: KEEP_FIRST_DUPLICATE=Boolean If SANITIZE=true keep the first record when we find more than one record with the same KEEP_FIRST_DUPLICATE=Boolean If SANITIZE=true keep the first record when we find more than one record with the same Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: name for R1/R2/unpaired reads respectively. For paired end reads, keeps only the first R1 name for R1/R2/unpaired reads respectively. For paired end reads, keeps only the first R1 Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: and R2 found respectively, and discards all unpaired reads. Duplicates do not refer to the and R2 found respectively, and discards all unpaired reads. Duplicates do not refer to the Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: duplicate flag in the FLAG field, but instead reads with the same name. Default value: duplicate flag in the FLAG field, but instead reads with the same name. Default value: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: false. This option can be set to 'null' to clear the default value. Possible values: false. This option can be set to 'null' to clear the default value. Possible values: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: {true, false} {true, false} Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: SAMPLE_ALIAS=String SAMPLE_ALIAS=String Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: ALIAS=String The sample alias to use in the reverted output file. This will override the existing ALIAS=String The sample alias to use in the reverted output file. This will override the existing Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: sample alias in the file and is used only if all the read groups in the input file have sample alias in the file and is used only if all the read groups in the input file have Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: the same sample alias. Default value: null. the same sample alias. Default value: null. Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: LIBRARY_NAME=String LIBRARY_NAME=String Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: LIB=String The library name to use in the reverted output file. This will override the existing LIB=String The library name to use in the reverted output file. This will override the existing Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: sample alias in the file and is used only if all the read groups in the input file have sample alias in the file and is used only if all the read groups in the input file have Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: the same library name. Default value: null. the same library name. Default value: null. Test: Test method testMutexOutputMapVsOutput(picard.sam.RevertSamTest) produced standard out/err: Running Test: Test method testNoInput(picard.sam.RevertSamTest) Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: ERROR: Option 'INPUT' is required. Gradle suite > Gradle test > picard.sam.RevertSamTest.testNoInput STANDARD_ERROR ERROR: Option 'INPUT' is required. Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: USAGE: RevertSam [options] USAGE: RevertSam [options] Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#RevertSam Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#RevertSam Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Reverts SAM or BAM files to a previous state. This tool removes or restores certain properties of the SAM records, Reverts SAM or BAM files to a previous state. This tool removes or restores certain properties of the SAM records, Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: including alignment information, which can be used to produce an unmapped BAM (uBAM) from a previously aligned BAM. It including alignment information, which can be used to produce an unmapped BAM (uBAM) from a previously aligned BAM. It Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: is also capable of restoring the original quality scores of a BAM file that has already undergone base quality score is also capable of restoring the original quality scores of a BAM file that has already undergone base quality score Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: recalibration (BQSR) if theoriginal qualities were retained. recalibration (BQSR) if theoriginal qualities were retained. Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Examples Examples Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Example with single output: Example with single output: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: java -jar picard.jar RevertSam \ java -jar picard.jar RevertSam \ Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: O=reverted.bam O=reverted.bam Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Example outputting by read group with output map: Example outputting by read group with output map: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: java -jar picard.jar RevertSam \ java -jar picard.jar RevertSam \ Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: OUTPUT_BY_READGROUP=true \ OUTPUT_BY_READGROUP=true \ Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: OUTPUT_MAP=reverted_bam_paths.tsv OUTPUT_MAP=reverted_bam_paths.tsv Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Will output a BAM/SAM file per read group. Will output a BAM/SAM file per read group. Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Example outputting by read group without output map: Example outputting by read group without output map: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: java -jar picard.jar RevertSam \ java -jar picard.jar RevertSam \ Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: I=input.bam \ I=input.bam \ Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: OUTPUT_BY_READGROUP=true \ OUTPUT_BY_READGROUP=true \ Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: O=/write/reverted/read/group/bams/in/this/dir O=/write/reverted/read/group/bams/in/this/dir Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Will output a BAM file per read group. Output format can be overridden with the OUTPUT_BY_READGROUP_FILE_FORMAT option. Will output a BAM file per read group. Output format can be overridden with the OUTPUT_BY_READGROUP_FILE_FORMAT option. Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Note: If the program fails due to a SAM validation error, consider setting the VALIDATION_STRINGENCY option to LENIENT Note: If the program fails due to a SAM validation error, consider setting the VALIDATION_STRINGENCY option to LENIENT Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: or SILENT if the failures are expected to be obviated by the reversion process (e.g. invalid alignment information will or SILENT if the failures are expected to be obviated by the reversion process (e.g. invalid alignment information will Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: be obviated when the REMOVE_ALIGNMENT_INFORMATION option is used). be obviated when the REMOVE_ALIGNMENT_INFORMATION option is used). Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Version: null Version: null Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Options: Options: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: --help --help Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: --stdhelp --stdhelp Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: tools. tools. Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: INPUT=File INPUT=File Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: I=File The input SAM/BAM file to revert the state of. Required. I=File The input SAM/BAM file to revert the state of. Required. Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: OUTPUT=File OUTPUT=File Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: O=File The output SAM/BAM file to create, or an output directory if OUTPUT_BY_READGROUP is true. O=File The output SAM/BAM file to create, or an output directory if OUTPUT_BY_READGROUP is true. Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Required. Cannot be used in conjuction with option(s) OUTPUT_MAP (OM) Required. Cannot be used in conjuction with option(s) OUTPUT_MAP (OM) Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: OUTPUT_MAP=File OUTPUT_MAP=File Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: OM=File Tab separated file with two columns, READ_GROUP_ID and OUTPUT, providing file mapping only OM=File Tab separated file with two columns, READ_GROUP_ID and OUTPUT, providing file mapping only Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: used if OUTPUT_BY_READGROUP is true. Required. Cannot be used in conjuction with used if OUTPUT_BY_READGROUP is true. Required. Cannot be used in conjuction with Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: option(s) OUTPUT (O) option(s) OUTPUT (O) Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: OUTPUT_BY_READGROUP=Boolean OUTPUT_BY_READGROUP=Boolean Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: OBR=Boolean When true, outputs each read group in a separate file. Default value: false. This option OBR=Boolean When true, outputs each read group in a separate file. Default value: false. This option Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: can be set to 'null' to clear the default value. Possible values: {true, false} can be set to 'null' to clear the default value. Possible values: {true, false} Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: RESTORE_HARDCLIPS=Boolean RESTORE_HARDCLIPS=Boolean Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: RHC=Boolean When true, restores reads and qualities of records with hard-clips containing XB and XQ RHC=Boolean When true, restores reads and qualities of records with hard-clips containing XB and XQ Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: tags. Default value: true. This option can be set to 'null' to clear the default value. tags. Default value: true. This option can be set to 'null' to clear the default value. Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Possible values: {true, false} Possible values: {true, false} Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: OUTPUT_BY_READGROUP_FILE_FORMAT=FileType OUTPUT_BY_READGROUP_FILE_FORMAT=FileType Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: OBRFF=FileType When using OUTPUT_BY_READGROUP, the output file format can be set to a certain format. OBRFF=FileType When using OUTPUT_BY_READGROUP, the output file format can be set to a certain format. Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Default value: dynamic. This option can be set to 'null' to clear the default value. Default value: dynamic. This option can be set to 'null' to clear the default value. Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Possible values: { Possible values: { Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: sam (Generate SAM files.) sam (Generate SAM files.) Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: bam (Generate BAM files.) bam (Generate BAM files.) Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: cram (Generate CRAM files.) cram (Generate CRAM files.) Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: dynamic (Generate files based on the extention of INPUT.) dynamic (Generate files based on the extention of INPUT.) Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: } } Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: SORT_ORDER=SortOrder SORT_ORDER=SortOrder Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: SO=SortOrder The sort order to create the reverted output file with. Default value: queryname. This SO=SortOrder The sort order to create the reverted output file with. Default value: queryname. This Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: option can be set to 'null' to clear the default value. Possible values: {unsorted, option can be set to 'null' to clear the default value. Possible values: {unsorted, Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: queryname, coordinate, duplicate, unknown} queryname, coordinate, duplicate, unknown} Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: RESTORE_ORIGINAL_QUALITIES=Boolean RESTORE_ORIGINAL_QUALITIES=Boolean Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: OQ=Boolean True to restore original qualities from the OQ field to the QUAL field if available. OQ=Boolean True to restore original qualities from the OQ field to the QUAL field if available. Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Default value: true. This option can be set to 'null' to clear the default value. Possible Default value: true. This option can be set to 'null' to clear the default value. Possible Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: values: {true, false} values: {true, false} Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: REMOVE_DUPLICATE_INFORMATION=Boolean REMOVE_DUPLICATE_INFORMATION=Boolean Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Remove duplicate read flags from all reads. Note that if this is false and Remove duplicate read flags from all reads. Note that if this is false and Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: REMOVE_ALIGNMENT_INFORMATION==true, the output may have the unusual but sometimes REMOVE_ALIGNMENT_INFORMATION==true, the output may have the unusual but sometimes Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: desirable trait of having unmapped reads that are marked as duplicates. Default value: desirable trait of having unmapped reads that are marked as duplicates. Default value: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: true. This option can be set to 'null' to clear the default value. Possible values: {true, true. This option can be set to 'null' to clear the default value. Possible values: {true, Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: false} false} Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: REMOVE_ALIGNMENT_INFORMATION=Boolean REMOVE_ALIGNMENT_INFORMATION=Boolean Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Remove all alignment information from the file. Default value: true. This option can be Remove all alignment information from the file. Default value: true. This option can be Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: set to 'null' to clear the default value. Possible values: {true, false} set to 'null' to clear the default value. Possible values: {true, false} Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: ATTRIBUTE_TO_CLEAR=String When removing alignment information, the set of optional tags to remove. Default value: ATTRIBUTE_TO_CLEAR=String When removing alignment information, the set of optional tags to remove. Default value: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: [NM, UQ, PG, MD, MQ, SA, MC, AS]. This option can be set to 'null' to clear the default [NM, UQ, PG, MD, MQ, SA, MC, AS]. This option can be set to 'null' to clear the default Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: value. This option may be specified 0 or more times. This option can be set to 'null' to value. This option may be specified 0 or more times. This option can be set to 'null' to Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: clear the default list. clear the default list. Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: SANITIZE=Boolean WARNING: This option is potentially destructive. If enabled will discard reads in order to SANITIZE=Boolean WARNING: This option is potentially destructive. If enabled will discard reads in order to Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: produce a consistent output BAM. Reads discarded include (but are not limited to) paired produce a consistent output BAM. Reads discarded include (but are not limited to) paired Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: reads with missing mates, duplicated records, records with mismatches in length of bases reads with missing mates, duplicated records, records with mismatches in length of bases Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: and qualities. This option can only be enabled if the output sort order is queryname and and qualities. This option can only be enabled if the output sort order is queryname and Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: will always cause sorting to occur. Default value: false. This option can be set to will always cause sorting to occur. Default value: false. This option can be set to Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: 'null' to clear the default value. Possible values: {true, false} 'null' to clear the default value. Possible values: {true, false} Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: MAX_DISCARD_FRACTION=Double If SANITIZE=true and higher than MAX_DISCARD_FRACTION reads are discarded due to MAX_DISCARD_FRACTION=Double If SANITIZE=true and higher than MAX_DISCARD_FRACTION reads are discarded due to Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: sanitization thenthe program will exit with an Exception instead of exiting cleanly. sanitization thenthe program will exit with an Exception instead of exiting cleanly. Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Output BAM will still be valid. Default value: 0.01. This option can be set to 'null' to Output BAM will still be valid. Default value: 0.01. This option can be set to 'null' to Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: clear the default value. clear the default value. Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: KEEP_FIRST_DUPLICATE=Boolean If SANITIZE=true keep the first record when we find more than one record with the same KEEP_FIRST_DUPLICATE=Boolean If SANITIZE=true keep the first record when we find more than one record with the same Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: name for R1/R2/unpaired reads respectively. For paired end reads, keeps only the first R1 name for R1/R2/unpaired reads respectively. For paired end reads, keeps only the first R1 Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: and R2 found respectively, and discards all unpaired reads. Duplicates do not refer to the and R2 found respectively, and discards all unpaired reads. Duplicates do not refer to the Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: duplicate flag in the FLAG field, but instead reads with the same name. Default value: duplicate flag in the FLAG field, but instead reads with the same name. Default value: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: false. This option can be set to 'null' to clear the default value. Possible values: false. This option can be set to 'null' to clear the default value. Possible values: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: {true, false} {true, false} Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: SAMPLE_ALIAS=String SAMPLE_ALIAS=String Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: ALIAS=String The sample alias to use in the reverted output file. This will override the existing ALIAS=String The sample alias to use in the reverted output file. This will override the existing Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: sample alias in the file and is used only if all the read groups in the input file have sample alias in the file and is used only if all the read groups in the input file have Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: the same sample alias. Default value: null. the same sample alias. Default value: null. Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: LIBRARY_NAME=String LIBRARY_NAME=String Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: LIB=String The library name to use in the reverted output file. This will override the existing LIB=String The library name to use in the reverted output file. This will override the existing Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: sample alias in the file and is used only if all the read groups in the input file have sample alias in the file and is used only if all the read groups in the input file have Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: the same library name. Default value: null. the same library name. Default value: null. Test: Test method testNoInput(picard.sam.RevertSamTest) produced standard out/err: Running Test: Test method testNoRgInfoOutputByRg(picard.sam.RevertSamTest) Test: Test method testNoRgInfoOutputByRg(picard.sam.RevertSamTest) produced standard out/err: INFO 2024-07-02 12:02:03 RevertSam Gradle suite > Gradle test > picard.sam.RevertSamTest.testNoRgInfoOutputByRg STANDARD_ERROR INFO 2024-07-02 12:02:03 RevertSam Test: Test method testNoRgInfoOutputByRg(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoRgInfoOutputByRg(picard.sam.RevertSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testNoRgInfoOutputByRg(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testNoRgInfoOutputByRg(picard.sam.RevertSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testNoRgInfoOutputByRg(picard.sam.RevertSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testNoRgInfoOutputByRg(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testNoRgInfoOutputByRg(picard.sam.RevertSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testNoRgInfoOutputByRg(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testNoRgInfoOutputByRg(picard.sam.RevertSamTest) produced standard out/err: ********** RevertSam -I testdata/picard/sam/bam2fastq/paired/bad/missing-rg-info.sam -OUTPUT_BY_READGROUP true -O . ********** RevertSam -I testdata/picard/sam/bam2fastq/paired/bad/missing-rg-info.sam -OUTPUT_BY_READGROUP true -O . Test: Test method testNoRgInfoOutputByRg(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testNoRgInfoOutputByRg(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoRgInfoOutputByRg(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoRgInfoOutputByRg(picard.sam.RevertSamTest) produced standard out/err: 12:02:03.025 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:03.025 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoRgInfoOutputByRg(picard.sam.RevertSamTest) produced standard out/err: 12:02:03.025 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:03.025 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoRgInfoOutputByRg(picard.sam.RevertSamTest) produced standard out/err: 12:02:03.026 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:03.026 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoRgInfoOutputByRg(picard.sam.RevertSamTest) produced standard out/err: 12:02:03.026 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:03.026 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoRgInfoOutputByRg(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:03 GMT+14:00 2024] RevertSam INPUT=testdata/picard/sam/bam2fastq/paired/bad/missing-rg-info.sam OUTPUT=. OUTPUT_BY_READGROUP=true RESTORE_HARDCLIPS=true OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic SORT_ORDER=queryname RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS] SANITIZE=false MAX_DISCARD_FRACTION=0.01 KEEP_FIRST_DUPLICATE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:03 GMT+14:00 2024] RevertSam INPUT=testdata/picard/sam/bam2fastq/paired/bad/missing-rg-info.sam OUTPUT=. OUTPUT_BY_READGROUP=true RESTORE_HARDCLIPS=true OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic SORT_ORDER=queryname RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS] SANITIZE=false MAX_DISCARD_FRACTION=0.01 KEEP_FIRST_DUPLICATE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testNoRgInfoOutputByRg(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testNoRgInfoOutputByRg(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:03 GMT+14:00 2024] picard.sam.RevertSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:03 GMT+14:00 2024] picard.sam.RevertSam done. Elapsed time: 0.00 minutes. Test: Test method testNoRgInfoOutputByRg(picard.sam.RevertSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testNoRgInfoOutputByRg(picard.sam.RevertSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testNoRgInfoSanitize(picard.sam.RevertSamTest) Test: Test method testNoRgInfoSanitize(picard.sam.RevertSamTest) produced standard out/err: INFO 2024-07-02 12:02:03 RevertSam Gradle suite > Gradle test > picard.sam.RevertSamTest.testNoRgInfoSanitize STANDARD_ERROR INFO 2024-07-02 12:02:03 RevertSam Test: Test method testNoRgInfoSanitize(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoRgInfoSanitize(picard.sam.RevertSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testNoRgInfoSanitize(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testNoRgInfoSanitize(picard.sam.RevertSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testNoRgInfoSanitize(picard.sam.RevertSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testNoRgInfoSanitize(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testNoRgInfoSanitize(picard.sam.RevertSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testNoRgInfoSanitize(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testNoRgInfoSanitize(picard.sam.RevertSamTest) produced standard out/err: ********** RevertSam -I testdata/picard/sam/bam2fastq/paired/bad/missing-rg-info.sam -SANITIZE true -O /tmp/no-rg-reverted834931276417519677.sam ********** RevertSam -I testdata/picard/sam/bam2fastq/paired/bad/missing-rg-info.sam -SANITIZE true -O /tmp/no-rg-reverted834931276417519677.sam Test: Test method testNoRgInfoSanitize(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testNoRgInfoSanitize(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoRgInfoSanitize(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testNoRgInfoSanitize(picard.sam.RevertSamTest) produced standard out/err: 12:02:03.112 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:03.112 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoRgInfoSanitize(picard.sam.RevertSamTest) produced standard out/err: 12:02:03.112 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:03.112 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoRgInfoSanitize(picard.sam.RevertSamTest) produced standard out/err: 12:02:03.112 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:03.112 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoRgInfoSanitize(picard.sam.RevertSamTest) produced standard out/err: 12:02:03.112 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:03.112 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoRgInfoSanitize(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:03 GMT+14:00 2024] RevertSam INPUT=testdata/picard/sam/bam2fastq/paired/bad/missing-rg-info.sam OUTPUT=/tmp/no-rg-reverted834931276417519677.sam SANITIZE=true OUTPUT_BY_READGROUP=false RESTORE_HARDCLIPS=true OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic SORT_ORDER=queryname RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS] MAX_DISCARD_FRACTION=0.01 KEEP_FIRST_DUPLICATE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:03 GMT+14:00 2024] RevertSam INPUT=testdata/picard/sam/bam2fastq/paired/bad/missing-rg-info.sam OUTPUT=/tmp/no-rg-reverted834931276417519677.sam SANITIZE=true OUTPUT_BY_READGROUP=false RESTORE_HARDCLIPS=true OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic SORT_ORDER=queryname RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS] MAX_DISCARD_FRACTION=0.01 KEEP_FIRST_DUPLICATE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testNoRgInfoSanitize(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testNoRgInfoSanitize(picard.sam.RevertSamTest) produced standard out/err: INFO 2024-07-02 12:02:03 RevertSam Discarded 0 out of 240 (0.000%) reads in order to sanitize output. INFO 2024-07-02 12:02:03 RevertSam Discarded 0 out of 240 (0.000%) reads in order to sanitize output. Test: Test method testNoRgInfoSanitize(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:03 GMT+14:00 2024] picard.sam.RevertSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:03 GMT+14:00 2024] picard.sam.RevertSam done. Elapsed time: 0.00 minutes. Test: Test method testNoRgInfoSanitize(picard.sam.RevertSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testOutputByReadGroupWithOutputMap(picard.sam.RevertSamTest) Test: Test method testOutputByReadGroupWithOutputMap(picard.sam.RevertSamTest) produced standard out/err: outputFile: /tmp/pbuilder2/tmpPicardTest17059270206359872886/my_rg0.sam Gradle suite > Gradle test > picard.sam.RevertSamTest.testOutputByReadGroupWithOutputMap STANDARD_OUT outputFile: /tmp/pbuilder2/tmpPicardTest17059270206359872886/my_rg0.sam Test: Test method testOutputByReadGroupWithOutputMap(picard.sam.RevertSamTest) produced standard out/err: outputFile: /tmp/pbuilder2/tmpPicardTest17059270206359872886/rg1.cram outputFile: /tmp/pbuilder2/tmpPicardTest17059270206359872886/rg1.cram Test: Test method testOutputByReadGroupWithOutputMap(picard.sam.RevertSamTest) produced standard out/err: outputFile: /tmp/pbuilder2/tmpPicardTest17059270206359872886/my_rg2.bam outputFile: /tmp/pbuilder2/tmpPicardTest17059270206359872886/my_rg2.bam Test: Test method testOutputByReadGroupWithOutputMap(picard.sam.RevertSamTest) produced standard out/err: outputFile: /tmp/pbuilder2/tmpPicardTest17059270206359872886/my_rg3.sam outputFile: /tmp/pbuilder2/tmpPicardTest17059270206359872886/my_rg3.sam Test: Test method testOutputByReadGroupWithOutputMap(picard.sam.RevertSamTest) produced standard out/err: INFO 2024-07-02 12:02:03 RevertSam Gradle suite > Gradle test > picard.sam.RevertSamTest.testOutputByReadGroupWithOutputMap STANDARD_ERROR INFO 2024-07-02 12:02:03 RevertSam Test: Test method testOutputByReadGroupWithOutputMap(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testOutputByReadGroupWithOutputMap(picard.sam.RevertSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOutputByReadGroupWithOutputMap(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testOutputByReadGroupWithOutputMap(picard.sam.RevertSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOutputByReadGroupWithOutputMap(picard.sam.RevertSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOutputByReadGroupWithOutputMap(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testOutputByReadGroupWithOutputMap(picard.sam.RevertSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOutputByReadGroupWithOutputMap(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testOutputByReadGroupWithOutputMap(picard.sam.RevertSamTest) produced standard out/err: ********** RevertSam -INPUT testdata/picard/sam/revert_sam_basic.sam -OUTPUT_BY_READGROUP true -OUTPUT_MAP /tmp/pbuilder2/picardRevertSamTestOutputMap8927518002615877297.txt -REFERENCE_SEQUENCE testdata/picard/reference/test.fasta -SORT_ORDER queryname -REMOVE_DUPLICATE_INFORMATION true -REMOVE_ALIGNMENT_INFORMATION true -RESTORE_ORIGINAL_QUALITIES true -SAMPLE_ALIAS test_sample_1 -LIBRARY_NAME test_library_1 -ATTRIBUTE_TO_CLEAR NM ********** RevertSam -INPUT testdata/picard/sam/revert_sam_basic.sam -OUTPUT_BY_READGROUP true -OUTPUT_MAP /tmp/pbuilder2/picardRevertSamTestOutputMap8927518002615877297.txt -REFERENCE_SEQUENCE testdata/picard/reference/test.fasta -SORT_ORDER queryname -REMOVE_DUPLICATE_INFORMATION true -REMOVE_ALIGNMENT_INFORMATION true -RESTORE_ORIGINAL_QUALITIES true -SAMPLE_ALIAS test_sample_1 -LIBRARY_NAME test_library_1 -ATTRIBUTE_TO_CLEAR NM Test: Test method testOutputByReadGroupWithOutputMap(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testOutputByReadGroupWithOutputMap(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testOutputByReadGroupWithOutputMap(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testOutputByReadGroupWithOutputMap(picard.sam.RevertSamTest) produced standard out/err: 12:02:03.299 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:03.299 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOutputByReadGroupWithOutputMap(picard.sam.RevertSamTest) produced standard out/err: 12:02:03.299 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:03.299 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOutputByReadGroupWithOutputMap(picard.sam.RevertSamTest) produced standard out/err: 12:02:03.299 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:03.299 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOutputByReadGroupWithOutputMap(picard.sam.RevertSamTest) produced standard out/err: 12:02:03.299 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:03.299 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOutputByReadGroupWithOutputMap(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:03 GMT+14:00 2024] RevertSam INPUT=testdata/picard/sam/revert_sam_basic.sam OUTPUT_MAP=/tmp/pbuilder2/picardRevertSamTestOutputMap8927518002615877297.txt OUTPUT_BY_READGROUP=true SORT_ORDER=queryname RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS, NM] SAMPLE_ALIAS=test_sample_1 LIBRARY_NAME=test_library_1 REFERENCE_SEQUENCE=testdata/picard/reference/test.fasta RESTORE_HARDCLIPS=true OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic SANITIZE=false MAX_DISCARD_FRACTION=0.01 KEEP_FIRST_DUPLICATE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:03 GMT+14:00 2024] RevertSam INPUT=testdata/picard/sam/revert_sam_basic.sam OUTPUT_MAP=/tmp/pbuilder2/picardRevertSamTestOutputMap8927518002615877297.txt OUTPUT_BY_READGROUP=true SORT_ORDER=queryname RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS, NM] SAMPLE_ALIAS=test_sample_1 LIBRARY_NAME=test_library_1 REFERENCE_SEQUENCE=testdata/picard/reference/test.fasta RESTORE_HARDCLIPS=true OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic SANITIZE=false MAX_DISCARD_FRACTION=0.01 KEEP_FIRST_DUPLICATE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOutputByReadGroupWithOutputMap(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOutputByReadGroupWithOutputMap(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:03 GMT+14:00 2024] picard.sam.RevertSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:03 GMT+14:00 2024] picard.sam.RevertSam done. Elapsed time: 0.00 minutes. Test: Test method testOutputByReadGroupWithOutputMap(picard.sam.RevertSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testSampleLibraryOverride[0](NewSample, null)(picard.sam.RevertSamTest) Test: Test method testSampleLibraryOverride[0](NewSample, null)(picard.sam.RevertSamTest) produced standard out/err: INFO 2024-07-02 12:02:03 RevertSam Gradle suite > Gradle test > picard.sam.RevertSamTest.testSampleLibraryOverride[0](NewSample, null) STANDARD_ERROR INFO 2024-07-02 12:02:03 RevertSam Test: Test method testSampleLibraryOverride[0](NewSample, null)(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testSampleLibraryOverride[0](NewSample, null)(picard.sam.RevertSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSampleLibraryOverride[0](NewSample, null)(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testSampleLibraryOverride[0](NewSample, null)(picard.sam.RevertSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSampleLibraryOverride[0](NewSample, null)(picard.sam.RevertSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSampleLibraryOverride[0](NewSample, null)(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testSampleLibraryOverride[0](NewSample, null)(picard.sam.RevertSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSampleLibraryOverride[0](NewSample, null)(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testSampleLibraryOverride[0](NewSample, null)(picard.sam.RevertSamTest) produced standard out/err: ********** RevertSam -INPUT testdata/picard/sam/revert_sam_sample_library_override.sam -OUTPUT /tmp/bad15313798491287231760.sam -SAMPLE_ALIAS NewSample ********** RevertSam -INPUT testdata/picard/sam/revert_sam_sample_library_override.sam -OUTPUT /tmp/bad15313798491287231760.sam -SAMPLE_ALIAS NewSample Test: Test method testSampleLibraryOverride[0](NewSample, null)(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testSampleLibraryOverride[0](NewSample, null)(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testSampleLibraryOverride[0](NewSample, null)(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testSampleLibraryOverride[0](NewSample, null)(picard.sam.RevertSamTest) produced standard out/err: 12:02:03.810 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:03.810 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSampleLibraryOverride[0](NewSample, null)(picard.sam.RevertSamTest) produced standard out/err: 12:02:03.810 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:03.810 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSampleLibraryOverride[0](NewSample, null)(picard.sam.RevertSamTest) produced standard out/err: 12:02:03.811 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:03.811 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSampleLibraryOverride[0](NewSample, null)(picard.sam.RevertSamTest) produced standard out/err: 12:02:03.811 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:03.811 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSampleLibraryOverride[0](NewSample, null)(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:03 GMT+14:00 2024] RevertSam INPUT=testdata/picard/sam/revert_sam_sample_library_override.sam OUTPUT=/tmp/bad15313798491287231760.sam SAMPLE_ALIAS=NewSample OUTPUT_BY_READGROUP=false RESTORE_HARDCLIPS=true OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic SORT_ORDER=queryname RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS] SANITIZE=false MAX_DISCARD_FRACTION=0.01 KEEP_FIRST_DUPLICATE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:03 GMT+14:00 2024] RevertSam INPUT=testdata/picard/sam/revert_sam_sample_library_override.sam OUTPUT=/tmp/bad15313798491287231760.sam SAMPLE_ALIAS=NewSample OUTPUT_BY_READGROUP=false RESTORE_HARDCLIPS=true OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic SORT_ORDER=queryname RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS] SANITIZE=false MAX_DISCARD_FRACTION=0.01 KEEP_FIRST_DUPLICATE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSampleLibraryOverride[0](NewSample, null)(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSampleLibraryOverride[0](NewSample, null)(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:03 GMT+14:00 2024] picard.sam.RevertSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:03 GMT+14:00 2024] picard.sam.RevertSam done. Elapsed time: 0.00 minutes. Test: Test method testSampleLibraryOverride[0](NewSample, null)(picard.sam.RevertSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testSampleLibraryOverride[0](NewSample, null)(picard.sam.RevertSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testSampleLibraryOverride[1](null, NewLibrary)(picard.sam.RevertSamTest) Test: Test method testSampleLibraryOverride[1](null, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: INFO 2024-07-02 12:02:03 RevertSam Gradle suite > Gradle test > picard.sam.RevertSamTest.testSampleLibraryOverride[1](null, NewLibrary) STANDARD_ERROR INFO 2024-07-02 12:02:03 RevertSam Test: Test method testSampleLibraryOverride[1](null, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testSampleLibraryOverride[1](null, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSampleLibraryOverride[1](null, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testSampleLibraryOverride[1](null, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSampleLibraryOverride[1](null, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSampleLibraryOverride[1](null, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testSampleLibraryOverride[1](null, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSampleLibraryOverride[1](null, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testSampleLibraryOverride[1](null, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: ********** RevertSam -INPUT testdata/picard/sam/revert_sam_sample_library_override.sam -OUTPUT /tmp/bad12047350881204926565.sam -LIBRARY_NAME NewLibrary ********** RevertSam -INPUT testdata/picard/sam/revert_sam_sample_library_override.sam -OUTPUT /tmp/bad12047350881204926565.sam -LIBRARY_NAME NewLibrary Test: Test method testSampleLibraryOverride[1](null, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testSampleLibraryOverride[1](null, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testSampleLibraryOverride[1](null, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testSampleLibraryOverride[1](null, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: 12:02:03.914 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:03.914 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSampleLibraryOverride[1](null, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: 12:02:03.914 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:03.914 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSampleLibraryOverride[1](null, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: 12:02:03.914 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:03.914 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSampleLibraryOverride[1](null, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: 12:02:03.914 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:03.914 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSampleLibraryOverride[1](null, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:03 GMT+14:00 2024] RevertSam INPUT=testdata/picard/sam/revert_sam_sample_library_override.sam OUTPUT=/tmp/bad12047350881204926565.sam LIBRARY_NAME=NewLibrary OUTPUT_BY_READGROUP=false RESTORE_HARDCLIPS=true OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic SORT_ORDER=queryname RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS] SANITIZE=false MAX_DISCARD_FRACTION=0.01 KEEP_FIRST_DUPLICATE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:03 GMT+14:00 2024] RevertSam INPUT=testdata/picard/sam/revert_sam_sample_library_override.sam OUTPUT=/tmp/bad12047350881204926565.sam LIBRARY_NAME=NewLibrary OUTPUT_BY_READGROUP=false RESTORE_HARDCLIPS=true OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic SORT_ORDER=queryname RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS] SANITIZE=false MAX_DISCARD_FRACTION=0.01 KEEP_FIRST_DUPLICATE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSampleLibraryOverride[1](null, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:03 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSampleLibraryOverride[1](null, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:03 GMT+14:00 2024] picard.sam.RevertSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:03 GMT+14:00 2024] picard.sam.RevertSam done. Elapsed time: 0.00 minutes. Test: Test method testSampleLibraryOverride[1](null, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testSampleLibraryOverride[1](null, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testSampleLibraryOverride[2](NewSample, NewLibrary)(picard.sam.RevertSamTest) Test: Test method testSampleLibraryOverride[2](NewSample, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: INFO 2024-07-02 12:02:04 RevertSam Gradle suite > Gradle test > picard.sam.RevertSamTest.testSampleLibraryOverride[2](NewSample, NewLibrary) STANDARD_ERROR INFO 2024-07-02 12:02:04 RevertSam Test: Test method testSampleLibraryOverride[2](NewSample, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testSampleLibraryOverride[2](NewSample, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSampleLibraryOverride[2](NewSample, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testSampleLibraryOverride[2](NewSample, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSampleLibraryOverride[2](NewSample, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSampleLibraryOverride[2](NewSample, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testSampleLibraryOverride[2](NewSample, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSampleLibraryOverride[2](NewSample, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testSampleLibraryOverride[2](NewSample, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: ********** RevertSam -INPUT testdata/picard/sam/revert_sam_sample_library_override.sam -OUTPUT /tmp/bad9158597457399392319.sam -SAMPLE_ALIAS NewSample -LIBRARY_NAME NewLibrary ********** RevertSam -INPUT testdata/picard/sam/revert_sam_sample_library_override.sam -OUTPUT /tmp/bad9158597457399392319.sam -SAMPLE_ALIAS NewSample -LIBRARY_NAME NewLibrary Test: Test method testSampleLibraryOverride[2](NewSample, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testSampleLibraryOverride[2](NewSample, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testSampleLibraryOverride[2](NewSample, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testSampleLibraryOverride[2](NewSample, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: 12:02:04.017 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:04.017 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSampleLibraryOverride[2](NewSample, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: 12:02:04.017 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:04.017 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSampleLibraryOverride[2](NewSample, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: 12:02:04.017 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:04.017 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSampleLibraryOverride[2](NewSample, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: 12:02:04.017 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:04.017 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSampleLibraryOverride[2](NewSample, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:04 GMT+14:00 2024] RevertSam INPUT=testdata/picard/sam/revert_sam_sample_library_override.sam OUTPUT=/tmp/bad9158597457399392319.sam SAMPLE_ALIAS=NewSample LIBRARY_NAME=NewLibrary OUTPUT_BY_READGROUP=false RESTORE_HARDCLIPS=true OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic SORT_ORDER=queryname RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS] SANITIZE=false MAX_DISCARD_FRACTION=0.01 KEEP_FIRST_DUPLICATE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:04 GMT+14:00 2024] RevertSam INPUT=testdata/picard/sam/revert_sam_sample_library_override.sam OUTPUT=/tmp/bad9158597457399392319.sam SAMPLE_ALIAS=NewSample LIBRARY_NAME=NewLibrary OUTPUT_BY_READGROUP=false RESTORE_HARDCLIPS=true OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic SORT_ORDER=queryname RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS] SANITIZE=false MAX_DISCARD_FRACTION=0.01 KEEP_FIRST_DUPLICATE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSampleLibraryOverride[2](NewSample, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSampleLibraryOverride[2](NewSample, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:04 GMT+14:00 2024] picard.sam.RevertSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:04 GMT+14:00 2024] picard.sam.RevertSam done. Elapsed time: 0.00 minutes. Test: Test method testSampleLibraryOverride[2](NewSample, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testSampleLibraryOverride[2](NewSample, NewLibrary)(picard.sam.RevertSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testSanitizeAndDeduplicateRecords(picard.sam.RevertSamTest) Test: Test method testSanitizeAndDeduplicateRecords(picard.sam.RevertSamTest) produced standard out/err: INFO 2024-07-02 12:02:04 RevertSam Gradle suite > Gradle test > picard.sam.RevertSamTest.testSanitizeAndDeduplicateRecords STANDARD_ERROR INFO 2024-07-02 12:02:04 RevertSam Test: Test method testSanitizeAndDeduplicateRecords(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testSanitizeAndDeduplicateRecords(picard.sam.RevertSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSanitizeAndDeduplicateRecords(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testSanitizeAndDeduplicateRecords(picard.sam.RevertSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSanitizeAndDeduplicateRecords(picard.sam.RevertSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSanitizeAndDeduplicateRecords(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testSanitizeAndDeduplicateRecords(picard.sam.RevertSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSanitizeAndDeduplicateRecords(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testSanitizeAndDeduplicateRecords(picard.sam.RevertSamTest) produced standard out/err: ********** RevertSam -I /tmp/test-input-santize-and-deduplicate-records12917943695109469010.sam -SANITIZE true -KEEP_FIRST_DUPLICATE true -MAX_DISCARD_FRACTION 1 -O /tmp/test-output-santize-and-deduplicate-records5538182464962226383.sam ********** RevertSam -I /tmp/test-input-santize-and-deduplicate-records12917943695109469010.sam -SANITIZE true -KEEP_FIRST_DUPLICATE true -MAX_DISCARD_FRACTION 1 -O /tmp/test-output-santize-and-deduplicate-records5538182464962226383.sam Test: Test method testSanitizeAndDeduplicateRecords(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testSanitizeAndDeduplicateRecords(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testSanitizeAndDeduplicateRecords(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testSanitizeAndDeduplicateRecords(picard.sam.RevertSamTest) produced standard out/err: 12:02:04.067 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:04.067 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSanitizeAndDeduplicateRecords(picard.sam.RevertSamTest) produced standard out/err: 12:02:04.067 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:04.067 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSanitizeAndDeduplicateRecords(picard.sam.RevertSamTest) produced standard out/err: 12:02:04.067 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:04.067 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSanitizeAndDeduplicateRecords(picard.sam.RevertSamTest) produced standard out/err: 12:02:04.067 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:04.067 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSanitizeAndDeduplicateRecords(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:04 GMT+14:00 2024] RevertSam INPUT=/tmp/test-input-santize-and-deduplicate-records12917943695109469010.sam OUTPUT=/tmp/test-output-santize-and-deduplicate-records5538182464962226383.sam SANITIZE=true MAX_DISCARD_FRACTION=1.0 KEEP_FIRST_DUPLICATE=true OUTPUT_BY_READGROUP=false RESTORE_HARDCLIPS=true OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic SORT_ORDER=queryname RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:04 GMT+14:00 2024] RevertSam INPUT=/tmp/test-input-santize-and-deduplicate-records12917943695109469010.sam OUTPUT=/tmp/test-output-santize-and-deduplicate-records5538182464962226383.sam SANITIZE=true MAX_DISCARD_FRACTION=1.0 KEEP_FIRST_DUPLICATE=true OUTPUT_BY_READGROUP=false RESTORE_HARDCLIPS=true OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic SORT_ORDER=queryname RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS] VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSanitizeAndDeduplicateRecords(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSanitizeAndDeduplicateRecords(picard.sam.RevertSamTest) produced standard out/err: WARNING 2024-07-02 12:02:04 RevertSam Skipping read group 3 with no reads WARNING 2024-07-02 12:02:04 RevertSam Skipping read group 3 with no reads Test: Test method testSanitizeAndDeduplicateRecords(picard.sam.RevertSamTest) produced standard out/err: INFO 2024-07-02 12:02:04 RevertSam Detected quality format for 0: Standard INFO 2024-07-02 12:02:04 RevertSam Detected quality format for 0: Standard Test: Test method testSanitizeAndDeduplicateRecords(picard.sam.RevertSamTest) produced standard out/err: INFO 2024-07-02 12:02:04 RevertSam Detected quality format for 1: Standard INFO 2024-07-02 12:02:04 RevertSam Detected quality format for 1: Standard Test: Test method testSanitizeAndDeduplicateRecords(picard.sam.RevertSamTest) produced standard out/err: INFO 2024-07-02 12:02:04 RevertSam Detected quality format for 2: Standard INFO 2024-07-02 12:02:04 RevertSam Detected quality format for 2: Standard Test: Test method testSanitizeAndDeduplicateRecords(picard.sam.RevertSamTest) produced standard out/err: INFO 2024-07-02 12:02:04 RevertSam Discarded 4 out of 12 (33.333%) reads in order to sanitize output. INFO 2024-07-02 12:02:04 RevertSam Discarded 4 out of 12 (33.333%) reads in order to sanitize output. Test: Test method testSanitizeAndDeduplicateRecords(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:04 GMT+14:00 2024] picard.sam.RevertSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:04 GMT+14:00 2024] picard.sam.RevertSam done. Elapsed time: 0.00 minutes. Test: Test method testSanitizeAndDeduplicateRecords(picard.sam.RevertSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testSingleEnd(picard.sam.RevertSamTest) Test: Test method testSingleEnd(picard.sam.RevertSamTest) produced standard out/err: INFO 2024-07-02 12:02:04 RevertSam Gradle suite > Gradle test > picard.sam.RevertSamTest.testSingleEnd STANDARD_ERROR INFO 2024-07-02 12:02:04 RevertSam Test: Test method testSingleEnd(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testSingleEnd(picard.sam.RevertSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleEnd(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testSingleEnd(picard.sam.RevertSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleEnd(picard.sam.RevertSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleEnd(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testSingleEnd(picard.sam.RevertSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleEnd(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testSingleEnd(picard.sam.RevertSamTest) produced standard out/err: ********** RevertSam -INPUT testdata/picard/sam/revert_sam_single_end.sam -OUTPUT /tmp/single_end_reverted1235920597601934396.sam ********** RevertSam -INPUT testdata/picard/sam/revert_sam_single_end.sam -OUTPUT /tmp/single_end_reverted1235920597601934396.sam Test: Test method testSingleEnd(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testSingleEnd(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testSingleEnd(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testSingleEnd(picard.sam.RevertSamTest) produced standard out/err: 12:02:04.120 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:04.120 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleEnd(picard.sam.RevertSamTest) produced standard out/err: 12:02:04.120 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:04.120 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleEnd(picard.sam.RevertSamTest) produced standard out/err: 12:02:04.120 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:04.120 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleEnd(picard.sam.RevertSamTest) produced standard out/err: 12:02:04.120 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:04.120 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleEnd(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:04 GMT+14:00 2024] RevertSam INPUT=testdata/picard/sam/revert_sam_single_end.sam OUTPUT=/tmp/single_end_reverted1235920597601934396.sam OUTPUT_BY_READGROUP=false RESTORE_HARDCLIPS=true OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic SORT_ORDER=queryname RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS] SANITIZE=false MAX_DISCARD_FRACTION=0.01 KEEP_FIRST_DUPLICATE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:04 GMT+14:00 2024] RevertSam INPUT=testdata/picard/sam/revert_sam_single_end.sam OUTPUT=/tmp/single_end_reverted1235920597601934396.sam OUTPUT_BY_READGROUP=false RESTORE_HARDCLIPS=true OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic SORT_ORDER=queryname RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS] SANITIZE=false MAX_DISCARD_FRACTION=0.01 KEEP_FIRST_DUPLICATE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleEnd(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleEnd(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:04 GMT+14:00 2024] picard.sam.RevertSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:04 GMT+14:00 2024] picard.sam.RevertSam done. Elapsed time: 0.00 minutes. Test: Test method testSingleEnd(picard.sam.RevertSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testSingleEnd(picard.sam.RevertSamTest) produced standard out/err: WARNING 2024-07-02 12:02:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:02:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testSingleEnd(picard.sam.RevertSamTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.RevertSamTest.testSingleEnd STANDARD_OUT No errors found Running Test: Test method testSingleEndSanitize(picard.sam.RevertSamTest) Test: Test method testSingleEndSanitize(picard.sam.RevertSamTest) produced standard out/err: INFO 2024-07-02 12:02:04 RevertSam Gradle suite > Gradle test > picard.sam.RevertSamTest.testSingleEndSanitize STANDARD_ERROR INFO 2024-07-02 12:02:04 RevertSam Test: Test method testSingleEndSanitize(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testSingleEndSanitize(picard.sam.RevertSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSingleEndSanitize(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testSingleEndSanitize(picard.sam.RevertSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSingleEndSanitize(picard.sam.RevertSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSingleEndSanitize(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testSingleEndSanitize(picard.sam.RevertSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSingleEndSanitize(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testSingleEndSanitize(picard.sam.RevertSamTest) produced standard out/err: ********** RevertSam -INPUT testdata/picard/sam/revert_sam_single_end.sam -OUTPUT /tmp/single_end_reverted11313091028476556736.sam -SANITIZE true ********** RevertSam -INPUT testdata/picard/sam/revert_sam_single_end.sam -OUTPUT /tmp/single_end_reverted11313091028476556736.sam -SANITIZE true Test: Test method testSingleEndSanitize(picard.sam.RevertSamTest) produced standard out/err: ********** ********** Test: Test method testSingleEndSanitize(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testSingleEndSanitize(picard.sam.RevertSamTest) produced standard out/err: Test: Test method testSingleEndSanitize(picard.sam.RevertSamTest) produced standard out/err: 12:02:04.151 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:04.151 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleEndSanitize(picard.sam.RevertSamTest) produced standard out/err: 12:02:04.152 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:04.152 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleEndSanitize(picard.sam.RevertSamTest) produced standard out/err: 12:02:04.152 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:04.152 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSingleEndSanitize(picard.sam.RevertSamTest) produced standard out/err: 12:02:04.152 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:04.152 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSingleEndSanitize(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:04 GMT+14:00 2024] RevertSam INPUT=testdata/picard/sam/revert_sam_single_end.sam OUTPUT=/tmp/single_end_reverted11313091028476556736.sam SANITIZE=true OUTPUT_BY_READGROUP=false RESTORE_HARDCLIPS=true OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic SORT_ORDER=queryname RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS] MAX_DISCARD_FRACTION=0.01 KEEP_FIRST_DUPLICATE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:04 GMT+14:00 2024] RevertSam INPUT=testdata/picard/sam/revert_sam_single_end.sam OUTPUT=/tmp/single_end_reverted11313091028476556736.sam SANITIZE=true OUTPUT_BY_READGROUP=false RESTORE_HARDCLIPS=true OUTPUT_BY_READGROUP_FILE_FORMAT=dynamic SORT_ORDER=queryname RESTORE_ORIGINAL_QUALITIES=true REMOVE_DUPLICATE_INFORMATION=true REMOVE_ALIGNMENT_INFORMATION=true ATTRIBUTE_TO_CLEAR=[NM, UQ, PG, MD, MQ, SA, MC, AS] MAX_DISCARD_FRACTION=0.01 KEEP_FIRST_DUPLICATE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSingleEndSanitize(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:04 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSingleEndSanitize(picard.sam.RevertSamTest) produced standard out/err: INFO 2024-07-02 12:02:04 RevertSam Detected quality format for A: Standard INFO 2024-07-02 12:02:04 RevertSam Detected quality format for A: Standard Test: Test method testSingleEndSanitize(picard.sam.RevertSamTest) produced standard out/err: INFO 2024-07-02 12:02:04 RevertSam Discarded 0 out of 3 (0.000%) reads in order to sanitize output. INFO 2024-07-02 12:02:04 RevertSam Discarded 0 out of 3 (0.000%) reads in order to sanitize output. Test: Test method testSingleEndSanitize(picard.sam.RevertSamTest) produced standard out/err: [Tue Jul 02 12:02:04 GMT+14:00 2024] picard.sam.RevertSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:04 GMT+14:00 2024] picard.sam.RevertSam done. Elapsed time: 0.00 minutes. Test: Test method testSingleEndSanitize(picard.sam.RevertSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testValidateOutputParamsByReadGroupBadHeaderMap(picard.sam.RevertSamTest) Running Test: Test method testValidateOutputParamsByReadGroupDirValid(picard.sam.RevertSamTest) Running Test: Test method testValidateOutputParamsByReadGroupMapValid(picard.sam.RevertSamTest) Running Test: Test method testValidateOutputParamsByReadGroupMissingMap(picard.sam.RevertSamTest) Running Test: Test method testValidateOutputParamsByReadGroupNoMapOrDir(picard.sam.RevertSamTest) Running Test: Test method testValidateOutputParamsNotByReadGroupDir(picard.sam.RevertSamTest) Running Test: Test method testValidateOutputParamsNotByReadGroupMap(picard.sam.RevertSamTest) Running Test: Test method testValidateOutputParamsNotByReadGroupNoOutput(picard.sam.RevertSamTest) Running Test: Test method testValidateOutputParamsNotByReadGroupValid(picard.sam.RevertSamTest) Running Test: Test method testSamComparison[0](genomic_sorted.sam, unsorted.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) Test: Test method testSamComparison[0](genomic_sorted.sam, unsorted.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: Sort order differs. Gradle suite > Gradle test > picard.sam.util.SamComparisonTest.testSamComparison[0](genomic_sorted.sam, unsorted.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false) STANDARD_OUT Sort order differs. Test: Test method testSamComparison[0](genomic_sorted.sam, unsorted.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: File 1: coordinate File 1: coordinate Test: Test method testSamComparison[0](genomic_sorted.sam, unsorted.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: File 2: null File 2: null Test: Test method testSamComparison[0](genomic_sorted.sam, unsorted.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: Sort Order differs. Sort Order differs. Test: Test method testSamComparison[0](genomic_sorted.sam, unsorted.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: File 1: coordinate File 1: coordinate Test: Test method testSamComparison[0](genomic_sorted.sam, unsorted.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: File 2: unsorted File 2: unsorted Test: Test method testSamComparison[0](genomic_sorted.sam, unsorted.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: Cannot compare alignments if sort orders differ. Cannot compare alignments if sort orders differ. Test: Test method testSamComparison[0](genomic_sorted.sam, unsorted.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: Sort order differs. Sort order differs. Test: Test method testSamComparison[0](genomic_sorted.sam, unsorted.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: File 1: null File 1: null Test: Test method testSamComparison[0](genomic_sorted.sam, unsorted.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: File 2: coordinate File 2: coordinate Test: Test method testSamComparison[0](genomic_sorted.sam, unsorted.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: Sort Order differs. Sort Order differs. Test: Test method testSamComparison[0](genomic_sorted.sam, unsorted.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: File 1: unsorted File 1: unsorted Test: Test method testSamComparison[0](genomic_sorted.sam, unsorted.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: File 2: coordinate File 2: coordinate Test: Test method testSamComparison[0](genomic_sorted.sam, unsorted.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: Cannot compare alignments if sort orders differ. Cannot compare alignments if sort orders differ. Running Test: Test method testSamComparison[1](genomic_sorted.sam, chr21.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) Test: Test method testSamComparison[1](genomic_sorted.sam, chr21.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: Name of sequence record 1 differs. Gradle suite > Gradle test > picard.sam.util.SamComparisonTest.testSamComparison[1](genomic_sorted.sam, chr21.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false) STANDARD_OUT Name of sequence record 1 differs. Test: Test method testSamComparison[1](genomic_sorted.sam, chr21.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: File 1: chr20 File 1: chr20 Test: Test method testSamComparison[1](genomic_sorted.sam, chr21.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: File 2: chr21 File 2: chr21 Test: Test method testSamComparison[1](genomic_sorted.sam, chr21.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: Cannot compare coordinate-sorted SAM files because sequence dictionaries differ. Cannot compare coordinate-sorted SAM files because sequence dictionaries differ. Test: Test method testSamComparison[1](genomic_sorted.sam, chr21.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: Name of sequence record 1 differs. Name of sequence record 1 differs. Test: Test method testSamComparison[1](genomic_sorted.sam, chr21.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: File 1: chr21 File 1: chr21 Test: Test method testSamComparison[1](genomic_sorted.sam, chr21.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: File 2: chr20 File 2: chr20 Test: Test method testSamComparison[1](genomic_sorted.sam, chr21.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: Cannot compare coordinate-sorted SAM files because sequence dictionaries differ. Cannot compare coordinate-sorted SAM files because sequence dictionaries differ. Running Test: Test method testSamComparison[2](genomic_sorted.sam, bigger_seq_dict.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) Test: Test method testSamComparison[2](genomic_sorted.sam, bigger_seq_dict.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: Length of sequence dictionaries differs. Gradle suite > Gradle test > picard.sam.util.SamComparisonTest.testSamComparison[2](genomic_sorted.sam, bigger_seq_dict.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false) STANDARD_OUT Length of sequence dictionaries differs. Test: Test method testSamComparison[2](genomic_sorted.sam, bigger_seq_dict.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: File 1: 1 File 1: 1 Test: Test method testSamComparison[2](genomic_sorted.sam, bigger_seq_dict.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: File 2: 2 File 2: 2 Test: Test method testSamComparison[2](genomic_sorted.sam, bigger_seq_dict.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: Cannot compare coordinate-sorted SAM files because sequence dictionaries differ. Cannot compare coordinate-sorted SAM files because sequence dictionaries differ. Test: Test method testSamComparison[2](genomic_sorted.sam, bigger_seq_dict.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: Length of sequence dictionaries differs. Length of sequence dictionaries differs. Test: Test method testSamComparison[2](genomic_sorted.sam, bigger_seq_dict.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: File 1: 2 File 1: 2 Test: Test method testSamComparison[2](genomic_sorted.sam, bigger_seq_dict.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: File 2: 1 File 2: 1 Test: Test method testSamComparison[2](genomic_sorted.sam, bigger_seq_dict.sam, false, false, 0, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: Cannot compare coordinate-sorted SAM files because sequence dictionaries differ. Cannot compare coordinate-sorted SAM files because sequence dictionaries differ. Running Test: Test method testSamComparison[3](bigger_seq_dict.sam, bigger_seq_dict.sam, false, false, 2, 0, 0, 0, 0, 0, 0, 0, true)(picard.sam.util.SamComparisonTest) Running Test: Test method testSamComparison[4](genomic_sorted.sam, genomic_sorted.sam, false, false, 2, 0, 0, 0, 0, 0, 0, 0, true)(picard.sam.util.SamComparisonTest) Running Test: Test method testSamComparison[5](genomic_sorted.sam, has_non_primary.sam, false, false, 2, 0, 0, 0, 0, 0, 0, 0, true)(picard.sam.util.SamComparisonTest) Running Test: Test method testSamComparison[6](genomic_sorted_5.sam, genomic_sorted_5_plus.sam, false, false, 3, 2, 0, 0, 0, 3, 0, 0, false)(picard.sam.util.SamComparisonTest) Running Test: Test method testSamComparison[7](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, false, false, 2, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) Test: Test method testSamComparison[7](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, false, false, 2, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: File format version differs. Gradle suite > Gradle test > picard.sam.util.SamComparisonTest.testSamComparison[7](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, false, false, 2, 0, 0, 0, 0, 0, 0, 0, false) STANDARD_OUT File format version differs. Test: Test method testSamComparison[7](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, false, false, 2, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: File 1: 1.0 File 1: 1.0 Test: Test method testSamComparison[7](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, false, false, 2, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: File 2: 1.6 File 2: 1.6 Test: Test method testSamComparison[7](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, false, false, 2, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: File format version differs. File format version differs. Test: Test method testSamComparison[7](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, false, false, 2, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: File 1: 1.6 File 1: 1.6 Test: Test method testSamComparison[7](genomic_sorted.sam, genomic_sorted_sam_v1.6.sam, false, false, 2, 0, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) produced standard out/err: File 2: 1.0 File 2: 1.0 Running Test: Test method testSamComparison[8](group_same_coord.sam, group_same_coord_diff_order.sam, false, false, 3, 0, 0, 0, 0, 1, 2, 0, false)(picard.sam.util.SamComparisonTest) Running Test: Test method testSamComparison[9](genomic_sorted_same_position.sam, genomic_sorted_same_position.sam, false, false, 2, 0, 0, 0, 0, 0, 0, 0, true)(picard.sam.util.SamComparisonTest) Running Test: Test method testSamComparison[10](group_same_coord.sam, diff_coords.sam, false, false, 0, 5, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) Running Test: Test method testSamComparison[11](genomic_sorted.sam, unmapped_first.sam, false, false, 1, 0, 0, 0, 1, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) Running Test: Test method testSamComparison[12](genomic_sorted.sam, unmapped_second.sam, false, false, 1, 0, 0, 0, 1, 0, 0, 1, false)(picard.sam.util.SamComparisonTest) Running Test: Test method testSamComparison[13](unmapped_first.sam, unmapped_second.sam, false, false, 0, 0, 0, 1, 1, 0, 0, 1, false)(picard.sam.util.SamComparisonTest) Running Test: Test method testSamComparison[14](unmapped_first.sam, unmapped_first.sam, false, false, 1, 0, 1, 0, 0, 0, 0, 0, true)(picard.sam.util.SamComparisonTest) Running Test: Test method testSamComparison[15](unsorted.sam, unsorted.sam, false, false, 2, 0, 0, 0, 0, 0, 0, 0, true)(picard.sam.util.SamComparisonTest) Running Test: Test method testSamComparison[16](unsorted.sam, unsorted2.sam, false, false, 0, 1, 0, 0, 0, 0, 1, 0, false)(picard.sam.util.SamComparisonTest) Running Test: Test method testSamComparison[17](duplicate_base.sam, duplicate_four_mismatch_strict.sam, true, false, 14, 0, 0, 0, 0, 0, 0, 0, true)(picard.sam.util.SamComparisonTest) Running Test: Test method testSamComparison[18](duplicate_base.sam, duplicate_four_mismatch_lenient_one_align_differ.sam, true, false, 13, 1, 0, 0, 0, 0, 0, 4, false)(picard.sam.util.SamComparisonTest) Running Test: Test method testSamComparison[19](duplicate_base.sam, duplicate_two_mismatch_lenient.sam, true, false, 14, 0, 0, 0, 0, 0, 0, 2, false)(picard.sam.util.SamComparisonTest) Running Test: Test method testSamComparison[20](duplicate_base.sam, duplicate_four_mismatch_lenient.sam, true, false, 14, 0, 0, 0, 0, 0, 0, 4, false)(picard.sam.util.SamComparisonTest) Running Test: Test method testSamComparison[21](duplicate_base.sam, duplicate_four_mismatch_strict.sam, false, false, 14, 0, 0, 0, 0, 0, 0, 4, false)(picard.sam.util.SamComparisonTest) Running Test: Test method testSamComparison[22](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, true, false, 14, 0, 0, 0, 0, 0, 0, 0, true)(picard.sam.util.SamComparisonTest) Running Test: Test method testSamComparison[23](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_one_align_differ_queryname.sam, true, false, 13, 1, 0, 0, 0, 0, 0, 4, false)(picard.sam.util.SamComparisonTest) Running Test: Test method testSamComparison[24](duplicate_base_queryname.sam, duplicate_two_mismatch_lenient_queryname.sam, true, false, 14, 0, 0, 0, 0, 0, 0, 2, false)(picard.sam.util.SamComparisonTest) Running Test: Test method testSamComparison[25](duplicate_base_queryname.sam, duplicate_four_mismatch_lenient_queryname.sam, true, false, 14, 0, 0, 0, 0, 0, 0, 4, false)(picard.sam.util.SamComparisonTest) Running Test: Test method testSamComparison[26](duplicate_base_queryname.sam, duplicate_four_mismatch_strict_queryname.sam, false, false, 14, 0, 0, 0, 0, 0, 0, 4, false)(picard.sam.util.SamComparisonTest) Running Test: Test method testSamComparison[27](genomic_sorted.sam, mq0_2.sam, false, true, 1, 1, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) Running Test: Test method testSamComparison[28](mq0_1.sam, mq0_2.sam, false, true, 2, 0, 0, 0, 0, 0, 0, 0, true)(picard.sam.util.SamComparisonTest) Running Test: Test method testSamComparison[29](mq0_1.sam, mq0_2.sam, false, false, 1, 1, 0, 0, 0, 0, 0, 0, false)(picard.sam.util.SamComparisonTest) Running Test: Test method testConvert[0](testdata/picard/sam/SamFormatConverterTest/unmapped.sam, testdata/picard/sam/SamFormatConverterTest/unmapped.bam, .bam)(picard.sam.SamFormatConverterTest) Test: Test method testConvert[0](testdata/picard/sam/SamFormatConverterTest/unmapped.sam, testdata/picard/sam/SamFormatConverterTest/unmapped.bam, .bam)(picard.sam.SamFormatConverterTest) produced standard out/err: WARNING 2024-07-02 12:02:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Gradle suite > Gradle test > picard.sam.SamFormatConverterTest.testConvert[0](testdata/picard/sam/SamFormatConverterTest/unmapped.sam, testdata/picard/sam/SamFormatConverterTest/unmapped.bam, .bam) STANDARD_ERROR WARNING 2024-07-02 12:02:04 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testConvert[0](testdata/picard/sam/SamFormatConverterTest/unmapped.sam, testdata/picard/sam/SamFormatConverterTest/unmapped.bam, .bam)(picard.sam.SamFormatConverterTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.SamFormatConverterTest.testConvert[0](testdata/picard/sam/SamFormatConverterTest/unmapped.sam, testdata/picard/sam/SamFormatConverterTest/unmapped.bam, .bam) STANDARD_OUT No errors found Running Test: Test method testConvert[1](testdata/picard/sam/SamFormatConverterTest/unmapped.sam, testdata/picard/sam/SamFormatConverterTest/unmapped.cram, .cram)(picard.sam.SamFormatConverterTest) Test: Test method testConvert[1](testdata/picard/sam/SamFormatConverterTest/unmapped.sam, testdata/picard/sam/SamFormatConverterTest/unmapped.cram, .cram)(picard.sam.SamFormatConverterTest) produced standard out/err: WARNING 2024-07-02 12:02:05 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Gradle suite > Gradle test > picard.sam.SamFormatConverterTest.testConvert[1](testdata/picard/sam/SamFormatConverterTest/unmapped.sam, testdata/picard/sam/SamFormatConverterTest/unmapped.cram, .cram) STANDARD_ERROR WARNING 2024-07-02 12:02:05 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testConvert[1](testdata/picard/sam/SamFormatConverterTest/unmapped.sam, testdata/picard/sam/SamFormatConverterTest/unmapped.cram, .cram)(picard.sam.SamFormatConverterTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.SamFormatConverterTest.testConvert[1](testdata/picard/sam/SamFormatConverterTest/unmapped.sam, testdata/picard/sam/SamFormatConverterTest/unmapped.cram, .cram) STANDARD_OUT No errors found Running Test: Test method testConvert[2](testdata/picard/sam/SamFormatConverterTest/unmapped.bam, testdata/picard/sam/SamFormatConverterTest/unmapped.cram, .cram)(picard.sam.SamFormatConverterTest) Test: Test method testConvert[2](testdata/picard/sam/SamFormatConverterTest/unmapped.bam, testdata/picard/sam/SamFormatConverterTest/unmapped.cram, .cram)(picard.sam.SamFormatConverterTest) produced standard out/err: WARNING 2024-07-02 12:02:05 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Gradle suite > Gradle test > picard.sam.SamFormatConverterTest.testConvert[2](testdata/picard/sam/SamFormatConverterTest/unmapped.bam, testdata/picard/sam/SamFormatConverterTest/unmapped.cram, .cram) STANDARD_ERROR WARNING 2024-07-02 12:02:05 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testConvert[2](testdata/picard/sam/SamFormatConverterTest/unmapped.bam, testdata/picard/sam/SamFormatConverterTest/unmapped.cram, .cram)(picard.sam.SamFormatConverterTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.SamFormatConverterTest.testConvert[2](testdata/picard/sam/SamFormatConverterTest/unmapped.bam, testdata/picard/sam/SamFormatConverterTest/unmapped.cram, .cram) STANDARD_OUT No errors found Running Test: Test method testConvert[3](testdata/picard/sam/SamFormatConverterTest/unmapped.bam, testdata/picard/sam/SamFormatConverterTest/unmapped.sam, .sam)(picard.sam.SamFormatConverterTest) Test: Test method testConvert[3](testdata/picard/sam/SamFormatConverterTest/unmapped.bam, testdata/picard/sam/SamFormatConverterTest/unmapped.sam, .sam)(picard.sam.SamFormatConverterTest) produced standard out/err: WARNING 2024-07-02 12:02:05 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Gradle suite > Gradle test > picard.sam.SamFormatConverterTest.testConvert[3](testdata/picard/sam/SamFormatConverterTest/unmapped.bam, testdata/picard/sam/SamFormatConverterTest/unmapped.sam, .sam) STANDARD_ERROR WARNING 2024-07-02 12:02:05 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testConvert[3](testdata/picard/sam/SamFormatConverterTest/unmapped.bam, testdata/picard/sam/SamFormatConverterTest/unmapped.sam, .sam)(picard.sam.SamFormatConverterTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.SamFormatConverterTest.testConvert[3](testdata/picard/sam/SamFormatConverterTest/unmapped.bam, testdata/picard/sam/SamFormatConverterTest/unmapped.sam, .sam) STANDARD_OUT No errors found Running Test: Test method testConvert[4](testdata/picard/sam/SamFormatConverterTest/unmapped.cram, testdata/picard/sam/SamFormatConverterTest/unmapped.bam, .bam)(picard.sam.SamFormatConverterTest) Test: Test method testConvert[4](testdata/picard/sam/SamFormatConverterTest/unmapped.cram, testdata/picard/sam/SamFormatConverterTest/unmapped.bam, .bam)(picard.sam.SamFormatConverterTest) produced standard out/err: WARNING 2024-07-02 12:02:05 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Gradle suite > Gradle test > picard.sam.SamFormatConverterTest.testConvert[4](testdata/picard/sam/SamFormatConverterTest/unmapped.cram, testdata/picard/sam/SamFormatConverterTest/unmapped.bam, .bam) STANDARD_ERROR WARNING 2024-07-02 12:02:05 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testConvert[4](testdata/picard/sam/SamFormatConverterTest/unmapped.cram, testdata/picard/sam/SamFormatConverterTest/unmapped.bam, .bam)(picard.sam.SamFormatConverterTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.SamFormatConverterTest.testConvert[4](testdata/picard/sam/SamFormatConverterTest/unmapped.cram, testdata/picard/sam/SamFormatConverterTest/unmapped.bam, .bam) STANDARD_OUT No errors found Running Test: Test method testConvert[5](testdata/picard/sam/SamFormatConverterTest/unmapped.cram, testdata/picard/sam/SamFormatConverterTest/unmapped.sam, .sam)(picard.sam.SamFormatConverterTest) Test: Test method testConvert[5](testdata/picard/sam/SamFormatConverterTest/unmapped.cram, testdata/picard/sam/SamFormatConverterTest/unmapped.sam, .sam)(picard.sam.SamFormatConverterTest) produced standard out/err: WARNING 2024-07-02 12:02:05 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Gradle suite > Gradle test > picard.sam.SamFormatConverterTest.testConvert[5](testdata/picard/sam/SamFormatConverterTest/unmapped.cram, testdata/picard/sam/SamFormatConverterTest/unmapped.sam, .sam) STANDARD_ERROR WARNING 2024-07-02 12:02:05 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testConvert[5](testdata/picard/sam/SamFormatConverterTest/unmapped.cram, testdata/picard/sam/SamFormatConverterTest/unmapped.sam, .sam)(picard.sam.SamFormatConverterTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.SamFormatConverterTest.testConvert[5](testdata/picard/sam/SamFormatConverterTest/unmapped.cram, testdata/picard/sam/SamFormatConverterTest/unmapped.sam, .sam) STANDARD_OUT No errors found Running Test: Test method testBadFile[0](bad/unpaired-mate.sam)(picard.sam.SamToFastqTest) Test: Test method testBadFile[0](bad/unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: INFO 2024-07-02 12:02:05 SamToFastq Gradle suite > Gradle test > picard.sam.SamToFastqTest.testBadFile[0](bad/unpaired-mate.sam) STANDARD_ERROR INFO 2024-07-02 12:02:05 SamToFastq Test: Test method testBadFile[0](bad/unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testBadFile[0](bad/unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadFile[0](bad/unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testBadFile[0](bad/unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadFile[0](bad/unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadFile[0](bad/unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testBadFile[0](bad/unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadFile[0](bad/unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testBadFile[0](bad/unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/bad/unpaired-mate.sam -FASTQ /tmp/tt-pair1.6958861242052517335.fastq -SECOND_END_FASTQ /tmp/tt-pair2.12154093645883855498.fastq ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/bad/unpaired-mate.sam -FASTQ /tmp/tt-pair1.6958861242052517335.fastq -SECOND_END_FASTQ /tmp/tt-pair2.12154093645883855498.fastq Test: Test method testBadFile[0](bad/unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testBadFile[0](bad/unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testBadFile[0](bad/unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testBadFile[0](bad/unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:05.788 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:05.788 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadFile[0](bad/unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:05.788 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:05.788 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadFile[0](bad/unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:05.788 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:05.788 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadFile[0](bad/unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:05.788 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:05.788 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadFile[0](bad/unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:05 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/bad/unpaired-mate.sam FASTQ=/tmp/tt-pair1.6958861242052517335.fastq SECOND_END_FASTQ=/tmp/tt-pair2.12154093645883855498.fastq OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:05 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/bad/unpaired-mate.sam FASTQ=/tmp/tt-pair1.6958861242052517335.fastq SECOND_END_FASTQ=/tmp/tt-pair2.12154093645883855498.fastq OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBadFile[0](bad/unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBadFile[0](bad/unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:05 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:05 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. Test: Test method testBadFile[0](bad/unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testBadFile[0](bad/unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testBadGroupedFile[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) Test: Test method testBadGroupedFile[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: INFO 2024-07-02 12:02:05 SamToFastq Gradle suite > Gradle test > picard.sam.SamToFastqTest.testBadGroupedFile[0](bad/grouped-unpaired-mate.sam) STANDARD_ERROR INFO 2024-07-02 12:02:05 SamToFastq Test: Test method testBadGroupedFile[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testBadGroupedFile[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadGroupedFile[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testBadGroupedFile[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadGroupedFile[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadGroupedFile[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testBadGroupedFile[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadGroupedFile[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testBadGroupedFile[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** SamToFastq -INPUT testdata/picard/sam/bam2fastq/paired/bad/grouped-unpaired-mate.sam -FASTQ /tmp/pair12384574424004856340.fastq -SECOND_END_FASTQ /tmp/pair28027117258366614985.fastq ********** SamToFastq -INPUT testdata/picard/sam/bam2fastq/paired/bad/grouped-unpaired-mate.sam -FASTQ /tmp/pair12384574424004856340.fastq -SECOND_END_FASTQ /tmp/pair28027117258366614985.fastq Test: Test method testBadGroupedFile[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testBadGroupedFile[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testBadGroupedFile[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testBadGroupedFile[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:05.859 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:05.859 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadGroupedFile[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:05.860 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:05.860 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadGroupedFile[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:05.860 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:05.860 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadGroupedFile[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:05.860 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:05.860 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadGroupedFile[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:05 GMT+14:00 2024] SamToFastq INPUT=testdata/picard/sam/bam2fastq/paired/bad/grouped-unpaired-mate.sam FASTQ=/tmp/pair12384574424004856340.fastq SECOND_END_FASTQ=/tmp/pair28027117258366614985.fastq OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:05 GMT+14:00 2024] SamToFastq INPUT=testdata/picard/sam/bam2fastq/paired/bad/grouped-unpaired-mate.sam FASTQ=/tmp/pair12384574424004856340.fastq SECOND_END_FASTQ=/tmp/pair28027117258366614985.fastq OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBadGroupedFile[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBadGroupedFile[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:05 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:05 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. Test: Test method testBadGroupedFile[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testBadGroupedFile[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testBadGroupedFileOutputPerRg[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) Test: Test method testBadGroupedFileOutputPerRg[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: INFO 2024-07-02 12:02:05 SamToFastq Gradle suite > Gradle test > picard.sam.SamToFastqTest.testBadGroupedFileOutputPerRg[0](bad/grouped-unpaired-mate.sam) STANDARD_ERROR INFO 2024-07-02 12:02:05 SamToFastq Test: Test method testBadGroupedFileOutputPerRg[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testBadGroupedFileOutputPerRg[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBadGroupedFileOutputPerRg[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testBadGroupedFileOutputPerRg[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBadGroupedFileOutputPerRg[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBadGroupedFileOutputPerRg[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testBadGroupedFileOutputPerRg[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBadGroupedFileOutputPerRg[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testBadGroupedFileOutputPerRg[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** SamToFastq -INPUT testdata/picard/sam/bam2fastq/paired/bad/grouped-unpaired-mate.sam -OUTPUT_DIR /tmp/pbuilder2/ -OUTPUT_PER_RG true ********** SamToFastq -INPUT testdata/picard/sam/bam2fastq/paired/bad/grouped-unpaired-mate.sam -OUTPUT_DIR /tmp/pbuilder2/ -OUTPUT_PER_RG true Test: Test method testBadGroupedFileOutputPerRg[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testBadGroupedFileOutputPerRg[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testBadGroupedFileOutputPerRg[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testBadGroupedFileOutputPerRg[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:05.932 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:05.932 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadGroupedFileOutputPerRg[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:05.932 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:05.932 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadGroupedFileOutputPerRg[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:05.932 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:05.932 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBadGroupedFileOutputPerRg[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:05.932 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:05.932 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBadGroupedFileOutputPerRg[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:05 GMT+14:00 2024] SamToFastq INPUT=testdata/picard/sam/bam2fastq/paired/bad/grouped-unpaired-mate.sam OUTPUT_PER_RG=true OUTPUT_DIR=/tmp/pbuilder2 COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:05 GMT+14:00 2024] SamToFastq INPUT=testdata/picard/sam/bam2fastq/paired/bad/grouped-unpaired-mate.sam OUTPUT_PER_RG=true OUTPUT_DIR=/tmp/pbuilder2 COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBadGroupedFileOutputPerRg[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:05 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBadGroupedFileOutputPerRg[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:05 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:05 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. Test: Test method testBadGroupedFileOutputPerRg[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testBadGroupedFileOutputPerRg[0](bad/grouped-unpaired-mate.sam)(picard.sam.SamToFastqTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testClipping[0](null, AAAAAAAAAA, 1111111111, AAAAAAAAAA, 1111111111, CCCCCCCCCC, 2222222222, GGGGGGGGGG, 2222222222, No clipping test)(picard.sam.SamToFastqTest) Test: Test method testClipping[0](null, AAAAAAAAAA, 1111111111, AAAAAAAAAA, 1111111111, CCCCCCCCCC, 2222222222, GGGGGGGGGG, 2222222222, No clipping test)(picard.sam.SamToFastqTest) produced standard out/err: INFO 2024-07-02 12:02:06 SamToFastq Gradle suite > Gradle test > picard.sam.SamToFastqTest.testClipping[0](null, AAAAAAAAAA, 1111111111, AAAAAAAAAA, 1111111111, CCCCCCCCCC, 2222222222, GGGGGGGGGG, 2222222222, No clipping test) STANDARD_ERROR INFO 2024-07-02 12:02:06 SamToFastq Test: Test method testClipping[0](null, AAAAAAAAAA, 1111111111, AAAAAAAAAA, 1111111111, CCCCCCCCCC, 2222222222, GGGGGGGGGG, 2222222222, No clipping test)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testClipping[0](null, AAAAAAAAAA, 1111111111, AAAAAAAAAA, 1111111111, CCCCCCCCCC, 2222222222, GGGGGGGGGG, 2222222222, No clipping test)(picard.sam.SamToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testClipping[0](null, AAAAAAAAAA, 1111111111, AAAAAAAAAA, 1111111111, CCCCCCCCCC, 2222222222, GGGGGGGGGG, 2222222222, No clipping test)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testClipping[0](null, AAAAAAAAAA, 1111111111, AAAAAAAAAA, 1111111111, CCCCCCCCCC, 2222222222, GGGGGGGGGG, 2222222222, No clipping test)(picard.sam.SamToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testClipping[0](null, AAAAAAAAAA, 1111111111, AAAAAAAAAA, 1111111111, CCCCCCCCCC, 2222222222, GGGGGGGGGG, 2222222222, No clipping test)(picard.sam.SamToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testClipping[0](null, AAAAAAAAAA, 1111111111, AAAAAAAAAA, 1111111111, CCCCCCCCCC, 2222222222, GGGGGGGGGG, 2222222222, No clipping test)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testClipping[0](null, AAAAAAAAAA, 1111111111, AAAAAAAAAA, 1111111111, CCCCCCCCCC, 2222222222, GGGGGGGGGG, 2222222222, No clipping test)(picard.sam.SamToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testClipping[0](null, AAAAAAAAAA, 1111111111, AAAAAAAAAA, 1111111111, CCCCCCCCCC, 2222222222, GGGGGGGGGG, 2222222222, No clipping test)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testClipping[0](null, AAAAAAAAAA, 1111111111, AAAAAAAAAA, 1111111111, CCCCCCCCCC, 2222222222, GGGGGGGGGG, 2222222222, No clipping test)(picard.sam.SamToFastqTest) produced standard out/err: ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/clipping_test.sam -FASTQ /tmp/clippingtest114006169016371027847fastq -SECOND_END_FASTQ /tmp/clippingtest24959637556324793783fastq ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/clipping_test.sam -FASTQ /tmp/clippingtest114006169016371027847fastq -SECOND_END_FASTQ /tmp/clippingtest24959637556324793783fastq Test: Test method testClipping[0](null, AAAAAAAAAA, 1111111111, AAAAAAAAAA, 1111111111, CCCCCCCCCC, 2222222222, GGGGGGGGGG, 2222222222, No clipping test)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testClipping[0](null, AAAAAAAAAA, 1111111111, AAAAAAAAAA, 1111111111, CCCCCCCCCC, 2222222222, GGGGGGGGGG, 2222222222, No clipping test)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testClipping[0](null, AAAAAAAAAA, 1111111111, AAAAAAAAAA, 1111111111, CCCCCCCCCC, 2222222222, GGGGGGGGGG, 2222222222, No clipping test)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testClipping[0](null, AAAAAAAAAA, 1111111111, AAAAAAAAAA, 1111111111, CCCCCCCCCC, 2222222222, GGGGGGGGGG, 2222222222, No clipping test)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.015 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:06.015 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testClipping[0](null, AAAAAAAAAA, 1111111111, AAAAAAAAAA, 1111111111, CCCCCCCCCC, 2222222222, GGGGGGGGGG, 2222222222, No clipping test)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.015 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:06.015 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testClipping[0](null, AAAAAAAAAA, 1111111111, AAAAAAAAAA, 1111111111, CCCCCCCCCC, 2222222222, GGGGGGGGGG, 2222222222, No clipping test)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.015 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:06.015 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testClipping[0](null, AAAAAAAAAA, 1111111111, AAAAAAAAAA, 1111111111, CCCCCCCCCC, 2222222222, GGGGGGGGGG, 2222222222, No clipping test)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.015 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:06.015 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testClipping[0](null, AAAAAAAAAA, 1111111111, AAAAAAAAAA, 1111111111, CCCCCCCCCC, 2222222222, GGGGGGGGGG, 2222222222, No clipping test)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/clipping_test.sam FASTQ=/tmp/clippingtest114006169016371027847fastq SECOND_END_FASTQ=/tmp/clippingtest24959637556324793783fastq OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:06 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/clipping_test.sam FASTQ=/tmp/clippingtest114006169016371027847fastq SECOND_END_FASTQ=/tmp/clippingtest24959637556324793783fastq OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testClipping[0](null, AAAAAAAAAA, 1111111111, AAAAAAAAAA, 1111111111, CCCCCCCCCC, 2222222222, GGGGGGGGGG, 2222222222, No clipping test)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testClipping[0](null, AAAAAAAAAA, 1111111111, AAAAAAAAAA, 1111111111, CCCCCCCCCC, 2222222222, GGGGGGGGGG, 2222222222, No clipping test)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:06 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. Test: Test method testClipping[0](null, AAAAAAAAAA, 1111111111, AAAAAAAAAA, 1111111111, CCCCCCCCCC, 2222222222, GGGGGGGGGG, 2222222222, No clipping test)(picard.sam.SamToFastqTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testClipping[1](X, AAAAAAA, 1111111, AAAAAA, 111111, CCCCCCCC, 22222222, GGGGGG, 222222, Cut clipped bases test)(picard.sam.SamToFastqTest) Test: Test method testClipping[1](X, AAAAAAA, 1111111, AAAAAA, 111111, CCCCCCCC, 22222222, GGGGGG, 222222, Cut clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: INFO 2024-07-02 12:02:06 SamToFastq Gradle suite > Gradle test > picard.sam.SamToFastqTest.testClipping[1](X, AAAAAAA, 1111111, AAAAAA, 111111, CCCCCCCC, 22222222, GGGGGG, 222222, Cut clipped bases test) STANDARD_ERROR INFO 2024-07-02 12:02:06 SamToFastq Test: Test method testClipping[1](X, AAAAAAA, 1111111, AAAAAA, 111111, CCCCCCCC, 22222222, GGGGGG, 222222, Cut clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testClipping[1](X, AAAAAAA, 1111111, AAAAAA, 111111, CCCCCCCC, 22222222, GGGGGG, 222222, Cut clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testClipping[1](X, AAAAAAA, 1111111, AAAAAA, 111111, CCCCCCCC, 22222222, GGGGGG, 222222, Cut clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testClipping[1](X, AAAAAAA, 1111111, AAAAAA, 111111, CCCCCCCC, 22222222, GGGGGG, 222222, Cut clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testClipping[1](X, AAAAAAA, 1111111, AAAAAA, 111111, CCCCCCCC, 22222222, GGGGGG, 222222, Cut clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testClipping[1](X, AAAAAAA, 1111111, AAAAAA, 111111, CCCCCCCC, 22222222, GGGGGG, 222222, Cut clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testClipping[1](X, AAAAAAA, 1111111, AAAAAA, 111111, CCCCCCCC, 22222222, GGGGGG, 222222, Cut clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testClipping[1](X, AAAAAAA, 1111111, AAAAAA, 111111, CCCCCCCC, 22222222, GGGGGG, 222222, Cut clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testClipping[1](X, AAAAAAA, 1111111, AAAAAA, 111111, CCCCCCCC, 22222222, GGGGGG, 222222, Cut clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/clipping_test.sam -FASTQ /tmp/clippingtest16737222120754322366fastq -SECOND_END_FASTQ /tmp/clippingtest216024408532092647363fastq -CLIPPING_ACTION X -CLIPPING_ATTRIBUTE XT ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/clipping_test.sam -FASTQ /tmp/clippingtest16737222120754322366fastq -SECOND_END_FASTQ /tmp/clippingtest216024408532092647363fastq -CLIPPING_ACTION X -CLIPPING_ATTRIBUTE XT Test: Test method testClipping[1](X, AAAAAAA, 1111111, AAAAAA, 111111, CCCCCCCC, 22222222, GGGGGG, 222222, Cut clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testClipping[1](X, AAAAAAA, 1111111, AAAAAA, 111111, CCCCCCCC, 22222222, GGGGGG, 222222, Cut clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testClipping[1](X, AAAAAAA, 1111111, AAAAAA, 111111, CCCCCCCC, 22222222, GGGGGG, 222222, Cut clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testClipping[1](X, AAAAAAA, 1111111, AAAAAA, 111111, CCCCCCCC, 22222222, GGGGGG, 222222, Cut clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.094 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:06.094 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testClipping[1](X, AAAAAAA, 1111111, AAAAAA, 111111, CCCCCCCC, 22222222, GGGGGG, 222222, Cut clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.094 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:06.094 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testClipping[1](X, AAAAAAA, 1111111, AAAAAA, 111111, CCCCCCCC, 22222222, GGGGGG, 222222, Cut clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.094 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:06.094 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testClipping[1](X, AAAAAAA, 1111111, AAAAAA, 111111, CCCCCCCC, 22222222, GGGGGG, 222222, Cut clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.094 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:06.094 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testClipping[1](X, AAAAAAA, 1111111, AAAAAA, 111111, CCCCCCCC, 22222222, GGGGGG, 222222, Cut clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/clipping_test.sam FASTQ=/tmp/clippingtest16737222120754322366fastq SECOND_END_FASTQ=/tmp/clippingtest216024408532092647363fastq CLIPPING_ATTRIBUTE=XT CLIPPING_ACTION=X OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:06 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/clipping_test.sam FASTQ=/tmp/clippingtest16737222120754322366fastq SECOND_END_FASTQ=/tmp/clippingtest216024408532092647363fastq CLIPPING_ATTRIBUTE=XT CLIPPING_ACTION=X OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testClipping[1](X, AAAAAAA, 1111111, AAAAAA, 111111, CCCCCCCC, 22222222, GGGGGG, 222222, Cut clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testClipping[1](X, AAAAAAA, 1111111, AAAAAA, 111111, CCCCCCCC, 22222222, GGGGGG, 222222, Cut clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:06 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. Test: Test method testClipping[1](X, AAAAAAA, 1111111, AAAAAA, 111111, CCCCCCCC, 22222222, GGGGGG, 222222, Cut clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testClipping[2](N, AAAAAAANNN, 1111111111, AAAAAANNNN, 1111111111, CCCCCCCCNN, 2222222222, GGGGGGNNNN, 2222222222, Mask clipped bases test)(picard.sam.SamToFastqTest) Test: Test method testClipping[2](N, AAAAAAANNN, 1111111111, AAAAAANNNN, 1111111111, CCCCCCCCNN, 2222222222, GGGGGGNNNN, 2222222222, Mask clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: INFO 2024-07-02 12:02:06 SamToFastq Gradle suite > Gradle test > picard.sam.SamToFastqTest.testClipping[2](N, AAAAAAANNN, 1111111111, AAAAAANNNN, 1111111111, CCCCCCCCNN, 2222222222, GGGGGGNNNN, 2222222222, Mask clipped bases test) STANDARD_ERROR INFO 2024-07-02 12:02:06 SamToFastq Test: Test method testClipping[2](N, AAAAAAANNN, 1111111111, AAAAAANNNN, 1111111111, CCCCCCCCNN, 2222222222, GGGGGGNNNN, 2222222222, Mask clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testClipping[2](N, AAAAAAANNN, 1111111111, AAAAAANNNN, 1111111111, CCCCCCCCNN, 2222222222, GGGGGGNNNN, 2222222222, Mask clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testClipping[2](N, AAAAAAANNN, 1111111111, AAAAAANNNN, 1111111111, CCCCCCCCNN, 2222222222, GGGGGGNNNN, 2222222222, Mask clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testClipping[2](N, AAAAAAANNN, 1111111111, AAAAAANNNN, 1111111111, CCCCCCCCNN, 2222222222, GGGGGGNNNN, 2222222222, Mask clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testClipping[2](N, AAAAAAANNN, 1111111111, AAAAAANNNN, 1111111111, CCCCCCCCNN, 2222222222, GGGGGGNNNN, 2222222222, Mask clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testClipping[2](N, AAAAAAANNN, 1111111111, AAAAAANNNN, 1111111111, CCCCCCCCNN, 2222222222, GGGGGGNNNN, 2222222222, Mask clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testClipping[2](N, AAAAAAANNN, 1111111111, AAAAAANNNN, 1111111111, CCCCCCCCNN, 2222222222, GGGGGGNNNN, 2222222222, Mask clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testClipping[2](N, AAAAAAANNN, 1111111111, AAAAAANNNN, 1111111111, CCCCCCCCNN, 2222222222, GGGGGGNNNN, 2222222222, Mask clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testClipping[2](N, AAAAAAANNN, 1111111111, AAAAAANNNN, 1111111111, CCCCCCCCNN, 2222222222, GGGGGGNNNN, 2222222222, Mask clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/clipping_test.sam -FASTQ /tmp/clippingtest17570146371606990246fastq -SECOND_END_FASTQ /tmp/clippingtest27702660905638902222fastq -CLIPPING_ACTION N -CLIPPING_ATTRIBUTE XT ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/clipping_test.sam -FASTQ /tmp/clippingtest17570146371606990246fastq -SECOND_END_FASTQ /tmp/clippingtest27702660905638902222fastq -CLIPPING_ACTION N -CLIPPING_ATTRIBUTE XT Test: Test method testClipping[2](N, AAAAAAANNN, 1111111111, AAAAAANNNN, 1111111111, CCCCCCCCNN, 2222222222, GGGGGGNNNN, 2222222222, Mask clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testClipping[2](N, AAAAAAANNN, 1111111111, AAAAAANNNN, 1111111111, CCCCCCCCNN, 2222222222, GGGGGGNNNN, 2222222222, Mask clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testClipping[2](N, AAAAAAANNN, 1111111111, AAAAAANNNN, 1111111111, CCCCCCCCNN, 2222222222, GGGGGGNNNN, 2222222222, Mask clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testClipping[2](N, AAAAAAANNN, 1111111111, AAAAAANNNN, 1111111111, CCCCCCCCNN, 2222222222, GGGGGGNNNN, 2222222222, Mask clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.171 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:06.171 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testClipping[2](N, AAAAAAANNN, 1111111111, AAAAAANNNN, 1111111111, CCCCCCCCNN, 2222222222, GGGGGGNNNN, 2222222222, Mask clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.171 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:06.171 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testClipping[2](N, AAAAAAANNN, 1111111111, AAAAAANNNN, 1111111111, CCCCCCCCNN, 2222222222, GGGGGGNNNN, 2222222222, Mask clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.171 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:06.171 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testClipping[2](N, AAAAAAANNN, 1111111111, AAAAAANNNN, 1111111111, CCCCCCCCNN, 2222222222, GGGGGGNNNN, 2222222222, Mask clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.171 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:06.171 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testClipping[2](N, AAAAAAANNN, 1111111111, AAAAAANNNN, 1111111111, CCCCCCCCNN, 2222222222, GGGGGGNNNN, 2222222222, Mask clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/clipping_test.sam FASTQ=/tmp/clippingtest17570146371606990246fastq SECOND_END_FASTQ=/tmp/clippingtest27702660905638902222fastq CLIPPING_ATTRIBUTE=XT CLIPPING_ACTION=N OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:06 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/clipping_test.sam FASTQ=/tmp/clippingtest17570146371606990246fastq SECOND_END_FASTQ=/tmp/clippingtest27702660905638902222fastq CLIPPING_ATTRIBUTE=XT CLIPPING_ACTION=N OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testClipping[2](N, AAAAAAANNN, 1111111111, AAAAAANNNN, 1111111111, CCCCCCCCNN, 2222222222, GGGGGGNNNN, 2222222222, Mask clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testClipping[2](N, AAAAAAANNN, 1111111111, AAAAAANNNN, 1111111111, CCCCCCCCNN, 2222222222, GGGGGGNNNN, 2222222222, Mask clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:06 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. Test: Test method testClipping[2](N, AAAAAAANNN, 1111111111, AAAAAANNNN, 1111111111, CCCCCCCCNN, 2222222222, GGGGGGNNNN, 2222222222, Mask clipped bases test)(picard.sam.SamToFastqTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testClipping[3](2, AAAAAAAAAA, 1111111###, AAAAAAAAAA, 111111####, CCCCCCCCCC, 22222222##, GGGGGGGGGG, 222222####, Change clipped qualities test)(picard.sam.SamToFastqTest) Test: Test method testClipping[3](2, AAAAAAAAAA, 1111111###, AAAAAAAAAA, 111111####, CCCCCCCCCC, 22222222##, GGGGGGGGGG, 222222####, Change clipped qualities test)(picard.sam.SamToFastqTest) produced standard out/err: INFO 2024-07-02 12:02:06 SamToFastq Gradle suite > Gradle test > picard.sam.SamToFastqTest.testClipping[3](2, AAAAAAAAAA, 1111111###, AAAAAAAAAA, 111111####, CCCCCCCCCC, 22222222##, GGGGGGGGGG, 222222####, Change clipped qualities test) STANDARD_ERROR INFO 2024-07-02 12:02:06 SamToFastq Test: Test method testClipping[3](2, AAAAAAAAAA, 1111111###, AAAAAAAAAA, 111111####, CCCCCCCCCC, 22222222##, GGGGGGGGGG, 222222####, Change clipped qualities test)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testClipping[3](2, AAAAAAAAAA, 1111111###, AAAAAAAAAA, 111111####, CCCCCCCCCC, 22222222##, GGGGGGGGGG, 222222####, Change clipped qualities test)(picard.sam.SamToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testClipping[3](2, AAAAAAAAAA, 1111111###, AAAAAAAAAA, 111111####, CCCCCCCCCC, 22222222##, GGGGGGGGGG, 222222####, Change clipped qualities test)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testClipping[3](2, AAAAAAAAAA, 1111111###, AAAAAAAAAA, 111111####, CCCCCCCCCC, 22222222##, GGGGGGGGGG, 222222####, Change clipped qualities test)(picard.sam.SamToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testClipping[3](2, AAAAAAAAAA, 1111111###, AAAAAAAAAA, 111111####, CCCCCCCCCC, 22222222##, GGGGGGGGGG, 222222####, Change clipped qualities test)(picard.sam.SamToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testClipping[3](2, AAAAAAAAAA, 1111111###, AAAAAAAAAA, 111111####, CCCCCCCCCC, 22222222##, GGGGGGGGGG, 222222####, Change clipped qualities test)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testClipping[3](2, AAAAAAAAAA, 1111111###, AAAAAAAAAA, 111111####, CCCCCCCCCC, 22222222##, GGGGGGGGGG, 222222####, Change clipped qualities test)(picard.sam.SamToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testClipping[3](2, AAAAAAAAAA, 1111111###, AAAAAAAAAA, 111111####, CCCCCCCCCC, 22222222##, GGGGGGGGGG, 222222####, Change clipped qualities test)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testClipping[3](2, AAAAAAAAAA, 1111111###, AAAAAAAAAA, 111111####, CCCCCCCCCC, 22222222##, GGGGGGGGGG, 222222####, Change clipped qualities test)(picard.sam.SamToFastqTest) produced standard out/err: ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/clipping_test.sam -FASTQ /tmp/clippingtest19774369231823369454fastq -SECOND_END_FASTQ /tmp/clippingtest21127466535411686640fastq -CLIPPING_ACTION 2 -CLIPPING_ATTRIBUTE XT ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/clipping_test.sam -FASTQ /tmp/clippingtest19774369231823369454fastq -SECOND_END_FASTQ /tmp/clippingtest21127466535411686640fastq -CLIPPING_ACTION 2 -CLIPPING_ATTRIBUTE XT Test: Test method testClipping[3](2, AAAAAAAAAA, 1111111###, AAAAAAAAAA, 111111####, CCCCCCCCCC, 22222222##, GGGGGGGGGG, 222222####, Change clipped qualities test)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testClipping[3](2, AAAAAAAAAA, 1111111###, AAAAAAAAAA, 111111####, CCCCCCCCCC, 22222222##, GGGGGGGGGG, 222222####, Change clipped qualities test)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testClipping[3](2, AAAAAAAAAA, 1111111###, AAAAAAAAAA, 111111####, CCCCCCCCCC, 22222222##, GGGGGGGGGG, 222222####, Change clipped qualities test)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testClipping[3](2, AAAAAAAAAA, 1111111###, AAAAAAAAAA, 111111####, CCCCCCCCCC, 22222222##, GGGGGGGGGG, 222222####, Change clipped qualities test)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.261 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:06.261 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testClipping[3](2, AAAAAAAAAA, 1111111###, AAAAAAAAAA, 111111####, CCCCCCCCCC, 22222222##, GGGGGGGGGG, 222222####, Change clipped qualities test)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.261 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:06.261 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testClipping[3](2, AAAAAAAAAA, 1111111###, AAAAAAAAAA, 111111####, CCCCCCCCCC, 22222222##, GGGGGGGGGG, 222222####, Change clipped qualities test)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.262 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:06.262 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testClipping[3](2, AAAAAAAAAA, 1111111###, AAAAAAAAAA, 111111####, CCCCCCCCCC, 22222222##, GGGGGGGGGG, 222222####, Change clipped qualities test)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.262 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:06.262 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testClipping[3](2, AAAAAAAAAA, 1111111###, AAAAAAAAAA, 111111####, CCCCCCCCCC, 22222222##, GGGGGGGGGG, 222222####, Change clipped qualities test)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/clipping_test.sam FASTQ=/tmp/clippingtest19774369231823369454fastq SECOND_END_FASTQ=/tmp/clippingtest21127466535411686640fastq CLIPPING_ATTRIBUTE=XT CLIPPING_ACTION=2 OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:06 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/clipping_test.sam FASTQ=/tmp/clippingtest19774369231823369454fastq SECOND_END_FASTQ=/tmp/clippingtest21127466535411686640fastq CLIPPING_ATTRIBUTE=XT CLIPPING_ACTION=2 OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testClipping[3](2, AAAAAAAAAA, 1111111###, AAAAAAAAAA, 111111####, CCCCCCCCCC, 22222222##, GGGGGGGGGG, 222222####, Change clipped qualities test)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testClipping[3](2, AAAAAAAAAA, 1111111###, AAAAAAAAAA, 111111####, CCCCCCCCCC, 22222222##, GGGGGGGGGG, 222222####, Change clipped qualities test)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:06 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. Test: Test method testClipping[3](2, AAAAAAAAAA, 1111111###, AAAAAAAAAA, 111111####, CCCCCCCCCC, 22222222##, GGGGGGGGGG, 222222####, Change clipped qualities test)(picard.sam.SamToFastqTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testFileCompression[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) Test: Test method testFileCompression[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: INFO 2024-07-02 12:02:06 SamToFastq Gradle suite > Gradle test > picard.sam.SamToFastqTest.testFileCompression[0](ok/sorted-pair.sam) STANDARD_ERROR INFO 2024-07-02 12:02:06 SamToFastq Test: Test method testFileCompression[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testFileCompression[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFileCompression[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testFileCompression[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFileCompression[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFileCompression[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testFileCompression[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFileCompression[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testFileCompression[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam -FASTQ /tmp/pair113180045237050741509.fastq.gz -SECOND_END_FASTQ /tmp/pair211597133614651828721.fastq.gz ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam -FASTQ /tmp/pair113180045237050741509.fastq.gz -SECOND_END_FASTQ /tmp/pair211597133614651828721.fastq.gz Test: Test method testFileCompression[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testFileCompression[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testFileCompression[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testFileCompression[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.337 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:06.337 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFileCompression[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.337 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:06.337 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFileCompression[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.337 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:06.337 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFileCompression[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.337 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:06.337 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFileCompression[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam FASTQ=/tmp/pair113180045237050741509.fastq.gz SECOND_END_FASTQ=/tmp/pair211597133614651828721.fastq.gz OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:06 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam FASTQ=/tmp/pair113180045237050741509.fastq.gz SECOND_END_FASTQ=/tmp/pair211597133614651828721.fastq.gz OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFileCompression[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFileCompression[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:06 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. Test: Test method testFileCompression[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testFileCompression[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) Test: Test method testFileCompression[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: INFO 2024-07-02 12:02:06 SamToFastq Gradle suite > Gradle test > picard.sam.SamToFastqTest.testFileCompression[1](ok/sorted-pair-no-rg.sam) STANDARD_ERROR INFO 2024-07-02 12:02:06 SamToFastq Test: Test method testFileCompression[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testFileCompression[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFileCompression[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testFileCompression[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFileCompression[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFileCompression[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testFileCompression[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFileCompression[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testFileCompression[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair-no-rg.sam -FASTQ /tmp/pair11409669725972516744.fastq.gz -SECOND_END_FASTQ /tmp/pair210128230629107231720.fastq.gz ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair-no-rg.sam -FASTQ /tmp/pair11409669725972516744.fastq.gz -SECOND_END_FASTQ /tmp/pair210128230629107231720.fastq.gz Test: Test method testFileCompression[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testFileCompression[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testFileCompression[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testFileCompression[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.411 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:06.411 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFileCompression[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.411 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:06.411 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFileCompression[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.411 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:06.411 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFileCompression[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.411 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:06.411 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFileCompression[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair-no-rg.sam FASTQ=/tmp/pair11409669725972516744.fastq.gz SECOND_END_FASTQ=/tmp/pair210128230629107231720.fastq.gz OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:06 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair-no-rg.sam FASTQ=/tmp/pair11409669725972516744.fastq.gz SECOND_END_FASTQ=/tmp/pair210128230629107231720.fastq.gz OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFileCompression[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFileCompression[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:06 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. Test: Test method testFileCompression[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testFileCompression[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) Test: Test method testFileCompression[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: INFO 2024-07-02 12:02:06 SamToFastq Gradle suite > Gradle test > picard.sam.SamToFastqTest.testFileCompression[2](ok/last-pair-mates-flipped.sam) STANDARD_ERROR INFO 2024-07-02 12:02:06 SamToFastq Test: Test method testFileCompression[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testFileCompression[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFileCompression[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testFileCompression[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFileCompression[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFileCompression[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testFileCompression[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFileCompression[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testFileCompression[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/last-pair-mates-flipped.sam -FASTQ /tmp/pair13916987748707008496.fastq.gz -SECOND_END_FASTQ /tmp/pair27042887625246539630.fastq.gz ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/last-pair-mates-flipped.sam -FASTQ /tmp/pair13916987748707008496.fastq.gz -SECOND_END_FASTQ /tmp/pair27042887625246539630.fastq.gz Test: Test method testFileCompression[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testFileCompression[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testFileCompression[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testFileCompression[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.487 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:06.487 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFileCompression[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.487 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:06.487 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFileCompression[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.488 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:06.488 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFileCompression[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.488 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:06.488 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFileCompression[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/last-pair-mates-flipped.sam FASTQ=/tmp/pair13916987748707008496.fastq.gz SECOND_END_FASTQ=/tmp/pair27042887625246539630.fastq.gz OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:06 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/last-pair-mates-flipped.sam FASTQ=/tmp/pair13916987748707008496.fastq.gz SECOND_END_FASTQ=/tmp/pair27042887625246539630.fastq.gz OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFileCompression[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFileCompression[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:06 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. Test: Test method testFileCompression[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testFileCompression[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) Test: Test method testFileCompression[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: INFO 2024-07-02 12:02:06 SamToFastq Gradle suite > Gradle test > picard.sam.SamToFastqTest.testFileCompression[3](ok/first-mate-bof-last-mate-eof.sam) STANDARD_ERROR INFO 2024-07-02 12:02:06 SamToFastq Test: Test method testFileCompression[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testFileCompression[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testFileCompression[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testFileCompression[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testFileCompression[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testFileCompression[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testFileCompression[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testFileCompression[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testFileCompression[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/first-mate-bof-last-mate-eof.sam -FASTQ /tmp/pair118339523838434469413.fastq.gz -SECOND_END_FASTQ /tmp/pair26865406536588965911.fastq.gz ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/first-mate-bof-last-mate-eof.sam -FASTQ /tmp/pair118339523838434469413.fastq.gz -SECOND_END_FASTQ /tmp/pair26865406536588965911.fastq.gz Test: Test method testFileCompression[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testFileCompression[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testFileCompression[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testFileCompression[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.563 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:06.563 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFileCompression[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.564 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:06.564 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFileCompression[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.564 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:06.564 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testFileCompression[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.564 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:06.564 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testFileCompression[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/first-mate-bof-last-mate-eof.sam FASTQ=/tmp/pair118339523838434469413.fastq.gz SECOND_END_FASTQ=/tmp/pair26865406536588965911.fastq.gz OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:06 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/first-mate-bof-last-mate-eof.sam FASTQ=/tmp/pair118339523838434469413.fastq.gz SECOND_END_FASTQ=/tmp/pair26865406536588965911.fastq.gz OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testFileCompression[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testFileCompression[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:06 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. Test: Test method testFileCompression[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testMissingRgFile[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) Test: Test method testMissingRgFile[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: INFO 2024-07-02 12:02:06 SamToFastq Gradle suite > Gradle test > picard.sam.SamToFastqTest.testMissingRgFile[0](bad/missing-rg-info.sam) STANDARD_ERROR INFO 2024-07-02 12:02:06 SamToFastq Test: Test method testMissingRgFile[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testMissingRgFile[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingRgFile[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testMissingRgFile[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingRgFile[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingRgFile[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testMissingRgFile[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingRgFile[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testMissingRgFile[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/bad/missing-rg-info.sam -FASTQ /tmp/pair116887798188110947856.fastq -SECOND_END_FASTQ /tmp/pair24496534734386081125.fastq ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/bad/missing-rg-info.sam -FASTQ /tmp/pair116887798188110947856.fastq -SECOND_END_FASTQ /tmp/pair24496534734386081125.fastq Test: Test method testMissingRgFile[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testMissingRgFile[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testMissingRgFile[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testMissingRgFile[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.653 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:06.653 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingRgFile[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.653 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:06.653 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingRgFile[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.654 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:06.654 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingRgFile[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.654 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:06.654 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingRgFile[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/bad/missing-rg-info.sam FASTQ=/tmp/pair116887798188110947856.fastq SECOND_END_FASTQ=/tmp/pair24496534734386081125.fastq OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:06 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/bad/missing-rg-info.sam FASTQ=/tmp/pair116887798188110947856.fastq SECOND_END_FASTQ=/tmp/pair24496534734386081125.fastq OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingRgFile[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingRgFile[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:06 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. Test: Test method testMissingRgFile[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testMissingRgFileOutputPerRg[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) Test: Test method testMissingRgFileOutputPerRg[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: INFO 2024-07-02 12:02:06 SamToFastq Gradle suite > Gradle test > picard.sam.SamToFastqTest.testMissingRgFileOutputPerRg[0](bad/missing-rg-info.sam) STANDARD_ERROR INFO 2024-07-02 12:02:06 SamToFastq Test: Test method testMissingRgFileOutputPerRg[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testMissingRgFileOutputPerRg[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testMissingRgFileOutputPerRg[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testMissingRgFileOutputPerRg[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testMissingRgFileOutputPerRg[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testMissingRgFileOutputPerRg[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testMissingRgFileOutputPerRg[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testMissingRgFileOutputPerRg[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testMissingRgFileOutputPerRg[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** SamToFastq -INPUT testdata/picard/sam/bam2fastq/paired/bad/missing-rg-info.sam -OUTPUT_DIR /tmp/pbuilder2/ -OUTPUT_PER_RG true ********** SamToFastq -INPUT testdata/picard/sam/bam2fastq/paired/bad/missing-rg-info.sam -OUTPUT_DIR /tmp/pbuilder2/ -OUTPUT_PER_RG true Test: Test method testMissingRgFileOutputPerRg[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testMissingRgFileOutputPerRg[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testMissingRgFileOutputPerRg[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testMissingRgFileOutputPerRg[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.755 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:06.755 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingRgFileOutputPerRg[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.755 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:06.755 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingRgFileOutputPerRg[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.755 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:06.755 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testMissingRgFileOutputPerRg[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.755 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:06.755 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testMissingRgFileOutputPerRg[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] SamToFastq INPUT=testdata/picard/sam/bam2fastq/paired/bad/missing-rg-info.sam OUTPUT_PER_RG=true OUTPUT_DIR=/tmp/pbuilder2 COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:06 GMT+14:00 2024] SamToFastq INPUT=testdata/picard/sam/bam2fastq/paired/bad/missing-rg-info.sam OUTPUT_PER_RG=true OUTPUT_DIR=/tmp/pbuilder2 COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testMissingRgFileOutputPerRg[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testMissingRgFileOutputPerRg[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:06 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. Test: Test method testMissingRgFileOutputPerRg[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testMissingRgFileOutputPerRg[0](bad/missing-rg-info.sam)(picard.sam.SamToFastqTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testOkFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) Test: Test method testOkFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: INFO 2024-07-02 12:02:06 SamToFastq Gradle suite > Gradle test > picard.sam.SamToFastqTest.testOkFile[0](ok/sorted-pair.sam) STANDARD_ERROR INFO 2024-07-02 12:02:06 SamToFastq Test: Test method testOkFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testOkFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOkFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOkFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOkFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOkFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam -FASTQ /tmp/pair115930850973347543725.fastq -SECOND_END_FASTQ /tmp/pair26198476426436720894.fastq ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam -FASTQ /tmp/pair115930850973347543725.fastq -SECOND_END_FASTQ /tmp/pair26198476426436720894.fastq Test: Test method testOkFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testOkFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testOkFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.825 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:06.825 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOkFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.833 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:06.833 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOkFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.833 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:06.833 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOkFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.833 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:06.833 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOkFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam FASTQ=/tmp/pair115930850973347543725.fastq SECOND_END_FASTQ=/tmp/pair26198476426436720894.fastq OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:06 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam FASTQ=/tmp/pair115930850973347543725.fastq SECOND_END_FASTQ=/tmp/pair26198476426436720894.fastq OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOkFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOkFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:06 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. Test: Test method testOkFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testOkFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) Test: Test method testOkFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: INFO 2024-07-02 12:02:06 SamToFastq Gradle suite > Gradle test > picard.sam.SamToFastqTest.testOkFile[1](ok/sorted-pair-no-rg.sam) STANDARD_ERROR INFO 2024-07-02 12:02:06 SamToFastq Test: Test method testOkFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testOkFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOkFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOkFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOkFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOkFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair-no-rg.sam -FASTQ /tmp/pair117963795530510164869.fastq -SECOND_END_FASTQ /tmp/pair23687953860798194110.fastq ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair-no-rg.sam -FASTQ /tmp/pair117963795530510164869.fastq -SECOND_END_FASTQ /tmp/pair23687953860798194110.fastq Test: Test method testOkFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testOkFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testOkFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.911 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:06.911 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOkFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.911 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:06.911 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOkFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.911 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:06.911 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOkFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.911 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:06.911 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOkFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair-no-rg.sam FASTQ=/tmp/pair117963795530510164869.fastq SECOND_END_FASTQ=/tmp/pair23687953860798194110.fastq OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:06 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair-no-rg.sam FASTQ=/tmp/pair117963795530510164869.fastq SECOND_END_FASTQ=/tmp/pair23687953860798194110.fastq OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOkFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOkFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:06 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. Test: Test method testOkFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testOkFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) Test: Test method testOkFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: INFO 2024-07-02 12:02:06 SamToFastq Gradle suite > Gradle test > picard.sam.SamToFastqTest.testOkFile[2](ok/last-pair-mates-flipped.sam) STANDARD_ERROR INFO 2024-07-02 12:02:06 SamToFastq Test: Test method testOkFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testOkFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOkFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOkFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOkFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOkFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/last-pair-mates-flipped.sam -FASTQ /tmp/pair115752041723297919127.fastq -SECOND_END_FASTQ /tmp/pair23549349645287921033.fastq ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/last-pair-mates-flipped.sam -FASTQ /tmp/pair115752041723297919127.fastq -SECOND_END_FASTQ /tmp/pair23549349645287921033.fastq Test: Test method testOkFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testOkFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testOkFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.995 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:06.995 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOkFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.995 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:06.995 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOkFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.996 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:06.996 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOkFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:06.996 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:06.996 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOkFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/last-pair-mates-flipped.sam FASTQ=/tmp/pair115752041723297919127.fastq SECOND_END_FASTQ=/tmp/pair23549349645287921033.fastq OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:06 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/last-pair-mates-flipped.sam FASTQ=/tmp/pair115752041723297919127.fastq SECOND_END_FASTQ=/tmp/pair23549349645287921033.fastq OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOkFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:06 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOkFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:07 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:07 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. Test: Test method testOkFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testOkFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) Test: Test method testOkFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: INFO 2024-07-02 12:02:07 SamToFastq Gradle suite > Gradle test > picard.sam.SamToFastqTest.testOkFile[3](ok/first-mate-bof-last-mate-eof.sam) STANDARD_ERROR INFO 2024-07-02 12:02:07 SamToFastq Test: Test method testOkFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testOkFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOkFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOkFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOkFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOkFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/first-mate-bof-last-mate-eof.sam -FASTQ /tmp/pair112545200130172470603.fastq -SECOND_END_FASTQ /tmp/pair2218976940162810737.fastq ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/first-mate-bof-last-mate-eof.sam -FASTQ /tmp/pair112545200130172470603.fastq -SECOND_END_FASTQ /tmp/pair2218976940162810737.fastq Test: Test method testOkFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testOkFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testOkFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.081 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:07.081 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOkFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.081 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:07.081 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOkFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.081 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:07.081 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOkFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.081 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:07.081 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOkFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:07 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/first-mate-bof-last-mate-eof.sam FASTQ=/tmp/pair112545200130172470603.fastq SECOND_END_FASTQ=/tmp/pair2218976940162810737.fastq OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:07 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/first-mate-bof-last-mate-eof.sam FASTQ=/tmp/pair112545200130172470603.fastq SECOND_END_FASTQ=/tmp/pair2218976940162810737.fastq OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOkFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOkFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:07 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:07 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. Test: Test method testOkFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@3fc2f5a3)(picard.sam.SamToFastqTest) Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@3fc2f5a3)(picard.sam.SamToFastqTest) produced standard out/err: INFO 2024-07-02 12:02:07 SamToFastq Gradle suite > Gradle test > picard.sam.SamToFastqTest.testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@3fc2f5a3) STANDARD_ERROR INFO 2024-07-02 12:02:07 SamToFastq Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@3fc2f5a3)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@3fc2f5a3)(picard.sam.SamToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@3fc2f5a3)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@3fc2f5a3)(picard.sam.SamToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@3fc2f5a3)(picard.sam.SamToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@3fc2f5a3)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@3fc2f5a3)(picard.sam.SamToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@3fc2f5a3)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@3fc2f5a3)(picard.sam.SamToFastqTest) produced standard out/err: ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/grouped-last-pair-mates-flipped.sam -OUTPUT_PER_RG true -OUTPUT_DIR /tmp/pbuilder2/ ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/grouped-last-pair-mates-flipped.sam -OUTPUT_PER_RG true -OUTPUT_DIR /tmp/pbuilder2/ Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@3fc2f5a3)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@3fc2f5a3)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@3fc2f5a3)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@3fc2f5a3)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.156 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:07.156 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@3fc2f5a3)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.156 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:07.156 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@3fc2f5a3)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.156 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:07.156 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@3fc2f5a3)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.156 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:07.156 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@3fc2f5a3)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:07 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/grouped-last-pair-mates-flipped.sam OUTPUT_PER_RG=true OUTPUT_DIR=/tmp/pbuilder2 COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:07 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/grouped-last-pair-mates-flipped.sam OUTPUT_PER_RG=true OUTPUT_DIR=/tmp/pbuilder2 COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@3fc2f5a3)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@3fc2f5a3)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:07 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:07 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@3fc2f5a3)(picard.sam.SamToFastqTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testOkInterleavedFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) Test: Test method testOkInterleavedFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: INFO 2024-07-02 12:02:07 SamToFastq Gradle suite > Gradle test > picard.sam.SamToFastqTest.testOkInterleavedFile[0](ok/sorted-pair.sam) STANDARD_ERROR INFO 2024-07-02 12:02:07 SamToFastq Test: Test method testOkInterleavedFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testOkInterleavedFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOkInterleavedFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkInterleavedFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOkInterleavedFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOkInterleavedFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkInterleavedFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOkInterleavedFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkInterleavedFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam -FASTQ /tmp/pair18040812264999563310.fastq -INTERLEAVE true ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam -FASTQ /tmp/pair18040812264999563310.fastq -INTERLEAVE true Test: Test method testOkInterleavedFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkInterleavedFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testOkInterleavedFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testOkInterleavedFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.252 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:07.252 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOkInterleavedFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.252 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:07.252 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOkInterleavedFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.252 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:07.252 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOkInterleavedFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.252 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:07.252 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOkInterleavedFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:07 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam FASTQ=/tmp/pair18040812264999563310.fastq INTERLEAVE=true OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:07 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam FASTQ=/tmp/pair18040812264999563310.fastq INTERLEAVE=true OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOkInterleavedFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOkInterleavedFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:07 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:07 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. Test: Test method testOkInterleavedFile[0](ok/sorted-pair.sam)(picard.sam.SamToFastqTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testOkInterleavedFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) Test: Test method testOkInterleavedFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: INFO 2024-07-02 12:02:07 SamToFastq Gradle suite > Gradle test > picard.sam.SamToFastqTest.testOkInterleavedFile[1](ok/sorted-pair-no-rg.sam) STANDARD_ERROR INFO 2024-07-02 12:02:07 SamToFastq Test: Test method testOkInterleavedFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testOkInterleavedFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOkInterleavedFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkInterleavedFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOkInterleavedFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOkInterleavedFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkInterleavedFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOkInterleavedFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkInterleavedFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair-no-rg.sam -FASTQ /tmp/pair17323597834672753335.fastq -INTERLEAVE true ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair-no-rg.sam -FASTQ /tmp/pair17323597834672753335.fastq -INTERLEAVE true Test: Test method testOkInterleavedFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkInterleavedFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testOkInterleavedFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testOkInterleavedFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.335 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:07.335 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOkInterleavedFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.335 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:07.335 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOkInterleavedFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.335 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:07.335 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOkInterleavedFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.335 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:07.335 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOkInterleavedFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:07 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair-no-rg.sam FASTQ=/tmp/pair17323597834672753335.fastq INTERLEAVE=true OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:07 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair-no-rg.sam FASTQ=/tmp/pair17323597834672753335.fastq INTERLEAVE=true OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOkInterleavedFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOkInterleavedFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:07 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:07 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. Test: Test method testOkInterleavedFile[1](ok/sorted-pair-no-rg.sam)(picard.sam.SamToFastqTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testOkInterleavedFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) Test: Test method testOkInterleavedFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: INFO 2024-07-02 12:02:07 SamToFastq Gradle suite > Gradle test > picard.sam.SamToFastqTest.testOkInterleavedFile[2](ok/last-pair-mates-flipped.sam) STANDARD_ERROR INFO 2024-07-02 12:02:07 SamToFastq Test: Test method testOkInterleavedFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testOkInterleavedFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOkInterleavedFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkInterleavedFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOkInterleavedFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOkInterleavedFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkInterleavedFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOkInterleavedFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkInterleavedFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/last-pair-mates-flipped.sam -FASTQ /tmp/pair11947964113737532112.fastq -INTERLEAVE true ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/last-pair-mates-flipped.sam -FASTQ /tmp/pair11947964113737532112.fastq -INTERLEAVE true Test: Test method testOkInterleavedFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkInterleavedFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testOkInterleavedFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testOkInterleavedFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.410 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:07.410 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOkInterleavedFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.410 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:07.410 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOkInterleavedFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.410 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:07.410 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOkInterleavedFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.410 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:07.410 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOkInterleavedFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:07 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/last-pair-mates-flipped.sam FASTQ=/tmp/pair11947964113737532112.fastq INTERLEAVE=true OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:07 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/last-pair-mates-flipped.sam FASTQ=/tmp/pair11947964113737532112.fastq INTERLEAVE=true OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOkInterleavedFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOkInterleavedFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:07 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:07 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. Test: Test method testOkInterleavedFile[2](ok/last-pair-mates-flipped.sam)(picard.sam.SamToFastqTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testOkInterleavedFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) Test: Test method testOkInterleavedFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: INFO 2024-07-02 12:02:07 SamToFastq Gradle suite > Gradle test > picard.sam.SamToFastqTest.testOkInterleavedFile[3](ok/first-mate-bof-last-mate-eof.sam) STANDARD_ERROR INFO 2024-07-02 12:02:07 SamToFastq Test: Test method testOkInterleavedFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testOkInterleavedFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOkInterleavedFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkInterleavedFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOkInterleavedFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOkInterleavedFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkInterleavedFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOkInterleavedFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkInterleavedFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/first-mate-bof-last-mate-eof.sam -FASTQ /tmp/pair7907110655160200299.fastq -INTERLEAVE true ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/first-mate-bof-last-mate-eof.sam -FASTQ /tmp/pair7907110655160200299.fastq -INTERLEAVE true Test: Test method testOkInterleavedFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testOkInterleavedFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testOkInterleavedFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testOkInterleavedFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.487 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:07.487 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOkInterleavedFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.487 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:07.487 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOkInterleavedFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.488 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:07.488 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOkInterleavedFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.488 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:07.488 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOkInterleavedFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:07 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/first-mate-bof-last-mate-eof.sam FASTQ=/tmp/pair7907110655160200299.fastq INTERLEAVE=true OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:07 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/first-mate-bof-last-mate-eof.sam FASTQ=/tmp/pair7907110655160200299.fastq INTERLEAVE=true OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOkInterleavedFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOkInterleavedFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:07 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:07 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. Test: Test method testOkInterleavedFile[3](ok/first-mate-bof-last-mate-eof.sam)(picard.sam.SamToFastqTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testTrimming[0](ok/sorted-pair.sam, 6, 7, 7, 5, 8, 8)(picard.sam.SamToFastqTest) Test: Test method testTrimming[0](ok/sorted-pair.sam, 6, 7, 7, 5, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: INFO 2024-07-02 12:02:07 SamToFastq Gradle suite > Gradle test > picard.sam.SamToFastqTest.testTrimming[0](ok/sorted-pair.sam, 6, 7, 7, 5, 8, 8) STANDARD_ERROR INFO 2024-07-02 12:02:07 SamToFastq Test: Test method testTrimming[0](ok/sorted-pair.sam, 6, 7, 7, 5, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testTrimming[0](ok/sorted-pair.sam, 6, 7, 7, 5, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTrimming[0](ok/sorted-pair.sam, 6, 7, 7, 5, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testTrimming[0](ok/sorted-pair.sam, 6, 7, 7, 5, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTrimming[0](ok/sorted-pair.sam, 6, 7, 7, 5, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTrimming[0](ok/sorted-pair.sam, 6, 7, 7, 5, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testTrimming[0](ok/sorted-pair.sam, 6, 7, 7, 5, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTrimming[0](ok/sorted-pair.sam, 6, 7, 7, 5, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testTrimming[0](ok/sorted-pair.sam, 6, 7, 7, 5, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam -FASTQ /tmp/pair115101347242199994022.fastq -SECOND_END_FASTQ /tmp/pair23942529118315246443.fastq -READ1_TRIM 6 -READ1_MAX_BASES_TO_WRITE 7 -READ2_TRIM 5 -READ2_MAX_BASES_TO_WRITE 8 ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam -FASTQ /tmp/pair115101347242199994022.fastq -SECOND_END_FASTQ /tmp/pair23942529118315246443.fastq -READ1_TRIM 6 -READ1_MAX_BASES_TO_WRITE 7 -READ2_TRIM 5 -READ2_MAX_BASES_TO_WRITE 8 Test: Test method testTrimming[0](ok/sorted-pair.sam, 6, 7, 7, 5, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testTrimming[0](ok/sorted-pair.sam, 6, 7, 7, 5, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testTrimming[0](ok/sorted-pair.sam, 6, 7, 7, 5, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testTrimming[0](ok/sorted-pair.sam, 6, 7, 7, 5, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.567 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:07.567 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTrimming[0](ok/sorted-pair.sam, 6, 7, 7, 5, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.567 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:07.567 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTrimming[0](ok/sorted-pair.sam, 6, 7, 7, 5, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.567 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:07.567 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTrimming[0](ok/sorted-pair.sam, 6, 7, 7, 5, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.567 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:07.567 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTrimming[0](ok/sorted-pair.sam, 6, 7, 7, 5, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:07 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam FASTQ=/tmp/pair115101347242199994022.fastq SECOND_END_FASTQ=/tmp/pair23942529118315246443.fastq READ1_TRIM=6 READ1_MAX_BASES_TO_WRITE=7 READ2_TRIM=5 READ2_MAX_BASES_TO_WRITE=8 OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:07 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam FASTQ=/tmp/pair115101347242199994022.fastq SECOND_END_FASTQ=/tmp/pair23942529118315246443.fastq READ1_TRIM=6 READ1_MAX_BASES_TO_WRITE=7 READ2_TRIM=5 READ2_MAX_BASES_TO_WRITE=8 OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTrimming[0](ok/sorted-pair.sam, 6, 7, 7, 5, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTrimming[0](ok/sorted-pair.sam, 6, 7, 7, 5, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:07 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:07 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. Test: Test method testTrimming[0](ok/sorted-pair.sam, 6, 7, 7, 5, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testTrimming[1](ok/sorted-pair.sam, 7, 7, 6, 3, 8, 8)(picard.sam.SamToFastqTest) Test: Test method testTrimming[1](ok/sorted-pair.sam, 7, 7, 6, 3, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: INFO 2024-07-02 12:02:07 SamToFastq Gradle suite > Gradle test > picard.sam.SamToFastqTest.testTrimming[1](ok/sorted-pair.sam, 7, 7, 6, 3, 8, 8) STANDARD_ERROR INFO 2024-07-02 12:02:07 SamToFastq Test: Test method testTrimming[1](ok/sorted-pair.sam, 7, 7, 6, 3, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testTrimming[1](ok/sorted-pair.sam, 7, 7, 6, 3, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTrimming[1](ok/sorted-pair.sam, 7, 7, 6, 3, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testTrimming[1](ok/sorted-pair.sam, 7, 7, 6, 3, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTrimming[1](ok/sorted-pair.sam, 7, 7, 6, 3, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTrimming[1](ok/sorted-pair.sam, 7, 7, 6, 3, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testTrimming[1](ok/sorted-pair.sam, 7, 7, 6, 3, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTrimming[1](ok/sorted-pair.sam, 7, 7, 6, 3, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testTrimming[1](ok/sorted-pair.sam, 7, 7, 6, 3, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam -FASTQ /tmp/pair15934641858254107130.fastq -SECOND_END_FASTQ /tmp/pair29565117998025361112.fastq -READ1_TRIM 7 -READ1_MAX_BASES_TO_WRITE 7 -READ2_TRIM 3 -READ2_MAX_BASES_TO_WRITE 8 ********** SamToFastq -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam -FASTQ /tmp/pair15934641858254107130.fastq -SECOND_END_FASTQ /tmp/pair29565117998025361112.fastq -READ1_TRIM 7 -READ1_MAX_BASES_TO_WRITE 7 -READ2_TRIM 3 -READ2_MAX_BASES_TO_WRITE 8 Test: Test method testTrimming[1](ok/sorted-pair.sam, 7, 7, 6, 3, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: ********** ********** Test: Test method testTrimming[1](ok/sorted-pair.sam, 7, 7, 6, 3, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testTrimming[1](ok/sorted-pair.sam, 7, 7, 6, 3, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: Test: Test method testTrimming[1](ok/sorted-pair.sam, 7, 7, 6, 3, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.651 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:07.651 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTrimming[1](ok/sorted-pair.sam, 7, 7, 6, 3, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.651 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:07.651 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTrimming[1](ok/sorted-pair.sam, 7, 7, 6, 3, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.651 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:07.651 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTrimming[1](ok/sorted-pair.sam, 7, 7, 6, 3, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: 12:02:07.651 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:07.651 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTrimming[1](ok/sorted-pair.sam, 7, 7, 6, 3, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:07 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam FASTQ=/tmp/pair15934641858254107130.fastq SECOND_END_FASTQ=/tmp/pair29565117998025361112.fastq READ1_TRIM=7 READ1_MAX_BASES_TO_WRITE=7 READ2_TRIM=3 READ2_MAX_BASES_TO_WRITE=8 OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:07 GMT+14:00 2024] SamToFastq INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam FASTQ=/tmp/pair15934641858254107130.fastq SECOND_END_FASTQ=/tmp/pair29565117998025361112.fastq READ1_TRIM=7 READ1_MAX_BASES_TO_WRITE=7 READ2_TRIM=3 READ2_MAX_BASES_TO_WRITE=8 OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTrimming[1](ok/sorted-pair.sam, 7, 7, 6, 3, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTrimming[1](ok/sorted-pair.sam, 7, 7, 6, 3, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: [Tue Jul 02 12:02:07 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:07 GMT+14:00 2024] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes. Test: Test method testTrimming[1](ok/sorted-pair.sam, 7, 7, 6, 3, 8, 8)(picard.sam.SamToFastqTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: INFO 2024-07-02 12:02:07 SamToFastqWithTags Gradle suite > Gradle test > picard.sam.SamToFastqWithTagsTest.argumentCombinations[0](null, null, null, 1) STANDARD_ERROR INFO 2024-07-02 12:02:07 SamToFastqWithTags Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** SamToFastqWithTags -INPUT testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam -FASTQ /tmp/input8939579462171568704.fastq -SECOND_END_FASTQ /tmp/input_212853943181380220409.fastq ********** SamToFastqWithTags -INPUT testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam -FASTQ /tmp/input8939579462171568704.fastq -SECOND_END_FASTQ /tmp/input_212853943181380220409.fastq Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ERROR: Option 'SEQUENCE_TAG_GROUP' must be specified at least 1 times. ERROR: Option 'SEQUENCE_TAG_GROUP' must be specified at least 1 times. Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: USAGE: SamToFastqWithTags [options] USAGE: SamToFastqWithTags [options] Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#SamToFastqWithTags Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#SamToFastqWithTags Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Converts a SAM or BAM file to FASTQ alongside FASTQs created from tags. Extracts read sequences and qualities from the Converts a SAM or BAM file to FASTQ alongside FASTQs created from tags. Extracts read sequences and qualities from the Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: input SAM/BAM file and SAM/BAM tags and writes them into the output file in Sanger FASTQ format. See MAQ FASTQ input SAM/BAM file and SAM/BAM tags and writes them into the output file in Sanger FASTQ format. See MAQ FASTQ Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: specification (http://maq.sourceforge.net/fastq.shtml) for details. specification (http://maq.sourceforge.net/fastq.shtml) for details. Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: The following example will create two FASTQs from tags. One will be converted with the base sequence coming from the The following example will create two FASTQs from tags. One will be converted with the base sequence coming from the Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: "CR" tag and base quality from the "CY" tag. The other fastq will be converted with the base sequence coming from the "CR" tag and base quality from the "CY" tag. The other fastq will be converted with the base sequence coming from the Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: "CB" and "UR" tags concatenated together with no separator (not specified on command line) with the base qualities "CB" and "UR" tags concatenated together with no separator (not specified on command line) with the base qualities Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: coming from the "CY" and "UY" tags concatenated together. The two files will be named CR.fastq and CB_UR.fastq. coming from the "CY" and "UY" tags concatenated together. The two files will be named CR.fastq and CB_UR.fastq. Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: java -jar picard.jar SamToFastqWithTags java -jar picard.jar SamToFastqWithTags Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: I=input.bam I=input.bam Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: FASTQ=output.fastq FASTQ=output.fastq Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: SEQUENCE_TAG_GROUP=CR SEQUENCE_TAG_GROUP=CR Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: QUALITY_TAG_GROUP=CY QUALITY_TAG_GROUP=CY Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: SEQUENCE_TAG_GROUP="CB,UR" SEQUENCE_TAG_GROUP="CB,UR" Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: QUALITY_TAG_GROUP="CY,UY" QUALITY_TAG_GROUP="CY,UY" Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Version: null Version: null Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Options: Options: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: --help --help Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: tools. tools. Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: SEQUENCE_TAG_GROUP=String SEQUENCE_TAG_GROUP=String Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: STG=String List of comma separated tag values to extract from Input SAM/BAM to be used as read STG=String List of comma separated tag values to extract from Input SAM/BAM to be used as read Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: sequence Default value: null. This option must be specified at least 1 times. sequence Default value: null. This option must be specified at least 1 times. Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: QUALITY_TAG_GROUP=String QUALITY_TAG_GROUP=String Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: QTG=String List of comma separated tag values to extract from Input SAM/BAM to be used as read QTG=String List of comma separated tag values to extract from Input SAM/BAM to be used as read Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: qualities Default value: null. This option may be specified 0 or more times. qualities Default value: null. This option may be specified 0 or more times. Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: TAG_GROUP_SEPERATOR=String TAG_GROUP_SEPERATOR=String Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: SEP=String List of any sequences (e.g. 'AACCTG`) to put in between each comma separated list of SEP=String List of any sequences (e.g. 'AACCTG`) to put in between each comma separated list of Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: sequence tags in each SEQUENCE_TAG_GROUP (STG) Default value: null. This option may be sequence tags in each SEQUENCE_TAG_GROUP (STG) Default value: null. This option may be Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: specified 0 or more times. specified 0 or more times. Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: COMPRESS_OUTPUTS_PER_TAG_GROUP=Boolean COMPRESS_OUTPUTS_PER_TAG_GROUP=Boolean Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: GZOPTG=Boolean Compress output FASTQ files per Tag grouping using gzip and append a .gz extension to the GZOPTG=Boolean Compress output FASTQ files per Tag grouping using gzip and append a .gz extension to the Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: file names. Default value: false. This option can be set to 'null' to clear the default file names. Default value: false. This option can be set to 'null' to clear the default Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: I=File Input SAM/BAM file to extract reads from Required. I=File Input SAM/BAM file to extract reads from Required. Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: FASTQ=File FASTQ=File Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: F=File Output FASTQ file (single-end fastq or, if paired, first end of the pair FASTQ). F=File Output FASTQ file (single-end fastq or, if paired, first end of the pair FASTQ). Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Required. Cannot be used in conjuction with option(s) OUTPUT_DIR (ODIR) Required. Cannot be used in conjuction with option(s) OUTPUT_DIR (ODIR) Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: COMPRESS_OUTPUTS_PER_RG (GZOPRG) OUTPUT_PER_RG (OPRG) COMPRESS_OUTPUTS_PER_RG (GZOPRG) OUTPUT_PER_RG (OPRG) Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: SECOND_END_FASTQ=File SECOND_END_FASTQ=File Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: F2=File Output FASTQ file (if paired, second end of the pair FASTQ). Default value: null. Cannot F2=File Output FASTQ file (if paired, second end of the pair FASTQ). Default value: null. Cannot Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: be used in conjuction with option(s) COMPRESS_OUTPUTS_PER_RG (GZOPRG) OUTPUT_PER_RG (OPRG) be used in conjuction with option(s) COMPRESS_OUTPUTS_PER_RG (GZOPRG) OUTPUT_PER_RG (OPRG) Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: UNPAIRED_FASTQ=File UNPAIRED_FASTQ=File Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: FU=File Output FASTQ file for unpaired reads; may only be provided in paired-FASTQ mode Default FU=File Output FASTQ file for unpaired reads; may only be provided in paired-FASTQ mode Default Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: value: null. Cannot be used in conjuction with option(s) COMPRESS_OUTPUTS_PER_RG (GZOPRG) value: null. Cannot be used in conjuction with option(s) COMPRESS_OUTPUTS_PER_RG (GZOPRG) Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: OUTPUT_PER_RG (OPRG) OUTPUT_PER_RG (OPRG) Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: OUTPUT_PER_RG=Boolean OUTPUT_PER_RG=Boolean Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: OPRG=Boolean Output a FASTQ file per read group (two FASTQ files per read group if the group is OPRG=Boolean Output a FASTQ file per read group (two FASTQ files per read group if the group is Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: paired). Default value: false. This option can be set to 'null' to clear the default paired). Default value: false. This option can be set to 'null' to clear the default Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: value. Possible values: {true, false} Cannot be used in conjuction with option(s) value. Possible values: {true, false} Cannot be used in conjuction with option(s) Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: SECOND_END_FASTQ (F2) UNPAIRED_FASTQ (FU) FASTQ (F) SECOND_END_FASTQ (F2) UNPAIRED_FASTQ (FU) FASTQ (F) Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: COMPRESS_OUTPUTS_PER_RG=Boolean COMPRESS_OUTPUTS_PER_RG=Boolean Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: GZOPRG=Boolean Compress output FASTQ files per read group using gzip and append a .gz extension to the GZOPRG=Boolean Compress output FASTQ files per read group using gzip and append a .gz extension to the Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: file names. Default value: false. This option can be set to 'null' to clear the default file names. Default value: false. This option can be set to 'null' to clear the default Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: value. Possible values: {true, false} Cannot be used in conjuction with option(s) value. Possible values: {true, false} Cannot be used in conjuction with option(s) Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: SECOND_END_FASTQ (F2) UNPAIRED_FASTQ (FU) FASTQ (F) SECOND_END_FASTQ (F2) UNPAIRED_FASTQ (FU) FASTQ (F) Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: RG_TAG=String RG_TAG=String Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: RGT=String The read group tag (PU or ID) to be used to output a FASTQ file per read group. Default RGT=String The read group tag (PU or ID) to be used to output a FASTQ file per read group. Default Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: value: PU. This option can be set to 'null' to clear the default value. value: PU. This option can be set to 'null' to clear the default value. Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: OUTPUT_DIR=File OUTPUT_DIR=File Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ODIR=File Directory in which to output the FASTQ file(s). Used only when OUTPUT_PER_RG is true. ODIR=File Directory in which to output the FASTQ file(s). Used only when OUTPUT_PER_RG is true. Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Default value: null. Default value: null. Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: RE_REVERSE=Boolean RE_REVERSE=Boolean Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: RC=Boolean Re-reverse bases and qualities of reads with negative strand flag set before writing them RC=Boolean Re-reverse bases and qualities of reads with negative strand flag set before writing them Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: to FASTQ Default value: true. This option can be set to 'null' to clear the default to FASTQ Default value: true. This option can be set to 'null' to clear the default Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: INTERLEAVE=Boolean INTERLEAVE=Boolean Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: INTER=Boolean Will generate an interleaved fastq if paired, each line will have /1 or /2 to describe INTER=Boolean Will generate an interleaved fastq if paired, each line will have /1 or /2 to describe Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: which end it came from Default value: false. This option can be set to 'null' to clear which end it came from Default value: false. This option can be set to 'null' to clear Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: the default value. Possible values: {true, false} the default value. Possible values: {true, false} Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: INCLUDE_NON_PF_READS=Boolean INCLUDE_NON_PF_READS=Boolean Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: NON_PF=Boolean Include non-PF reads from the SAM file into the output FASTQ files. PF means 'passes NON_PF=Boolean Include non-PF reads from the SAM file into the output FASTQ files. PF means 'passes Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: filtering'. Reads whose 'not passing quality controls' flag is set are non-PF reads. See filtering'. Reads whose 'not passing quality controls' flag is set are non-PF reads. See Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: GATK Dictionary for more info. Default value: false. This option can be set to 'null' to GATK Dictionary for more info. Default value: false. This option can be set to 'null' to Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: clear the default value. Possible values: {true, false} clear the default value. Possible values: {true, false} Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: CLIPPING_ATTRIBUTE=String CLIPPING_ATTRIBUTE=String Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: CLIP_ATTR=String The attribute that stores the position at which the SAM record should be clipped Default CLIP_ATTR=String The attribute that stores the position at which the SAM record should be clipped Default Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: value: null. value: null. Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: CLIPPING_ACTION=String CLIPPING_ACTION=String Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: CLIP_ACT=String The action that should be taken with clipped reads: 'X' means the reads and qualities CLIP_ACT=String The action that should be taken with clipped reads: 'X' means the reads and qualities Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: the clipped region; and any integer means that the base qualities should be set to that the clipped region; and any integer means that the base qualities should be set to that Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: value in the clipped region. Default value: null. value in the clipped region. Default value: null. Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: CLIPPING_MIN_LENGTH=Integer CLIPPING_MIN_LENGTH=Integer Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: CLIP_MIN=Integer When performing clipping with the CLIPPING_ATTRIBUTE and CLIPPING_ACTION parameters, CLIP_MIN=Integer When performing clipping with the CLIPPING_ATTRIBUTE and CLIPPING_ACTION parameters, Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ensure that the resulting reads after clipping are at least CLIPPING_MIN_LENGTH bases ensure that the resulting reads after clipping are at least CLIPPING_MIN_LENGTH bases Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: long. If the original read is shorter than CLIPPING_MIN_LENGTH then the original read long. If the original read is shorter than CLIPPING_MIN_LENGTH then the original read Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: length will be maintained. Default value: 0. This option can be set to 'null' to clear length will be maintained. Default value: 0. This option can be set to 'null' to clear Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: the default value. the default value. Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: READ1_TRIM=Integer READ1_TRIM=Integer Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: R1_TRIM=Integer The number of bases to trim from the beginning of read 1. Default value: 0. This option R1_TRIM=Integer The number of bases to trim from the beginning of read 1. Default value: 0. This option Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: can be set to 'null' to clear the default value. can be set to 'null' to clear the default value. Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: READ1_MAX_BASES_TO_WRITE=Integer READ1_MAX_BASES_TO_WRITE=Integer Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: R1_MAX_BASES=Integer The maximum number of bases to write from read 1 after trimming. If there are fewer than R1_MAX_BASES=Integer The maximum number of bases to write from read 1 after trimming. If there are fewer than Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: this many bases left after trimming, all will be written. If this value is null then all this many bases left after trimming, all will be written. If this value is null then all Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: bases left after trimming will be written. Default value: null. bases left after trimming will be written. Default value: null. Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: READ2_TRIM=Integer READ2_TRIM=Integer Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: R2_TRIM=Integer The number of bases to trim from the beginning of read 2. Default value: 0. This option R2_TRIM=Integer The number of bases to trim from the beginning of read 2. Default value: 0. This option Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: can be set to 'null' to clear the default value. can be set to 'null' to clear the default value. Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: READ2_MAX_BASES_TO_WRITE=Integer READ2_MAX_BASES_TO_WRITE=Integer Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: R2_MAX_BASES=Integer The maximum number of bases to write from read 2 after trimming. If there are fewer than R2_MAX_BASES=Integer The maximum number of bases to write from read 2 after trimming. If there are fewer than Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: this many bases left after trimming, all will be written. If this value is null then all this many bases left after trimming, all will be written. If this value is null then all Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: bases left after trimming will be written. Default value: null. bases left after trimming will be written. Default value: null. Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: QUALITY=Integer QUALITY=Integer Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Q=Integer End-trim reads using the phred/bwa quality trimming algorithm and this quality. Default Q=Integer End-trim reads using the phred/bwa quality trimming algorithm and this quality. Default Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: value: null. value: null. Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: INCLUDE_NON_PRIMARY_ALIGNMENTS=Boolean INCLUDE_NON_PRIMARY_ALIGNMENTS=Boolean Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: If true, include non-primary alignments in the output. Support of non-primary alignments If true, include non-primary alignments in the output. Support of non-primary alignments Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: there are paired reads with non-primary alignments. Default value: false. This option can there are paired reads with non-primary alignments. Default value: false. This option can Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: be set to 'null' to clear the default value. Possible values: {true, false} be set to 'null' to clear the default value. Possible values: {true, false} Test: Test method argumentCombinations[0](null, null, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Running Test: Test method argumentCombinations[1]([Ljava.lang.String;@61183ae6, null, null, 0)(picard.sam.SamToFastqWithTagsTest) Test: Test method argumentCombinations[1]([Ljava.lang.String;@61183ae6, null, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: INFO 2024-07-02 12:02:07 SamToFastqWithTags Gradle suite > Gradle test > picard.sam.SamToFastqWithTagsTest.argumentCombinations[1]([Ljava.lang.String;@61183ae6, null, null, 0) STANDARD_ERROR INFO 2024-07-02 12:02:07 SamToFastqWithTags Test: Test method argumentCombinations[1]([Ljava.lang.String;@61183ae6, null, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[1]([Ljava.lang.String;@61183ae6, null, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method argumentCombinations[1]([Ljava.lang.String;@61183ae6, null, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method argumentCombinations[1]([Ljava.lang.String;@61183ae6, null, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method argumentCombinations[1]([Ljava.lang.String;@61183ae6, null, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method argumentCombinations[1]([Ljava.lang.String;@61183ae6, null, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method argumentCombinations[1]([Ljava.lang.String;@61183ae6, null, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method argumentCombinations[1]([Ljava.lang.String;@61183ae6, null, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method argumentCombinations[1]([Ljava.lang.String;@61183ae6, null, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** SamToFastqWithTags -INPUT testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam -FASTQ /tmp/input10099505611072485225.fastq -SECOND_END_FASTQ /tmp/input_28646365910156293120.fastq -STG UR,CR -STG CR,UR ********** SamToFastqWithTags -INPUT testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam -FASTQ /tmp/input10099505611072485225.fastq -SECOND_END_FASTQ /tmp/input_28646365910156293120.fastq -STG UR,CR -STG CR,UR Test: Test method argumentCombinations[1]([Ljava.lang.String;@61183ae6, null, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method argumentCombinations[1]([Ljava.lang.String;@61183ae6, null, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[1]([Ljava.lang.String;@61183ae6, null, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[1]([Ljava.lang.String;@61183ae6, null, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:07.889 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:07.889 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method argumentCombinations[1]([Ljava.lang.String;@61183ae6, null, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:07.889 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:07.889 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method argumentCombinations[1]([Ljava.lang.String;@61183ae6, null, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:07.889 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:07.889 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method argumentCombinations[1]([Ljava.lang.String;@61183ae6, null, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:07.889 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:07.889 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method argumentCombinations[1]([Ljava.lang.String;@61183ae6, null, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:07 GMT+14:00 2024] SamToFastqWithTags SEQUENCE_TAG_GROUP=[UR,CR, CR,UR] INPUT=testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam FASTQ=/tmp/input10099505611072485225.fastq SECOND_END_FASTQ=/tmp/input_28646365910156293120.fastq COMPRESS_OUTPUTS_PER_TAG_GROUP=false OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:07 GMT+14:00 2024] SamToFastqWithTags SEQUENCE_TAG_GROUP=[UR,CR, CR,UR] INPUT=testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam FASTQ=/tmp/input10099505611072485225.fastq SECOND_END_FASTQ=/tmp/input_28646365910156293120.fastq COMPRESS_OUTPUTS_PER_TAG_GROUP=false OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method argumentCombinations[1]([Ljava.lang.String;@61183ae6, null, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:07 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method argumentCombinations[1]([Ljava.lang.String;@61183ae6, null, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:07 GMT+14:00 2024] picard.sam.SamToFastqWithTags done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:07 GMT+14:00 2024] picard.sam.SamToFastqWithTags done. Elapsed time: 0.00 minutes. Test: Test method argumentCombinations[1]([Ljava.lang.String;@61183ae6, null, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: INFO 2024-07-02 12:02:07 SamToFastqWithTags Gradle suite > Gradle test > picard.sam.SamToFastqWithTagsTest.argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1) STANDARD_ERROR INFO 2024-07-02 12:02:07 SamToFastqWithTags Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** SamToFastqWithTags -INPUT testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam -FASTQ /tmp/input6372531406297211814.fastq -SECOND_END_FASTQ /tmp/input_217859195475093641342.fastq -STG UR,CR -STG CR,UR -QTG UY ********** SamToFastqWithTags -INPUT testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam -FASTQ /tmp/input6372531406297211814.fastq -SECOND_END_FASTQ /tmp/input_217859195475093641342.fastq -STG UR,CR -STG CR,UR -QTG UY Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:07.957 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 12:02:07.957 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: USAGE: SamToFastqWithTags [options] USAGE: SamToFastqWithTags [options] Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#SamToFastqWithTags Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#SamToFastqWithTags Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Converts a SAM or BAM file to FASTQ alongside FASTQs created from tags. Extracts read sequences and qualities from the Converts a SAM or BAM file to FASTQ alongside FASTQs created from tags. Extracts read sequences and qualities from the Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: input SAM/BAM file and SAM/BAM tags and writes them into the output file in Sanger FASTQ format. See MAQ FASTQ input SAM/BAM file and SAM/BAM tags and writes them into the output file in Sanger FASTQ format. See MAQ FASTQ Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: specification (http://maq.sourceforge.net/fastq.shtml) for details. specification (http://maq.sourceforge.net/fastq.shtml) for details. Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: The following example will create two FASTQs from tags. One will be converted with the base sequence coming from the The following example will create two FASTQs from tags. One will be converted with the base sequence coming from the Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: "CR" tag and base quality from the "CY" tag. The other fastq will be converted with the base sequence coming from the "CR" tag and base quality from the "CY" tag. The other fastq will be converted with the base sequence coming from the Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: "CB" and "UR" tags concatenated together with no separator (not specified on command line) with the base qualities "CB" and "UR" tags concatenated together with no separator (not specified on command line) with the base qualities Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: coming from the "CY" and "UY" tags concatenated together. The two files will be named CR.fastq and CB_UR.fastq. coming from the "CY" and "UY" tags concatenated together. The two files will be named CR.fastq and CB_UR.fastq. Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: java -jar picard.jar SamToFastqWithTags java -jar picard.jar SamToFastqWithTags Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: I=input.bam I=input.bam Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: FASTQ=output.fastq FASTQ=output.fastq Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: SEQUENCE_TAG_GROUP=CR SEQUENCE_TAG_GROUP=CR Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: QUALITY_TAG_GROUP=CY QUALITY_TAG_GROUP=CY Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: SEQUENCE_TAG_GROUP="CB,UR" SEQUENCE_TAG_GROUP="CB,UR" Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: QUALITY_TAG_GROUP="CY,UY" QUALITY_TAG_GROUP="CY,UY" Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Version: null Version: null Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Options: Options: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: --help --help Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: tools. tools. Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: SEQUENCE_TAG_GROUP=String SEQUENCE_TAG_GROUP=String Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: STG=String List of comma separated tag values to extract from Input SAM/BAM to be used as read STG=String List of comma separated tag values to extract from Input SAM/BAM to be used as read Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: sequence Default value: null. This option must be specified at least 1 times. sequence Default value: null. This option must be specified at least 1 times. Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: QUALITY_TAG_GROUP=String QUALITY_TAG_GROUP=String Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: QTG=String List of comma separated tag values to extract from Input SAM/BAM to be used as read QTG=String List of comma separated tag values to extract from Input SAM/BAM to be used as read Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: qualities Default value: null. This option may be specified 0 or more times. qualities Default value: null. This option may be specified 0 or more times. Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: TAG_GROUP_SEPERATOR=String TAG_GROUP_SEPERATOR=String Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: SEP=String List of any sequences (e.g. 'AACCTG`) to put in between each comma separated list of SEP=String List of any sequences (e.g. 'AACCTG`) to put in between each comma separated list of Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: sequence tags in each SEQUENCE_TAG_GROUP (STG) Default value: null. This option may be sequence tags in each SEQUENCE_TAG_GROUP (STG) Default value: null. This option may be Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: specified 0 or more times. specified 0 or more times. Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: COMPRESS_OUTPUTS_PER_TAG_GROUP=Boolean COMPRESS_OUTPUTS_PER_TAG_GROUP=Boolean Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: GZOPTG=Boolean Compress output FASTQ files per Tag grouping using gzip and append a .gz extension to the GZOPTG=Boolean Compress output FASTQ files per Tag grouping using gzip and append a .gz extension to the Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: file names. Default value: false. This option can be set to 'null' to clear the default file names. Default value: false. This option can be set to 'null' to clear the default Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: I=File Input SAM/BAM file to extract reads from Required. I=File Input SAM/BAM file to extract reads from Required. Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: FASTQ=File FASTQ=File Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: F=File Output FASTQ file (single-end fastq or, if paired, first end of the pair FASTQ). F=File Output FASTQ file (single-end fastq or, if paired, first end of the pair FASTQ). Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Required. Cannot be used in conjuction with option(s) OUTPUT_DIR (ODIR) Required. Cannot be used in conjuction with option(s) OUTPUT_DIR (ODIR) Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: COMPRESS_OUTPUTS_PER_RG (GZOPRG) OUTPUT_PER_RG (OPRG) COMPRESS_OUTPUTS_PER_RG (GZOPRG) OUTPUT_PER_RG (OPRG) Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: SECOND_END_FASTQ=File SECOND_END_FASTQ=File Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: F2=File Output FASTQ file (if paired, second end of the pair FASTQ). Default value: null. Cannot F2=File Output FASTQ file (if paired, second end of the pair FASTQ). Default value: null. Cannot Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: be used in conjuction with option(s) COMPRESS_OUTPUTS_PER_RG (GZOPRG) OUTPUT_PER_RG (OPRG) be used in conjuction with option(s) COMPRESS_OUTPUTS_PER_RG (GZOPRG) OUTPUT_PER_RG (OPRG) Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: UNPAIRED_FASTQ=File UNPAIRED_FASTQ=File Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: FU=File Output FASTQ file for unpaired reads; may only be provided in paired-FASTQ mode Default FU=File Output FASTQ file for unpaired reads; may only be provided in paired-FASTQ mode Default Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: value: null. Cannot be used in conjuction with option(s) COMPRESS_OUTPUTS_PER_RG (GZOPRG) value: null. Cannot be used in conjuction with option(s) COMPRESS_OUTPUTS_PER_RG (GZOPRG) Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: OUTPUT_PER_RG (OPRG) OUTPUT_PER_RG (OPRG) Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: OUTPUT_PER_RG=Boolean OUTPUT_PER_RG=Boolean Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: OPRG=Boolean Output a FASTQ file per read group (two FASTQ files per read group if the group is OPRG=Boolean Output a FASTQ file per read group (two FASTQ files per read group if the group is Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: paired). Default value: false. This option can be set to 'null' to clear the default paired). Default value: false. This option can be set to 'null' to clear the default Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: value. Possible values: {true, false} Cannot be used in conjuction with option(s) value. Possible values: {true, false} Cannot be used in conjuction with option(s) Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: SECOND_END_FASTQ (F2) UNPAIRED_FASTQ (FU) FASTQ (F) SECOND_END_FASTQ (F2) UNPAIRED_FASTQ (FU) FASTQ (F) Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: COMPRESS_OUTPUTS_PER_RG=Boolean COMPRESS_OUTPUTS_PER_RG=Boolean Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: GZOPRG=Boolean Compress output FASTQ files per read group using gzip and append a .gz extension to the GZOPRG=Boolean Compress output FASTQ files per read group using gzip and append a .gz extension to the Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: file names. Default value: false. This option can be set to 'null' to clear the default file names. Default value: false. This option can be set to 'null' to clear the default Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: value. Possible values: {true, false} Cannot be used in conjuction with option(s) value. Possible values: {true, false} Cannot be used in conjuction with option(s) Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: SECOND_END_FASTQ (F2) UNPAIRED_FASTQ (FU) FASTQ (F) SECOND_END_FASTQ (F2) UNPAIRED_FASTQ (FU) FASTQ (F) Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: RG_TAG=String RG_TAG=String Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: RGT=String The read group tag (PU or ID) to be used to output a FASTQ file per read group. Default RGT=String The read group tag (PU or ID) to be used to output a FASTQ file per read group. Default Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: value: PU. This option can be set to 'null' to clear the default value. value: PU. This option can be set to 'null' to clear the default value. Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: OUTPUT_DIR=File OUTPUT_DIR=File Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ODIR=File Directory in which to output the FASTQ file(s). Used only when OUTPUT_PER_RG is true. ODIR=File Directory in which to output the FASTQ file(s). Used only when OUTPUT_PER_RG is true. Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Default value: null. Default value: null. Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: RE_REVERSE=Boolean RE_REVERSE=Boolean Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: RC=Boolean Re-reverse bases and qualities of reads with negative strand flag set before writing them RC=Boolean Re-reverse bases and qualities of reads with negative strand flag set before writing them Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: to FASTQ Default value: true. This option can be set to 'null' to clear the default to FASTQ Default value: true. This option can be set to 'null' to clear the default Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: INTERLEAVE=Boolean INTERLEAVE=Boolean Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: INTER=Boolean Will generate an interleaved fastq if paired, each line will have /1 or /2 to describe INTER=Boolean Will generate an interleaved fastq if paired, each line will have /1 or /2 to describe Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: which end it came from Default value: false. This option can be set to 'null' to clear which end it came from Default value: false. This option can be set to 'null' to clear Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: the default value. Possible values: {true, false} the default value. Possible values: {true, false} Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: INCLUDE_NON_PF_READS=Boolean INCLUDE_NON_PF_READS=Boolean Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: NON_PF=Boolean Include non-PF reads from the SAM file into the output FASTQ files. PF means 'passes NON_PF=Boolean Include non-PF reads from the SAM file into the output FASTQ files. PF means 'passes Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: filtering'. Reads whose 'not passing quality controls' flag is set are non-PF reads. See filtering'. Reads whose 'not passing quality controls' flag is set are non-PF reads. See Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: GATK Dictionary for more info. Default value: false. This option can be set to 'null' to GATK Dictionary for more info. Default value: false. This option can be set to 'null' to Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: clear the default value. Possible values: {true, false} clear the default value. Possible values: {true, false} Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: CLIPPING_ATTRIBUTE=String CLIPPING_ATTRIBUTE=String Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: CLIP_ATTR=String The attribute that stores the position at which the SAM record should be clipped Default CLIP_ATTR=String The attribute that stores the position at which the SAM record should be clipped Default Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: value: null. value: null. Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: CLIPPING_ACTION=String CLIPPING_ACTION=String Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: CLIP_ACT=String The action that should be taken with clipped reads: 'X' means the reads and qualities CLIP_ACT=String The action that should be taken with clipped reads: 'X' means the reads and qualities Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: the clipped region; and any integer means that the base qualities should be set to that the clipped region; and any integer means that the base qualities should be set to that Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: value in the clipped region. Default value: null. value in the clipped region. Default value: null. Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: CLIPPING_MIN_LENGTH=Integer CLIPPING_MIN_LENGTH=Integer Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: CLIP_MIN=Integer When performing clipping with the CLIPPING_ATTRIBUTE and CLIPPING_ACTION parameters, CLIP_MIN=Integer When performing clipping with the CLIPPING_ATTRIBUTE and CLIPPING_ACTION parameters, Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ensure that the resulting reads after clipping are at least CLIPPING_MIN_LENGTH bases ensure that the resulting reads after clipping are at least CLIPPING_MIN_LENGTH bases Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: long. If the original read is shorter than CLIPPING_MIN_LENGTH then the original read long. If the original read is shorter than CLIPPING_MIN_LENGTH then the original read Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: length will be maintained. Default value: 0. This option can be set to 'null' to clear length will be maintained. Default value: 0. This option can be set to 'null' to clear Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: the default value. the default value. Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: READ1_TRIM=Integer READ1_TRIM=Integer Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: R1_TRIM=Integer The number of bases to trim from the beginning of read 1. Default value: 0. This option R1_TRIM=Integer The number of bases to trim from the beginning of read 1. Default value: 0. This option Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: can be set to 'null' to clear the default value. can be set to 'null' to clear the default value. Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: READ1_MAX_BASES_TO_WRITE=Integer READ1_MAX_BASES_TO_WRITE=Integer Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: R1_MAX_BASES=Integer The maximum number of bases to write from read 1 after trimming. If there are fewer than R1_MAX_BASES=Integer The maximum number of bases to write from read 1 after trimming. If there are fewer than Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: this many bases left after trimming, all will be written. If this value is null then all this many bases left after trimming, all will be written. If this value is null then all Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: bases left after trimming will be written. Default value: null. bases left after trimming will be written. Default value: null. Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: READ2_TRIM=Integer READ2_TRIM=Integer Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: R2_TRIM=Integer The number of bases to trim from the beginning of read 2. Default value: 0. This option R2_TRIM=Integer The number of bases to trim from the beginning of read 2. Default value: 0. This option Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: can be set to 'null' to clear the default value. can be set to 'null' to clear the default value. Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: READ2_MAX_BASES_TO_WRITE=Integer READ2_MAX_BASES_TO_WRITE=Integer Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: R2_MAX_BASES=Integer The maximum number of bases to write from read 2 after trimming. If there are fewer than R2_MAX_BASES=Integer The maximum number of bases to write from read 2 after trimming. If there are fewer than Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: this many bases left after trimming, all will be written. If this value is null then all this many bases left after trimming, all will be written. If this value is null then all Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: bases left after trimming will be written. Default value: null. bases left after trimming will be written. Default value: null. Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: QUALITY=Integer QUALITY=Integer Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Q=Integer End-trim reads using the phred/bwa quality trimming algorithm and this quality. Default Q=Integer End-trim reads using the phred/bwa quality trimming algorithm and this quality. Default Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: value: null. value: null. Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: INCLUDE_NON_PRIMARY_ALIGNMENTS=Boolean INCLUDE_NON_PRIMARY_ALIGNMENTS=Boolean Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: If true, include non-primary alignments in the output. Support of non-primary alignments If true, include non-primary alignments in the output. Support of non-primary alignments Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: there are paired reads with non-primary alignments. Default value: false. This option can there are paired reads with non-primary alignments. Default value: false. This option can Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: be set to 'null' to clear the default value. Possible values: {true, false} be set to 'null' to clear the default value. Possible values: {true, false} Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[2]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@55e27142, null, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: QUALITY_TAG_GROUP size must be equal to SEQUENCE_TAG_GROUP or not be specified at all. QUALITY_TAG_GROUP size must be equal to SEQUENCE_TAG_GROUP or not be specified at all. Running Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 SamToFastqWithTags Gradle suite > Gradle test > picard.sam.SamToFastqWithTagsTest.argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1) STANDARD_ERROR INFO 2024-07-02 12:02:08 SamToFastqWithTags Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** SamToFastqWithTags -INPUT testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam -FASTQ /tmp/input148869123669747602.fastq -SECOND_END_FASTQ /tmp/input_214236600764486646166.fastq -STG UR,CR -STG CR,UR -SEP AAAAA ********** SamToFastqWithTags -INPUT testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam -FASTQ /tmp/input148869123669747602.fastq -SECOND_END_FASTQ /tmp/input_214236600764486646166.fastq -STG UR,CR -STG CR,UR -SEP AAAAA Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.031 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser 12:02:08.031 WARN LegacyCommandLineArgumentParser - Hidden arguments are always printed in LegacyCommandLineArgumentParser Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: USAGE: SamToFastqWithTags [options] USAGE: SamToFastqWithTags [options] Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#SamToFastqWithTags Documentation: http://broadinstitute.github.io/picard/command-line-overview.html#SamToFastqWithTags Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Converts a SAM or BAM file to FASTQ alongside FASTQs created from tags. Extracts read sequences and qualities from the Converts a SAM or BAM file to FASTQ alongside FASTQs created from tags. Extracts read sequences and qualities from the Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: input SAM/BAM file and SAM/BAM tags and writes them into the output file in Sanger FASTQ format. See MAQ FASTQ input SAM/BAM file and SAM/BAM tags and writes them into the output file in Sanger FASTQ format. See MAQ FASTQ Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: specification (http://maq.sourceforge.net/fastq.shtml) for details. specification (http://maq.sourceforge.net/fastq.shtml) for details. Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: The following example will create two FASTQs from tags. One will be converted with the base sequence coming from the The following example will create two FASTQs from tags. One will be converted with the base sequence coming from the Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: "CR" tag and base quality from the "CY" tag. The other fastq will be converted with the base sequence coming from the "CR" tag and base quality from the "CY" tag. The other fastq will be converted with the base sequence coming from the Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: "CB" and "UR" tags concatenated together with no separator (not specified on command line) with the base qualities "CB" and "UR" tags concatenated together with no separator (not specified on command line) with the base qualities Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: coming from the "CY" and "UY" tags concatenated together. The two files will be named CR.fastq and CB_UR.fastq. coming from the "CY" and "UY" tags concatenated together. The two files will be named CR.fastq and CB_UR.fastq. Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: java -jar picard.jar SamToFastqWithTags java -jar picard.jar SamToFastqWithTags Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: I=input.bam I=input.bam Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: FASTQ=output.fastq FASTQ=output.fastq Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: SEQUENCE_TAG_GROUP=CR SEQUENCE_TAG_GROUP=CR Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: QUALITY_TAG_GROUP=CY QUALITY_TAG_GROUP=CY Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: SEQUENCE_TAG_GROUP="CB,UR" SEQUENCE_TAG_GROUP="CB,UR" Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: QUALITY_TAG_GROUP="CY,UY" QUALITY_TAG_GROUP="CY,UY" Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Version: null Version: null Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Options: Options: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: --help --help Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: -h Displays options specific to this tool. -h Displays options specific to this tool. Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: --stdhelp --stdhelp Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: -H Displays options specific to this tool AND options common to all Picard command line -H Displays options specific to this tool AND options common to all Picard command line Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: tools. tools. Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: --version Displays program version. --version Displays program version. Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: SEQUENCE_TAG_GROUP=String SEQUENCE_TAG_GROUP=String Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: STG=String List of comma separated tag values to extract from Input SAM/BAM to be used as read STG=String List of comma separated tag values to extract from Input SAM/BAM to be used as read Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: sequence Default value: null. This option must be specified at least 1 times. sequence Default value: null. This option must be specified at least 1 times. Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: QUALITY_TAG_GROUP=String QUALITY_TAG_GROUP=String Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: QTG=String List of comma separated tag values to extract from Input SAM/BAM to be used as read QTG=String List of comma separated tag values to extract from Input SAM/BAM to be used as read Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: qualities Default value: null. This option may be specified 0 or more times. qualities Default value: null. This option may be specified 0 or more times. Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: TAG_GROUP_SEPERATOR=String TAG_GROUP_SEPERATOR=String Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: SEP=String List of any sequences (e.g. 'AACCTG`) to put in between each comma separated list of SEP=String List of any sequences (e.g. 'AACCTG`) to put in between each comma separated list of Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: sequence tags in each SEQUENCE_TAG_GROUP (STG) Default value: null. This option may be sequence tags in each SEQUENCE_TAG_GROUP (STG) Default value: null. This option may be Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: specified 0 or more times. specified 0 or more times. Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: COMPRESS_OUTPUTS_PER_TAG_GROUP=Boolean COMPRESS_OUTPUTS_PER_TAG_GROUP=Boolean Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: GZOPTG=Boolean Compress output FASTQ files per Tag grouping using gzip and append a .gz extension to the GZOPTG=Boolean Compress output FASTQ files per Tag grouping using gzip and append a .gz extension to the Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: file names. Default value: false. This option can be set to 'null' to clear the default file names. Default value: false. This option can be set to 'null' to clear the default Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: INPUT=File INPUT=File Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: I=File Input SAM/BAM file to extract reads from Required. I=File Input SAM/BAM file to extract reads from Required. Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: FASTQ=File FASTQ=File Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: F=File Output FASTQ file (single-end fastq or, if paired, first end of the pair FASTQ). F=File Output FASTQ file (single-end fastq or, if paired, first end of the pair FASTQ). Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Required. Cannot be used in conjuction with option(s) OUTPUT_DIR (ODIR) Required. Cannot be used in conjuction with option(s) OUTPUT_DIR (ODIR) Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: COMPRESS_OUTPUTS_PER_RG (GZOPRG) OUTPUT_PER_RG (OPRG) COMPRESS_OUTPUTS_PER_RG (GZOPRG) OUTPUT_PER_RG (OPRG) Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: SECOND_END_FASTQ=File SECOND_END_FASTQ=File Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: F2=File Output FASTQ file (if paired, second end of the pair FASTQ). Default value: null. Cannot F2=File Output FASTQ file (if paired, second end of the pair FASTQ). Default value: null. Cannot Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: be used in conjuction with option(s) COMPRESS_OUTPUTS_PER_RG (GZOPRG) OUTPUT_PER_RG (OPRG) be used in conjuction with option(s) COMPRESS_OUTPUTS_PER_RG (GZOPRG) OUTPUT_PER_RG (OPRG) Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: UNPAIRED_FASTQ=File UNPAIRED_FASTQ=File Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: FU=File Output FASTQ file for unpaired reads; may only be provided in paired-FASTQ mode Default FU=File Output FASTQ file for unpaired reads; may only be provided in paired-FASTQ mode Default Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: value: null. Cannot be used in conjuction with option(s) COMPRESS_OUTPUTS_PER_RG (GZOPRG) value: null. Cannot be used in conjuction with option(s) COMPRESS_OUTPUTS_PER_RG (GZOPRG) Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: OUTPUT_PER_RG (OPRG) OUTPUT_PER_RG (OPRG) Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: OUTPUT_PER_RG=Boolean OUTPUT_PER_RG=Boolean Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: OPRG=Boolean Output a FASTQ file per read group (two FASTQ files per read group if the group is OPRG=Boolean Output a FASTQ file per read group (two FASTQ files per read group if the group is Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: paired). Default value: false. This option can be set to 'null' to clear the default paired). Default value: false. This option can be set to 'null' to clear the default Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: value. Possible values: {true, false} Cannot be used in conjuction with option(s) value. Possible values: {true, false} Cannot be used in conjuction with option(s) Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: SECOND_END_FASTQ (F2) UNPAIRED_FASTQ (FU) FASTQ (F) SECOND_END_FASTQ (F2) UNPAIRED_FASTQ (FU) FASTQ (F) Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: COMPRESS_OUTPUTS_PER_RG=Boolean COMPRESS_OUTPUTS_PER_RG=Boolean Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: GZOPRG=Boolean Compress output FASTQ files per read group using gzip and append a .gz extension to the GZOPRG=Boolean Compress output FASTQ files per read group using gzip and append a .gz extension to the Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: file names. Default value: false. This option can be set to 'null' to clear the default file names. Default value: false. This option can be set to 'null' to clear the default Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: value. Possible values: {true, false} Cannot be used in conjuction with option(s) value. Possible values: {true, false} Cannot be used in conjuction with option(s) Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: SECOND_END_FASTQ (F2) UNPAIRED_FASTQ (FU) FASTQ (F) SECOND_END_FASTQ (F2) UNPAIRED_FASTQ (FU) FASTQ (F) Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: RG_TAG=String RG_TAG=String Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: RGT=String The read group tag (PU or ID) to be used to output a FASTQ file per read group. Default RGT=String The read group tag (PU or ID) to be used to output a FASTQ file per read group. Default Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: value: PU. This option can be set to 'null' to clear the default value. value: PU. This option can be set to 'null' to clear the default value. Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: OUTPUT_DIR=File OUTPUT_DIR=File Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ODIR=File Directory in which to output the FASTQ file(s). Used only when OUTPUT_PER_RG is true. ODIR=File Directory in which to output the FASTQ file(s). Used only when OUTPUT_PER_RG is true. Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Default value: null. Default value: null. Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: RE_REVERSE=Boolean RE_REVERSE=Boolean Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: RC=Boolean Re-reverse bases and qualities of reads with negative strand flag set before writing them RC=Boolean Re-reverse bases and qualities of reads with negative strand flag set before writing them Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: to FASTQ Default value: true. This option can be set to 'null' to clear the default to FASTQ Default value: true. This option can be set to 'null' to clear the default Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: value. Possible values: {true, false} value. Possible values: {true, false} Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: INTERLEAVE=Boolean INTERLEAVE=Boolean Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: INTER=Boolean Will generate an interleaved fastq if paired, each line will have /1 or /2 to describe INTER=Boolean Will generate an interleaved fastq if paired, each line will have /1 or /2 to describe Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: which end it came from Default value: false. This option can be set to 'null' to clear which end it came from Default value: false. This option can be set to 'null' to clear Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: the default value. Possible values: {true, false} the default value. Possible values: {true, false} Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: INCLUDE_NON_PF_READS=Boolean INCLUDE_NON_PF_READS=Boolean Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: NON_PF=Boolean Include non-PF reads from the SAM file into the output FASTQ files. PF means 'passes NON_PF=Boolean Include non-PF reads from the SAM file into the output FASTQ files. PF means 'passes Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: filtering'. Reads whose 'not passing quality controls' flag is set are non-PF reads. See filtering'. Reads whose 'not passing quality controls' flag is set are non-PF reads. See Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: GATK Dictionary for more info. Default value: false. This option can be set to 'null' to GATK Dictionary for more info. Default value: false. This option can be set to 'null' to Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: clear the default value. Possible values: {true, false} clear the default value. Possible values: {true, false} Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: CLIPPING_ATTRIBUTE=String CLIPPING_ATTRIBUTE=String Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: CLIP_ATTR=String The attribute that stores the position at which the SAM record should be clipped Default CLIP_ATTR=String The attribute that stores the position at which the SAM record should be clipped Default Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: value: null. value: null. Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: CLIPPING_ACTION=String CLIPPING_ACTION=String Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: CLIP_ACT=String The action that should be taken with clipped reads: 'X' means the reads and qualities CLIP_ACT=String The action that should be taken with clipped reads: 'X' means the reads and qualities Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: the clipped region; and any integer means that the base qualities should be set to that the clipped region; and any integer means that the base qualities should be set to that Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: value in the clipped region. Default value: null. value in the clipped region. Default value: null. Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: CLIPPING_MIN_LENGTH=Integer CLIPPING_MIN_LENGTH=Integer Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: CLIP_MIN=Integer When performing clipping with the CLIPPING_ATTRIBUTE and CLIPPING_ACTION parameters, CLIP_MIN=Integer When performing clipping with the CLIPPING_ATTRIBUTE and CLIPPING_ACTION parameters, Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ensure that the resulting reads after clipping are at least CLIPPING_MIN_LENGTH bases ensure that the resulting reads after clipping are at least CLIPPING_MIN_LENGTH bases Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: long. If the original read is shorter than CLIPPING_MIN_LENGTH then the original read long. If the original read is shorter than CLIPPING_MIN_LENGTH then the original read Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: length will be maintained. Default value: 0. This option can be set to 'null' to clear length will be maintained. Default value: 0. This option can be set to 'null' to clear Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: the default value. the default value. Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: READ1_TRIM=Integer READ1_TRIM=Integer Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: R1_TRIM=Integer The number of bases to trim from the beginning of read 1. Default value: 0. This option R1_TRIM=Integer The number of bases to trim from the beginning of read 1. Default value: 0. This option Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: can be set to 'null' to clear the default value. can be set to 'null' to clear the default value. Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: READ1_MAX_BASES_TO_WRITE=Integer READ1_MAX_BASES_TO_WRITE=Integer Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: R1_MAX_BASES=Integer The maximum number of bases to write from read 1 after trimming. If there are fewer than R1_MAX_BASES=Integer The maximum number of bases to write from read 1 after trimming. If there are fewer than Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: this many bases left after trimming, all will be written. If this value is null then all this many bases left after trimming, all will be written. If this value is null then all Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: bases left after trimming will be written. Default value: null. bases left after trimming will be written. Default value: null. Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: READ2_TRIM=Integer READ2_TRIM=Integer Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: R2_TRIM=Integer The number of bases to trim from the beginning of read 2. Default value: 0. This option R2_TRIM=Integer The number of bases to trim from the beginning of read 2. Default value: 0. This option Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: can be set to 'null' to clear the default value. can be set to 'null' to clear the default value. Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: READ2_MAX_BASES_TO_WRITE=Integer READ2_MAX_BASES_TO_WRITE=Integer Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: R2_MAX_BASES=Integer The maximum number of bases to write from read 2 after trimming. If there are fewer than R2_MAX_BASES=Integer The maximum number of bases to write from read 2 after trimming. If there are fewer than Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: this many bases left after trimming, all will be written. If this value is null then all this many bases left after trimming, all will be written. If this value is null then all Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: bases left after trimming will be written. Default value: null. bases left after trimming will be written. Default value: null. Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: QUALITY=Integer QUALITY=Integer Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Q=Integer End-trim reads using the phred/bwa quality trimming algorithm and this quality. Default Q=Integer End-trim reads using the phred/bwa quality trimming algorithm and this quality. Default Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: value: null. value: null. Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: INCLUDE_NON_PRIMARY_ALIGNMENTS=Boolean INCLUDE_NON_PRIMARY_ALIGNMENTS=Boolean Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: If true, include non-primary alignments in the output. Support of non-primary alignments If true, include non-primary alignments in the output. Support of non-primary alignments Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: there are paired reads with non-primary alignments. Default value: false. This option can there are paired reads with non-primary alignments. Default value: false. This option can Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: be set to 'null' to clear the default value. Possible values: {true, false} be set to 'null' to clear the default value. Possible values: {true, false} Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[3]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@1421b69b, 1)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: TAG_GROUP_SEPERATOR size must be equal to SEQUENCE_TAG_GROUP or not be specified at all. TAG_GROUP_SEPERATOR size must be equal to SEQUENCE_TAG_GROUP or not be specified at all. Running Test: Test method argumentCombinations[4]([Ljava.lang.String;@1dc2b4d2, [Ljava.lang.String;@f021b8f, null, 0)(picard.sam.SamToFastqWithTagsTest) Test: Test method argumentCombinations[4]([Ljava.lang.String;@1dc2b4d2, [Ljava.lang.String;@f021b8f, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 SamToFastqWithTags Gradle suite > Gradle test > picard.sam.SamToFastqWithTagsTest.argumentCombinations[4]([Ljava.lang.String;@1dc2b4d2, [Ljava.lang.String;@f021b8f, null, 0) STANDARD_ERROR INFO 2024-07-02 12:02:08 SamToFastqWithTags Test: Test method argumentCombinations[4]([Ljava.lang.String;@1dc2b4d2, [Ljava.lang.String;@f021b8f, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[4]([Ljava.lang.String;@1dc2b4d2, [Ljava.lang.String;@f021b8f, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method argumentCombinations[4]([Ljava.lang.String;@1dc2b4d2, [Ljava.lang.String;@f021b8f, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method argumentCombinations[4]([Ljava.lang.String;@1dc2b4d2, [Ljava.lang.String;@f021b8f, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method argumentCombinations[4]([Ljava.lang.String;@1dc2b4d2, [Ljava.lang.String;@f021b8f, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method argumentCombinations[4]([Ljava.lang.String;@1dc2b4d2, [Ljava.lang.String;@f021b8f, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method argumentCombinations[4]([Ljava.lang.String;@1dc2b4d2, [Ljava.lang.String;@f021b8f, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method argumentCombinations[4]([Ljava.lang.String;@1dc2b4d2, [Ljava.lang.String;@f021b8f, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method argumentCombinations[4]([Ljava.lang.String;@1dc2b4d2, [Ljava.lang.String;@f021b8f, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** SamToFastqWithTags -INPUT testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam -FASTQ /tmp/input9745387418931024146.fastq -SECOND_END_FASTQ /tmp/input_213893845824264587136.fastq -STG UR,CR -QTG CY,UY ********** SamToFastqWithTags -INPUT testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam -FASTQ /tmp/input9745387418931024146.fastq -SECOND_END_FASTQ /tmp/input_213893845824264587136.fastq -STG UR,CR -QTG CY,UY Test: Test method argumentCombinations[4]([Ljava.lang.String;@1dc2b4d2, [Ljava.lang.String;@f021b8f, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method argumentCombinations[4]([Ljava.lang.String;@1dc2b4d2, [Ljava.lang.String;@f021b8f, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[4]([Ljava.lang.String;@1dc2b4d2, [Ljava.lang.String;@f021b8f, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[4]([Ljava.lang.String;@1dc2b4d2, [Ljava.lang.String;@f021b8f, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.099 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.099 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method argumentCombinations[4]([Ljava.lang.String;@1dc2b4d2, [Ljava.lang.String;@f021b8f, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.099 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.099 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method argumentCombinations[4]([Ljava.lang.String;@1dc2b4d2, [Ljava.lang.String;@f021b8f, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.099 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.099 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method argumentCombinations[4]([Ljava.lang.String;@1dc2b4d2, [Ljava.lang.String;@f021b8f, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.099 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.099 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method argumentCombinations[4]([Ljava.lang.String;@1dc2b4d2, [Ljava.lang.String;@f021b8f, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] SamToFastqWithTags SEQUENCE_TAG_GROUP=[UR,CR] QUALITY_TAG_GROUP=[CY,UY] INPUT=testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam FASTQ=/tmp/input9745387418931024146.fastq SECOND_END_FASTQ=/tmp/input_213893845824264587136.fastq COMPRESS_OUTPUTS_PER_TAG_GROUP=false OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:08 GMT+14:00 2024] SamToFastqWithTags SEQUENCE_TAG_GROUP=[UR,CR] QUALITY_TAG_GROUP=[CY,UY] INPUT=testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam FASTQ=/tmp/input9745387418931024146.fastq SECOND_END_FASTQ=/tmp/input_213893845824264587136.fastq COMPRESS_OUTPUTS_PER_TAG_GROUP=false OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method argumentCombinations[4]([Ljava.lang.String;@1dc2b4d2, [Ljava.lang.String;@f021b8f, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method argumentCombinations[4]([Ljava.lang.String;@1dc2b4d2, [Ljava.lang.String;@f021b8f, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SamToFastqWithTags done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SamToFastqWithTags done. Elapsed time: 0.00 minutes. Test: Test method argumentCombinations[4]([Ljava.lang.String;@1dc2b4d2, [Ljava.lang.String;@f021b8f, null, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method argumentCombinations[5]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@23510878, 0)(picard.sam.SamToFastqWithTagsTest) Test: Test method argumentCombinations[5]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@23510878, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 SamToFastqWithTags Gradle suite > Gradle test > picard.sam.SamToFastqWithTagsTest.argumentCombinations[5]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@23510878, 0) STANDARD_ERROR INFO 2024-07-02 12:02:08 SamToFastqWithTags Test: Test method argumentCombinations[5]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@23510878, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[5]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@23510878, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method argumentCombinations[5]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@23510878, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method argumentCombinations[5]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@23510878, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method argumentCombinations[5]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@23510878, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method argumentCombinations[5]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@23510878, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method argumentCombinations[5]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@23510878, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method argumentCombinations[5]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@23510878, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method argumentCombinations[5]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@23510878, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** SamToFastqWithTags -INPUT testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam -FASTQ /tmp/input16849042468641057677.fastq -SECOND_END_FASTQ /tmp/input_211940153278238659359.fastq -STG UR,CR -STG CR,UR -SEP AAA -SEP AAAAA ********** SamToFastqWithTags -INPUT testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam -FASTQ /tmp/input16849042468641057677.fastq -SECOND_END_FASTQ /tmp/input_211940153278238659359.fastq -STG UR,CR -STG CR,UR -SEP AAA -SEP AAAAA Test: Test method argumentCombinations[5]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@23510878, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method argumentCombinations[5]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@23510878, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[5]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@23510878, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[5]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@23510878, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.131 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.131 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method argumentCombinations[5]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@23510878, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.131 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.131 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method argumentCombinations[5]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@23510878, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.131 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.131 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method argumentCombinations[5]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@23510878, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.131 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.131 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method argumentCombinations[5]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@23510878, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] SamToFastqWithTags SEQUENCE_TAG_GROUP=[UR,CR, CR,UR] TAG_GROUP_SEPERATOR=[AAA, AAAAA] INPUT=testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam FASTQ=/tmp/input16849042468641057677.fastq SECOND_END_FASTQ=/tmp/input_211940153278238659359.fastq COMPRESS_OUTPUTS_PER_TAG_GROUP=false OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:08 GMT+14:00 2024] SamToFastqWithTags SEQUENCE_TAG_GROUP=[UR,CR, CR,UR] TAG_GROUP_SEPERATOR=[AAA, AAAAA] INPUT=testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam FASTQ=/tmp/input16849042468641057677.fastq SECOND_END_FASTQ=/tmp/input_211940153278238659359.fastq COMPRESS_OUTPUTS_PER_TAG_GROUP=false OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method argumentCombinations[5]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@23510878, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method argumentCombinations[5]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@23510878, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SamToFastqWithTags done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SamToFastqWithTags done. Elapsed time: 0.00 minutes. Test: Test method argumentCombinations[5]([Ljava.lang.String;@61183ae6, null, [Ljava.lang.String;@23510878, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method argumentCombinations[6]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@2359b887, [Ljava.lang.String;@c57438b, 0)(picard.sam.SamToFastqWithTagsTest) Test: Test method argumentCombinations[6]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@2359b887, [Ljava.lang.String;@c57438b, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 SamToFastqWithTags Gradle suite > Gradle test > picard.sam.SamToFastqWithTagsTest.argumentCombinations[6]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@2359b887, [Ljava.lang.String;@c57438b, 0) STANDARD_ERROR INFO 2024-07-02 12:02:08 SamToFastqWithTags Test: Test method argumentCombinations[6]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@2359b887, [Ljava.lang.String;@c57438b, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[6]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@2359b887, [Ljava.lang.String;@c57438b, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method argumentCombinations[6]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@2359b887, [Ljava.lang.String;@c57438b, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method argumentCombinations[6]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@2359b887, [Ljava.lang.String;@c57438b, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method argumentCombinations[6]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@2359b887, [Ljava.lang.String;@c57438b, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method argumentCombinations[6]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@2359b887, [Ljava.lang.String;@c57438b, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method argumentCombinations[6]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@2359b887, [Ljava.lang.String;@c57438b, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method argumentCombinations[6]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@2359b887, [Ljava.lang.String;@c57438b, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method argumentCombinations[6]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@2359b887, [Ljava.lang.String;@c57438b, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** SamToFastqWithTags -INPUT testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam -FASTQ /tmp/input15250986191349288937.fastq -SECOND_END_FASTQ /tmp/input_216539797000960458824.fastq -STG UR,CR -STG CR,UR -QTG CY -QTG CY,UY -SEP AAA -SEP AAAAA ********** SamToFastqWithTags -INPUT testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam -FASTQ /tmp/input15250986191349288937.fastq -SECOND_END_FASTQ /tmp/input_216539797000960458824.fastq -STG UR,CR -STG CR,UR -QTG CY -QTG CY,UY -SEP AAA -SEP AAAAA Test: Test method argumentCombinations[6]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@2359b887, [Ljava.lang.String;@c57438b, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method argumentCombinations[6]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@2359b887, [Ljava.lang.String;@c57438b, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[6]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@2359b887, [Ljava.lang.String;@c57438b, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method argumentCombinations[6]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@2359b887, [Ljava.lang.String;@c57438b, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.160 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.160 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method argumentCombinations[6]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@2359b887, [Ljava.lang.String;@c57438b, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.160 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.160 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method argumentCombinations[6]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@2359b887, [Ljava.lang.String;@c57438b, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.160 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.160 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method argumentCombinations[6]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@2359b887, [Ljava.lang.String;@c57438b, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.160 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.160 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method argumentCombinations[6]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@2359b887, [Ljava.lang.String;@c57438b, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] SamToFastqWithTags SEQUENCE_TAG_GROUP=[UR,CR, CR,UR] QUALITY_TAG_GROUP=[CY, CY,UY] TAG_GROUP_SEPERATOR=[AAA, AAAAA] INPUT=testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam FASTQ=/tmp/input15250986191349288937.fastq SECOND_END_FASTQ=/tmp/input_216539797000960458824.fastq COMPRESS_OUTPUTS_PER_TAG_GROUP=false OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:08 GMT+14:00 2024] SamToFastqWithTags SEQUENCE_TAG_GROUP=[UR,CR, CR,UR] QUALITY_TAG_GROUP=[CY, CY,UY] TAG_GROUP_SEPERATOR=[AAA, AAAAA] INPUT=testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam FASTQ=/tmp/input15250986191349288937.fastq SECOND_END_FASTQ=/tmp/input_216539797000960458824.fastq COMPRESS_OUTPUTS_PER_TAG_GROUP=false OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method argumentCombinations[6]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@2359b887, [Ljava.lang.String;@c57438b, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method argumentCombinations[6]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@2359b887, [Ljava.lang.String;@c57438b, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SamToFastqWithTags done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SamToFastqWithTags done. Elapsed time: 0.00 minutes. Test: Test method argumentCombinations[6]([Ljava.lang.String;@61183ae6, [Ljava.lang.String;@2359b887, [Ljava.lang.String;@c57438b, 0)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@2049376f)(picard.sam.SamToFastqWithTagsTest) Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@2049376f)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 SamToFastqWithTags Gradle suite > Gradle test > picard.sam.SamToFastqWithTagsTest.testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@2049376f) STANDARD_ERROR INFO 2024-07-02 12:02:08 SamToFastqWithTags Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@2049376f)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@2049376f)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@2049376f)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@2049376f)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@2049376f)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@2049376f)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@2049376f)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@2049376f)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@2049376f)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** SamToFastqWithTags -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/grouped-last-pair-mates-flipped.sam -OUTPUT_PER_RG true -OUTPUT_DIR /tmp/pbuilder2/ -INTERLEAVE true -STG CR,UR -QTG CY,UY ********** SamToFastqWithTags -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/grouped-last-pair-mates-flipped.sam -OUTPUT_PER_RG true -OUTPUT_DIR /tmp/pbuilder2/ -INTERLEAVE true -STG CR,UR -QTG CY,UY Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@2049376f)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@2049376f)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@2049376f)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@2049376f)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.202 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.202 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@2049376f)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.202 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.202 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@2049376f)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.202 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.202 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@2049376f)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.202 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.202 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@2049376f)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] SamToFastqWithTags SEQUENCE_TAG_GROUP=[CR,UR] QUALITY_TAG_GROUP=[CY,UY] INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/grouped-last-pair-mates-flipped.sam OUTPUT_PER_RG=true OUTPUT_DIR=/tmp/pbuilder2 INTERLEAVE=true COMPRESS_OUTPUTS_PER_TAG_GROUP=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:08 GMT+14:00 2024] SamToFastqWithTags SEQUENCE_TAG_GROUP=[CR,UR] QUALITY_TAG_GROUP=[CY,UY] INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/grouped-last-pair-mates-flipped.sam OUTPUT_PER_RG=true OUTPUT_DIR=/tmp/pbuilder2 INTERLEAVE=true COMPRESS_OUTPUTS_PER_TAG_GROUP=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@2049376f)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@2049376f)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SamToFastqWithTags done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SamToFastqWithTags done. Elapsed time: 0.00 minutes. Test: Test method testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, [Ljava.lang.String;@2049376f)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testQueryNonExistantTag[0](ok/sorted-single.sam)(picard.sam.SamToFastqWithTagsTest) Test: Test method testQueryNonExistantTag[0](ok/sorted-single.sam)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 SamToFastqWithTags Gradle suite > Gradle test > picard.sam.SamToFastqWithTagsTest.testQueryNonExistantTag[0](ok/sorted-single.sam) STANDARD_ERROR INFO 2024-07-02 12:02:08 SamToFastqWithTags Test: Test method testQueryNonExistantTag[0](ok/sorted-single.sam)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method testQueryNonExistantTag[0](ok/sorted-single.sam)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testQueryNonExistantTag[0](ok/sorted-single.sam)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method testQueryNonExistantTag[0](ok/sorted-single.sam)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testQueryNonExistantTag[0](ok/sorted-single.sam)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testQueryNonExistantTag[0](ok/sorted-single.sam)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method testQueryNonExistantTag[0](ok/sorted-single.sam)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testQueryNonExistantTag[0](ok/sorted-single.sam)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method testQueryNonExistantTag[0](ok/sorted-single.sam)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** SamToFastqWithTags -INPUT testdata/picard/sam/bam2fastq/paired/ok/sorted-single.sam -FASTQ /tmp/input1738436026729235603.fastq -STG BR ********** SamToFastqWithTags -INPUT testdata/picard/sam/bam2fastq/paired/ok/sorted-single.sam -FASTQ /tmp/input1738436026729235603.fastq -STG BR Test: Test method testQueryNonExistantTag[0](ok/sorted-single.sam)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method testQueryNonExistantTag[0](ok/sorted-single.sam)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method testQueryNonExistantTag[0](ok/sorted-single.sam)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method testQueryNonExistantTag[0](ok/sorted-single.sam)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.264 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.264 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testQueryNonExistantTag[0](ok/sorted-single.sam)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.264 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.264 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testQueryNonExistantTag[0](ok/sorted-single.sam)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.264 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.264 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testQueryNonExistantTag[0](ok/sorted-single.sam)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.264 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.264 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testQueryNonExistantTag[0](ok/sorted-single.sam)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] SamToFastqWithTags SEQUENCE_TAG_GROUP=[BR] INPUT=testdata/picard/sam/bam2fastq/paired/ok/sorted-single.sam FASTQ=/tmp/input1738436026729235603.fastq COMPRESS_OUTPUTS_PER_TAG_GROUP=false OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:08 GMT+14:00 2024] SamToFastqWithTags SEQUENCE_TAG_GROUP=[BR] INPUT=testdata/picard/sam/bam2fastq/paired/ok/sorted-single.sam FASTQ=/tmp/input1738436026729235603.fastq COMPRESS_OUTPUTS_PER_TAG_GROUP=false OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testQueryNonExistantTag[0](ok/sorted-single.sam)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testQueryNonExistantTag[0](ok/sorted-single.sam)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SamToFastqWithTags done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SamToFastqWithTags done. Elapsed time: 0.00 minutes. Test: Test method testQueryNonExistantTag[0](ok/sorted-single.sam)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testQueryNonExistantTag[0](ok/sorted-single.sam)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testTagGroupFastq[0]([Ljava.lang.String;@2b4e01fe, [Ljava.lang.String;@365a687, null, AAAAA, 11111, CCCCC, 22222, null, null, null, null, One Sequence Tag Group)(picard.sam.SamToFastqWithTagsTest) Test: Test method testTagGroupFastq[0]([Ljava.lang.String;@2b4e01fe, [Ljava.lang.String;@365a687, null, AAAAA, 11111, CCCCC, 22222, null, null, null, null, One Sequence Tag Group)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 SamToFastqWithTags Gradle suite > Gradle test > picard.sam.SamToFastqWithTagsTest.testTagGroupFastq[0]([Ljava.lang.String;@2b4e01fe, [Ljava.lang.String;@365a687, null, AAAAA, 11111, CCCCC, 22222, null, null, null, null, One Sequence Tag Group) STANDARD_ERROR INFO 2024-07-02 12:02:08 SamToFastqWithTags Test: Test method testTagGroupFastq[0]([Ljava.lang.String;@2b4e01fe, [Ljava.lang.String;@365a687, null, AAAAA, 11111, CCCCC, 22222, null, null, null, null, One Sequence Tag Group)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method testTagGroupFastq[0]([Ljava.lang.String;@2b4e01fe, [Ljava.lang.String;@365a687, null, AAAAA, 11111, CCCCC, 22222, null, null, null, null, One Sequence Tag Group)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTagGroupFastq[0]([Ljava.lang.String;@2b4e01fe, [Ljava.lang.String;@365a687, null, AAAAA, 11111, CCCCC, 22222, null, null, null, null, One Sequence Tag Group)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method testTagGroupFastq[0]([Ljava.lang.String;@2b4e01fe, [Ljava.lang.String;@365a687, null, AAAAA, 11111, CCCCC, 22222, null, null, null, null, One Sequence Tag Group)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTagGroupFastq[0]([Ljava.lang.String;@2b4e01fe, [Ljava.lang.String;@365a687, null, AAAAA, 11111, CCCCC, 22222, null, null, null, null, One Sequence Tag Group)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTagGroupFastq[0]([Ljava.lang.String;@2b4e01fe, [Ljava.lang.String;@365a687, null, AAAAA, 11111, CCCCC, 22222, null, null, null, null, One Sequence Tag Group)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method testTagGroupFastq[0]([Ljava.lang.String;@2b4e01fe, [Ljava.lang.String;@365a687, null, AAAAA, 11111, CCCCC, 22222, null, null, null, null, One Sequence Tag Group)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTagGroupFastq[0]([Ljava.lang.String;@2b4e01fe, [Ljava.lang.String;@365a687, null, AAAAA, 11111, CCCCC, 22222, null, null, null, null, One Sequence Tag Group)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method testTagGroupFastq[0]([Ljava.lang.String;@2b4e01fe, [Ljava.lang.String;@365a687, null, AAAAA, 11111, CCCCC, 22222, null, null, null, null, One Sequence Tag Group)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** SamToFastqWithTags -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-single.sam -FASTQ /tmp/testtag12894283001876594448fastq -STG CR -QTG CY ********** SamToFastqWithTags -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-single.sam -FASTQ /tmp/testtag12894283001876594448fastq -STG CR -QTG CY Test: Test method testTagGroupFastq[0]([Ljava.lang.String;@2b4e01fe, [Ljava.lang.String;@365a687, null, AAAAA, 11111, CCCCC, 22222, null, null, null, null, One Sequence Tag Group)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method testTagGroupFastq[0]([Ljava.lang.String;@2b4e01fe, [Ljava.lang.String;@365a687, null, AAAAA, 11111, CCCCC, 22222, null, null, null, null, One Sequence Tag Group)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method testTagGroupFastq[0]([Ljava.lang.String;@2b4e01fe, [Ljava.lang.String;@365a687, null, AAAAA, 11111, CCCCC, 22222, null, null, null, null, One Sequence Tag Group)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method testTagGroupFastq[0]([Ljava.lang.String;@2b4e01fe, [Ljava.lang.String;@365a687, null, AAAAA, 11111, CCCCC, 22222, null, null, null, null, One Sequence Tag Group)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.312 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.312 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTagGroupFastq[0]([Ljava.lang.String;@2b4e01fe, [Ljava.lang.String;@365a687, null, AAAAA, 11111, CCCCC, 22222, null, null, null, null, One Sequence Tag Group)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.312 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.312 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTagGroupFastq[0]([Ljava.lang.String;@2b4e01fe, [Ljava.lang.String;@365a687, null, AAAAA, 11111, CCCCC, 22222, null, null, null, null, One Sequence Tag Group)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.312 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.312 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTagGroupFastq[0]([Ljava.lang.String;@2b4e01fe, [Ljava.lang.String;@365a687, null, AAAAA, 11111, CCCCC, 22222, null, null, null, null, One Sequence Tag Group)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.312 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.312 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTagGroupFastq[0]([Ljava.lang.String;@2b4e01fe, [Ljava.lang.String;@365a687, null, AAAAA, 11111, CCCCC, 22222, null, null, null, null, One Sequence Tag Group)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] SamToFastqWithTags SEQUENCE_TAG_GROUP=[CR] QUALITY_TAG_GROUP=[CY] INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-single.sam FASTQ=/tmp/testtag12894283001876594448fastq COMPRESS_OUTPUTS_PER_TAG_GROUP=false OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:08 GMT+14:00 2024] SamToFastqWithTags SEQUENCE_TAG_GROUP=[CR] QUALITY_TAG_GROUP=[CY] INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-single.sam FASTQ=/tmp/testtag12894283001876594448fastq COMPRESS_OUTPUTS_PER_TAG_GROUP=false OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTagGroupFastq[0]([Ljava.lang.String;@2b4e01fe, [Ljava.lang.String;@365a687, null, AAAAA, 11111, CCCCC, 22222, null, null, null, null, One Sequence Tag Group)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTagGroupFastq[0]([Ljava.lang.String;@2b4e01fe, [Ljava.lang.String;@365a687, null, AAAAA, 11111, CCCCC, 22222, null, null, null, null, One Sequence Tag Group)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SamToFastqWithTags done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SamToFastqWithTags done. Elapsed time: 0.00 minutes. Test: Test method testTagGroupFastq[0]([Ljava.lang.String;@2b4e01fe, [Ljava.lang.String;@365a687, null, AAAAA, 11111, CCCCC, 22222, null, null, null, null, One Sequence Tag Group)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testTagGroupFastq[1]([Ljava.lang.String;@7f8e52fa, [Ljava.lang.String;@6efab7c0, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, null, null, null, null, One Sequence Tag Group with Two Tags)(picard.sam.SamToFastqWithTagsTest) Test: Test method testTagGroupFastq[1]([Ljava.lang.String;@7f8e52fa, [Ljava.lang.String;@6efab7c0, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, null, null, null, null, One Sequence Tag Group with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 SamToFastqWithTags Gradle suite > Gradle test > picard.sam.SamToFastqWithTagsTest.testTagGroupFastq[1]([Ljava.lang.String;@7f8e52fa, [Ljava.lang.String;@6efab7c0, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, null, null, null, null, One Sequence Tag Group with Two Tags) STANDARD_ERROR INFO 2024-07-02 12:02:08 SamToFastqWithTags Test: Test method testTagGroupFastq[1]([Ljava.lang.String;@7f8e52fa, [Ljava.lang.String;@6efab7c0, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, null, null, null, null, One Sequence Tag Group with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method testTagGroupFastq[1]([Ljava.lang.String;@7f8e52fa, [Ljava.lang.String;@6efab7c0, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, null, null, null, null, One Sequence Tag Group with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTagGroupFastq[1]([Ljava.lang.String;@7f8e52fa, [Ljava.lang.String;@6efab7c0, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, null, null, null, null, One Sequence Tag Group with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method testTagGroupFastq[1]([Ljava.lang.String;@7f8e52fa, [Ljava.lang.String;@6efab7c0, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, null, null, null, null, One Sequence Tag Group with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTagGroupFastq[1]([Ljava.lang.String;@7f8e52fa, [Ljava.lang.String;@6efab7c0, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, null, null, null, null, One Sequence Tag Group with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTagGroupFastq[1]([Ljava.lang.String;@7f8e52fa, [Ljava.lang.String;@6efab7c0, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, null, null, null, null, One Sequence Tag Group with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method testTagGroupFastq[1]([Ljava.lang.String;@7f8e52fa, [Ljava.lang.String;@6efab7c0, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, null, null, null, null, One Sequence Tag Group with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTagGroupFastq[1]([Ljava.lang.String;@7f8e52fa, [Ljava.lang.String;@6efab7c0, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, null, null, null, null, One Sequence Tag Group with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method testTagGroupFastq[1]([Ljava.lang.String;@7f8e52fa, [Ljava.lang.String;@6efab7c0, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, null, null, null, null, One Sequence Tag Group with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** SamToFastqWithTags -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-single.sam -FASTQ /tmp/testtag8478896174613794281fastq -STG CR,UR -QTG CY,UY ********** SamToFastqWithTags -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-single.sam -FASTQ /tmp/testtag8478896174613794281fastq -STG CR,UR -QTG CY,UY Test: Test method testTagGroupFastq[1]([Ljava.lang.String;@7f8e52fa, [Ljava.lang.String;@6efab7c0, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, null, null, null, null, One Sequence Tag Group with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method testTagGroupFastq[1]([Ljava.lang.String;@7f8e52fa, [Ljava.lang.String;@6efab7c0, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, null, null, null, null, One Sequence Tag Group with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method testTagGroupFastq[1]([Ljava.lang.String;@7f8e52fa, [Ljava.lang.String;@6efab7c0, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, null, null, null, null, One Sequence Tag Group with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method testTagGroupFastq[1]([Ljava.lang.String;@7f8e52fa, [Ljava.lang.String;@6efab7c0, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, null, null, null, null, One Sequence Tag Group with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.365 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.365 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTagGroupFastq[1]([Ljava.lang.String;@7f8e52fa, [Ljava.lang.String;@6efab7c0, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, null, null, null, null, One Sequence Tag Group with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.365 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.365 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTagGroupFastq[1]([Ljava.lang.String;@7f8e52fa, [Ljava.lang.String;@6efab7c0, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, null, null, null, null, One Sequence Tag Group with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.365 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.365 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTagGroupFastq[1]([Ljava.lang.String;@7f8e52fa, [Ljava.lang.String;@6efab7c0, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, null, null, null, null, One Sequence Tag Group with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.365 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.365 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTagGroupFastq[1]([Ljava.lang.String;@7f8e52fa, [Ljava.lang.String;@6efab7c0, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, null, null, null, null, One Sequence Tag Group with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] SamToFastqWithTags SEQUENCE_TAG_GROUP=[CR,UR] QUALITY_TAG_GROUP=[CY,UY] INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-single.sam FASTQ=/tmp/testtag8478896174613794281fastq COMPRESS_OUTPUTS_PER_TAG_GROUP=false OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:08 GMT+14:00 2024] SamToFastqWithTags SEQUENCE_TAG_GROUP=[CR,UR] QUALITY_TAG_GROUP=[CY,UY] INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-single.sam FASTQ=/tmp/testtag8478896174613794281fastq COMPRESS_OUTPUTS_PER_TAG_GROUP=false OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTagGroupFastq[1]([Ljava.lang.String;@7f8e52fa, [Ljava.lang.String;@6efab7c0, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, null, null, null, null, One Sequence Tag Group with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTagGroupFastq[1]([Ljava.lang.String;@7f8e52fa, [Ljava.lang.String;@6efab7c0, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, null, null, null, null, One Sequence Tag Group with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SamToFastqWithTags done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SamToFastqWithTags done. Elapsed time: 0.00 minutes. Test: Test method testTagGroupFastq[1]([Ljava.lang.String;@7f8e52fa, [Ljava.lang.String;@6efab7c0, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, null, null, null, null, One Sequence Tag Group with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testTagGroupFastq[2]([Ljava.lang.String;@4371d0c1, [Ljava.lang.String;@1caf4cc7, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, TTTAAAAA, 22211111, GGGCCCCC, 11122222, Two Sequence Tag Groups with Two Tags)(picard.sam.SamToFastqWithTagsTest) Test: Test method testTagGroupFastq[2]([Ljava.lang.String;@4371d0c1, [Ljava.lang.String;@1caf4cc7, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, TTTAAAAA, 22211111, GGGCCCCC, 11122222, Two Sequence Tag Groups with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 SamToFastqWithTags Gradle suite > Gradle test > picard.sam.SamToFastqWithTagsTest.testTagGroupFastq[2]([Ljava.lang.String;@4371d0c1, [Ljava.lang.String;@1caf4cc7, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, TTTAAAAA, 22211111, GGGCCCCC, 11122222, Two Sequence Tag Groups with Two Tags) STANDARD_ERROR INFO 2024-07-02 12:02:08 SamToFastqWithTags Test: Test method testTagGroupFastq[2]([Ljava.lang.String;@4371d0c1, [Ljava.lang.String;@1caf4cc7, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, TTTAAAAA, 22211111, GGGCCCCC, 11122222, Two Sequence Tag Groups with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method testTagGroupFastq[2]([Ljava.lang.String;@4371d0c1, [Ljava.lang.String;@1caf4cc7, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, TTTAAAAA, 22211111, GGGCCCCC, 11122222, Two Sequence Tag Groups with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTagGroupFastq[2]([Ljava.lang.String;@4371d0c1, [Ljava.lang.String;@1caf4cc7, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, TTTAAAAA, 22211111, GGGCCCCC, 11122222, Two Sequence Tag Groups with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method testTagGroupFastq[2]([Ljava.lang.String;@4371d0c1, [Ljava.lang.String;@1caf4cc7, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, TTTAAAAA, 22211111, GGGCCCCC, 11122222, Two Sequence Tag Groups with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTagGroupFastq[2]([Ljava.lang.String;@4371d0c1, [Ljava.lang.String;@1caf4cc7, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, TTTAAAAA, 22211111, GGGCCCCC, 11122222, Two Sequence Tag Groups with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTagGroupFastq[2]([Ljava.lang.String;@4371d0c1, [Ljava.lang.String;@1caf4cc7, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, TTTAAAAA, 22211111, GGGCCCCC, 11122222, Two Sequence Tag Groups with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method testTagGroupFastq[2]([Ljava.lang.String;@4371d0c1, [Ljava.lang.String;@1caf4cc7, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, TTTAAAAA, 22211111, GGGCCCCC, 11122222, Two Sequence Tag Groups with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTagGroupFastq[2]([Ljava.lang.String;@4371d0c1, [Ljava.lang.String;@1caf4cc7, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, TTTAAAAA, 22211111, GGGCCCCC, 11122222, Two Sequence Tag Groups with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method testTagGroupFastq[2]([Ljava.lang.String;@4371d0c1, [Ljava.lang.String;@1caf4cc7, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, TTTAAAAA, 22211111, GGGCCCCC, 11122222, Two Sequence Tag Groups with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** SamToFastqWithTags -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-single.sam -FASTQ /tmp/testtag5299634637253686619fastq -STG CR,UR -STG UR,CR -QTG CY,UY -QTG UY,CY ********** SamToFastqWithTags -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-single.sam -FASTQ /tmp/testtag5299634637253686619fastq -STG CR,UR -STG UR,CR -QTG CY,UY -QTG UY,CY Test: Test method testTagGroupFastq[2]([Ljava.lang.String;@4371d0c1, [Ljava.lang.String;@1caf4cc7, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, TTTAAAAA, 22211111, GGGCCCCC, 11122222, Two Sequence Tag Groups with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method testTagGroupFastq[2]([Ljava.lang.String;@4371d0c1, [Ljava.lang.String;@1caf4cc7, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, TTTAAAAA, 22211111, GGGCCCCC, 11122222, Two Sequence Tag Groups with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method testTagGroupFastq[2]([Ljava.lang.String;@4371d0c1, [Ljava.lang.String;@1caf4cc7, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, TTTAAAAA, 22211111, GGGCCCCC, 11122222, Two Sequence Tag Groups with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method testTagGroupFastq[2]([Ljava.lang.String;@4371d0c1, [Ljava.lang.String;@1caf4cc7, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, TTTAAAAA, 22211111, GGGCCCCC, 11122222, Two Sequence Tag Groups with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.411 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.411 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTagGroupFastq[2]([Ljava.lang.String;@4371d0c1, [Ljava.lang.String;@1caf4cc7, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, TTTAAAAA, 22211111, GGGCCCCC, 11122222, Two Sequence Tag Groups with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.411 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.411 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTagGroupFastq[2]([Ljava.lang.String;@4371d0c1, [Ljava.lang.String;@1caf4cc7, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, TTTAAAAA, 22211111, GGGCCCCC, 11122222, Two Sequence Tag Groups with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.411 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.411 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTagGroupFastq[2]([Ljava.lang.String;@4371d0c1, [Ljava.lang.String;@1caf4cc7, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, TTTAAAAA, 22211111, GGGCCCCC, 11122222, Two Sequence Tag Groups with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.411 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.411 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTagGroupFastq[2]([Ljava.lang.String;@4371d0c1, [Ljava.lang.String;@1caf4cc7, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, TTTAAAAA, 22211111, GGGCCCCC, 11122222, Two Sequence Tag Groups with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] SamToFastqWithTags SEQUENCE_TAG_GROUP=[CR,UR, UR,CR] QUALITY_TAG_GROUP=[CY,UY, UY,CY] INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-single.sam FASTQ=/tmp/testtag5299634637253686619fastq COMPRESS_OUTPUTS_PER_TAG_GROUP=false OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:08 GMT+14:00 2024] SamToFastqWithTags SEQUENCE_TAG_GROUP=[CR,UR, UR,CR] QUALITY_TAG_GROUP=[CY,UY, UY,CY] INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-single.sam FASTQ=/tmp/testtag5299634637253686619fastq COMPRESS_OUTPUTS_PER_TAG_GROUP=false OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTagGroupFastq[2]([Ljava.lang.String;@4371d0c1, [Ljava.lang.String;@1caf4cc7, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, TTTAAAAA, 22211111, GGGCCCCC, 11122222, Two Sequence Tag Groups with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTagGroupFastq[2]([Ljava.lang.String;@4371d0c1, [Ljava.lang.String;@1caf4cc7, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, TTTAAAAA, 22211111, GGGCCCCC, 11122222, Two Sequence Tag Groups with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SamToFastqWithTags done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SamToFastqWithTags done. Elapsed time: 0.00 minutes. Test: Test method testTagGroupFastq[2]([Ljava.lang.String;@4371d0c1, [Ljava.lang.String;@1caf4cc7, null, AAAAATTT, 11111222, CCCCCGGG, 22222111, TTTAAAAA, 22211111, GGGCCCCC, 11122222, Two Sequence Tag Groups with Two Tags)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testTagGroupFastq[3]([Ljava.lang.String;@2b1aaadd, [Ljava.lang.String;@68be99b, [Ljava.lang.String;@224d9dc1, AAAAAATGCTTT, 11111~~~~222, CCCCCATGCGGG, 22222~~~~111, TTTCGTAAAAAA, 222~~~~11111, GGGCGTACCCCC, 111~~~~22222, Two Sequence Tag Groups with Two Tags with Separators)(picard.sam.SamToFastqWithTagsTest) Test: Test method testTagGroupFastq[3]([Ljava.lang.String;@2b1aaadd, [Ljava.lang.String;@68be99b, [Ljava.lang.String;@224d9dc1, AAAAAATGCTTT, 11111~~~~222, CCCCCATGCGGG, 22222~~~~111, TTTCGTAAAAAA, 222~~~~11111, GGGCGTACCCCC, 111~~~~22222, Two Sequence Tag Groups with Two Tags with Separators)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 SamToFastqWithTags Gradle suite > Gradle test > picard.sam.SamToFastqWithTagsTest.testTagGroupFastq[3]([Ljava.lang.String;@2b1aaadd, [Ljava.lang.String;@68be99b, [Ljava.lang.String;@224d9dc1, AAAAAATGCTTT, 11111~~~~222, CCCCCATGCGGG, 22222~~~~111, TTTCGTAAAAAA, 222~~~~11111, GGGCGTACCCCC, 111~~~~22222, Two Sequence Tag Groups with Two Tags with Separators) STANDARD_ERROR INFO 2024-07-02 12:02:08 SamToFastqWithTags Test: Test method testTagGroupFastq[3]([Ljava.lang.String;@2b1aaadd, [Ljava.lang.String;@68be99b, [Ljava.lang.String;@224d9dc1, AAAAAATGCTTT, 11111~~~~222, CCCCCATGCGGG, 22222~~~~111, TTTCGTAAAAAA, 222~~~~11111, GGGCGTACCCCC, 111~~~~22222, Two Sequence Tag Groups with Two Tags with Separators)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method testTagGroupFastq[3]([Ljava.lang.String;@2b1aaadd, [Ljava.lang.String;@68be99b, [Ljava.lang.String;@224d9dc1, AAAAAATGCTTT, 11111~~~~222, CCCCCATGCGGG, 22222~~~~111, TTTCGTAAAAAA, 222~~~~11111, GGGCGTACCCCC, 111~~~~22222, Two Sequence Tag Groups with Two Tags with Separators)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testTagGroupFastq[3]([Ljava.lang.String;@2b1aaadd, [Ljava.lang.String;@68be99b, [Ljava.lang.String;@224d9dc1, AAAAAATGCTTT, 11111~~~~222, CCCCCATGCGGG, 22222~~~~111, TTTCGTAAAAAA, 222~~~~11111, GGGCGTACCCCC, 111~~~~22222, Two Sequence Tag Groups with Two Tags with Separators)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method testTagGroupFastq[3]([Ljava.lang.String;@2b1aaadd, [Ljava.lang.String;@68be99b, [Ljava.lang.String;@224d9dc1, AAAAAATGCTTT, 11111~~~~222, CCCCCATGCGGG, 22222~~~~111, TTTCGTAAAAAA, 222~~~~11111, GGGCGTACCCCC, 111~~~~22222, Two Sequence Tag Groups with Two Tags with Separators)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testTagGroupFastq[3]([Ljava.lang.String;@2b1aaadd, [Ljava.lang.String;@68be99b, [Ljava.lang.String;@224d9dc1, AAAAAATGCTTT, 11111~~~~222, CCCCCATGCGGG, 22222~~~~111, TTTCGTAAAAAA, 222~~~~11111, GGGCGTACCCCC, 111~~~~22222, Two Sequence Tag Groups with Two Tags with Separators)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testTagGroupFastq[3]([Ljava.lang.String;@2b1aaadd, [Ljava.lang.String;@68be99b, [Ljava.lang.String;@224d9dc1, AAAAAATGCTTT, 11111~~~~222, CCCCCATGCGGG, 22222~~~~111, TTTCGTAAAAAA, 222~~~~11111, GGGCGTACCCCC, 111~~~~22222, Two Sequence Tag Groups with Two Tags with Separators)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method testTagGroupFastq[3]([Ljava.lang.String;@2b1aaadd, [Ljava.lang.String;@68be99b, [Ljava.lang.String;@224d9dc1, AAAAAATGCTTT, 11111~~~~222, CCCCCATGCGGG, 22222~~~~111, TTTCGTAAAAAA, 222~~~~11111, GGGCGTACCCCC, 111~~~~22222, Two Sequence Tag Groups with Two Tags with Separators)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testTagGroupFastq[3]([Ljava.lang.String;@2b1aaadd, [Ljava.lang.String;@68be99b, [Ljava.lang.String;@224d9dc1, AAAAAATGCTTT, 11111~~~~222, CCCCCATGCGGG, 22222~~~~111, TTTCGTAAAAAA, 222~~~~11111, GGGCGTACCCCC, 111~~~~22222, Two Sequence Tag Groups with Two Tags with Separators)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method testTagGroupFastq[3]([Ljava.lang.String;@2b1aaadd, [Ljava.lang.String;@68be99b, [Ljava.lang.String;@224d9dc1, AAAAAATGCTTT, 11111~~~~222, CCCCCATGCGGG, 22222~~~~111, TTTCGTAAAAAA, 222~~~~11111, GGGCGTACCCCC, 111~~~~22222, Two Sequence Tag Groups with Two Tags with Separators)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** SamToFastqWithTags -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-single.sam -FASTQ /tmp/testtag15354162029530858313fastq -STG CR,UR -STG UR,CR -QTG CY,UY -QTG UY,CY -SEP ATGC -SEP CGTA ********** SamToFastqWithTags -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-single.sam -FASTQ /tmp/testtag15354162029530858313fastq -STG CR,UR -STG UR,CR -QTG CY,UY -QTG UY,CY -SEP ATGC -SEP CGTA Test: Test method testTagGroupFastq[3]([Ljava.lang.String;@2b1aaadd, [Ljava.lang.String;@68be99b, [Ljava.lang.String;@224d9dc1, AAAAAATGCTTT, 11111~~~~222, CCCCCATGCGGG, 22222~~~~111, TTTCGTAAAAAA, 222~~~~11111, GGGCGTACCCCC, 111~~~~22222, Two Sequence Tag Groups with Two Tags with Separators)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: ********** ********** Test: Test method testTagGroupFastq[3]([Ljava.lang.String;@2b1aaadd, [Ljava.lang.String;@68be99b, [Ljava.lang.String;@224d9dc1, AAAAAATGCTTT, 11111~~~~222, CCCCCATGCGGG, 22222~~~~111, TTTCGTAAAAAA, 222~~~~11111, GGGCGTACCCCC, 111~~~~22222, Two Sequence Tag Groups with Two Tags with Separators)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method testTagGroupFastq[3]([Ljava.lang.String;@2b1aaadd, [Ljava.lang.String;@68be99b, [Ljava.lang.String;@224d9dc1, AAAAAATGCTTT, 11111~~~~222, CCCCCATGCGGG, 22222~~~~111, TTTCGTAAAAAA, 222~~~~11111, GGGCGTACCCCC, 111~~~~22222, Two Sequence Tag Groups with Two Tags with Separators)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Test: Test method testTagGroupFastq[3]([Ljava.lang.String;@2b1aaadd, [Ljava.lang.String;@68be99b, [Ljava.lang.String;@224d9dc1, AAAAAATGCTTT, 11111~~~~222, CCCCCATGCGGG, 22222~~~~111, TTTCGTAAAAAA, 222~~~~11111, GGGCGTACCCCC, 111~~~~22222, Two Sequence Tag Groups with Two Tags with Separators)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.475 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.475 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTagGroupFastq[3]([Ljava.lang.String;@2b1aaadd, [Ljava.lang.String;@68be99b, [Ljava.lang.String;@224d9dc1, AAAAAATGCTTT, 11111~~~~222, CCCCCATGCGGG, 22222~~~~111, TTTCGTAAAAAA, 222~~~~11111, GGGCGTACCCCC, 111~~~~22222, Two Sequence Tag Groups with Two Tags with Separators)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.475 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.475 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTagGroupFastq[3]([Ljava.lang.String;@2b1aaadd, [Ljava.lang.String;@68be99b, [Ljava.lang.String;@224d9dc1, AAAAAATGCTTT, 11111~~~~222, CCCCCATGCGGG, 22222~~~~111, TTTCGTAAAAAA, 222~~~~11111, GGGCGTACCCCC, 111~~~~22222, Two Sequence Tag Groups with Two Tags with Separators)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.475 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.475 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testTagGroupFastq[3]([Ljava.lang.String;@2b1aaadd, [Ljava.lang.String;@68be99b, [Ljava.lang.String;@224d9dc1, AAAAAATGCTTT, 11111~~~~222, CCCCCATGCGGG, 22222~~~~111, TTTCGTAAAAAA, 222~~~~11111, GGGCGTACCCCC, 111~~~~22222, Two Sequence Tag Groups with Two Tags with Separators)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: 12:02:08.475 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.475 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testTagGroupFastq[3]([Ljava.lang.String;@2b1aaadd, [Ljava.lang.String;@68be99b, [Ljava.lang.String;@224d9dc1, AAAAAATGCTTT, 11111~~~~222, CCCCCATGCGGG, 22222~~~~111, TTTCGTAAAAAA, 222~~~~11111, GGGCGTACCCCC, 111~~~~22222, Two Sequence Tag Groups with Two Tags with Separators)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] SamToFastqWithTags SEQUENCE_TAG_GROUP=[CR,UR, UR,CR] QUALITY_TAG_GROUP=[CY,UY, UY,CY] TAG_GROUP_SEPERATOR=[ATGC, CGTA] INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-single.sam FASTQ=/tmp/testtag15354162029530858313fastq COMPRESS_OUTPUTS_PER_TAG_GROUP=false OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:08 GMT+14:00 2024] SamToFastqWithTags SEQUENCE_TAG_GROUP=[CR,UR, UR,CR] QUALITY_TAG_GROUP=[CY,UY, UY,CY] TAG_GROUP_SEPERATOR=[ATGC, CGTA] INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/bam2fastq/paired/ok/sorted-single.sam FASTQ=/tmp/testtag15354162029530858313fastq COMPRESS_OUTPUTS_PER_TAG_GROUP=false OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testTagGroupFastq[3]([Ljava.lang.String;@2b1aaadd, [Ljava.lang.String;@68be99b, [Ljava.lang.String;@224d9dc1, AAAAAATGCTTT, 11111~~~~222, CCCCCATGCGGG, 22222~~~~111, TTTCGTAAAAAA, 222~~~~11111, GGGCGTACCCCC, 111~~~~22222, Two Sequence Tag Groups with Two Tags with Separators)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testTagGroupFastq[3]([Ljava.lang.String;@2b1aaadd, [Ljava.lang.String;@68be99b, [Ljava.lang.String;@224d9dc1, AAAAAATGCTTT, 11111~~~~222, CCCCCATGCGGG, 22222~~~~111, TTTCGTAAAAAA, 222~~~~11111, GGGCGTACCCCC, 111~~~~22222, Two Sequence Tag Groups with Two Tags with Separators)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SamToFastqWithTags done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SamToFastqWithTags done. Elapsed time: 0.00 minutes. Test: Test method testTagGroupFastq[3]([Ljava.lang.String;@2b1aaadd, [Ljava.lang.String;@68be99b, [Ljava.lang.String;@224d9dc1, AAAAAATGCTTT, 11111~~~~222, CCCCCATGCGGG, 22222~~~~111, TTTCGTAAAAAA, 222~~~~11111, GGGCGTACCCCC, 111~~~~22222, Two Sequence Tag Groups with Two Tags with Separators)(picard.sam.SamToFastqWithTagsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testSegregateReference[0](NNNNNAAAAANNNNNN, 1, [fake1:1-5 + ., fake1:6-10 + ., fake1:11-16 + .])(picard.util.ScatterIntervalsByNsTest) Running Test: Test method testSegregateReference[1](NNNNNAAAAANNNNNN, 5, [fake1:1-5 + ., fake1:6-10 + ., fake1:11-16 + .])(picard.util.ScatterIntervalsByNsTest) Running Test: Test method testSegregateReference[2](NNNNNAAAnANNNNNN, 6, [fake1:1-5 + ., fake1:6-10 + ., fake1:11-16 + .])(picard.util.ScatterIntervalsByNsTest) Running Test: Test method testSegregateReference[3](AnTGCNNNNNACGTCG, 1, [fake1:1-5 + ., fake1:6-10 + ., fake1:11-16 + .])(picard.util.ScatterIntervalsByNsTest) Test: Test method testSegregateReference[3](AnTGCNNNNNACGTCG, 1, [fake1:1-5 + ., fake1:6-10 + ., fake1:11-16 + .])(picard.util.ScatterIntervalsByNsTest) produced standard out/err: INFO 2024-07-02 12:02:08 ScatterIntervalsByNs found 10 intervals. Elapsed time: 00:00:00s. Time for last 10: 0s. Last read position: fake1:1 Gradle suite > Gradle test > picard.util.ScatterIntervalsByNsTest.testSegregateReference[3](AnTGCNNNNNACGTCG, 1, [fake1:1-5 + ., fake1:6-10 + ., fake1:11-16 + .]) STANDARD_ERROR INFO 2024-07-02 12:02:08 ScatterIntervalsByNs found 10 intervals. Elapsed time: 00:00:00s. Time for last 10: 0s. Last read position: fake1:1 Running Test: Test method testSegregateReference[4](ACTGCNNNNNACGTCG, 4, [fake1:1-5 + ., fake1:6-10 + ., fake1:11-16 + .])(picard.util.ScatterIntervalsByNsTest) Running Test: Test method testSegregateReference[5](ACTGCNNNNNACgctG, 5, [fake1:1-16 + .])(picard.util.ScatterIntervalsByNsTest) Running Test: Test method testSegregateReference[6](ACNGCNNNNNACnTNG, 5, [fake1:1-16 + .])(picard.util.ScatterIntervalsByNsTest) Running Test: Test method testSegregateReference[7](ACNGCNNNNNACnTNG, 0, [fake1:1-2 + ., fake1:3-3 + ., fake1:4-5 + ., fake1:6-10 + ., fake1:11-12 + ., fake1:13-13 + ., fake1:14-14 + ., fake1:15-15 + ., fake1:16-16 + .])(picard.util.ScatterIntervalsByNsTest) Test: Test method testSegregateReference[7](ACNGCNNNNNACnTNG, 0, [fake1:1-2 + ., fake1:3-3 + ., fake1:4-5 + ., fake1:6-10 + ., fake1:11-12 + ., fake1:13-13 + ., fake1:14-14 + ., fake1:15-15 + ., fake1:16-16 + .])(picard.util.ScatterIntervalsByNsTest) produced standard out/err: INFO 2024-07-02 12:02:08 ScatterIntervalsByNs found 20 intervals. Elapsed time: 00:00:00s. Time for last 10: 0s. Last read position: fake1:4 Gradle suite > Gradle test > picard.util.ScatterIntervalsByNsTest.testSegregateReference[7](ACNGCNNNNNACnTNG, 0, [fake1:1-2 + ., fake1:3-3 + ., fake1:4-5 + ., fake1:6-10 + ., fake1:11-12 + ., fake1:13-13 + ., fake1:14-14 + ., fake1:15-15 + ., fake1:16-16 + .]) STANDARD_ERROR INFO 2024-07-02 12:02:08 ScatterIntervalsByNs found 20 intervals. Elapsed time: 00:00:00s. Time for last 10: 0s. Last read position: fake1:4 Running Test: Test method testSegregateReference[8](AAAAAAAAAAACnTNG, 0, [fake1:1-12 + ., fake1:13-13 + ., fake1:14-14 + ., fake1:15-15 + ., fake1:16-16 + .])(picard.util.ScatterIntervalsByNsTest) Test: Test method testSegregateReference[8](AAAAAAAAAAACnTNG, 0, [fake1:1-12 + ., fake1:13-13 + ., fake1:14-14 + ., fake1:15-15 + ., fake1:16-16 + .])(picard.util.ScatterIntervalsByNsTest) produced standard out/err: INFO 2024-07-02 12:02:08 ScatterIntervalsByNs found 30 intervals. Elapsed time: 00:00:00s. Time for last 10: 0s. Last read position: fake1:15 Gradle suite > Gradle test > picard.util.ScatterIntervalsByNsTest.testSegregateReference[8](AAAAAAAAAAACnTNG, 0, [fake1:1-12 + ., fake1:13-13 + ., fake1:14-14 + ., fake1:15-15 + ., fake1:16-16 + .]) STANDARD_ERROR INFO 2024-07-02 12:02:08 ScatterIntervalsByNs found 30 intervals. Elapsed time: 00:00:00s. Time for last 10: 0s. Last read position: fake1:15 Running Test: Test method testSegregateReference[9](AAAAAAAAAAACATNG, 0, [fake1:1-14 + ., fake1:15-15 + ., fake1:16-16 + .])(picard.util.ScatterIntervalsByNsTest) Running Test: Test method testSegregateReference[10](ANCNNGCNNNNNACNTNGN, 1, [fake1:1-3 + ., fake1:4-5 + ., fake1:6-7 + ., fake1:8-12 + ., fake1:13-18 + ., fake1:19-19 + .])(picard.util.ScatterIntervalsByNsTest) Test: Test method testSegregateReference[10](ANCNNGCNNNNNACNTNGN, 1, [fake1:1-3 + ., fake1:4-5 + ., fake1:6-7 + ., fake1:8-12 + ., fake1:13-18 + ., fake1:19-19 + .])(picard.util.ScatterIntervalsByNsTest) produced standard out/err: INFO 2024-07-02 12:02:08 ScatterIntervalsByNs found 40 intervals. Elapsed time: 00:00:00s. Time for last 10: 0s. Last read position: fake1:19 Gradle suite > Gradle test > picard.util.ScatterIntervalsByNsTest.testSegregateReference[10](ANCNNGCNNNNNACNTNGN, 1, [fake1:1-3 + ., fake1:4-5 + ., fake1:6-7 + ., fake1:8-12 + ., fake1:13-18 + ., fake1:19-19 + .]) STANDARD_ERROR INFO 2024-07-02 12:02:08 ScatterIntervalsByNs found 40 intervals. Elapsed time: 00:00:00s. Time for last 10: 0s. Last read position: fake1:19 Running Test: Test method testSegregateReference[11](ANCNNGCNNNNNACNTNGN, 0, [fake1:1-1 + ., fake1:2-2 + ., fake1:3-3 + ., fake1:4-5 + ., fake1:6-7 + ., fake1:8-12 + ., fake1:13-14 + ., fake1:15-15 + ., fake1:16-16 + ., fake1:17-17 + ., fake1:18-18 + ., fake1:19-19 + .])(picard.util.ScatterIntervalsByNsTest) Test: Test method testSegregateReference[11](ANCNNGCNNNNNACNTNGN, 0, [fake1:1-1 + ., fake1:2-2 + ., fake1:3-3 + ., fake1:4-5 + ., fake1:6-7 + ., fake1:8-12 + ., fake1:13-14 + ., fake1:15-15 + ., fake1:16-16 + ., fake1:17-17 + ., fake1:18-18 + ., fake1:19-19 + .])(picard.util.ScatterIntervalsByNsTest) produced standard out/err: INFO 2024-07-02 12:02:08 ScatterIntervalsByNs found 50 intervals. Elapsed time: 00:00:00s. Time for last 10: 0s. Last read position: fake1:17 Gradle suite > Gradle test > picard.util.ScatterIntervalsByNsTest.testSegregateReference[11](ANCNNGCNNNNNACNTNGN, 0, [fake1:1-1 + ., fake1:2-2 + ., fake1:3-3 + ., fake1:4-5 + ., fake1:6-7 + ., fake1:8-12 + ., fake1:13-14 + ., fake1:15-15 + ., fake1:16-16 + ., fake1:17-17 + ., fake1:18-18 + ., fake1:19-19 + .]) STANDARD_ERROR INFO 2024-07-02 12:02:08 ScatterIntervalsByNs found 50 intervals. Elapsed time: 00:00:00s. Time for last 10: 0s. Last read position: fake1:17 Running Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 SortSam Gradle suite > Gradle test > picard.sam.SetNmMdAndUqTagsTest.testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta) STANDARD_ERROR INFO 2024-07-02 12:02:08 SortSam Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** SortSam -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/Sort7015079448219025308.bam -SORT_ORDER coordinate ********** SortSam -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/Sort7015079448219025308.bam -SORT_ORDER coordinate Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.507 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.507 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.507 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.507 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.507 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.507 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.507 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.507 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] SortSam INPUT=testdata/picard/sam/aligned.sam OUTPUT=/tmp/Sort7015079448219025308.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:08 GMT+14:00 2024] SortSam INPUT=testdata/picard/sam/aligned.sam OUTPUT=/tmp/Sort7015079448219025308.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 SortSam Finished reading inputs, merging and writing to output now. INFO 2024-07-02 12:02:08 SortSam Finished reading inputs, merging and writing to output now. Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.00 minutes. Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 SetNmMdAndUqTags INFO 2024-07-02 12:02:08 SetNmMdAndUqTags Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** SetNmMdAndUqTags -INPUT /tmp/Sort7015079448219025308.bam -OUTPUT /tmp/Fix8817863419938362643.bam -REFERENCE_SEQUENCE testdata/picard/sam/merger.fasta ********** SetNmMdAndUqTags -INPUT /tmp/Sort7015079448219025308.bam -OUTPUT /tmp/Fix8817863419938362643.bam -REFERENCE_SEQUENCE testdata/picard/sam/merger.fasta Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.537 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.537 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.537 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.537 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.537 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.537 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.537 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.537 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] SetNmMdAndUqTags INPUT=/tmp/Sort7015079448219025308.bam OUTPUT=/tmp/Fix8817863419938362643.bam REFERENCE_SEQUENCE=testdata/picard/sam/merger.fasta IS_BISULFITE_SEQUENCE=false SET_ONLY_UQ=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:08 GMT+14:00 2024] SetNmMdAndUqTags INPUT=/tmp/Sort7015079448219025308.bam OUTPUT=/tmp/Fix8817863419938362643.bam REFERENCE_SEQUENCE=testdata/picard/sam/merger.fasta IS_BISULFITE_SEQUENCE=false SET_ONLY_UQ=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SetNmMdAndUqTags done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SetNmMdAndUqTags done. Elapsed time: 0.00 minutes. Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 ValidateSamFile INFO 2024-07-02 12:02:08 ValidateSamFile Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ValidateSamFile -INPUT /tmp/Fix8817863419938362643.bam -OUTPUT /tmp/Sort1899633635551465414.validation_report -MODE VERBOSE -REFERENCE_SEQUENCE testdata/picard/sam/merger.fasta ********** ValidateSamFile -INPUT /tmp/Fix8817863419938362643.bam -OUTPUT /tmp/Sort1899633635551465414.validation_report -MODE VERBOSE -REFERENCE_SEQUENCE testdata/picard/sam/merger.fasta Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.563 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.563 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.563 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.563 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.563 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.563 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.563 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.563 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/Fix8817863419938362643.bam OUTPUT=/tmp/Sort1899633635551465414.validation_report MODE=VERBOSE REFERENCE_SEQUENCE=testdata/picard/sam/merger.fasta MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:08 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/Fix8817863419938362643.bam OUTPUT=/tmp/Sort1899633635551465414.validation_report MODE=VERBOSE REFERENCE_SEQUENCE=testdata/picard/sam/merger.fasta MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testValidSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 SortSam Gradle suite > Gradle test > picard.sam.SetNmMdAndUqTagsTest.testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta) STANDARD_ERROR INFO 2024-07-02 12:02:08 SortSam Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** SortSam -INPUT testdata/picard/sam/aligned_queryname_sorted.sam -OUTPUT /tmp/Sort18445284905299908118.bam -SORT_ORDER coordinate ********** SortSam -INPUT testdata/picard/sam/aligned_queryname_sorted.sam -OUTPUT /tmp/Sort18445284905299908118.bam -SORT_ORDER coordinate Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.577 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.577 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.577 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.577 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.578 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.578 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.578 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.578 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] SortSam INPUT=testdata/picard/sam/aligned_queryname_sorted.sam OUTPUT=/tmp/Sort18445284905299908118.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:08 GMT+14:00 2024] SortSam INPUT=testdata/picard/sam/aligned_queryname_sorted.sam OUTPUT=/tmp/Sort18445284905299908118.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 SortSam Finished reading inputs, merging and writing to output now. INFO 2024-07-02 12:02:08 SortSam Finished reading inputs, merging and writing to output now. Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.00 minutes. Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 SetNmMdAndUqTags INFO 2024-07-02 12:02:08 SetNmMdAndUqTags Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** SetNmMdAndUqTags -INPUT /tmp/Sort18445284905299908118.bam -OUTPUT /tmp/Fix16399477720078456105.bam -REFERENCE_SEQUENCE testdata/picard/sam/merger.fasta ********** SetNmMdAndUqTags -INPUT /tmp/Sort18445284905299908118.bam -OUTPUT /tmp/Fix16399477720078456105.bam -REFERENCE_SEQUENCE testdata/picard/sam/merger.fasta Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.610 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.610 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.610 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.610 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.610 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.610 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.610 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.610 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] SetNmMdAndUqTags INPUT=/tmp/Sort18445284905299908118.bam OUTPUT=/tmp/Fix16399477720078456105.bam REFERENCE_SEQUENCE=testdata/picard/sam/merger.fasta IS_BISULFITE_SEQUENCE=false SET_ONLY_UQ=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:08 GMT+14:00 2024] SetNmMdAndUqTags INPUT=/tmp/Sort18445284905299908118.bam OUTPUT=/tmp/Fix16399477720078456105.bam REFERENCE_SEQUENCE=testdata/picard/sam/merger.fasta IS_BISULFITE_SEQUENCE=false SET_ONLY_UQ=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SetNmMdAndUqTags done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SetNmMdAndUqTags done. Elapsed time: 0.00 minutes. Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 ValidateSamFile INFO 2024-07-02 12:02:08 ValidateSamFile Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ValidateSamFile -INPUT /tmp/Fix16399477720078456105.bam -OUTPUT /tmp/Sort11943563943457731902.validation_report -MODE VERBOSE -REFERENCE_SEQUENCE testdata/picard/sam/merger.fasta ********** ValidateSamFile -INPUT /tmp/Fix16399477720078456105.bam -OUTPUT /tmp/Sort11943563943457731902.validation_report -MODE VERBOSE -REFERENCE_SEQUENCE testdata/picard/sam/merger.fasta Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.619 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.619 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.619 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.619 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.619 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.619 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.619 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.619 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/Fix16399477720078456105.bam OUTPUT=/tmp/Sort11943563943457731902.validation_report MODE=VERBOSE REFERENCE_SEQUENCE=testdata/picard/sam/merger.fasta MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:08 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/Fix16399477720078456105.bam OUTPUT=/tmp/Sort11943563943457731902.validation_report MODE=VERBOSE REFERENCE_SEQUENCE=testdata/picard/sam/merger.fasta MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testValidSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 SortSam Gradle suite > Gradle test > picard.sam.SetNmMdAndUqTagsTest.testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta) STANDARD_ERROR INFO 2024-07-02 12:02:08 SortSam Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** SortSam -INPUT testdata/picard/sam/aligned_queryname_sorted.sam -OUTPUT /tmp/Sort3209308544528171228.bam -SORT_ORDER coordinate ********** SortSam -INPUT testdata/picard/sam/aligned_queryname_sorted.sam -OUTPUT /tmp/Sort3209308544528171228.bam -SORT_ORDER coordinate Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.647 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.647 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.647 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.647 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.647 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.647 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.647 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.647 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] SortSam INPUT=testdata/picard/sam/aligned_queryname_sorted.sam OUTPUT=/tmp/Sort3209308544528171228.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:08 GMT+14:00 2024] SortSam INPUT=testdata/picard/sam/aligned_queryname_sorted.sam OUTPUT=/tmp/Sort3209308544528171228.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 SortSam Finished reading inputs, merging and writing to output now. INFO 2024-07-02 12:02:08 SortSam Finished reading inputs, merging and writing to output now. Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.00 minutes. Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 SetNmMdAndUqTags INFO 2024-07-02 12:02:08 SetNmMdAndUqTags Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** SetNmMdAndUqTags -INPUT /tmp/Sort3209308544528171228.bam -OUTPUT /tmp/Fix14248892765227411258.bam -REFERENCE_SEQUENCE testdata/picard/sam/merger.fasta ********** SetNmMdAndUqTags -INPUT /tmp/Sort3209308544528171228.bam -OUTPUT /tmp/Fix14248892765227411258.bam -REFERENCE_SEQUENCE testdata/picard/sam/merger.fasta Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.667 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.667 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.667 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.667 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.667 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.667 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.667 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.667 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] SetNmMdAndUqTags INPUT=/tmp/Sort3209308544528171228.bam OUTPUT=/tmp/Fix14248892765227411258.bam REFERENCE_SEQUENCE=testdata/picard/sam/merger.fasta IS_BISULFITE_SEQUENCE=false SET_ONLY_UQ=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:08 GMT+14:00 2024] SetNmMdAndUqTags INPUT=/tmp/Sort3209308544528171228.bam OUTPUT=/tmp/Fix14248892765227411258.bam REFERENCE_SEQUENCE=testdata/picard/sam/merger.fasta IS_BISULFITE_SEQUENCE=false SET_ONLY_UQ=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SetNmMdAndUqTags done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SetNmMdAndUqTags done. Elapsed time: 0.00 minutes. Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 ValidateSamFile INFO 2024-07-02 12:02:08 ValidateSamFile Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ValidateSamFile -INPUT /tmp/Fix14248892765227411258.bam -OUTPUT /tmp/Sort17340475896517410893.validation_report -MODE VERBOSE -REFERENCE_SEQUENCE testdata/picard/sam/merger.fasta ********** ValidateSamFile -INPUT /tmp/Fix14248892765227411258.bam -OUTPUT /tmp/Sort17340475896517410893.validation_report -MODE VERBOSE -REFERENCE_SEQUENCE testdata/picard/sam/merger.fasta Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.690 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.690 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.690 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.690 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.690 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.690 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.690 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.690 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/Fix14248892765227411258.bam OUTPUT=/tmp/Sort17340475896517410893.validation_report MODE=VERBOSE REFERENCE_SEQUENCE=testdata/picard/sam/merger.fasta MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:08 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/Fix14248892765227411258.bam OUTPUT=/tmp/Sort17340475896517410893.validation_report MODE=VERBOSE REFERENCE_SEQUENCE=testdata/picard/sam/merger.fasta MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testValidSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 SortSam Gradle suite > Gradle test > picard.sam.SetNmMdAndUqTagsTest.testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta) STANDARD_ERROR INFO 2024-07-02 12:02:08 SortSam Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** SortSam -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/Sort11980624862110866990.bam -SORT_ORDER coordinate ********** SortSam -INPUT testdata/picard/sam/aligned.sam -OUTPUT /tmp/Sort11980624862110866990.bam -SORT_ORDER coordinate Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.704 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.704 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.704 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.704 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.704 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.704 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.704 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.704 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] SortSam INPUT=testdata/picard/sam/aligned.sam OUTPUT=/tmp/Sort11980624862110866990.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:08 GMT+14:00 2024] SortSam INPUT=testdata/picard/sam/aligned.sam OUTPUT=/tmp/Sort11980624862110866990.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 SortSam Finished reading inputs, merging and writing to output now. INFO 2024-07-02 12:02:08 SortSam Finished reading inputs, merging and writing to output now. Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.00 minutes. Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 SetNmMdAndUqTags INFO 2024-07-02 12:02:08 SetNmMdAndUqTags Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** SetNmMdAndUqTags -INPUT /tmp/Sort11980624862110866990.bam -OUTPUT /tmp/Fix12072573575931088212.bam -REFERENCE_SEQUENCE testdata/picard/sam/merger.fasta -SET_ONLY_UQ true ********** SetNmMdAndUqTags -INPUT /tmp/Sort11980624862110866990.bam -OUTPUT /tmp/Fix12072573575931088212.bam -REFERENCE_SEQUENCE testdata/picard/sam/merger.fasta -SET_ONLY_UQ true Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.724 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.724 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.724 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.724 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.724 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.724 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.724 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.724 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] SetNmMdAndUqTags INPUT=/tmp/Sort11980624862110866990.bam OUTPUT=/tmp/Fix12072573575931088212.bam SET_ONLY_UQ=true REFERENCE_SEQUENCE=testdata/picard/sam/merger.fasta IS_BISULFITE_SEQUENCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:08 GMT+14:00 2024] SetNmMdAndUqTags INPUT=/tmp/Sort11980624862110866990.bam OUTPUT=/tmp/Fix12072573575931088212.bam SET_ONLY_UQ=true REFERENCE_SEQUENCE=testdata/picard/sam/merger.fasta IS_BISULFITE_SEQUENCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SetNmMdAndUqTags done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SetNmMdAndUqTags done. Elapsed time: 0.00 minutes. Test: Test method testValidUqSort[0](testdata/picard/sam/aligned.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 SortSam Gradle suite > Gradle test > picard.sam.SetNmMdAndUqTagsTest.testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta) STANDARD_ERROR INFO 2024-07-02 12:02:08 SortSam Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** SortSam -INPUT testdata/picard/sam/aligned_queryname_sorted.sam -OUTPUT /tmp/Sort5090229625097463925.bam -SORT_ORDER coordinate ********** SortSam -INPUT testdata/picard/sam/aligned_queryname_sorted.sam -OUTPUT /tmp/Sort5090229625097463925.bam -SORT_ORDER coordinate Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.754 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.754 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.754 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.754 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.754 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.754 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.754 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.754 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] SortSam INPUT=testdata/picard/sam/aligned_queryname_sorted.sam OUTPUT=/tmp/Sort5090229625097463925.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:08 GMT+14:00 2024] SortSam INPUT=testdata/picard/sam/aligned_queryname_sorted.sam OUTPUT=/tmp/Sort5090229625097463925.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 SortSam Finished reading inputs, merging and writing to output now. INFO 2024-07-02 12:02:08 SortSam Finished reading inputs, merging and writing to output now. Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.00 minutes. Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 SetNmMdAndUqTags INFO 2024-07-02 12:02:08 SetNmMdAndUqTags Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** SetNmMdAndUqTags -INPUT /tmp/Sort5090229625097463925.bam -OUTPUT /tmp/Fix16218134788765937409.bam -REFERENCE_SEQUENCE testdata/picard/sam/merger.fasta -SET_ONLY_UQ true ********** SetNmMdAndUqTags -INPUT /tmp/Sort5090229625097463925.bam -OUTPUT /tmp/Fix16218134788765937409.bam -REFERENCE_SEQUENCE testdata/picard/sam/merger.fasta -SET_ONLY_UQ true Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.775 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.775 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.775 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.775 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.775 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.775 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.775 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.775 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] SetNmMdAndUqTags INPUT=/tmp/Sort5090229625097463925.bam OUTPUT=/tmp/Fix16218134788765937409.bam SET_ONLY_UQ=true REFERENCE_SEQUENCE=testdata/picard/sam/merger.fasta IS_BISULFITE_SEQUENCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:08 GMT+14:00 2024] SetNmMdAndUqTags INPUT=/tmp/Sort5090229625097463925.bam OUTPUT=/tmp/Fix16218134788765937409.bam SET_ONLY_UQ=true REFERENCE_SEQUENCE=testdata/picard/sam/merger.fasta IS_BISULFITE_SEQUENCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SetNmMdAndUqTags done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SetNmMdAndUqTags done. Elapsed time: 0.00 minutes. Test: Test method testValidUqSort[1](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 SortSam Gradle suite > Gradle test > picard.sam.SetNmMdAndUqTagsTest.testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta) STANDARD_ERROR INFO 2024-07-02 12:02:08 SortSam Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** SortSam -INPUT testdata/picard/sam/aligned_queryname_sorted.sam -OUTPUT /tmp/Sort8545065612369989875.bam -SORT_ORDER coordinate ********** SortSam -INPUT testdata/picard/sam/aligned_queryname_sorted.sam -OUTPUT /tmp/Sort8545065612369989875.bam -SORT_ORDER coordinate Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.799 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.799 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.799 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.799 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.799 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.799 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.799 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.799 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] SortSam INPUT=testdata/picard/sam/aligned_queryname_sorted.sam OUTPUT=/tmp/Sort8545065612369989875.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:08 GMT+14:00 2024] SortSam INPUT=testdata/picard/sam/aligned_queryname_sorted.sam OUTPUT=/tmp/Sort8545065612369989875.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 SortSam Finished reading inputs, merging and writing to output now. INFO 2024-07-02 12:02:08 SortSam Finished reading inputs, merging and writing to output now. Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.00 minutes. Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: INFO 2024-07-02 12:02:08 SetNmMdAndUqTags INFO 2024-07-02 12:02:08 SetNmMdAndUqTags Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** SetNmMdAndUqTags -INPUT /tmp/Sort8545065612369989875.bam -OUTPUT /tmp/Fix7136142835530479609.bam -REFERENCE_SEQUENCE testdata/picard/sam/merger.fasta -SET_ONLY_UQ true ********** SetNmMdAndUqTags -INPUT /tmp/Sort8545065612369989875.bam -OUTPUT /tmp/Fix7136142835530479609.bam -REFERENCE_SEQUENCE testdata/picard/sam/merger.fasta -SET_ONLY_UQ true Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: ********** ********** Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.811 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.811 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.811 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.811 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.812 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.812 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: 12:02:08.812 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.812 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] SetNmMdAndUqTags INPUT=/tmp/Sort8545065612369989875.bam OUTPUT=/tmp/Fix7136142835530479609.bam SET_ONLY_UQ=true REFERENCE_SEQUENCE=testdata/picard/sam/merger.fasta IS_BISULFITE_SEQUENCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:08 GMT+14:00 2024] SetNmMdAndUqTags INPUT=/tmp/Sort8545065612369989875.bam OUTPUT=/tmp/Fix7136142835530479609.bam SET_ONLY_UQ=true REFERENCE_SEQUENCE=testdata/picard/sam/merger.fasta IS_BISULFITE_SEQUENCE=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SetNmMdAndUqTags done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SetNmMdAndUqTags done. Elapsed time: 0.00 minutes. Test: Test method testValidUqSort[2](testdata/picard/sam/aligned_queryname_sorted.sam, testdata/picard/sam/merger.fasta)(picard.sam.SetNmMdAndUqTagsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testFromCode[0](Male, 1)(picard.pedigree.SexTest) Running Test: Test method testFromCode[1](Female, 2)(picard.pedigree.SexTest) Running Test: Test method testFromCode[2](Unknown, 0)(picard.pedigree.SexTest) Running Test: Test method testFromString[0](Female, F)(picard.pedigree.SexTest) Running Test: Test method testFromString[1](Female, f)(picard.pedigree.SexTest) Running Test: Test method testFromString[2](Female, Female)(picard.pedigree.SexTest) Running Test: Test method testFromString[3](Female, female)(picard.pedigree.SexTest) Running Test: Test method testFromString[4](Male, M)(picard.pedigree.SexTest) Running Test: Test method testFromString[5](Male, m)(picard.pedigree.SexTest) Running Test: Test method testFromString[6](Male, Male)(picard.pedigree.SexTest) Running Test: Test method testFromString[7](Male, male)(picard.pedigree.SexTest) Running Test: Test method testFromString[8](Unknown, Unknown)(picard.pedigree.SexTest) Running Test: Test method testFromString[9](Unknown, U)(picard.pedigree.SexTest) Running Test: Test method testFromString[10](Unknown, unknown)(picard.pedigree.SexTest) Running Test: Test method testFromString[11](Unknown, u)(picard.pedigree.SexTest) Running Test: Test method testFromStringException(picard.pedigree.SexTest) Running Test: Test method bugTest(picard.sam.SortSamTest) Test: Test method bugTest(picard.sam.SortSamTest) produced standard out/err: INFO 2024-07-02 12:02:08 SortSam Gradle suite > Gradle test > picard.sam.SortSamTest.bugTest STANDARD_ERROR INFO 2024-07-02 12:02:08 SortSam Test: Test method bugTest(picard.sam.SortSamTest) produced standard out/err: Test: Test method bugTest(picard.sam.SortSamTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method bugTest(picard.sam.SortSamTest) produced standard out/err: ********** ********** Test: Test method bugTest(picard.sam.SortSamTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method bugTest(picard.sam.SortSamTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method bugTest(picard.sam.SortSamTest) produced standard out/err: ********** ********** Test: Test method bugTest(picard.sam.SortSamTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method bugTest(picard.sam.SortSamTest) produced standard out/err: ********** ********** Test: Test method bugTest(picard.sam.SortSamTest) produced standard out/err: ********** SortSam -I /tmp/testIn1064923465402366598.bam -O /tmp/testOut3064427180704994268.bam -SORT_ORDER coordinate ********** SortSam -I /tmp/testIn1064923465402366598.bam -O /tmp/testOut3064427180704994268.bam -SORT_ORDER coordinate Test: Test method bugTest(picard.sam.SortSamTest) produced standard out/err: ********** ********** Test: Test method bugTest(picard.sam.SortSamTest) produced standard out/err: Test: Test method bugTest(picard.sam.SortSamTest) produced standard out/err: Test: Test method bugTest(picard.sam.SortSamTest) produced standard out/err: 12:02:08.869 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.869 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method bugTest(picard.sam.SortSamTest) produced standard out/err: 12:02:08.875 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.875 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method bugTest(picard.sam.SortSamTest) produced standard out/err: 12:02:08.877 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:08.877 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method bugTest(picard.sam.SortSamTest) produced standard out/err: 12:02:08.877 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:08.877 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method bugTest(picard.sam.SortSamTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] SortSam INPUT=/tmp/testIn1064923465402366598.bam OUTPUT=/tmp/testOut3064427180704994268.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:08 GMT+14:00 2024] SortSam INPUT=/tmp/testIn1064923465402366598.bam OUTPUT=/tmp/testOut3064427180704994268.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method bugTest(picard.sam.SortSamTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:08 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method bugTest(picard.sam.SortSamTest) produced standard out/err: [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:08 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.00 minutes. Test: Test method bugTest(picard.sam.SortSamTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method bugTest(picard.sam.SortSamTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method basicPositiveTest(picard.sam.SplitSamByLibraryTest) Running Test: Test method testNoLibrarySpecified(picard.sam.SplitSamByLibraryTest) Test: Test method testNoLibrarySpecified(picard.sam.SplitSamByLibraryTest) produced standard out/err: ERROR 2024-07-02 12:02:08 SplitSamByLibrary No individual libraries are specified in the header of /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/invalid_coord_sort_order.sam Gradle suite > Gradle test > picard.sam.SplitSamByLibraryTest.testNoLibrarySpecified STANDARD_ERROR ERROR 2024-07-02 12:02:08 SplitSamByLibrary No individual libraries are specified in the header of /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/invalid_coord_sort_order.sam Running Test: Test method testNoUnknownFile(picard.sam.SplitSamByLibraryTest) Running Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: INFO 2024-07-02 12:02:09 SplitSamByNumberOfReads Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testNFiles STANDARD_ERROR INFO 2024-07-02 12:02:09 SplitSamByNumberOfReads Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** SplitSamByNumberOfReads -INPUT testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam -TOTAL_READS_IN_INPUT 10 -SPLIT_TO_N_FILES 2 -OUTPUT /tmp/pbuilder2/temp_dir9026668037570687093 ********** SplitSamByNumberOfReads -INPUT testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam -TOTAL_READS_IN_INPUT 10 -SPLIT_TO_N_FILES 2 -OUTPUT /tmp/pbuilder2/temp_dir9026668037570687093 Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.041 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.041 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.041 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.041 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.042 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.042 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.042 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.042 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] SplitSamByNumberOfReads INPUT=testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam SPLIT_TO_N_FILES=2 TOTAL_READS_IN_INPUT=10 OUTPUT=/tmp/pbuilder2/temp_dir9026668037570687093 SPLIT_TO_N_READS=0 OUT_PREFIX=shard VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:09 GMT+14:00 2024] SplitSamByNumberOfReads INPUT=testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam SPLIT_TO_N_FILES=2 TOTAL_READS_IN_INPUT=10 OUTPUT=/tmp/pbuilder2/temp_dir9026668037570687093 SPLIT_TO_N_READS=0 OUT_PREFIX=shard VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: WARNING 2024-07-02 12:02:09 SplitSamByNumberOfReads Input file's version is 1.0, but the current SAM format version is 1.6. Outputs will be written with current version. WARNING 2024-07-02 12:02:09 SplitSamByNumberOfReads Input file's version is 1.0, but the current SAM format version is 1.6. Outputs will be written with current version. Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.SplitSamByNumberOfReads done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.SplitSamByNumberOfReads done. Elapsed time: 0.00 minutes. Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: INFO 2024-07-02 12:02:09 ValidateSamFile INFO 2024-07-02 12:02:09 ValidateSamFile Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ValidateSamFile -I /tmp/pbuilder2/temp_dir9026668037570687093/shard_0001.bam ********** ValidateSamFile -I /tmp/pbuilder2/temp_dir9026668037570687093/shard_0001.bam Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.101 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.101 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.101 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.101 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.102 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.102 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.102 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.102 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/pbuilder2/temp_dir9026668037570687093/shard_0001.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:09 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/pbuilder2/temp_dir9026668037570687093/shard_0001.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: WARNING 2024-07-02 12:02:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:02:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testNFiles STANDARD_OUT No errors found Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testNFiles STANDARD_ERROR [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: INFO 2024-07-02 12:02:09 ValidateSamFile INFO 2024-07-02 12:02:09 ValidateSamFile Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ValidateSamFile -I /tmp/pbuilder2/temp_dir9026668037570687093/shard_0002.bam ********** ValidateSamFile -I /tmp/pbuilder2/temp_dir9026668037570687093/shard_0002.bam Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.145 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.145 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.145 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.145 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.145 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.145 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.145 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.145 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/pbuilder2/temp_dir9026668037570687093/shard_0002.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:09 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/pbuilder2/temp_dir9026668037570687093/shard_0002.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: WARNING 2024-07-02 12:02:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:02:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testNFiles STANDARD_OUT No errors found Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testNFiles STANDARD_ERROR [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testNFiles(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: INFO 2024-07-02 12:02:09 SplitSamByNumberOfReads Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testNoTotalReads STANDARD_ERROR INFO 2024-07-02 12:02:09 SplitSamByNumberOfReads Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** SplitSamByNumberOfReads -INPUT testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam -SPLIT_TO_N_READS 5 -OUTPUT /tmp/pbuilder2/temp_dir4553585683584734987 ********** SplitSamByNumberOfReads -INPUT testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam -SPLIT_TO_N_READS 5 -OUTPUT /tmp/pbuilder2/temp_dir4553585683584734987 Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.194 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.194 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.195 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.195 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.195 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.195 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.195 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.195 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] SplitSamByNumberOfReads INPUT=testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam SPLIT_TO_N_READS=5 OUTPUT=/tmp/pbuilder2/temp_dir4553585683584734987 SPLIT_TO_N_FILES=0 TOTAL_READS_IN_INPUT=0 OUT_PREFIX=shard VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:09 GMT+14:00 2024] SplitSamByNumberOfReads INPUT=testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam SPLIT_TO_N_READS=5 OUTPUT=/tmp/pbuilder2/temp_dir4553585683584734987 SPLIT_TO_N_FILES=0 TOTAL_READS_IN_INPUT=0 OUT_PREFIX=shard VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: WARNING 2024-07-02 12:02:09 SplitSamByNumberOfReads Input file's version is 1.0, but the current SAM format version is 1.6. Outputs will be written with current version. WARNING 2024-07-02 12:02:09 SplitSamByNumberOfReads Input file's version is 1.0, but the current SAM format version is 1.6. Outputs will be written with current version. Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: INFO 2024-07-02 12:02:09 SplitSamByNumberOfReads First pass traversal to count number of reads is beginning. If number of reads is known, use TOTAL_READS_IN_INPUT to skip first traversal. INFO 2024-07-02 12:02:09 SplitSamByNumberOfReads First pass traversal to count number of reads is beginning. If number of reads is known, use TOTAL_READS_IN_INPUT to skip first traversal. Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: INFO 2024-07-02 12:02:09 SplitSamByNumberOfReads First pass traversal to count number of reads ended, found 10 total reads. INFO 2024-07-02 12:02:09 SplitSamByNumberOfReads First pass traversal to count number of reads ended, found 10 total reads. Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.SplitSamByNumberOfReads done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.SplitSamByNumberOfReads done. Elapsed time: 0.00 minutes. Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: INFO 2024-07-02 12:02:09 ValidateSamFile INFO 2024-07-02 12:02:09 ValidateSamFile Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ValidateSamFile -I /tmp/pbuilder2/temp_dir4553585683584734987/shard_0001.bam ********** ValidateSamFile -I /tmp/pbuilder2/temp_dir4553585683584734987/shard_0001.bam Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.246 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.246 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.246 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.246 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.247 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.247 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.247 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.247 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/pbuilder2/temp_dir4553585683584734987/shard_0001.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:09 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/pbuilder2/temp_dir4553585683584734987/shard_0001.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: WARNING 2024-07-02 12:02:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:02:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testNoTotalReads STANDARD_OUT No errors found Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testNoTotalReads STANDARD_ERROR [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: INFO 2024-07-02 12:02:09 ValidateSamFile INFO 2024-07-02 12:02:09 ValidateSamFile Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ValidateSamFile -I /tmp/pbuilder2/temp_dir4553585683584734987/shard_0002.bam ********** ValidateSamFile -I /tmp/pbuilder2/temp_dir4553585683584734987/shard_0002.bam Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.294 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.294 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.294 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.294 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.295 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.295 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.295 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.295 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/pbuilder2/temp_dir4553585683584734987/shard_0002.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:09 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/pbuilder2/temp_dir4553585683584734987/shard_0002.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: WARNING 2024-07-02 12:02:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:02:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testNoTotalReads STANDARD_OUT No errors found Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testNoTotalReads STANDARD_ERROR [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testNoTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: INFO 2024-07-02 12:02:09 SplitSamByNumberOfReads Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testOkFile STANDARD_ERROR INFO 2024-07-02 12:02:09 SplitSamByNumberOfReads Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** SplitSamByNumberOfReads -INPUT testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam -TOTAL_READS_IN_INPUT 10 -SPLIT_TO_N_READS 5 -OUTPUT /tmp/pbuilder2/temp_dir14056693403671596907 ********** SplitSamByNumberOfReads -INPUT testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam -TOTAL_READS_IN_INPUT 10 -SPLIT_TO_N_READS 5 -OUTPUT /tmp/pbuilder2/temp_dir14056693403671596907 Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.339 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.339 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.339 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.339 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.339 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.339 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.339 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.339 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] SplitSamByNumberOfReads INPUT=testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam SPLIT_TO_N_READS=5 TOTAL_READS_IN_INPUT=10 OUTPUT=/tmp/pbuilder2/temp_dir14056693403671596907 SPLIT_TO_N_FILES=0 OUT_PREFIX=shard VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:09 GMT+14:00 2024] SplitSamByNumberOfReads INPUT=testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam SPLIT_TO_N_READS=5 TOTAL_READS_IN_INPUT=10 OUTPUT=/tmp/pbuilder2/temp_dir14056693403671596907 SPLIT_TO_N_FILES=0 OUT_PREFIX=shard VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: WARNING 2024-07-02 12:02:09 SplitSamByNumberOfReads Input file's version is 1.0, but the current SAM format version is 1.6. Outputs will be written with current version. WARNING 2024-07-02 12:02:09 SplitSamByNumberOfReads Input file's version is 1.0, but the current SAM format version is 1.6. Outputs will be written with current version. Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.SplitSamByNumberOfReads done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.SplitSamByNumberOfReads done. Elapsed time: 0.00 minutes. Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: INFO 2024-07-02 12:02:09 ValidateSamFile INFO 2024-07-02 12:02:09 ValidateSamFile Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ValidateSamFile -I /tmp/pbuilder2/temp_dir14056693403671596907/shard_0001.bam ********** ValidateSamFile -I /tmp/pbuilder2/temp_dir14056693403671596907/shard_0001.bam Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.393 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.393 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.393 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.393 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.394 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.394 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.394 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.394 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/pbuilder2/temp_dir14056693403671596907/shard_0001.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:09 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/pbuilder2/temp_dir14056693403671596907/shard_0001.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: WARNING 2024-07-02 12:02:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:02:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testOkFile STANDARD_OUT No errors found Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testOkFile STANDARD_ERROR [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: INFO 2024-07-02 12:02:09 ValidateSamFile INFO 2024-07-02 12:02:09 ValidateSamFile Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ValidateSamFile -I /tmp/pbuilder2/temp_dir14056693403671596907/shard_0002.bam ********** ValidateSamFile -I /tmp/pbuilder2/temp_dir14056693403671596907/shard_0002.bam Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.438 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.438 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.438 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.438 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.439 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.439 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.439 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.439 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/pbuilder2/temp_dir14056693403671596907/shard_0002.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:09 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/pbuilder2/temp_dir14056693403671596907/shard_0002.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: WARNING 2024-07-02 12:02:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:02:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testOkFile STANDARD_OUT No errors found Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testOkFile STANDARD_ERROR [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testOkFile(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: INFO 2024-07-02 12:02:09 SplitSamByNumberOfReads Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testOneOutput STANDARD_ERROR INFO 2024-07-02 12:02:09 SplitSamByNumberOfReads Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** SplitSamByNumberOfReads -INPUT testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam -TOTAL_READS_IN_INPUT 10 -SPLIT_TO_N_READS 10 -OUTPUT /tmp/pbuilder2/temp_dir4168384702272584676 ********** SplitSamByNumberOfReads -INPUT testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam -TOTAL_READS_IN_INPUT 10 -SPLIT_TO_N_READS 10 -OUTPUT /tmp/pbuilder2/temp_dir4168384702272584676 Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.486 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.486 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.486 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.486 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.486 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.486 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.486 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.486 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] SplitSamByNumberOfReads INPUT=testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam SPLIT_TO_N_READS=10 TOTAL_READS_IN_INPUT=10 OUTPUT=/tmp/pbuilder2/temp_dir4168384702272584676 SPLIT_TO_N_FILES=0 OUT_PREFIX=shard VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:09 GMT+14:00 2024] SplitSamByNumberOfReads INPUT=testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam SPLIT_TO_N_READS=10 TOTAL_READS_IN_INPUT=10 OUTPUT=/tmp/pbuilder2/temp_dir4168384702272584676 SPLIT_TO_N_FILES=0 OUT_PREFIX=shard VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: WARNING 2024-07-02 12:02:09 SplitSamByNumberOfReads Input file's version is 1.0, but the current SAM format version is 1.6. Outputs will be written with current version. WARNING 2024-07-02 12:02:09 SplitSamByNumberOfReads Input file's version is 1.0, but the current SAM format version is 1.6. Outputs will be written with current version. Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.SplitSamByNumberOfReads done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.SplitSamByNumberOfReads done. Elapsed time: 0.00 minutes. Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: INFO 2024-07-02 12:02:09 ValidateSamFile INFO 2024-07-02 12:02:09 ValidateSamFile Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ValidateSamFile -I /tmp/pbuilder2/temp_dir4168384702272584676/shard_0001.bam ********** ValidateSamFile -I /tmp/pbuilder2/temp_dir4168384702272584676/shard_0001.bam Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.535 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.535 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.535 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.535 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.535 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.535 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.535 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.535 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/pbuilder2/temp_dir4168384702272584676/shard_0001.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:09 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/pbuilder2/temp_dir4168384702272584676/shard_0001.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: WARNING 2024-07-02 12:02:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:02:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testOneOutput STANDARD_OUT No errors found Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testOneOutput STANDARD_ERROR [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testOneOutput(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: INFO 2024-07-02 12:02:09 SplitSamByNumberOfReads Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testOutPrefixWithZeros STANDARD_ERROR INFO 2024-07-02 12:02:09 SplitSamByNumberOfReads Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** SplitSamByNumberOfReads -INPUT testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam -SPLIT_TO_N_READS 5 -OUTPUT /tmp/pbuilder2/temp_dir4098257601207393879 -OUT_PREFIX Sample01 ********** SplitSamByNumberOfReads -INPUT testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam -SPLIT_TO_N_READS 5 -OUTPUT /tmp/pbuilder2/temp_dir4098257601207393879 -OUT_PREFIX Sample01 Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.583 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.583 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.583 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.583 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.584 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.584 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.584 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.584 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] SplitSamByNumberOfReads INPUT=testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam SPLIT_TO_N_READS=5 OUTPUT=/tmp/pbuilder2/temp_dir4098257601207393879 OUT_PREFIX=Sample01 SPLIT_TO_N_FILES=0 TOTAL_READS_IN_INPUT=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:09 GMT+14:00 2024] SplitSamByNumberOfReads INPUT=testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam SPLIT_TO_N_READS=5 OUTPUT=/tmp/pbuilder2/temp_dir4098257601207393879 OUT_PREFIX=Sample01 SPLIT_TO_N_FILES=0 TOTAL_READS_IN_INPUT=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: WARNING 2024-07-02 12:02:09 SplitSamByNumberOfReads Input file's version is 1.0, but the current SAM format version is 1.6. Outputs will be written with current version. WARNING 2024-07-02 12:02:09 SplitSamByNumberOfReads Input file's version is 1.0, but the current SAM format version is 1.6. Outputs will be written with current version. Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: INFO 2024-07-02 12:02:09 SplitSamByNumberOfReads First pass traversal to count number of reads is beginning. If number of reads is known, use TOTAL_READS_IN_INPUT to skip first traversal. INFO 2024-07-02 12:02:09 SplitSamByNumberOfReads First pass traversal to count number of reads is beginning. If number of reads is known, use TOTAL_READS_IN_INPUT to skip first traversal. Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: INFO 2024-07-02 12:02:09 SplitSamByNumberOfReads First pass traversal to count number of reads ended, found 10 total reads. INFO 2024-07-02 12:02:09 SplitSamByNumberOfReads First pass traversal to count number of reads ended, found 10 total reads. Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.SplitSamByNumberOfReads done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.SplitSamByNumberOfReads done. Elapsed time: 0.00 minutes. Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: INFO 2024-07-02 12:02:09 ValidateSamFile INFO 2024-07-02 12:02:09 ValidateSamFile Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ValidateSamFile -I /tmp/pbuilder2/temp_dir4098257601207393879/Sample01_0001.bam ********** ValidateSamFile -I /tmp/pbuilder2/temp_dir4098257601207393879/Sample01_0001.bam Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.697 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.697 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.697 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.697 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.697 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.697 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.697 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.697 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/pbuilder2/temp_dir4098257601207393879/Sample01_0001.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:09 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/pbuilder2/temp_dir4098257601207393879/Sample01_0001.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: WARNING 2024-07-02 12:02:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:02:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testOutPrefixWithZeros STANDARD_OUT No errors found Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testOutPrefixWithZeros STANDARD_ERROR [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: INFO 2024-07-02 12:02:09 ValidateSamFile INFO 2024-07-02 12:02:09 ValidateSamFile Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ValidateSamFile -I /tmp/pbuilder2/temp_dir4098257601207393879/Sample01_0002.bam ********** ValidateSamFile -I /tmp/pbuilder2/temp_dir4098257601207393879/Sample01_0002.bam Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.789 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.789 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.789 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.789 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.789 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.789 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.789 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.789 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/pbuilder2/temp_dir4098257601207393879/Sample01_0002.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:09 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/pbuilder2/temp_dir4098257601207393879/Sample01_0002.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: WARNING 2024-07-02 12:02:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:02:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testOutPrefixWithZeros STANDARD_OUT No errors found Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testOutPrefixWithZeros STANDARD_ERROR [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testOutPrefixWithZeros(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testStreamWithoutTotalReads(picard.sam.SplitSamByNumberOfReadsTest) Test: Test method testStreamWithoutTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: INFO 2024-07-02 12:02:09 SplitSamByNumberOfReads Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testStreamWithoutTotalReads STANDARD_ERROR INFO 2024-07-02 12:02:09 SplitSamByNumberOfReads Test: Test method testStreamWithoutTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testStreamWithoutTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testStreamWithoutTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testStreamWithoutTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testStreamWithoutTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testStreamWithoutTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testStreamWithoutTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testStreamWithoutTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testStreamWithoutTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** SplitSamByNumberOfReads -INPUT /dev/stdin -SPLIT_TO_N_READS 5 -OUTPUT /tmp/pbuilder2/temp_dir5365513551868389010 ********** SplitSamByNumberOfReads -INPUT /dev/stdin -SPLIT_TO_N_READS 5 -OUTPUT /tmp/pbuilder2/temp_dir5365513551868389010 Test: Test method testStreamWithoutTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testStreamWithoutTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testStreamWithoutTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testStreamWithoutTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.838 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.838 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testStreamWithoutTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.838 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.838 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testStreamWithoutTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.838 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.838 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testStreamWithoutTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.838 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.838 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testStreamWithoutTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] SplitSamByNumberOfReads INPUT=/dev/stdin SPLIT_TO_N_READS=5 OUTPUT=/tmp/pbuilder2/temp_dir5365513551868389010 SPLIT_TO_N_FILES=0 TOTAL_READS_IN_INPUT=0 OUT_PREFIX=shard VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:09 GMT+14:00 2024] SplitSamByNumberOfReads INPUT=/dev/stdin SPLIT_TO_N_READS=5 OUTPUT=/tmp/pbuilder2/temp_dir5365513551868389010 SPLIT_TO_N_FILES=0 TOTAL_READS_IN_INPUT=0 OUT_PREFIX=shard VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testStreamWithoutTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testStreamWithoutTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ERROR 2024-07-02 12:02:09 SplitSamByNumberOfReads INPUT is not a regular file: /dev/stdin. If TOTAL_READS_IN_INPUT is not supplied, INPUT cannot be a stream. ERROR 2024-07-02 12:02:09 SplitSamByNumberOfReads INPUT is not a regular file: /dev/stdin. If TOTAL_READS_IN_INPUT is not supplied, INPUT cannot be a stream. Test: Test method testStreamWithoutTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.SplitSamByNumberOfReads done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.SplitSamByNumberOfReads done. Elapsed time: 0.00 minutes. Test: Test method testStreamWithoutTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testStreamWithoutTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: INFO 2024-07-02 12:02:09 SplitSamByNumberOfReads Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testThreeReadTemplate STANDARD_ERROR INFO 2024-07-02 12:02:09 SplitSamByNumberOfReads Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** SplitSamByNumberOfReads -INPUT testdata/picard/sam/SplitSamByNumberOfReads/sorted-triplet.sam -TOTAL_READS_IN_INPUT 11 -SPLIT_TO_N_READS 2 -OUTPUT /tmp/pbuilder2/temp_dir6430531724184813940 ********** SplitSamByNumberOfReads -INPUT testdata/picard/sam/SplitSamByNumberOfReads/sorted-triplet.sam -TOTAL_READS_IN_INPUT 11 -SPLIT_TO_N_READS 2 -OUTPUT /tmp/pbuilder2/temp_dir6430531724184813940 Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.880 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.880 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.880 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.880 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.880 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.880 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.880 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.880 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] SplitSamByNumberOfReads INPUT=testdata/picard/sam/SplitSamByNumberOfReads/sorted-triplet.sam SPLIT_TO_N_READS=2 TOTAL_READS_IN_INPUT=11 OUTPUT=/tmp/pbuilder2/temp_dir6430531724184813940 SPLIT_TO_N_FILES=0 OUT_PREFIX=shard VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:09 GMT+14:00 2024] SplitSamByNumberOfReads INPUT=testdata/picard/sam/SplitSamByNumberOfReads/sorted-triplet.sam SPLIT_TO_N_READS=2 TOTAL_READS_IN_INPUT=11 OUTPUT=/tmp/pbuilder2/temp_dir6430531724184813940 SPLIT_TO_N_FILES=0 OUT_PREFIX=shard VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.SplitSamByNumberOfReads done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.SplitSamByNumberOfReads done. Elapsed time: 0.00 minutes. Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: INFO 2024-07-02 12:02:09 ValidateSamFile INFO 2024-07-02 12:02:09 ValidateSamFile Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ValidateSamFile -I /tmp/pbuilder2/temp_dir6430531724184813940/shard_0001.bam ********** ValidateSamFile -I /tmp/pbuilder2/temp_dir6430531724184813940/shard_0001.bam Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.947 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.947 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.947 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.947 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.947 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.947 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.947 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.947 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/pbuilder2/temp_dir6430531724184813940/shard_0001.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:09 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/pbuilder2/temp_dir6430531724184813940/shard_0001.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: WARNING 2024-07-02 12:02:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:02:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testThreeReadTemplate STANDARD_OUT No errors found Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testThreeReadTemplate STANDARD_ERROR [Tue Jul 02 12:02:09 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: INFO 2024-07-02 12:02:09 ValidateSamFile INFO 2024-07-02 12:02:09 ValidateSamFile Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ValidateSamFile -I /tmp/pbuilder2/temp_dir6430531724184813940/shard_0002.bam ********** ValidateSamFile -I /tmp/pbuilder2/temp_dir6430531724184813940/shard_0002.bam Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.992 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.992 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.992 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.992 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.992 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:09.992 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:09.992 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:09.992 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/pbuilder2/temp_dir6430531724184813940/shard_0002.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:09 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/pbuilder2/temp_dir6430531724184813940/shard_0002.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:09 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: WARNING 2024-07-02 12:02:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:02:09 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testThreeReadTemplate STANDARD_OUT No errors found Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:10 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testThreeReadTemplate STANDARD_ERROR [Tue Jul 02 12:02:10 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testThreeReadTemplate(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: INFO 2024-07-02 12:02:10 SplitSamByNumberOfReads Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testWrongTotalReads STANDARD_ERROR INFO 2024-07-02 12:02:10 SplitSamByNumberOfReads Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** SplitSamByNumberOfReads -INPUT testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam -TOTAL_READS_IN_INPUT 20 -SPLIT_TO_N_READS 5 -OUTPUT /tmp/pbuilder2/temp_dir2025424565695993405 ********** SplitSamByNumberOfReads -INPUT testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam -TOTAL_READS_IN_INPUT 20 -SPLIT_TO_N_READS 5 -OUTPUT /tmp/pbuilder2/temp_dir2025424565695993405 Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:10.059 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:10.059 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:10.059 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:10.059 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:10.059 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:10.059 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:10.059 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:10.059 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:10 GMT+14:00 2024] SplitSamByNumberOfReads INPUT=testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam SPLIT_TO_N_READS=5 TOTAL_READS_IN_INPUT=20 OUTPUT=/tmp/pbuilder2/temp_dir2025424565695993405 SPLIT_TO_N_FILES=0 OUT_PREFIX=shard VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:10 GMT+14:00 2024] SplitSamByNumberOfReads INPUT=testdata/picard/sam/SplitSamByNumberOfReads/sorted-pair.sam SPLIT_TO_N_READS=5 TOTAL_READS_IN_INPUT=20 OUTPUT=/tmp/pbuilder2/temp_dir2025424565695993405 SPLIT_TO_N_FILES=0 OUT_PREFIX=shard VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: WARNING 2024-07-02 12:02:10 SplitSamByNumberOfReads Input file's version is 1.0, but the current SAM format version is 1.6. Outputs will be written with current version. WARNING 2024-07-02 12:02:10 SplitSamByNumberOfReads Input file's version is 1.0, but the current SAM format version is 1.6. Outputs will be written with current version. Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: WARNING 2024-07-02 12:02:10 SplitSamByNumberOfReads The totalReads (20) provided does not match the reads found in the input file (10). Files may not be split evenly or number of files may not match what was requested. There were 2 files generated each with around 5 reads except the last file which contained 4 reads. WARNING 2024-07-02 12:02:10 SplitSamByNumberOfReads The totalReads (20) provided does not match the reads found in the input file (10). Files may not be split evenly or number of files may not match what was requested. There were 2 files generated each with around 5 reads except the last file which contained 4 reads. Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:10 GMT+14:00 2024] picard.sam.SplitSamByNumberOfReads done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:02:10 GMT+14:00 2024] picard.sam.SplitSamByNumberOfReads done. Elapsed time: 0.00 minutes. Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: INFO 2024-07-02 12:02:10 ValidateSamFile INFO 2024-07-02 12:02:10 ValidateSamFile Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ValidateSamFile -I /tmp/pbuilder2/temp_dir2025424565695993405/shard_0001.bam ********** ValidateSamFile -I /tmp/pbuilder2/temp_dir2025424565695993405/shard_0001.bam Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:10.116 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:10.116 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:10.116 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:10.116 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:10.116 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:10.116 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:10.116 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:10.116 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:10 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/pbuilder2/temp_dir2025424565695993405/shard_0001.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:10 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/pbuilder2/temp_dir2025424565695993405/shard_0001.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: WARNING 2024-07-02 12:02:10 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:02:10 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testWrongTotalReads STANDARD_OUT No errors found Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:10 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testWrongTotalReads STANDARD_ERROR [Tue Jul 02 12:02:10 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: INFO 2024-07-02 12:02:10 ValidateSamFile INFO 2024-07-02 12:02:10 ValidateSamFile Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ValidateSamFile -I /tmp/pbuilder2/temp_dir2025424565695993405/shard_0002.bam ********** ValidateSamFile -I /tmp/pbuilder2/temp_dir2025424565695993405/shard_0002.bam Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: ********** ********** Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:10.162 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:10.162 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:10.162 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:10.162 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:10.162 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:10.162 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: 12:02:10.162 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:10.162 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:10 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/pbuilder2/temp_dir2025424565695993405/shard_0002.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:10 GMT+14:00 2024] ValidateSamFile INPUT=/tmp/pbuilder2/temp_dir2025424565695993405/shard_0002.bam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: WARNING 2024-07-02 12:02:10 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:02:10 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testWrongTotalReads STANDARD_OUT No errors found Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: [Tue Jul 02 12:02:10 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.SplitSamByNumberOfReadsTest.testWrongTotalReads STANDARD_ERROR [Tue Jul 02 12:02:10 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testWrongTotalReads(picard.sam.SplitSamByNumberOfReadsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testSplit(picard.vcf.SplitVcfsTest) Test: Test method testSplit(picard.vcf.SplitVcfsTest) produced standard out/err: INFO 2024-07-02 12:02:10 SplitVcfs Gradle suite > Gradle test > picard.vcf.SplitVcfsTest.testSplit STANDARD_ERROR INFO 2024-07-02 12:02:10 SplitVcfs Test: Test method testSplit(picard.vcf.SplitVcfsTest) produced standard out/err: Test: Test method testSplit(picard.vcf.SplitVcfsTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testSplit(picard.vcf.SplitVcfsTest) produced standard out/err: ********** ********** Test: Test method testSplit(picard.vcf.SplitVcfsTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testSplit(picard.vcf.SplitVcfsTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testSplit(picard.vcf.SplitVcfsTest) produced standard out/err: ********** ********** Test: Test method testSplit(picard.vcf.SplitVcfsTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testSplit(picard.vcf.SplitVcfsTest) produced standard out/err: ********** ********** Test: Test method testSplit(picard.vcf.SplitVcfsTest) produced standard out/err: ********** SplitVcfs -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/CEUTrio-merged-indels-snps.vcf -SNP_OUTPUT /tmp/SplitVcfsTest1224990104212620623.tmp/split-vcfs-test-snps-delete-me.vcf -INDEL_OUTPUT /tmp/SplitVcfsTest1224990104212620623.tmp/split-vcfs-test-indels-delete-me.vcf ********** SplitVcfs -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/CEUTrio-merged-indels-snps.vcf -SNP_OUTPUT /tmp/SplitVcfsTest1224990104212620623.tmp/split-vcfs-test-snps-delete-me.vcf -INDEL_OUTPUT /tmp/SplitVcfsTest1224990104212620623.tmp/split-vcfs-test-indels-delete-me.vcf Test: Test method testSplit(picard.vcf.SplitVcfsTest) produced standard out/err: ********** ********** Test: Test method testSplit(picard.vcf.SplitVcfsTest) produced standard out/err: Test: Test method testSplit(picard.vcf.SplitVcfsTest) produced standard out/err: Test: Test method testSplit(picard.vcf.SplitVcfsTest) produced standard out/err: 12:02:10.214 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:10.214 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSplit(picard.vcf.SplitVcfsTest) produced standard out/err: 12:02:10.214 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:10.214 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSplit(picard.vcf.SplitVcfsTest) produced standard out/err: 12:02:10.214 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:02:10.214 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testSplit(picard.vcf.SplitVcfsTest) produced standard out/err: 12:02:10.214 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:02:10.214 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testSplit(picard.vcf.SplitVcfsTest) produced standard out/err: [Tue Jul 02 12:02:10 GMT+14:00 2024] SplitVcfs INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/CEUTrio-merged-indels-snps.vcf SNP_OUTPUT=/tmp/SplitVcfsTest1224990104212620623.tmp/split-vcfs-test-snps-delete-me.vcf INDEL_OUTPUT=/tmp/SplitVcfsTest1224990104212620623.tmp/split-vcfs-test-indels-delete-me.vcf STRICT=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:02:10 GMT+14:00 2024] SplitVcfs INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/CEUTrio-merged-indels-snps.vcf SNP_OUTPUT=/tmp/SplitVcfsTest1224990104212620623.tmp/split-vcfs-test-snps-delete-me.vcf INDEL_OUTPUT=/tmp/SplitVcfsTest1224990104212620623.tmp/split-vcfs-test-indels-delete-me.vcf STRICT=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testSplit(picard.vcf.SplitVcfsTest) produced standard out/err: [Tue Jul 02 12:02:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:02:10 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testSplit(picard.vcf.SplitVcfsTest) produced standard out/err: [Tue Jul 02 12:02:11 GMT+14:00 2024] picard.vcf.SplitVcfs done. Elapsed time: 0.02 minutes. [Tue Jul 02 12:02:11 GMT+14:00 2024] picard.vcf.SplitVcfs done. Elapsed time: 0.02 minutes. Test: Test method testSplit(picard.vcf.SplitVcfsTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method basicParsingTest(picard.util.TabbedTextFileWithHeaderParserTest) Running Test: Test method parsingWithColumnHeadersTest(picard.util.TabbedTextFileWithHeaderParserTest) Running Test: Test method independentTestOfDataProviderTest(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[0](public java.lang.Object[][] picard.sam.markduplicates.MarkDuplicatesTest.pgRecordChainingTestDataProvider(), class picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[1](public java.lang.Object[][] picard.sam.markduplicates.AbstractMarkDuplicatesCommandLineProgramTest.extensions(), class picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[2](public java.lang.Object[][] picard.sam.markduplicates.MarkDuplicatesTest.testDuplexUmiDataProvider(), class picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[3](public java.lang.Object[][] picard.sam.markduplicates.AbstractMarkDuplicatesCommandLineProgramTest.secondarySupplementaryData(), class picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[4](public java.lang.Object[][] picard.sam.markduplicates.MarkDuplicatesTest.testOpticalDuplicateDetectionDataProvider(), class picard.sam.markduplicates.MarkDuplicateWithMissingSampleBarcodeTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[5](public java.lang.Object[][] picard.sam.util.ReadNameParserTests.testReadNameParsingDataProvider(), class picard.sam.util.ReadNameParserTests)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[6](public java.lang.Object[][] picard.sam.util.ReadNameParserTests.testParseReadNameDataProvider(), class picard.sam.util.ReadNameParserTests)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[7](public java.lang.Object[][] picard.sam.util.PrimaryAlignmentKeyTest.negativeTestData(), class picard.sam.util.PrimaryAlignmentKeyTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[8](public java.lang.Object[][] picard.sam.util.PrimaryAlignmentKeyTest.positiveTestData(), class picard.sam.util.PrimaryAlignmentKeyTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[9](public java.lang.Object[][] picard.analysis.CollectWgsMetricsTest.wgsDataProvider(), class picard.analysis.CollectWgsMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[10](public java.lang.Object[][] picard.analysis.CollectWgsMetricsTest.wgsAlgorithm(), class picard.analysis.CollectWgsMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[11](public java.lang.Object[][] picard.illumina.parser.BclParserTest.getTileMaps(), class picard.illumina.parser.BclParserTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[12](public java.lang.Object[][] picard.illumina.parser.BclParserTest.eamssTestDat(), class picard.illumina.parser.BclParserTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[13](public java.lang.Object[][] picard.illumina.parser.BclParserTest.getMultiTileMaps(), class picard.illumina.parser.BclParserTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[14](public java.lang.Object[][] picard.illumina.parser.BclParserTest.eamssDataNo10GSeries(), class picard.illumina.parser.BclParserTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[15](public java.lang.Object[][] picard.illumina.parser.TileMetricsUtilTest.testCases(), class picard.illumina.parser.TileMetricsUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[16](public java.lang.Object[][] picard.vcf.CallingMetricAccumulatorTest.getSingletonSampleData(), class picard.vcf.CallingMetricAccumulatorTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[17](public java.lang.Object[][] picard.util.BedToIntervalListTest.testBedToIntervalListDataProvider(), class picard.util.BedToIntervalListTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[18](public java.lang.Object[][] picard.util.BedToIntervalListTest.testBedToIntervalListSequenceDictionaryDataProvider(), class picard.util.BedToIntervalListTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[19](public java.lang.Object[][] picard.util.BedToIntervalListTest.testBedToIntervalListSequenceDictionaryBadDataProvider(), class picard.util.BedToIntervalListTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[20](public java.lang.Object[][] picard.util.BedToIntervalListTest.testBedToIntervalListOutOfBoundsDataProvider(), class picard.util.BedToIntervalListTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[21](public java.lang.Object[][] picard.vcf.GenotypeConcordanceTest.genotypeConcordanceDetermineStateDataProvider(), class picard.vcf.GenotypeConcordanceTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[22](public java.lang.Object[][] picard.vcf.GenotypeConcordanceTest.getGenotypeConcordanceTestFileData(), class picard.vcf.GenotypeConcordanceTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[23](public java.lang.Object[][] picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.provideForTestIndelErrors(), class picard.sam.SamErrorMetric.CollectSamErrorMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[24](public java.lang.Object[][] picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.parseDirectiveBadData(), class picard.sam.SamErrorMetric.CollectSamErrorMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[25](public java.lang.Object[][] picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.oneCovariateIndelErrorMetricsDataProvider(), class picard.sam.SamErrorMetric.CollectSamErrorMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[26](public java.lang.Object[][] picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.readCycleBinData(), class picard.sam.SamErrorMetric.CollectSamErrorMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[27](public java.lang.Object[][] picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.provideForTestHasDeletionBeenProcessed(), class picard.sam.SamErrorMetric.CollectSamErrorMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[28](public java.lang.Object[][] picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.parseDirectiveData(), class picard.sam.SamErrorMetric.CollectSamErrorMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[29](public java.lang.Object[][] picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.readCycleBinDataError(), class picard.sam.SamErrorMetric.CollectSamErrorMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[30](public java.lang.Object[][] picard.sam.SamErrorMetric.CollectSamErrorMetricsTest.OneCovariateErrorMetricsDataProvider(), class picard.sam.SamErrorMetric.CollectSamErrorMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[31](public java.lang.Object[][] picard.illumina.CollectIlluminaBasecallingMetricsTest.testIndexedRunLane1DataProvider(), class picard.illumina.CollectIlluminaBasecallingMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[32](public static java.lang.Object[][] picard.vcf.UpdateVcfSequenceDictionaryTest.outputFies(), class picard.vcf.UpdateVcfSequenceDictionaryTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[33](public java.lang.Object[][] picard.sam.markduplicates.CheckDuplicateMarkingTest.checkDuplicateMarkingDataProvider(), class picard.sam.markduplicates.CheckDuplicateMarkingTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[34](public java.lang.Object[][] picard.util.ScatterIntervalsByNsTest.testSegregate(), class picard.util.ScatterIntervalsByNsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[35](public java.lang.Object[][] picard.vcf.FixVcfHeaderTest.testFixVcfHeaderDataProvider(), class picard.vcf.FixVcfHeaderTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[36](public java.lang.Object[][] picard.sam.DownsampleSamTest.repeatedDownsamplingProvider(), class picard.sam.DownsampleSamTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[37](public java.lang.Object[][] picard.sam.DownsampleSamTest.ValidArgumentsTestProvider(), class picard.sam.DownsampleSamTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[38](public java.lang.Object[][] picard.sam.FastqToSamTest.badFormatFiles(), class picard.sam.FastqToSamTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[39](public java.lang.Object[][] picard.sam.FastqToSamTest.okPairNames(), class picard.sam.FastqToSamTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[40](public java.lang.Object[][] picard.sam.FastqToSamTest.permissiveFormatFiles(), class picard.sam.FastqToSamTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[41](public java.lang.Object[][] picard.sam.FastqToSamTest.okVersionFiles(), class picard.sam.FastqToSamTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[42](public java.lang.Object[][] picard.sam.FastqToSamTest.okPairedFiles(), class picard.sam.FastqToSamTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[43](public java.lang.Object[][] picard.sam.FastqToSamTest.badPairNames(), class picard.sam.FastqToSamTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[44](public java.lang.Object[][] picard.sam.FastqToSamTest.badPairedFiles(), class picard.sam.FastqToSamTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[45](public java.lang.Object[][] picard.sam.FastqToSamTest.badVersionFiles(), class picard.sam.FastqToSamTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[46](public java.lang.Object[][] picard.illumina.parser.PosParserTest.singleTileData(), class picard.illumina.parser.PosParserTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[47](public java.lang.Object[][] picard.illumina.parser.PosParserTest.multiTileData(), class picard.illumina.parser.PosParserTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[48](public java.lang.Object[][] picard.sam.DuplicationMetricsTest.testMergeDataProvider(), class picard.sam.DuplicationMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[49](public java.lang.Object[][] picard.sam.markduplicates.AbstractMarkDuplicatesCommandLineProgramTest.extensions(), class picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[50](public java.lang.Object[][] picard.sam.markduplicates.AbstractMarkDuplicatesCommandLineProgramTest.secondarySupplementaryData(), class picard.sam.markduplicates.MarkDuplicatesSetSizeHistogramTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[51](public java.lang.Object[][] picard.analysis.WgsMetricsTest.testWgsMetricsMergeDataProvider(), class picard.analysis.WgsMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[52](public java.lang.Object[][] picard.analysis.AlignmentSummaryMetricsCollectorTest.get3PrimeSoftClipData(), class picard.analysis.AlignmentSummaryMetricsCollectorTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[53](java.lang.Object[][] picard.sam.SetNmMdAndUqTagsTest.testValidSortData(), class picard.sam.SetNmMdAndUqTagsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[54](public java.util.Iterator picard.illumina.DistanceMetricTest.distanceTestData(), class picard.illumina.DistanceMetricTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[55](public java.lang.Object[][] picard.analysis.directed.CollectHsMetricsTest.targetedIntervalDataProvider(), class picard.analysis.directed.CollectHsMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[56](public java.util.Iterator picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumorTest.testGetLikelihoodsData(), class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumorTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[57](public java.lang.Object[][] picard.illumina.parser.readers.PosFileReaderTest.invalidDataFiles(), class picard.illumina.parser.readers.PosFileReaderTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[58](public java.lang.Object[][] picard.sam.markduplicates.AbstractMarkDuplicatesCommandLineProgramTest.extensions(), class picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[59](public java.lang.Object[][] picard.sam.markduplicates.AbstractMarkDuplicatesCommandLineProgramTest.secondarySupplementaryData(), class picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[60](public java.util.Iterator picard.sam.ReorderSamTest.testDictionaryData() throws java.io.IOException, class picard.sam.ReorderSamTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[61](public java.lang.Object[][] picard.illumina.parser.readers.LocsFileReaderTest.invalidFiles(), class picard.illumina.parser.readers.LocsFileReaderTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[62](public java.lang.Object[][] picard.sam.markduplicates.ElcHashBasedDuplicatesFinderTest.searchDuplicatesDataProvider(), class picard.sam.markduplicates.ElcHashBasedDuplicatesFinderTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[63](public java.lang.Object[][] picard.sam.markduplicates.ElcHashBasedDuplicatesFinderTest.fillHistogramDataProvider(), class picard.sam.markduplicates.ElcHashBasedDuplicatesFinderTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[64](public java.lang.Object[][] picard.sam.SamFormatConverterTest.conversionCases(), class picard.sam.SamFormatConverterTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[65](public java.lang.Object[][] picard.sam.AbstractAlignmentMergerTest.readPositionIgnoringSoftClips(), class picard.sam.AbstractAlignmentMergerTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[66](public java.util.Iterator picard.sam.AbstractAlignmentMergerTest.overlapReadDataWithSwaps(), class picard.sam.AbstractAlignmentMergerTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[67](public java.lang.Object[][] picard.sam.AbstractAlignmentMergerTest.referencePositionAndReadPositions(), class picard.sam.AbstractAlignmentMergerTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[68](public java.lang.Object[][] picard.analysis.CompareMetricsTest.testCompareMetricValuesDataProvider(), class picard.analysis.CompareMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[69](public java.lang.Object[][] picard.analysis.CompareMetricsTest.testCompareMetricsDataProvider(), class picard.analysis.CompareMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[70](public java.lang.Object[][] picard.sam.markduplicates.MarkDuplicatesTest.pgRecordChainingTestDataProvider(), class picard.sam.markduplicates.MarkDuplicatesTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[71](public java.lang.Object[][] picard.sam.markduplicates.AbstractMarkDuplicatesCommandLineProgramTest.extensions(), class picard.sam.markduplicates.MarkDuplicatesTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[72](public java.lang.Object[][] picard.sam.markduplicates.MarkDuplicatesTest.testDuplexUmiDataProvider(), class picard.sam.markduplicates.MarkDuplicatesTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[73](public java.lang.Object[][] picard.sam.markduplicates.AbstractMarkDuplicatesCommandLineProgramTest.secondarySupplementaryData(), class picard.sam.markduplicates.MarkDuplicatesTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[74](public java.lang.Object[][] picard.sam.markduplicates.MarkDuplicatesTest.testOpticalDuplicateDetectionDataProvider(), class picard.sam.markduplicates.MarkDuplicatesTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[75](public java.lang.Object[][] picard.pedigree.PedFileTest.testFromSexMapDataProvider(), class picard.pedigree.PedFileTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[76](public java.lang.Object[][] picard.sam.SamErrorMetric.BaseErrorCalculationTest.testOverlappingErrorCalculatorWithManyReadsData() throws java.io.IOException, class picard.sam.SamErrorMetric.BaseErrorCalculationTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[77](public java.lang.Object[][] picard.arrays.illumina.InfiniumDataFileTest.byteArrayToIntDataProvider(), class picard.arrays.illumina.InfiniumDataFileTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[78](public java.lang.Object[][] picard.arrays.illumina.InfiniumDataFileTest.byteArrayToFloatDataProvider(), class picard.arrays.illumina.InfiniumDataFileTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[79](public java.lang.Object[][] picard.arrays.CollectArraysVariantCallingMetricsTest.testCollectArraysVariantCallingMetricsTestProvider(), class picard.arrays.CollectArraysVariantCallingMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[80](public java.lang.Object[][] picard.arrays.CollectArraysVariantCallingMetricsTest.testSexConcordanceTypesProvider(), class picard.arrays.CollectArraysVariantCallingMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[81](public java.lang.Object[][] picard.arrays.illumina.VcfToAdpcTest.vcfToAdpcBinCombinations(), class picard.arrays.illumina.VcfToAdpcTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[82](public java.util.Iterator picard.TestDataProviders.testAllDataProvidersData() throws java.lang.Exception, class picard.TestDataProviders)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[83](public java.lang.Object[][] picard.sam.markduplicates.AbstractMarkDuplicatesCommandLineProgramTest.extensions(), class picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[84](public java.lang.Object[][] picard.sam.markduplicates.AbstractMarkDuplicatesCommandLineProgramTest.secondarySupplementaryData(), class picard.sam.markduplicates.MarkDuplicatesWithMateCigarTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[85](private java.lang.Object[][] picard.illumina.IlluminaBasecallsToSamAdapterClippingTest.getIlluminaBasecallsToSamTestData(), class picard.illumina.IlluminaBasecallsToSamAdapterClippingTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[86](public java.lang.Object[][] picard.sam.RevertSamTest.getPostitiveTestData(), class picard.sam.RevertSamTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[87](public java.lang.Object[][] picard.sam.RevertSamTest.getNegativeTestData(), class picard.sam.RevertSamTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[88](public java.util.Iterator picard.util.LiftoverVcfTest.indelFlipDataWithOriginalAllele(), class picard.util.LiftoverVcfTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[89](public java.util.Iterator picard.util.LiftoverVcfTest.indelFlipData(), class picard.util.LiftoverVcfTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[90](public java.util.Iterator picard.util.LiftoverVcfTest.noCallAndSymbolicData(), class picard.util.LiftoverVcfTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[91](public java.lang.Object[][] picard.util.LiftoverVcfTest.dataTestHaplotypeProbabilitiesFromSequenceAddToProbs(), class picard.util.LiftoverVcfTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[92](public java.util.Iterator picard.util.LiftoverVcfTest.cleanIndelNoFlipData(), class picard.util.LiftoverVcfTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[93](public java.lang.Object[][] picard.util.LiftoverVcfTest.dataTestVcfSorted(), class picard.util.LiftoverVcfTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[94](public java.lang.Object[][] picard.util.LiftoverVcfTest.dataTestWriteOriginalPosition(), class picard.util.LiftoverVcfTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[95](public java.util.Iterator picard.util.LiftoverVcfTest.leftAlignAllelesData(), class picard.util.LiftoverVcfTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[96](public java.util.Iterator picard.util.LiftoverVcfTest.indelNoFlipData(), class picard.util.LiftoverVcfTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[97](public java.util.Iterator picard.util.LiftoverVcfTest.snpWithChangedRef(), class picard.util.LiftoverVcfTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[98](public java.lang.Object[][] picard.util.LiftoverVcfTest.liftoverReverseStrand(), class picard.util.LiftoverVcfTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[99](java.util.Iterator picard.util.LiftoverVcfTest.testWriteVcfData(), class picard.util.LiftoverVcfTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[100](public java.lang.Object[][] picard.sam.markduplicates.AsIsMarkDuplicatesTest.queryGroupedInput(), class picard.sam.markduplicates.AsIsMarkDuplicatesTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[101](public java.lang.Object[][] picard.sam.markduplicates.AsIsMarkDuplicatesTest.testSameUnclipped5PrimeOppositeStrandData(), class picard.sam.markduplicates.AsIsMarkDuplicatesTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[102](public java.lang.Object[][] picard.sam.markduplicates.MarkDuplicatesTest.pgRecordChainingTestDataProvider(), class picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[103](public java.lang.Object[][] picard.sam.markduplicates.AbstractMarkDuplicatesCommandLineProgramTest.extensions(), class picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[104](public java.lang.Object[][] picard.sam.markduplicates.MarkDuplicatesTest.testDuplexUmiDataProvider(), class picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[105](public java.lang.Object[][] picard.sam.markduplicates.AbstractMarkDuplicatesCommandLineProgramTest.secondarySupplementaryData(), class picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[106](public java.lang.Object[][] picard.sam.markduplicates.MarkDuplicatesTest.testOpticalDuplicateDetectionDataProvider(), class picard.sam.markduplicates.MarkDuplicateWithMissingReadTwoBarcodeTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[107](public java.lang.Object[][] picard.util.MathUtilTest.divideMethodTestCases(), class picard.util.MathUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[108](public java.lang.Object[][] picard.util.MathUtilTest.testMinWithArrayData(), class picard.util.MathUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[109](public java.lang.Object[][] picard.util.MathUtilTest.getProbabilityFromLogTestData(), class picard.util.MathUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[110](public java.lang.Object[][] picard.util.MathUtilTest.divideMethodFailTestCases(), class picard.util.MathUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[111](public java.lang.Object[][] picard.util.MathUtilTest.testSubtractMaxData(), class picard.util.MathUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[112](public java.lang.Object[][] picard.util.MathUtilTest.testMaxWithArrayData(), class picard.util.MathUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[113](public java.lang.Object[][] picard.util.MathUtilTest.testMinWithArrayShortData(), class picard.util.MathUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[114](public java.lang.Object[][] picard.util.MathUtilTest.divideDoubleTestCases(), class picard.util.MathUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[115](public java.lang.Object[][] picard.util.MathUtilTest.testMinWithArrayByteData(), class picard.util.MathUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[116](public java.lang.Object[][] picard.util.MathUtilTest.testMinWithArrayIntData(), class picard.util.MathUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[117](public java.lang.Object[][] picard.util.MathUtilTest.testMinWithArrayAndScalarData(), class picard.util.MathUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[118](public java.lang.Object[][] picard.util.MathUtilTest.seqMethodTestCases(), class picard.util.MathUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[119](public java.lang.Object[][] picard.util.MathUtilTest.testMaxWithArrayAndScalarData(), class picard.util.MathUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[120](public java.lang.Object[][] picard.util.MathUtilTest.pNormalizeLogProbabilityTestData(), class picard.util.MathUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[121](public java.lang.Object[][] picard.fingerprint.CrosscheckReadGroupFingerprintsTest.bamFilesLBs(), class picard.fingerprint.CrosscheckReadGroupFingerprintsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[122](public java.lang.Object[][] picard.fingerprint.CrosscheckReadGroupFingerprintsTest.newParametersData(), class picard.fingerprint.CrosscheckReadGroupFingerprintsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[123](public java.lang.Object[][] picard.fingerprint.CrosscheckReadGroupFingerprintsTest.bamFilesRGs(), class picard.fingerprint.CrosscheckReadGroupFingerprintsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[124](public java.lang.Object[][] picard.fingerprint.CrosscheckReadGroupFingerprintsTest.bamFilesSources(), class picard.fingerprint.CrosscheckReadGroupFingerprintsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[125](public java.lang.Object[][] picard.fingerprint.CrosscheckReadGroupFingerprintsTest.bamFilesSMs(), class picard.fingerprint.CrosscheckReadGroupFingerprintsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[126](public java.lang.Object[][] picard.illumina.parser.readers.AbstractIlluminaPositionFileReaderTest.invalidPositions(), class picard.illumina.parser.readers.AbstractIlluminaPositionFileReaderTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[127](public java.lang.Object[][] picard.illumina.parser.readers.AbstractIlluminaPositionFileReaderTest.invalidFileNames(), class picard.illumina.parser.readers.AbstractIlluminaPositionFileReaderTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[128](java.lang.Object[][] picard.analysis.CollectMultipleMetricsTest.extraArgumentValue(), class picard.analysis.CollectMultipleMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[129](private java.lang.Object[][] picard.util.TextFileParsersTest.getTabbedData(), class picard.util.TextFileParsersTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[130](private java.lang.Object[][] picard.util.TextFileParsersTest.getLeadingWhiteSpaceData(), class picard.util.TextFileParsersTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[131](private java.lang.Object[][] picard.util.TextFileParsersTest.getMultiFileParsingData(), class picard.util.TextFileParsersTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[132](private java.lang.Object[][] picard.util.TextFileParsersTest.getTooManyWordsData(), class picard.util.TextFileParsersTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[133](private java.lang.Object[][] picard.util.TextFileParsersTest.getNoGroupingData(), class picard.util.TextFileParsersTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[134](private java.lang.Object[][] picard.util.TextFileParsersTest.getWordCountCalculationData(), class picard.util.TextFileParsersTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[135](private java.lang.Object[][] picard.util.TextFileParsersTest.getBasicInputParserData(), class picard.util.TextFileParsersTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[136](java.lang.Object[][] picard.analysis.AdapterUtilityTest.testAdapterReadsData(), class picard.analysis.AdapterUtilityTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[137](public java.lang.Object[][] picard.illumina.parser.PerTileParserTest.seekingTests(), class picard.illumina.parser.PerTileParserTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[138](public java.lang.Object[][] picard.illumina.parser.PerTileParserTest.missingTiles(), class picard.illumina.parser.PerTileParserTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[139](public java.lang.Object[][] picard.illumina.CheckIlluminaDirectoryTest.positiveTestData(), class picard.illumina.CheckIlluminaDirectoryTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[140](public java.lang.Object[][] picard.illumina.CheckIlluminaDirectoryTest.negativeTestData(), class picard.illumina.CheckIlluminaDirectoryTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[141](public java.lang.Object[][] picard.vcf.filter.TestFilterVcf.goodInputVcfs(), class picard.vcf.filter.TestFilterVcf)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[142](public java.lang.Object[][] picard.analysis.TheoreticalSensitivityTest.trimDistributions(), class picard.analysis.TheoreticalSensitivityTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[143](public java.lang.Object[][] picard.analysis.TheoreticalSensitivityTest.fractionalAlleleSensDataProvider(), class picard.analysis.TheoreticalSensitivityTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[144](public java.lang.Object[][] picard.analysis.TheoreticalSensitivityTest.arbFracSensDataProvider(), class picard.analysis.TheoreticalSensitivityTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[145](public java.lang.Object[][] picard.analysis.TheoreticalSensitivityTest.equivalenceHetVsFull(), class picard.analysis.TheoreticalSensitivityTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[146](public java.lang.Object[][] picard.analysis.TheoreticalSensitivityTest.sumOfGaussians(), class picard.analysis.TheoreticalSensitivityTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[147](public java.lang.Object[][] picard.analysis.TheoreticalSensitivityTest.callingThreshold(), class picard.analysis.TheoreticalSensitivityTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[148](public java.lang.Object[][] picard.analysis.TheoreticalSensitivityTest.hetSensDataProvider(), class picard.analysis.TheoreticalSensitivityTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[149](private java.lang.Object[][] picard.sam.markduplicates.UmiUtilTest.testBrokenUmiDataProvider(), class picard.sam.markduplicates.UmiUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[150](private java.lang.Object[][] picard.sam.markduplicates.UmiUtilTest.testIsTopStrandDataProvider(), class picard.sam.markduplicates.UmiUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[151](public java.util.Iterator picard.analysis.replicates.CollectIndependentReplicatesMetricTest.simpleTestsData(), class picard.analysis.replicates.CollectIndependentReplicatesMetricTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[152](public java.lang.Object[][] picard.illumina.parser.FilterParserTest.failingVerifyTiles(), class picard.illumina.parser.FilterParserTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[153](public java.lang.Object[][] picard.illumina.parser.FilterParserTest.seekToTile(), class picard.illumina.parser.FilterParserTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[154](public java.lang.Object[][] picard.illumina.parser.FilterParserTest.passingTiles(), class picard.illumina.parser.FilterParserTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[155](public java.lang.Object[][] picard.util.IlluminaUtilTest.solexaQualStrToPhredsToPhreds(), class picard.util.IlluminaUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[156](public java.lang.Object[][] picard.util.IlluminaUtilTest.readNames(), class picard.util.IlluminaUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[157](private java.lang.Object[][] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testDuplexUmiDataProvider(), class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[158](public java.lang.Object[][] picard.sam.markduplicates.AbstractMarkDuplicatesCommandLineProgramTest.extensions(), class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[159](private java.lang.Object[][] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testUmiSetsDataProvider(), class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[160](private java.lang.Object[][] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testBadUmiSetsDataProvider(), class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[161](private java.lang.Object[][] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testEmptyUmiDataProvider(), class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[162](private java.lang.Object[][] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testMultipleLibraryUmiMetricsDataProvider(), class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[163](public java.lang.Object[][] picard.sam.markduplicates.AbstractMarkDuplicatesCommandLineProgramTest.secondarySupplementaryData(), class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[164](private java.lang.Object[][] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest.testUmiMetricsDataProvider(), class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[165](public java.lang.Object[][] picard.sam.MergeBamAlignmentTest.testFragmentMultiHitWithFilteringTestCases(), class picard.sam.MergeBamAlignmentTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[166](java.lang.Object[][] picard.sam.MergeBamAlignmentTest.mappedReadInUnmappedBamDataProvider(), class picard.sam.MergeBamAlignmentTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[167](public java.lang.Object[][] picard.sam.MergeBamAlignmentTest.getDataForMergingTest(), class picard.sam.MergeBamAlignmentTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[168](public java.lang.Object[][] picard.sam.MergeBamAlignmentTest.getDataForSortingTest(), class picard.sam.MergeBamAlignmentTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[169](public java.lang.Object[][] picard.sam.MergeBamAlignmentTest.testPairedMultiHitWithFilteringTestCases(), class picard.sam.MergeBamAlignmentTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[170](java.lang.Object[][] picard.sam.MergeBamAlignmentTest.brokenAlignedFiles(), class picard.sam.MergeBamAlignmentTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[171](public java.lang.Object[][] picard.sam.MergeBamAlignmentTest.UnmappedReadStrategiesProvider(), class picard.sam.MergeBamAlignmentTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[172](public java.lang.Object[][] picard.sam.MergeBamAlignmentTest.testShortFragmentWithIndelsClipping(), class picard.sam.MergeBamAlignmentTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[173](public java.lang.Object[][] picard.sam.MergeBamAlignmentTest.testEarliestFragmentStrategyDataProvider(), class picard.sam.MergeBamAlignmentTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[174](public java.lang.Object[][] picard.sam.MergeBamAlignmentTest.testBestFragmentMapqStrategyDataProvider(), class picard.sam.MergeBamAlignmentTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[175](public java.lang.Object[][] picard.sam.MergeBamAlignmentTest.testMostDistantStrategyDataProvider(), class picard.sam.MergeBamAlignmentTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[176](public java.lang.Object[][] picard.fingerprint.HaplotypeMapTest.haplotypeMapForWriting(), class picard.fingerprint.HaplotypeMapTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[177](public java.lang.Object[][] picard.fingerprint.HaplotypeMapTest.haplotypeMapReaderData(), class picard.fingerprint.HaplotypeMapTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[178](public java.lang.Object[][] picard.analysis.directed.CollectTargetedMetricsTest.theoreticalSensitivityDataProvider(), class picard.analysis.directed.CollectTargetedMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[179](public java.lang.Object[][] picard.analysis.directed.CollectTargetedMetricsTest.targetedIntervalDataProvider(), class picard.analysis.directed.CollectTargetedMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[180](public java.lang.Object[][] picard.illumina.parser.readers.FilterFileReaderTest.failingFilesForPicardException(), class picard.illumina.parser.readers.FilterFileReaderTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[181](public java.lang.Object[][] picard.illumina.parser.readers.FilterFileReaderTest.failingFilesForSAMException(), class picard.illumina.parser.readers.FilterFileReaderTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[182](public java.lang.Object[][] picard.sam.ValidateSamFileTest.indexFiles(), class picard.sam.ValidateSamFileTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[183](public java.lang.Object[][] picard.sam.ValidateSamFileTest.samFiles(), class picard.sam.ValidateSamFileTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[184](public java.lang.Object[][] picard.sam.markduplicates.AsIsMarkDuplicatesTest.queryGroupedInput(), class picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[185](public java.lang.Object[][] picard.sam.markduplicates.AsIsMarkDuplicatesTest.testSameUnclipped5PrimeOppositeStrandData(), class picard.sam.markduplicates.AsIsCollectDuplicateMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[186](public java.lang.Object[][] picard.util.AlleleSubsettingUtilsTest.makeUpdatePLsAndADData(), class picard.util.AlleleSubsettingUtilsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[187](java.util.Iterator picard.util.AlleleSubsettingUtilsTest.swapAlleleData(), class picard.util.AlleleSubsettingUtilsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[188](public java.lang.Object[][] picard.sam.FilterSamReadsTest.dataTestJsFilter(), class picard.sam.FilterSamReadsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[189](public java.lang.Object[][] picard.sam.FilterSamReadsTest.dataTestPairedIntervalFilter(), class picard.sam.FilterSamReadsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[190](public java.lang.Object[][] picard.sam.FilterSamReadsTest.dataTestTagFilter(), class picard.sam.FilterSamReadsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[191](public java.lang.Object[][] picard.sam.FilterSamReadsTest.badArgumentCombinationsdata(), class picard.sam.FilterSamReadsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[192](public java.lang.Object[][] picard.sam.FilterSamReadsTest.dataTestDebugOption(), class picard.sam.FilterSamReadsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[193](public java.lang.Object[][] picard.sam.FilterSamReadsTest.dataTestReadFilter(), class picard.sam.FilterSamReadsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[194](public java.lang.Object[][] picard.vcf.VcfToIntervalListTest.getVcfToIntervalListData(), class picard.vcf.VcfToIntervalListTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[195](public java.lang.Object[][] picard.util.UnsignedTypeUtilTest.uByteData(), class picard.util.UnsignedTypeUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[196](public java.lang.Object[][] picard.util.UnsignedTypeUtilTest.uIntData(), class picard.util.UnsignedTypeUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[197](public java.lang.Object[][] picard.util.UnsignedTypeUtilTest.uShortData(), class picard.util.UnsignedTypeUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[198](public java.util.Iterator picard.metrics.MetricBaseTest.getMetricClasses(), class picard.metrics.MetricBaseTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[199](public java.lang.Object[][] picard.sam.SamToFastqWithTagsTest.queryNonExistantTag(), class picard.sam.SamToFastqWithTagsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[200](public java.lang.Object[][] picard.sam.SamToFastqWithTagsTest.argumentCombinationsdata(), class picard.sam.SamToFastqWithTagsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[201](public java.lang.Object[][] picard.sam.SamToFastqWithTagsTest.testTagGroupFastqData(), class picard.sam.SamToFastqWithTagsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[202](public java.lang.Object[][] picard.sam.SamToFastqWithTagsTest.okGroupedFiles(), class picard.sam.SamToFastqWithTagsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[203](public java.lang.Object[][] picard.sam.markduplicates.ElcIdenticalBasesDuplicatesFinderTest.fillHistogramDataProvider(), class picard.sam.markduplicates.ElcIdenticalBasesDuplicatesFinderTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[204](public java.lang.Object[][] picard.sam.markduplicates.ElcIdenticalBasesDuplicatesFinderTest.searchDuplicatesDataProvider(), class picard.sam.markduplicates.ElcIdenticalBasesDuplicatesFinderTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[205](public java.lang.Object[][] picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest.testEquivalenceProvider(), class picard.analysis.artifacts.ConvertSequencingArtifactToOxoGTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[206](public java.lang.Object[][] picard.arrays.illumina.Build37ExtendedIlluminaManifestTest.testBuild37ExtendedIlluminaManifestDataProvider(), class picard.arrays.illumina.Build37ExtendedIlluminaManifestTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[207](public static java.util.Iterator picard.util.IntervalListScattererTest.testScatterTestcases(), class picard.util.IntervalListScattererTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[208](public java.lang.Object[][] picard.illumina.parser.IlluminaDataProviderTest.binaryData(), class picard.illumina.parser.IlluminaDataProviderTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[209](public java.lang.Object[][] picard.illumina.parser.IlluminaDataProviderTest.badData(), class picard.illumina.parser.IlluminaDataProviderTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[210](public java.lang.Object[][] picard.illumina.ReadStructureTest.substructureToReadStructureData(), class picard.illumina.ReadStructureTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[211](public java.lang.Object[][] picard.illumina.ReadStructureTest.invalidReadStructuresFromList(), class picard.illumina.ReadStructureTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[212](public java.lang.Object[][] picard.illumina.ReadStructureTest.substructureToReadStructureNegativeData(), class picard.illumina.ReadStructureTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[213](public java.lang.Object[][] picard.illumina.ReadStructureTest.validReadStructures(), class picard.illumina.ReadStructureTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[214](public java.lang.Object[][] picard.illumina.ReadStructureTest.invalidReadStructures(), class picard.illumina.ReadStructureTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[215](public java.lang.Object[][] picard.util.ClippingUtilityTest.testAdapterInAllReadPositionsDataProvider(), class picard.util.ClippingUtilityTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[216](public java.lang.Object[][] picard.util.ClippingUtilityTest.testAdapterListTruncationDataProvider(), class picard.util.ClippingUtilityTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[217](public java.lang.Object[][] picard.util.ClippingUtilityTest.getClipTestData(), class picard.util.ClippingUtilityTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[218](public java.lang.Object[][] picard.util.ClippingUtilityTest.getClipPairedTestData(), class picard.util.ClippingUtilityTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[219](public java.lang.Object[][] picard.sam.markduplicates.EstimateLibraryComplexityTest.createDataTestSimpleDuplicateWithMaxReadLength(), class picard.sam.markduplicates.EstimateLibraryComplexityTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[220](public java.lang.Object[][] picard.sam.markduplicates.EstimateLibraryComplexityTest.createDataTestMaxDiffRate(), class picard.sam.markduplicates.EstimateLibraryComplexityTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[221](public java.lang.Object[][] picard.sam.markduplicates.EstimateLibraryComplexityTest.createDataTestDefaultMinGroupCount(), class picard.sam.markduplicates.EstimateLibraryComplexityTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[222](public java.lang.Object[][] picard.sam.markduplicates.EstimateLibraryComplexityTest.createDataTestSimpleDuplicatesWithSecondaryAndSupplementaryRecords(), class picard.sam.markduplicates.EstimateLibraryComplexityTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[223](public java.lang.Object[][] picard.sam.markduplicates.EstimateLibraryComplexityTest.createDataTestSimpleDuplicate(), class picard.sam.markduplicates.EstimateLibraryComplexityTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[224](public java.lang.Object[][] picard.illumina.IlluminaLaneMetricsCollectorTest.testLaneMetricsDataProvider(), class picard.illumina.IlluminaLaneMetricsCollectorTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[225](public java.lang.Object[][] picard.illumina.IlluminaLaneMetricsCollectorTest.testCollectIlluminaLaneMetricsDataProvider(), class picard.illumina.IlluminaLaneMetricsCollectorTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[226](public java.lang.Object[][] picard.sam.CleanSamTest.testCleanSamDataProvider(), class picard.sam.CleanSamTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[227](public java.lang.Object[][] picard.sam.CleanSamTest.testCleanSamTesterDataProvider(), class picard.sam.CleanSamTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[228](public java.lang.Object[][] picard.arrays.GtcToVcfTest.badData(), class picard.arrays.GtcToVcfTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[229](public java.lang.Object[][] picard.util.LiftoverUtilsTest.swapRefAltData(), class picard.util.LiftoverUtilsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[230](public java.util.Iterator picard.util.LiftoverUtilsTest.allelesToStringData(), class picard.util.LiftoverUtilsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[231](java.lang.Object[][] picard.fingerprint.FingerprintCheckerTest.samFilesforFingerprinting(), class picard.fingerprint.FingerprintCheckerTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[232](public java.util.Iterator picard.fingerprint.FingerprintCheckerTest.pLohData(), class picard.fingerprint.FingerprintCheckerTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[233](java.lang.Object[][] picard.fingerprint.FingerprintCheckerTest.mergeIsDafeProvider(), class picard.fingerprint.FingerprintCheckerTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[234](public java.lang.Object[][] picard.fingerprint.FingerprintCheckerTest.testCheckFingerprintsSamDataProvider(), class picard.fingerprint.FingerprintCheckerTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[235](public java.util.Iterator picard.fingerprint.FingerprintCheckerTest.queryableData() throws java.io.IOException, class picard.fingerprint.FingerprintCheckerTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[236](public java.lang.Object[][] picard.fingerprint.FingerprintCheckerTest.testCheckFingerprintsSamDataProviderFail(), class picard.fingerprint.FingerprintCheckerTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[237](public java.lang.Object[][] picard.fingerprint.FingerprintCheckerTest.testCheckFingerprintsVcfDataProvider(), class picard.fingerprint.FingerprintCheckerTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[238](public java.lang.Object[][] picard.sam.markduplicates.MarkDuplicatesTest.pgRecordChainingTestDataProvider(), class picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[239](public java.lang.Object[][] picard.sam.markduplicates.AbstractMarkDuplicatesCommandLineProgramTest.extensions(), class picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[240](public java.lang.Object[][] picard.sam.markduplicates.MarkDuplicatesTest.testDuplexUmiDataProvider(), class picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[241](public java.lang.Object[][] picard.sam.markduplicates.AbstractMarkDuplicatesCommandLineProgramTest.secondarySupplementaryData(), class picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[242](public java.lang.Object[][] picard.sam.markduplicates.MarkDuplicatesTest.testOpticalDuplicateDetectionDataProvider(), class picard.sam.markduplicates.MarkDuplicateWithMissingReadOneBarcodeTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[243](public java.lang.Object[][] picard.sam.markduplicates.MarkDuplicatesTest.pgRecordChainingTestDataProvider(), class picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[244](public java.lang.Object[][] picard.sam.markduplicates.AbstractMarkDuplicatesCommandLineProgramTest.extensions(), class picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[245](public java.lang.Object[][] picard.sam.markduplicates.MarkDuplicatesTest.testDuplexUmiDataProvider(), class picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[246](public java.lang.Object[][] picard.sam.markduplicates.AbstractMarkDuplicatesCommandLineProgramTest.secondarySupplementaryData(), class picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[247](public java.lang.Object[][] picard.sam.markduplicates.MarkDuplicatesTest.testOpticalDuplicateDetectionDataProvider(), class picard.sam.markduplicates.MarkDuplicatesTestQueryNameSorted)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[248](public static java.lang.Object[][] picard.analysis.CollectRnaSeqMetricsTest.rRnaIntervalsFiles() throws java.io.IOException, class picard.analysis.CollectRnaSeqMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[249](public static java.lang.Object[][] picard.fingerprint.CalculateFingerprintMetricsTest.testFingerprintMetricData(), class picard.fingerprint.CalculateFingerprintMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[250](public static java.lang.Object[][] picard.fastq.BamToBfqTest.inputs() throws java.io.IOException, class picard.fastq.BamToBfqTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[251](public java.lang.Object[][] picard.illumina.parser.readers.ClocsFileReaderTest.multiBinPassingClocsFiles(), class picard.illumina.parser.readers.ClocsFileReaderTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[252](public java.lang.Object[][] picard.fingerprint.CrosscheckFingerprintsTest.cramsWithNoReference(), class picard.fingerprint.CrosscheckFingerprintsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[253](public java.util.Iterator picard.fingerprint.CrosscheckFingerprintsTest.checkSamplesCrosscheckAllWithMappingData(), class picard.fingerprint.CrosscheckFingerprintsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[254](public java.lang.Object[][] picard.fingerprint.CrosscheckFingerprintsTest.cramBamComparison(), class picard.fingerprint.CrosscheckFingerprintsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[255](public java.util.Iterator picard.fingerprint.CrosscheckFingerprintsTest.checkPathsData() throws java.io.IOException, class picard.fingerprint.CrosscheckFingerprintsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[256](public java.util.Iterator picard.fingerprint.CrosscheckFingerprintsTest.checkSamplesData(), class picard.fingerprint.CrosscheckFingerprintsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[257](public java.util.Iterator picard.fingerprint.CrosscheckFingerprintsTest.checkFilesData(), class picard.fingerprint.CrosscheckFingerprintsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[258](public java.lang.Object[][] picard.fingerprint.CrosscheckFingerprintsTest.bamFilesSMs(), class picard.fingerprint.CrosscheckFingerprintsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[259](public java.util.Iterator picard.fingerprint.CrosscheckFingerprintsTest.checkSampleMapFailuresData(), class picard.fingerprint.CrosscheckFingerprintsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[260](public java.util.Iterator picard.fingerprint.CrosscheckFingerprintsTest.checkSamplesCrosscheckAllData(), class picard.fingerprint.CrosscheckFingerprintsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[261](public java.lang.Object[][] picard.fingerprint.CrosscheckFingerprintsTest.bamFilesLBs(), class picard.fingerprint.CrosscheckFingerprintsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[262](public java.lang.Object[][] picard.fingerprint.CrosscheckFingerprintsTest.bamFilesSources(), class picard.fingerprint.CrosscheckFingerprintsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[263](public java.lang.Object[][] picard.fingerprint.CrosscheckFingerprintsTest.missingOrNoFingerprintingSitesData(), class picard.fingerprint.CrosscheckFingerprintsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[264](public java.lang.Object[][] picard.fingerprint.CrosscheckFingerprintsTest.bamAndCramFilesRGs(), class picard.fingerprint.CrosscheckFingerprintsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[265](public java.lang.Object[][] picard.illumina.parser.PerTilePerCycleParserTest.seekingTests(), class picard.illumina.parser.PerTilePerCycleParserTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[266](public java.lang.Object[][] picard.util.EditDistanceQueriesTest.levensteinDistanceSymmetricData(), class picard.util.EditDistanceQueriesTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[267](private java.lang.Object[][] picard.util.EditDistanceQueriesTest.levensteinDistanceWithNoCallsData(), class picard.util.EditDistanceQueriesTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[268](public static java.lang.Object[][] picard.analysis.CollectOxoGMetricsTest.rightOptions(), class picard.analysis.CollectOxoGMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[269](public static java.lang.Object[][] picard.analysis.CollectOxoGMetricsTest.wrongOptions(), class picard.analysis.CollectOxoGMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[270](public java.lang.Object[][] picard.illumina.parser.readers.BclReaderTest.failingFiles(), class picard.illumina.parser.readers.BclReaderTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[271](public java.lang.Object[][] picard.pedigree.SexTest.testSexDataProviderStr(), class picard.pedigree.SexTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[272](public java.lang.Object[][] picard.pedigree.SexTest.testSexDataProviderInt(), class picard.pedigree.SexTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[273](public java.lang.Object[][] picard.sam.CompareSAMsTest.compareSamsTestData(), class picard.sam.CompareSAMsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[274](public java.lang.Object[][] picard.illumina.ExtractIlluminaBarcodesTest.getQualityTestData(), class picard.illumina.ExtractIlluminaBarcodesTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[275](java.lang.Object[][] picard.illumina.ExtractIlluminaBarcodesTest.testDeltaData(), class picard.illumina.ExtractIlluminaBarcodesTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[276](public java.lang.Object[][] picard.illumina.parser.CycleIlluminaFileMapTest.iteratorTestData(), class picard.illumina.parser.CycleIlluminaFileMapTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[277](public java.lang.Object[][] picard.sam.markduplicates.AbstractMarkDuplicatesCommandLineProgramTest.extensions(), class picard.sam.markduplicates.CollectDuplicateMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[278](public java.lang.Object[][] picard.sam.markduplicates.AbstractMarkDuplicatesCommandLineProgramTest.secondarySupplementaryData(), class picard.sam.markduplicates.CollectDuplicateMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[279](public java.lang.Object[][] picard.illumina.IlluminaBasecallsToSamTest.variousConfigurationsData(), class picard.illumina.IlluminaBasecallsToSamTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[280](public java.lang.Object[][] picard.illumina.IlluminaBasecallsToSamTest.molecularBarcodeData(), class picard.illumina.IlluminaBasecallsToSamTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[281](public java.lang.Object[][] picard.illumina.IlluminaBasecallsToSamTest.multiplexedData(), class picard.illumina.IlluminaBasecallsToSamTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[282](public java.lang.Object[][] picard.sam.SamToFastqTest.missingRgFiles(), class picard.sam.SamToFastqTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[283](public java.lang.Object[][] picard.sam.SamToFastqTest.badFiles(), class picard.sam.SamToFastqTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[284](public java.lang.Object[][] picard.sam.SamToFastqTest.okFiles(), class picard.sam.SamToFastqTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[285](public java.lang.Object[][] picard.sam.SamToFastqTest.okGroupedFiles(), class picard.sam.SamToFastqTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[286](public java.lang.Object[][] picard.sam.SamToFastqTest.trimmedData(), class picard.sam.SamToFastqTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[287](public java.lang.Object[][] picard.sam.SamToFastqTest.clippingTests(), class picard.sam.SamToFastqTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[288](public java.lang.Object[][] picard.sam.SamToFastqTest.badGroupedFiles(), class picard.sam.SamToFastqTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[289](public java.lang.Object[][] picard.sam.SamErrorMetric.ReadBaseStratificationTest.baseStratifierData(), class picard.sam.SamErrorMetric.ReadBaseStratificationTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[290](public java.util.Iterator picard.sam.SamErrorMetric.ReadBaseStratificationTest.readsForChimericTest(), class picard.sam.SamErrorMetric.ReadBaseStratificationTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[291](public java.lang.Object[][] picard.sam.SamErrorMetric.ReadBaseStratificationTest.provideForTestGetIndelElement(), class picard.sam.SamErrorMetric.ReadBaseStratificationTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[292](public java.lang.Object[][] picard.sam.SamErrorMetric.ReadBaseStratificationTest.homopolymerStratifierData(), class picard.sam.SamErrorMetric.ReadBaseStratificationTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[293](public java.lang.Object[][] picard.illumina.parser.IlluminaFileUtilTest.invalidLanes(), class picard.illumina.parser.IlluminaFileUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[294](public java.lang.Object[][] picard.illumina.parser.IlluminaFileUtilTest.perTileFileUtils(), class picard.illumina.parser.IlluminaFileUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[295](public java.lang.Object[][] picard.illumina.parser.IlluminaFileUtilTest.testHasCbclsDataProvider(), class picard.illumina.parser.IlluminaFileUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[296](public java.lang.Object[][] picard.illumina.parser.IlluminaFileUtilTest.perTilePerCycleFileFormats(), class picard.illumina.parser.IlluminaFileUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[297](public java.lang.Object[][] picard.illumina.parser.IlluminaFileUtilTest.missingCycleDataRanges(), class picard.illumina.parser.IlluminaFileUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[298](public java.lang.Object[][] picard.illumina.parser.IlluminaFileUtilTest.missingTileFormats(), class picard.illumina.parser.IlluminaFileUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[299](public java.lang.Object[][] picard.illumina.parser.IlluminaFileUtilTest.validLanes(), class picard.illumina.parser.IlluminaFileUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[300](public java.lang.Object[][] picard.illumina.parser.IlluminaFileUtilTest.validLanesInvalidRegexes(), class picard.illumina.parser.IlluminaFileUtilTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[301](java.lang.Object[][] picard.fingerprint.CheckFingerprintTest.vcfsToFingerprint(), class picard.fingerprint.CheckFingerprintTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[302](java.lang.Object[][] picard.fingerprint.CheckFingerprintTest.samsToFingerprint(), class picard.fingerprint.CheckFingerprintTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[303](public java.lang.Object[][] picard.fingerprint.CheckFingerprintTest.badData(), class picard.fingerprint.CheckFingerprintTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[304](public java.lang.Object[][] picard.vcf.GatherVcfsTest.vcfshards(), class picard.vcf.GatherVcfsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[305](public java.util.Iterator picard.analysis.artifacts.TransitionTest.allTransitions(), class picard.analysis.artifacts.TransitionTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[306](public java.lang.Object[][] picard.analysis.artifacts.TransitionTest.badBases(), class picard.analysis.artifacts.TransitionTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[307](java.lang.Object[][] picard.sam.AddOATagTest.testIntervalListData(), class picard.sam.AddOATagTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[308](java.lang.Object[][] picard.sam.AddOATagTest.testOAData(), class picard.sam.AddOATagTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[309](public java.lang.Object[][] picard.fingerprint.HaplotypeProbabilitiesTest.dataTestpEvidenceGivenPriorFromGLs(), class picard.fingerprint.HaplotypeProbabilitiesTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[310](public java.lang.Object[][] picard.fingerprint.HaplotypeProbabilitiesTest.symmetricLODdata(), class picard.fingerprint.HaplotypeProbabilitiesTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[311](public java.lang.Object[][] picard.fingerprint.HaplotypeProbabilitiesTest.dataTestHaplotypeProbabilitiesFromSequenceAddToProbs(), class picard.fingerprint.HaplotypeProbabilitiesTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[312](public java.lang.Object[][] picard.fingerprint.HaplotypeProbabilitiesTest.dataTestHaplotypeProbabilitiesFromContaminatorSequenceAddToProbs(), class picard.fingerprint.HaplotypeProbabilitiesTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[313](public java.lang.Object[][] picard.sam.PositionBasedDownsampleSamTest.InvalidArgumentsTestProvider(), class picard.sam.PositionBasedDownsampleSamTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[314](public java.lang.Object[][] picard.sam.PositionBasedDownsampleSamTest.allowTwiceData(), class picard.sam.PositionBasedDownsampleSamTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[315](public java.lang.Object[][] picard.sam.PositionBasedDownsampleSamTest.ValidArgumentsTestProvider(), class picard.sam.PositionBasedDownsampleSamTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[316](java.lang.Object[][] picard.analysis.CollectAlignmentSummaryMetricsTest.TrueFalse(), class picard.analysis.CollectAlignmentSummaryMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[317](java.lang.Object[][] picard.analysis.CollectAlignmentSummaryMetricsTest.fileForTestReadLengthHistogram(), class picard.analysis.CollectAlignmentSummaryMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[318](public java.lang.Object[][] picard.analysis.MultiLevelCollectorTest.variedAccumulationLevels(), class picard.analysis.MultiLevelCollectorTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[319](public java.lang.Object[][] picard.vcf.AccumulateVariantCallingMetricsTest.shardDataProvider(), class picard.vcf.AccumulateVariantCallingMetricsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[320](public java.lang.Object[][] picard.sam.util.SamComparisonTest.samComparisonTestData(), class picard.sam.util.SamComparisonTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[321](public java.lang.Object[][] picard.util.IntervalListToolsTest.actionAndTotalBasesWithUniqueData(), class picard.util.IntervalListToolsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[322](public java.lang.Object[][] picard.util.IntervalListToolsTest.combineAbuttingIntervals(), class picard.util.IntervalListToolsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[323](public java.lang.Object[][] picard.util.IntervalListToolsTest.actionAndTotalBasesData(), class picard.util.IntervalListToolsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[324](public java.lang.Object[][] picard.util.IntervalListToolsTest.actionAndTotalBasesWithDontMergeAbuttingData(), class picard.util.IntervalListToolsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[325](public static java.util.Iterator picard.util.IntervalListToolsTest.testScatterTestcases(), class picard.util.IntervalListToolsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[326](public java.util.Iterator picard.util.IntervalListToolsTest.ActionsTest(), class picard.util.IntervalListToolsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[327](public java.lang.Object[][] picard.util.IntervalListToolsTest.actionAndTotalBasesWithInvertData(), class picard.util.IntervalListToolsTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[328](public java.lang.Object[][] picard.sam.markduplicates.AbstractMarkDuplicatesCommandLineProgramTest.extensions(), class picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[329](public java.lang.Object[][] picard.sam.markduplicates.AbstractMarkDuplicatesCommandLineProgramTest.secondarySupplementaryData(), class picard.sam.markduplicates.MarkDuplicatesTagRepresentativeReadIndexTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[330](public java.lang.Object[][] picard.illumina.parser.readers.MMapBackedIteratorFactoryTest.validTestDefs(), class picard.illumina.parser.readers.MMapBackedIteratorFactoryTest)(picard.TestDataProviders) Running Test: Test method testDataProviderswithDP[331](public java.lang.Object[][] picard.illumina.parser.readers.MMapBackedIteratorFactoryTest.invalidFileSizes(), class picard.illumina.parser.readers.MMapBackedIteratorFactoryTest)(picard.TestDataProviders) Running Test: Test method testAbFiltering(picard.vcf.filter.TestFilterVcf) Running Test: Test method testCombinedFiltering(picard.vcf.filter.TestFilterVcf) Running Test: Test method testDpFiltering(picard.vcf.filter.TestFilterVcf) Running Test: Test method testDpFilteringToVcf(picard.vcf.filter.TestFilterVcf) Running Test: Test method testFilteringToVcfWithNoSequenceDictionary(picard.vcf.filter.TestFilterVcf) Running Test: Test method testFsFiltering[0](testdata/picard/vcf/filter/testFiltering.vcf)(picard.vcf.filter.TestFilterVcf) Running Test: Test method testFsFiltering[1](testdata/picard/vcf/filter/testFilteringSitesOnly.vcf)(picard.vcf.filter.TestFilterVcf) Running Test: Test method testGqFiltering(picard.vcf.filter.TestFilterVcf) Running Test: Test method testJavaScript[0](testdata/picard/vcf/filter/testFiltering.vcf)(picard.vcf.filter.TestFilterVcf) Test: Test method testJavaScript[0](testdata/picard/vcf/filter/testFiltering.vcf)(picard.vcf.filter.TestFilterVcf) produced standard out/err: Warning: Nashorn engine is planned to be removed from a future JDK release Gradle suite > Gradle test > picard.vcf.filter.TestFilterVcf.testJavaScript[0](testdata/picard/vcf/filter/testFiltering.vcf) STANDARD_ERROR Warning: Nashorn engine is planned to be removed from a future JDK release Running Test: Test method testJavaScript[1](testdata/picard/vcf/filter/testFilteringSitesOnly.vcf)(picard.vcf.filter.TestFilterVcf) Test: Test method testJavaScript[1](testdata/picard/vcf/filter/testFilteringSitesOnly.vcf)(picard.vcf.filter.TestFilterVcf) produced standard out/err: Warning: Nashorn engine is planned to be removed from a future JDK release Gradle suite > Gradle test > picard.vcf.filter.TestFilterVcf.testJavaScript[1](testdata/picard/vcf/filter/testFilteringSitesOnly.vcf) STANDARD_ERROR Warning: Nashorn engine is planned to be removed from a future JDK release Running Test: Test method testNoFiltering[0](testdata/picard/vcf/filter/testFiltering.vcf)(picard.vcf.filter.TestFilterVcf) Running Test: Test method testNoFiltering[1](testdata/picard/vcf/filter/testFilteringSitesOnly.vcf)(picard.vcf.filter.TestFilterVcf) Running Test: Test method testMultiFileParsing[0](testdata/picard/util/whitespace_text_file.txt, testdata/picard/util/whitespace_text_file.txt)(picard.util.TextFileParsersTest) Running Test: Test method testMultiFileParsing[1](sun.nio.ch.ChannelInputStream@1904cead, sun.nio.ch.ChannelInputStream@3ae7faa9)(picard.util.TextFileParsersTest) Running Test: Test method testTabbedFileParser[0](testdata/picard/util/tabbed_text_file.txt)(picard.util.TextFileParsersTest) Running Test: Test method testTabbedFileParser[1](sun.nio.ch.ChannelInputStream@58764138)(picard.util.TextFileParsersTest) Running Test: Test method testTextFileParser[0](testdata/picard/util/whitespace_text_file.txt)(picard.util.TextFileParsersTest) Running Test: Test method testTextFileParser[1](sun.nio.ch.ChannelInputStream@474e0150)(picard.util.TextFileParsersTest) Running Test: Test method testTextFileParserLeadingWhitespace[0](testdata/picard/util/all_ones_text_file.txt)(picard.util.TextFileParsersTest) Running Test: Test method testTextFileParserLeadingWhitespace[1](sun.nio.ch.ChannelInputStream@282870)(picard.util.TextFileParsersTest) Running Test: Test method testTextFileParserNoGrouping[0](testdata/picard/util/no_grouping_file.txt)(picard.util.TextFileParsersTest) Running Test: Test method testTextFileParserNoGrouping[1](sun.nio.ch.ChannelInputStream@7deb1e55)(picard.util.TextFileParsersTest) Running Test: Test method testTooManyWords[0](testdata/picard/util/whitespace_text_file.txt)(picard.util.TextFileParsersTest) Running Test: Test method testTooManyWords[1](sun.nio.ch.ChannelInputStream@42be2c45)(picard.util.TextFileParsersTest) Running Test: Test method testWordCountCalculation[0](1 2 3, false, Tabs with all fields filled.)(picard.util.TextFileParsersTest) Running Test: Test method testWordCountCalculation[1](1 2 , false, Tabs with no final field.)(picard.util.TextFileParsersTest) Running Test: Test method testWordCountCalculation[2]( 2 3, false, Tabs with no first field.)(picard.util.TextFileParsersTest) Running Test: Test method testWordCountCalculation[3]( 2 , false, Tabs with no first or final field.)(picard.util.TextFileParsersTest) Running Test: Test method testWordCountCalculation[4](1 2 3, true, Spaces with all fields filled (grouping on).)(picard.util.TextFileParsersTest) Running Test: Test method testWordCountCalculation[5](1 2 3 , true, Spaces with no final field (grouping on).)(picard.util.TextFileParsersTest) Running Test: Test method testWordCountCalculation[6]( 2 3 4, true, Spaces with no first field (grouping on).)(picard.util.TextFileParsersTest) Running Test: Test method testWordCountCalculation[7]( 2 , false, Spaces with no first or final field.)(picard.util.TextFileParsersTest) Running Test: Test method testCentralLimitTheorem(picard.analysis.TheoreticalSensitivityTest) Running Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel Gradle suite > Gradle test > picard.analysis.TheoreticalSensitivityTest.testDeterministicQualityAndDepth STANDARD_ERROR INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testDeterministicQualityAndDepth(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating theoretical het sensitivity Running Test: Test method testDrawSumOfQScores[0](testdata/picard/analysis/TheoreticalSensitivity/test_Solexa-332667.wgs_metrics, 500, 0.03)(picard.analysis.TheoreticalSensitivityTest) Running Test: Test method testDrawSumOfQScores[1](testdata/picard/analysis/TheoreticalSensitivity/test_Solexa-332667.wgs_metrics, 20, 0.05)(picard.analysis.TheoreticalSensitivityTest) Running Test: Test method testDrawSumOfQScores[2](testdata/picard/analysis/TheoreticalSensitivity/test_Solexa-332667.wgs_metrics, 10, 0.1)(picard.analysis.TheoreticalSensitivityTest) Running Test: Test method testDrawSumOfQScores[3](testdata/picard/analysis/TheoreticalSensitivity/test_25103070136.targeted_pcr_metrics, 500, 0.03)(picard.analysis.TheoreticalSensitivityTest) Running Test: Test method testDrawSumOfQScores[4](testdata/picard/analysis/TheoreticalSensitivity/test_25103070136.targeted_pcr_metrics, 20, 0.05)(picard.analysis.TheoreticalSensitivityTest) Running Test: Test method testDrawSumOfQScores[5](testdata/picard/analysis/TheoreticalSensitivity/test_25103070136.targeted_pcr_metrics, 10, 0.1)(picard.analysis.TheoreticalSensitivityTest) Running Test: Test method testHetAltDepthDistribution(picard.analysis.TheoreticalSensitivityTest) Running Test: Test method testHetSensDistributions(picard.analysis.TheoreticalSensitivityTest) Test: Test method testHetSensDistributions(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel Gradle suite > Gradle test > picard.analysis.TheoreticalSensitivityTest.testHetSensDistributions STANDARD_ERROR INFO 2024-07-02 12:03:34 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testHetSensDistributions(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:03:34 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testHetSensDistributions(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:03:34 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testHetSensDistributions(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:35 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:03:35 TheoreticalSensitivity Calculating theoretical het sensitivity Running Test: Test method testHetSensTargeted[0](0.89734254, testdata/picard/analysis/TheoreticalSensitivity/test_Solexa-332667.wgs_metrics)(picard.analysis.TheoreticalSensitivityTest) Test: Test method testHetSensTargeted[0](0.89734254, testdata/picard/analysis/TheoreticalSensitivity/test_Solexa-332667.wgs_metrics)(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:36 TheoreticalSensitivity Creating Roulette Wheel Gradle suite > Gradle test > picard.analysis.TheoreticalSensitivityTest.testHetSensTargeted[0](0.89734254, testdata/picard/analysis/TheoreticalSensitivity/test_Solexa-332667.wgs_metrics) STANDARD_ERROR INFO 2024-07-02 12:03:36 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testHetSensTargeted[0](0.89734254, testdata/picard/analysis/TheoreticalSensitivity/test_Solexa-332667.wgs_metrics)(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:36 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:03:36 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testHetSensTargeted[0](0.89734254, testdata/picard/analysis/TheoreticalSensitivity/test_Solexa-332667.wgs_metrics)(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:36 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:03:36 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testHetSensTargeted[0](0.89734254, testdata/picard/analysis/TheoreticalSensitivity/test_Solexa-332667.wgs_metrics)(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:38 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:03:38 TheoreticalSensitivity Calculating theoretical het sensitivity Running Test: Test method testHetSensTargeted[1](0.95618666, testdata/picard/analysis/TheoreticalSensitivity/test_25103070136.targeted_pcr_metrics)(picard.analysis.TheoreticalSensitivityTest) Test: Test method testHetSensTargeted[1](0.95618666, testdata/picard/analysis/TheoreticalSensitivity/test_25103070136.targeted_pcr_metrics)(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:38 TheoreticalSensitivity Creating Roulette Wheel Gradle suite > Gradle test > picard.analysis.TheoreticalSensitivityTest.testHetSensTargeted[1](0.95618666, testdata/picard/analysis/TheoreticalSensitivity/test_25103070136.targeted_pcr_metrics) STANDARD_ERROR INFO 2024-07-02 12:03:38 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testHetSensTargeted[1](0.95618666, testdata/picard/analysis/TheoreticalSensitivity/test_25103070136.targeted_pcr_metrics)(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:38 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:03:38 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testHetSensTargeted[1](0.95618666, testdata/picard/analysis/TheoreticalSensitivity/test_25103070136.targeted_pcr_metrics)(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:03:38 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:03:38 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testHetSensTargeted[1](0.95618666, testdata/picard/analysis/TheoreticalSensitivity/test_25103070136.targeted_pcr_metrics)(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:04:00 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:04:00 TheoreticalSensitivity Calculating theoretical het sensitivity Running Test: Test method testHetVsArbitrary[0](testdata/picard/analysis/TheoreticalSensitivity/test_Solexa-332667.wgs_metrics, 0.02, 500)(picard.analysis.TheoreticalSensitivityTest) Test: Test method testHetVsArbitrary[0](testdata/picard/analysis/TheoreticalSensitivity/test_Solexa-332667.wgs_metrics, 0.02, 500)(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:04:02 TheoreticalSensitivity Creating Roulette Wheel Gradle suite > Gradle test > picard.analysis.TheoreticalSensitivityTest.testHetVsArbitrary[0](testdata/picard/analysis/TheoreticalSensitivity/test_Solexa-332667.wgs_metrics, 0.02, 500) STANDARD_ERROR INFO 2024-07-02 12:04:02 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testHetVsArbitrary[0](testdata/picard/analysis/TheoreticalSensitivity/test_Solexa-332667.wgs_metrics, 0.02, 500)(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:04:02 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:04:02 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testHetVsArbitrary[0](testdata/picard/analysis/TheoreticalSensitivity/test_Solexa-332667.wgs_metrics, 0.02, 500)(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:04:02 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:04:02 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testHetVsArbitrary[0](testdata/picard/analysis/TheoreticalSensitivity/test_Solexa-332667.wgs_metrics, 0.02, 500)(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:04:04 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:04:04 TheoreticalSensitivity Calculating theoretical het sensitivity Running Test: Test method testHetVsArbitrary[1](testdata/picard/analysis/TheoreticalSensitivity/test_25103070136.targeted_pcr_metrics, 0.01, 500)(picard.analysis.TheoreticalSensitivityTest) Test: Test method testHetVsArbitrary[1](testdata/picard/analysis/TheoreticalSensitivity/test_25103070136.targeted_pcr_metrics, 0.01, 500)(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:04:04 TheoreticalSensitivity Creating Roulette Wheel Gradle suite > Gradle test > picard.analysis.TheoreticalSensitivityTest.testHetVsArbitrary[1](testdata/picard/analysis/TheoreticalSensitivity/test_25103070136.targeted_pcr_metrics, 0.01, 500) STANDARD_ERROR INFO 2024-07-02 12:04:04 TheoreticalSensitivity Creating Roulette Wheel Test: Test method testHetVsArbitrary[1](testdata/picard/analysis/TheoreticalSensitivity/test_25103070136.targeted_pcr_metrics, 0.01, 500)(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:04:04 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2024-07-02 12:04:04 TheoreticalSensitivity Calculating quality sums from quality sampler Test: Test method testHetVsArbitrary[1](testdata/picard/analysis/TheoreticalSensitivity/test_25103070136.targeted_pcr_metrics, 0.01, 500)(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:04:04 TheoreticalSensitivity 0 sampling iterations completed INFO 2024-07-02 12:04:04 TheoreticalSensitivity 0 sampling iterations completed Test: Test method testHetVsArbitrary[1](testdata/picard/analysis/TheoreticalSensitivity/test_25103070136.targeted_pcr_metrics, 0.01, 500)(picard.analysis.TheoreticalSensitivityTest) produced standard out/err: INFO 2024-07-02 12:04:19 TheoreticalSensitivity Calculating theoretical het sensitivity INFO 2024-07-02 12:04:19 TheoreticalSensitivity Calculating theoretical het sensitivity Running Test: Test method testProportionsAboveThresholds(picard.analysis.TheoreticalSensitivityTest) Running Test: Test method testRouletteWheel(picard.analysis.TheoreticalSensitivityTest) Running Test: Test method testSensitivity[0](0.9, testdata/picard/analysis/TheoreticalSensitivity/test_Solexa-332667.wgs_metrics, 0.5, 400)(picard.analysis.TheoreticalSensitivityTest) Running Test: Test method testSensitivity[1](0.78, testdata/picard/analysis/TheoreticalSensitivity/test_Solexa-332667.wgs_metrics, 0.3, 400)(picard.analysis.TheoreticalSensitivityTest) Running Test: Test method testSensitivity[2](0.29, testdata/picard/analysis/TheoreticalSensitivity/test_Solexa-332667.wgs_metrics, 0.1, 500)(picard.analysis.TheoreticalSensitivityTest) Running Test: Test method testSensitivity[3](0.08, testdata/picard/analysis/TheoreticalSensitivity/test_Solexa-332667.wgs_metrics, 0.05, 500)(picard.analysis.TheoreticalSensitivityTest) Running Test: Test method testSensitivityAtConstantDepth[0](1.0, testdata/picard/analysis/TheoreticalSensitivity/test_Solexa-332667.wgs_metrics, 0.5, 30, 10000, 0.01)(picard.analysis.TheoreticalSensitivityTest) Running Test: Test method testSensitivityAtConstantDepth[1](0.78, testdata/picard/analysis/TheoreticalSensitivity/test_25103070136.targeted_pcr_metrics, 0.1, 30, 10000, 0.02)(picard.analysis.TheoreticalSensitivityTest) Running Test: Test method testSensitivityAtConstantDepth[2](0.26, testdata/picard/analysis/TheoreticalSensitivity/test_25103070136.targeted_pcr_metrics, 0.1, 10, 10000, 0.01)(picard.analysis.TheoreticalSensitivityTest) Running Test: Test method testTrimDistributions[0]([D@7c52a803, [D@26f5bcf2)(picard.analysis.TheoreticalSensitivityTest) Running Test: Test method testTrimDistributions[1]([D@37eea339, [D@5e150777)(picard.analysis.TheoreticalSensitivityTest) Running Test: Test method testTrimDistributions[2]([D@45d8351a, [D@76db1f3)(picard.analysis.TheoreticalSensitivityTest) Running Test: Test method testTrimDistributions[3]([D@459ecbe1, [D@41ea46ad)(picard.analysis.TheoreticalSensitivityTest) Running Test: Test method testTrimDistributions[4]([D@7309a360, [D@40fbaf23)(picard.analysis.TheoreticalSensitivityTest) Running Test: Test method testTrimDistributions[5]([D@6cc0c146, [D@52ec6d1d)(picard.analysis.TheoreticalSensitivityTest) Running Test: Test method testTrimDistributions[6]([D@2698e73b, [D@4cb8d85f)(picard.analysis.TheoreticalSensitivityTest) Running Test: Test method ensureSameVariantsReadAsSimpleVcfFileIterator(picard.vcf.processor.ThreadsafeTest) Running Test: Test method ensureTestDataActuallyHasWideVariantAtTenMillion(picard.vcf.processor.ThreadsafeTest) Running Test: Test method ensureUniqueVariantObservationsEspeciallyMultiAllelicOnesThatAppearAtChunkingBoundaries(picard.vcf.processor.ThreadsafeTest) Running Test: Test method testFilePresencePermutation[0](notNovaSeq, 0, [], true, false)(picard.illumina.parser.TileMetricsUtilTest) Running Test: Test method testFilePresencePermutation[1](novaSeqBaseFileOnly, 0, [], true, true)(picard.illumina.parser.TileMetricsUtilTest) Running Test: Test method testFilePresencePermutation[2](novaSeqSingleCycleFile, 1, [1], false, true)(picard.illumina.parser.TileMetricsUtilTest) Running Test: Test method testFilePresencePermutation[3](novaSeqBaseAndSingleCycleFile, 1, [1], true, true)(picard.illumina.parser.TileMetricsUtilTest) Running Test: Test method testFilePresencePermutation[4](novaSeqAllCycleFiles, 5, [1, 2, 3, 4, 5], false, true)(picard.illumina.parser.TileMetricsUtilTest) Running Test: Test method testFilePresencePermutation[5](novaSeqBaseAndAllCycleFiles, 5, [1, 2, 3, 4, 5], true, true)(picard.illumina.parser.TileMetricsUtilTest) Running Test: Test method testFilePresencePermutation[6](novaSeqSomeCycleFiles, 5, [2, 4], false, true)(picard.illumina.parser.TileMetricsUtilTest) Running Test: Test method testFilePresencePermutation[7](novaSeqBaseAndSomeCycleFiles, 5, [2, 4], true, true)(picard.illumina.parser.TileMetricsUtilTest) Running Test: Test method testMissingTileMetrics(picard.illumina.parser.TileMetricsUtilTest) Running Test: Test method testIdentityAfterTwoComplement[0](A>A)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testIdentityAfterTwoComplement[1](A>C)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testIdentityAfterTwoComplement[2](A>G)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testIdentityAfterTwoComplement[3](A>T)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testIdentityAfterTwoComplement[4](C>A)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testIdentityAfterTwoComplement[5](C>C)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testIdentityAfterTwoComplement[6](C>G)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testIdentityAfterTwoComplement[7](C>T)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testIdentityAfterTwoComplement[8](G>A)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testIdentityAfterTwoComplement[9](G>C)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testIdentityAfterTwoComplement[10](G>G)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testIdentityAfterTwoComplement[11](G>T)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testIdentityAfterTwoComplement[12](T>A)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testIdentityAfterTwoComplement[13](T>C)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testIdentityAfterTwoComplement[14](T>G)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testIdentityAfterTwoComplement[15](T>T)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testTransitionOfSelf[0](A>A)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testTransitionOfSelf[1](A>C)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testTransitionOfSelf[2](A>G)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testTransitionOfSelf[3](A>T)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testTransitionOfSelf[4](C>A)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testTransitionOfSelf[5](C>C)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testTransitionOfSelf[6](C>G)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testTransitionOfSelf[7](C>T)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testTransitionOfSelf[8](G>A)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testTransitionOfSelf[9](G>C)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testTransitionOfSelf[10](G>G)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testTransitionOfSelf[11](G>T)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testTransitionOfSelf[12](T>A)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testTransitionOfSelf[13](T>C)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testTransitionOfSelf[14](T>G)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testTransitionOfSelf[15](T>T)(picard.analysis.artifacts.TransitionTest) Running Test: Test method testBrokenUmi[0](ATCxG-AGCG)(picard.sam.markduplicates.UmiUtilTest) Running Test: Test method testBrokenUmi[1](A1C)(picard.sam.markduplicates.UmiUtilTest) Running Test: Test method testBrokenUmi[2](@Agtc)(picard.sam.markduplicates.UmiUtilTest) Running Test: Test method testBrokenUmi[3](TA/AC)(picard.sam.markduplicates.UmiUtilTest) Running Test: Test method testBrokenUmi[4](AT:CG)(picard.sam.markduplicates.UmiUtilTest) Running Test: Test method testIsTopStrand[0](0, 100, 0, 200, true, false, true, true, true, TOP)(picard.sam.markduplicates.UmiUtilTest) Running Test: Test method testIsTopStrand[1](0, 200, 0, 100, false, true, false, true, true, TOP)(picard.sam.markduplicates.UmiUtilTest) Running Test: Test method testIsTopStrand[2](0, 200, 0, 100, true, false, true, true, true, BOTTOM)(picard.sam.markduplicates.UmiUtilTest) Running Test: Test method testIsTopStrand[3](0, 100, 0, 200, false, true, false, true, true, BOTTOM)(picard.sam.markduplicates.UmiUtilTest) Running Test: Test method testIsTopStrand[4](0, 100, 0, 200, true, true, false, true, true, TOP)(picard.sam.markduplicates.UmiUtilTest) Running Test: Test method testIsTopStrand[5](0, 200, 0, 100, false, false, false, true, true, TOP)(picard.sam.markduplicates.UmiUtilTest) Running Test: Test method testIsTopStrand[6](0, 100, 0, 200, true, false, false, true, true, TOP)(picard.sam.markduplicates.UmiUtilTest) Running Test: Test method testIsTopStrand[7](0, 200, 0, 100, false, false, false, true, true, TOP)(picard.sam.markduplicates.UmiUtilTest) Running Test: Test method testIsTopStrand[8](0, 100, 0, 200, true, true, true, true, true, TOP)(picard.sam.markduplicates.UmiUtilTest) Running Test: Test method testIsTopStrand[9](0, 200, 0, 100, false, true, true, true, true, TOP)(picard.sam.markduplicates.UmiUtilTest) Running Test: Test method testIsTopStrand[10](0, 100, 1, 200, true, false, true, true, true, TOP)(picard.sam.markduplicates.UmiUtilTest) Running Test: Test method testIsTopStrand[11](0, 100, 1, 200, false, true, false, true, true, BOTTOM)(picard.sam.markduplicates.UmiUtilTest) Running Test: Test method testIsTopStrand[12](0, 100, 1, 200, true, true, false, true, true, TOP)(picard.sam.markduplicates.UmiUtilTest) Running Test: Test method testIsTopStrand[13](0, 100, 1, 200, false, false, false, true, true, BOTTOM)(picard.sam.markduplicates.UmiUtilTest) Running Test: Test method testIsTopStrand[14](0, 100, 1, 200, false, false, true, true, true, BOTTOM)(picard.sam.markduplicates.UmiUtilTest) Running Test: Test method testIsTopStrand[15](0, 100, 0, 200, true, false, true, false, true, UNKNOWN)(picard.sam.markduplicates.UmiUtilTest) Running Test: Test method testIsTopStrand[16](0, 100, 0, 200, true, false, true, true, false, UNKNOWN)(picard.sam.markduplicates.UmiUtilTest) Running Test: Test method testIsTopStrand[17](0, 100, 0, 200, true, false, true, false, false, UNKNOWN)(picard.sam.markduplicates.UmiUtilTest) Running Test: Test method uByteToIntTest[0](-1, 255)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uByteToIntTest[1](-2, 254)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uByteToIntTest[2](-128, 128)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uByteToIntTest[3](127, 127)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uByteToIntTest[4](112, 112)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uByteToIntTest[5](2, 2)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uByteToIntTest[6](1, 1)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uByteToIntTest[7](0, 0)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uByteToShortTest[0](-1, 255)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uByteToShortTest[1](-2, 254)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uByteToShortTest[2](-128, 128)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uByteToShortTest[3](127, 127)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uByteToShortTest[4](112, 112)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uByteToShortTest[5](2, 2)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uByteToShortTest[6](1, 1)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uByteToShortTest[7](0, 0)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uIntToLongTest[0](-1, 4294967295)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uIntToLongTest[1](-2, 4294967294)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uIntToLongTest[2](-2130624512, 2164342784)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uIntToLongTest[3](2147483647, 2147483647)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uIntToLongTest[4](273686784, 273686784)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uIntToLongTest[5](2, 2)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uIntToLongTest[6](1, 1)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uIntToLongTest[7](0, 0)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uShortToIntTest[0](-1, 65535)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uShortToIntTest[1](-2, 65534)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uShortToIntTest[2](-32735, 32801)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uShortToIntTest[3](32767, 32767)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uShortToIntTest[4](21829, 21829)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uShortToIntTest[5](2, 2)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uShortToIntTest[6](1, 1)(picard.util.UnsignedTypeUtilTest) Running Test: Test method uShortToIntTest[7](0, 0)(picard.util.UnsignedTypeUtilTest) Running Test: Test method testCaptureStdout(picard.vcf.UpdateVcfSequenceDictionaryTest) 12:04:32.620 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:32.651 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:32.674 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:32.674 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null [Tue Jul 02 12:04:32 GMT+14:00 2024] UpdateVcfSequenceDictionary --INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/vcfFormatTest.vcf --OUTPUT /dev/stdout --SEQUENCE_DICTIONARY /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/vcfFormatTest.bad_dict.vcf --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Tue Jul 02 12:04:32 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null [Tue Jul 02 12:04:33 GMT+14:00 2024] picard.vcf.UpdateVcfSequenceDictionary done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1337982976 Running Test: Test method testUpdateVcfSequenceDictionary[0](/tmp/UpdateVcfSequenceDictionaryTest3939800202067396609.tmpupdateVcfSequenceDictionaryTest-delete-me.vcf.gz)(picard.vcf.UpdateVcfSequenceDictionaryTest) Test: Test method testUpdateVcfSequenceDictionary[0](/tmp/UpdateVcfSequenceDictionaryTest3939800202067396609.tmpupdateVcfSequenceDictionaryTest-delete-me.vcf.gz)(picard.vcf.UpdateVcfSequenceDictionaryTest) produced standard out/err: 12:04:33.876 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.UpdateVcfSequenceDictionaryTest.testUpdateVcfSequenceDictionary[0](/tmp/UpdateVcfSequenceDictionaryTest3939800202067396609.tmpupdateVcfSequenceDictionaryTest-delete-me.vcf.gz) STANDARD_ERROR 12:04:33.876 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUpdateVcfSequenceDictionary[0](/tmp/UpdateVcfSequenceDictionaryTest3939800202067396609.tmpupdateVcfSequenceDictionaryTest-delete-me.vcf.gz)(picard.vcf.UpdateVcfSequenceDictionaryTest) produced standard out/err: 12:04:33.876 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:33.876 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUpdateVcfSequenceDictionary[0](/tmp/UpdateVcfSequenceDictionaryTest3939800202067396609.tmpupdateVcfSequenceDictionaryTest-delete-me.vcf.gz)(picard.vcf.UpdateVcfSequenceDictionaryTest) produced standard out/err: 12:04:33.876 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:33.876 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUpdateVcfSequenceDictionary[0](/tmp/UpdateVcfSequenceDictionaryTest3939800202067396609.tmpupdateVcfSequenceDictionaryTest-delete-me.vcf.gz)(picard.vcf.UpdateVcfSequenceDictionaryTest) produced standard out/err: 12:04:33.876 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:33.876 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUpdateVcfSequenceDictionary[0](/tmp/UpdateVcfSequenceDictionaryTest3939800202067396609.tmpupdateVcfSequenceDictionaryTest-delete-me.vcf.gz)(picard.vcf.UpdateVcfSequenceDictionaryTest) produced standard out/err: [Tue Jul 02 12:04:33 GMT+14:00 2024] UpdateVcfSequenceDictionary INPUT=testdata/picard/vcf/vcfFormatTest.vcf OUTPUT=/tmp/UpdateVcfSequenceDictionaryTest3939800202067396609.tmpupdateVcfSequenceDictionaryTest-delete-me.vcf.gz SEQUENCE_DICTIONARY=testdata/picard/vcf/vcfFormatTest.bad_dict.vcf VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:33 GMT+14:00 2024] UpdateVcfSequenceDictionary INPUT=testdata/picard/vcf/vcfFormatTest.vcf OUTPUT=/tmp/UpdateVcfSequenceDictionaryTest3939800202067396609.tmpupdateVcfSequenceDictionaryTest-delete-me.vcf.gz SEQUENCE_DICTIONARY=testdata/picard/vcf/vcfFormatTest.bad_dict.vcf VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testUpdateVcfSequenceDictionary[0](/tmp/UpdateVcfSequenceDictionaryTest3939800202067396609.tmpupdateVcfSequenceDictionaryTest-delete-me.vcf.gz)(picard.vcf.UpdateVcfSequenceDictionaryTest) produced standard out/err: [Tue Jul 02 12:04:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:33 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testUpdateVcfSequenceDictionary[0](/tmp/UpdateVcfSequenceDictionaryTest3939800202067396609.tmpupdateVcfSequenceDictionaryTest-delete-me.vcf.gz)(picard.vcf.UpdateVcfSequenceDictionaryTest) produced standard out/err: [Tue Jul 02 12:04:33 GMT+14:00 2024] picard.vcf.UpdateVcfSequenceDictionary done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:04:33 GMT+14:00 2024] picard.vcf.UpdateVcfSequenceDictionary done. Elapsed time: 0.00 minutes. Test: Test method testUpdateVcfSequenceDictionary[0](/tmp/UpdateVcfSequenceDictionaryTest3939800202067396609.tmpupdateVcfSequenceDictionaryTest-delete-me.vcf.gz)(picard.vcf.UpdateVcfSequenceDictionaryTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testUpdateVcfSequenceDictionary[1](/tmp/UpdateVcfSequenceDictionaryTest3939800202067396609.tmpupdateVcfSequenceDictionaryTest-delete-me.vcf)(picard.vcf.UpdateVcfSequenceDictionaryTest) Test: Test method testUpdateVcfSequenceDictionary[1](/tmp/UpdateVcfSequenceDictionaryTest3939800202067396609.tmpupdateVcfSequenceDictionaryTest-delete-me.vcf)(picard.vcf.UpdateVcfSequenceDictionaryTest) produced standard out/err: 12:04:34.027 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.UpdateVcfSequenceDictionaryTest.testUpdateVcfSequenceDictionary[1](/tmp/UpdateVcfSequenceDictionaryTest3939800202067396609.tmpupdateVcfSequenceDictionaryTest-delete-me.vcf) STANDARD_ERROR 12:04:34.027 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUpdateVcfSequenceDictionary[1](/tmp/UpdateVcfSequenceDictionaryTest3939800202067396609.tmpupdateVcfSequenceDictionaryTest-delete-me.vcf)(picard.vcf.UpdateVcfSequenceDictionaryTest) produced standard out/err: 12:04:34.027 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:34.027 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUpdateVcfSequenceDictionary[1](/tmp/UpdateVcfSequenceDictionaryTest3939800202067396609.tmpupdateVcfSequenceDictionaryTest-delete-me.vcf)(picard.vcf.UpdateVcfSequenceDictionaryTest) produced standard out/err: 12:04:34.027 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:34.027 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUpdateVcfSequenceDictionary[1](/tmp/UpdateVcfSequenceDictionaryTest3939800202067396609.tmpupdateVcfSequenceDictionaryTest-delete-me.vcf)(picard.vcf.UpdateVcfSequenceDictionaryTest) produced standard out/err: 12:04:34.027 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:34.027 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUpdateVcfSequenceDictionary[1](/tmp/UpdateVcfSequenceDictionaryTest3939800202067396609.tmpupdateVcfSequenceDictionaryTest-delete-me.vcf)(picard.vcf.UpdateVcfSequenceDictionaryTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] UpdateVcfSequenceDictionary INPUT=testdata/picard/vcf/vcfFormatTest.vcf OUTPUT=/tmp/UpdateVcfSequenceDictionaryTest3939800202067396609.tmpupdateVcfSequenceDictionaryTest-delete-me.vcf SEQUENCE_DICTIONARY=testdata/picard/vcf/vcfFormatTest.bad_dict.vcf VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:34 GMT+14:00 2024] UpdateVcfSequenceDictionary INPUT=testdata/picard/vcf/vcfFormatTest.vcf OUTPUT=/tmp/UpdateVcfSequenceDictionaryTest3939800202067396609.tmpupdateVcfSequenceDictionaryTest-delete-me.vcf SEQUENCE_DICTIONARY=testdata/picard/vcf/vcfFormatTest.bad_dict.vcf VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testUpdateVcfSequenceDictionary[1](/tmp/UpdateVcfSequenceDictionaryTest3939800202067396609.tmpupdateVcfSequenceDictionaryTest-delete-me.vcf)(picard.vcf.UpdateVcfSequenceDictionaryTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testUpdateVcfSequenceDictionary[1](/tmp/UpdateVcfSequenceDictionaryTest3939800202067396609.tmpupdateVcfSequenceDictionaryTest-delete-me.vcf)(picard.vcf.UpdateVcfSequenceDictionaryTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] picard.vcf.UpdateVcfSequenceDictionary done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:04:34 GMT+14:00 2024] picard.vcf.UpdateVcfSequenceDictionary done. Elapsed time: 0.00 minutes. Test: Test method testUpdateVcfSequenceDictionary[1](/tmp/UpdateVcfSequenceDictionaryTest3939800202067396609.tmpupdateVcfSequenceDictionaryTest-delete-me.vcf)(picard.vcf.UpdateVcfSequenceDictionaryTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testUpdateVcfSequenceDictionary[2](/dev/stdout)(picard.vcf.UpdateVcfSequenceDictionaryTest) Test: Test method testUpdateVcfSequenceDictionary[2](/dev/stdout)(picard.vcf.UpdateVcfSequenceDictionaryTest) produced standard out/err: 12:04:34.128 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.vcf.UpdateVcfSequenceDictionaryTest.testUpdateVcfSequenceDictionary[2](/dev/stdout) STANDARD_ERROR 12:04:34.128 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUpdateVcfSequenceDictionary[2](/dev/stdout)(picard.vcf.UpdateVcfSequenceDictionaryTest) produced standard out/err: 12:04:34.128 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:34.128 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUpdateVcfSequenceDictionary[2](/dev/stdout)(picard.vcf.UpdateVcfSequenceDictionaryTest) produced standard out/err: 12:04:34.128 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:34.128 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testUpdateVcfSequenceDictionary[2](/dev/stdout)(picard.vcf.UpdateVcfSequenceDictionaryTest) produced standard out/err: 12:04:34.128 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:34.128 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testUpdateVcfSequenceDictionary[2](/dev/stdout)(picard.vcf.UpdateVcfSequenceDictionaryTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] UpdateVcfSequenceDictionary INPUT=testdata/picard/vcf/vcfFormatTest.vcf OUTPUT=/dev/fd/2878 SEQUENCE_DICTIONARY=testdata/picard/vcf/vcfFormatTest.bad_dict.vcf VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:34 GMT+14:00 2024] UpdateVcfSequenceDictionary INPUT=testdata/picard/vcf/vcfFormatTest.vcf OUTPUT=/dev/fd/2878 SEQUENCE_DICTIONARY=testdata/picard/vcf/vcfFormatTest.bad_dict.vcf VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testUpdateVcfSequenceDictionary[2](/dev/stdout)(picard.vcf.UpdateVcfSequenceDictionaryTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testUpdateVcfSequenceDictionary[2](/dev/stdout)(picard.vcf.UpdateVcfSequenceDictionaryTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] picard.vcf.UpdateVcfSequenceDictionary done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:04:34 GMT+14:00 2024] picard.vcf.UpdateVcfSequenceDictionary done. Elapsed time: 0.00 minutes. Test: Test method testUpdateVcfSequenceDictionary[2](/dev/stdout)(picard.vcf.UpdateVcfSequenceDictionaryTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method test[0](nofile, -1)(picard.sam.ValidateSamFileTest) Test: Test method test[0](nofile, -1)(picard.sam.ValidateSamFileTest) produced standard out/err: INFO 2024-07-02 12:04:34 ValidateSamFile Gradle suite > Gradle test > picard.sam.ValidateSamFileTest.test[0](nofile, -1) STANDARD_ERROR INFO 2024-07-02 12:04:34 ValidateSamFile Test: Test method test[0](nofile, -1)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method test[0](nofile, -1)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method test[0](nofile, -1)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method test[0](nofile, -1)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method test[0](nofile, -1)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method test[0](nofile, -1)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method test[0](nofile, -1)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method test[0](nofile, -1)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method test[0](nofile, -1)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ValidateSamFile -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/nofile ********** ValidateSamFile -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/nofile Test: Test method test[0](nofile, -1)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method test[0](nofile, -1)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method test[0](nofile, -1)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method test[0](nofile, -1)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.291 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:34.291 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method test[0](nofile, -1)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.291 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:34.291 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method test[0](nofile, -1)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.291 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:34.291 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method test[0](nofile, -1)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.291 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:34.291 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method test[0](nofile, -1)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] ValidateSamFile INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/nofile MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:34 GMT+14:00 2024] ValidateSamFile INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/nofile MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method test[0](nofile, -1)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method test[0](nofile, -1)(picard.sam.ValidateSamFileTest) produced standard out/err: ERROR 2024-07-02 12:04:34 ValidateSamFile Cannot read non-existent file: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/nofile ERROR 2024-07-02 12:04:34 ValidateSamFile Cannot read non-existent file: file:///build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/nofile Test: Test method test[0](nofile, -1)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:04:34 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method test[0](nofile, -1)(picard.sam.ValidateSamFileTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method test[0](nofile, -1)(picard.sam.ValidateSamFileTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method test[1](good/sorted-pair.sam, 0)(picard.sam.ValidateSamFileTest) Test: Test method test[1](good/sorted-pair.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: INFO 2024-07-02 12:04:34 ValidateSamFile Gradle suite > Gradle test > picard.sam.ValidateSamFileTest.test[1](good/sorted-pair.sam, 0) STANDARD_ERROR INFO 2024-07-02 12:04:34 ValidateSamFile Test: Test method test[1](good/sorted-pair.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method test[1](good/sorted-pair.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method test[1](good/sorted-pair.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method test[1](good/sorted-pair.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method test[1](good/sorted-pair.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method test[1](good/sorted-pair.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method test[1](good/sorted-pair.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method test[1](good/sorted-pair.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method test[1](good/sorted-pair.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ValidateSamFile -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/good/sorted-pair.sam ********** ValidateSamFile -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/good/sorted-pair.sam Test: Test method test[1](good/sorted-pair.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method test[1](good/sorted-pair.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method test[1](good/sorted-pair.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method test[1](good/sorted-pair.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.354 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:34.354 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method test[1](good/sorted-pair.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.355 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:34.355 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method test[1](good/sorted-pair.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.355 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:34.355 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method test[1](good/sorted-pair.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.355 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:34.355 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method test[1](good/sorted-pair.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] ValidateSamFile INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/good/sorted-pair.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:34 GMT+14:00 2024] ValidateSamFile INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/good/sorted-pair.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method test[1](good/sorted-pair.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method test[1](good/sorted-pair.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING 2024-07-02 12:04:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:04:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method test[1](good/sorted-pair.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ValidateSamFileTest.test[1](good/sorted-pair.sam, 0) STANDARD_OUT No errors found Test: Test method test[1](good/sorted-pair.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ValidateSamFileTest.test[1](good/sorted-pair.sam, 0) STANDARD_ERROR [Tue Jul 02 12:04:34 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method test[1](good/sorted-pair.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method test[2](good/sorted-pair-v1.6.sam, 0)(picard.sam.ValidateSamFileTest) Test: Test method test[2](good/sorted-pair-v1.6.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: INFO 2024-07-02 12:04:34 ValidateSamFile Gradle suite > Gradle test > picard.sam.ValidateSamFileTest.test[2](good/sorted-pair-v1.6.sam, 0) STANDARD_ERROR INFO 2024-07-02 12:04:34 ValidateSamFile Test: Test method test[2](good/sorted-pair-v1.6.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method test[2](good/sorted-pair-v1.6.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method test[2](good/sorted-pair-v1.6.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method test[2](good/sorted-pair-v1.6.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method test[2](good/sorted-pair-v1.6.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method test[2](good/sorted-pair-v1.6.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method test[2](good/sorted-pair-v1.6.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method test[2](good/sorted-pair-v1.6.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method test[2](good/sorted-pair-v1.6.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ValidateSamFile -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/good/sorted-pair-v1.6.sam ********** ValidateSamFile -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/good/sorted-pair-v1.6.sam Test: Test method test[2](good/sorted-pair-v1.6.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method test[2](good/sorted-pair-v1.6.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method test[2](good/sorted-pair-v1.6.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method test[2](good/sorted-pair-v1.6.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.415 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:34.415 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method test[2](good/sorted-pair-v1.6.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.415 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:34.415 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method test[2](good/sorted-pair-v1.6.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.415 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:34.415 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method test[2](good/sorted-pair-v1.6.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.415 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:34.415 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method test[2](good/sorted-pair-v1.6.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] ValidateSamFile INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/good/sorted-pair-v1.6.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:34 GMT+14:00 2024] ValidateSamFile INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/good/sorted-pair-v1.6.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method test[2](good/sorted-pair-v1.6.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method test[2](good/sorted-pair-v1.6.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING 2024-07-02 12:04:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:04:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method test[2](good/sorted-pair-v1.6.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ValidateSamFileTest.test[2](good/sorted-pair-v1.6.sam, 0) STANDARD_OUT No errors found Test: Test method test[2](good/sorted-pair-v1.6.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ValidateSamFileTest.test[2](good/sorted-pair-v1.6.sam, 0) STANDARD_ERROR [Tue Jul 02 12:04:34 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method test[2](good/sorted-pair-v1.6.sam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method test[3](bad/unpaired-mate.sam, 3)(picard.sam.ValidateSamFileTest) Test: Test method test[3](bad/unpaired-mate.sam, 3)(picard.sam.ValidateSamFileTest) produced standard out/err: INFO 2024-07-02 12:04:34 ValidateSamFile Gradle suite > Gradle test > picard.sam.ValidateSamFileTest.test[3](bad/unpaired-mate.sam, 3) STANDARD_ERROR INFO 2024-07-02 12:04:34 ValidateSamFile Test: Test method test[3](bad/unpaired-mate.sam, 3)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method test[3](bad/unpaired-mate.sam, 3)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method test[3](bad/unpaired-mate.sam, 3)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method test[3](bad/unpaired-mate.sam, 3)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method test[3](bad/unpaired-mate.sam, 3)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method test[3](bad/unpaired-mate.sam, 3)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method test[3](bad/unpaired-mate.sam, 3)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method test[3](bad/unpaired-mate.sam, 3)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method test[3](bad/unpaired-mate.sam, 3)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ValidateSamFile -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/bad/unpaired-mate.sam ********** ValidateSamFile -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/bad/unpaired-mate.sam Test: Test method test[3](bad/unpaired-mate.sam, 3)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method test[3](bad/unpaired-mate.sam, 3)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method test[3](bad/unpaired-mate.sam, 3)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method test[3](bad/unpaired-mate.sam, 3)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.480 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:34.480 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method test[3](bad/unpaired-mate.sam, 3)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.480 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:34.480 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method test[3](bad/unpaired-mate.sam, 3)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.480 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:34.480 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method test[3](bad/unpaired-mate.sam, 3)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.480 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:34.480 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method test[3](bad/unpaired-mate.sam, 3)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] ValidateSamFile INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/bad/unpaired-mate.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:34 GMT+14:00 2024] ValidateSamFile INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/bad/unpaired-mate.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method test[3](bad/unpaired-mate.sam, 3)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method test[3](bad/unpaired-mate.sam, 3)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING 2024-07-02 12:04:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:04:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method test[3](bad/unpaired-mate.sam, 3)(picard.sam.ValidateSamFileTest) produced standard out/err: ERROR::MATE_NOT_FOUND:Read name bar:record:6, Mate not found for paired read Gradle suite > Gradle test > picard.sam.ValidateSamFileTest.test[3](bad/unpaired-mate.sam, 3) STANDARD_OUT ERROR::MATE_NOT_FOUND:Read name bar:record:6, Mate not found for paired read Test: Test method test[3](bad/unpaired-mate.sam, 3)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ValidateSamFileTest.test[3](bad/unpaired-mate.sam, 3) STANDARD_ERROR [Tue Jul 02 12:04:34 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method test[3](bad/unpaired-mate.sam, 3)(picard.sam.ValidateSamFileTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method test[3](bad/unpaired-mate.sam, 3)(picard.sam.ValidateSamFileTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: INFO 2024-07-02 12:04:34 ValidateSamFile Gradle suite > Gradle test > picard.sam.ValidateSamFileTest.test[4](bad/missing-rg-info.sam, 2) STANDARD_ERROR INFO 2024-07-02 12:04:34 ValidateSamFile Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ValidateSamFile -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/bad/missing-rg-info.sam ********** ValidateSamFile -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/bad/missing-rg-info.sam Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.555 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:34.555 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.555 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:34.555 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.556 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:34.556 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.556 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:34.556 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] ValidateSamFile INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/bad/missing-rg-info.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:34 GMT+14:00 2024] ValidateSamFile INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/bad/missing-rg-info.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING 2024-07-02 12:04:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:04:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: ERROR::MISSING_READ_GROUP:Read groups is empty Gradle suite > Gradle test > picard.sam.ValidateSamFileTest.test[4](bad/missing-rg-info.sam, 2) STANDARD_OUT ERROR::MISSING_READ_GROUP:Read groups is empty Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1101:17727:54981, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1101:17727:54981, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1101:17727:54981, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1101:17727:54981, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1101:32434:62066, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1101:32434:62066, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1101:32434:62066, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1101:32434:62066, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1106:24872:23759, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1106:24872:23759, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1106:24872:23759, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1106:24872:23759, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1106:7526:7884, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1106:7526:7884, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1106:7526:7884, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1106:7526:7884, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1107:25837:52503, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1107:25837:52503, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1107:25837:52503, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1107:25837:52503, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1107:27907:56933, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1107:27907:56933, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1107:27907:56933, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1107:27907:56933, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:10114:61099, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:10114:61099, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:10114:61099, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:10114:61099, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:8135:38509, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:8135:38509, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:8135:38509, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:8135:38509, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:8247:38350, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:8247:38350, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:8247:38350, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:8247:38350, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1109:8978:18203, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1109:8978:18203, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1109:8978:18203, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1109:8978:18203, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1110:18092:66233, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1110:18092:66233, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1110:18092:66233, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1110:18092:66233, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1111:15413:71999, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1111:15413:71999, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1111:15413:71999, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1111:15413:71999, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1111:9434:70997, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1111:9434:70997, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1111:9434:70997, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1111:9434:70997, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1112:6602:11066, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1112:6602:11066, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1112:6602:11066, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1112:6602:11066, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1112:8237:10380, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1112:8237:10380, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1112:8237:10380, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1112:8237:10380, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1113:22233:39194, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1113:22233:39194, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1113:22233:39194, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1113:22233:39194, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1113:24071:73353, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1113:24071:73353, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1113:24071:73353, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1113:24071:73353, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1115:5527:12050, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1115:5527:12050, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1115:5527:12050, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1115:5527:12050, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1115:9282:41761, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1115:9282:41761, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1115:9282:41761, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1115:9282:41761, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1118:29359:28119, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1118:29359:28119, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1118:29359:28119, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1118:29359:28119, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1119:14560:61627, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1119:14560:61627, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1119:14560:61627, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1119:14560:61627, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1120:21178:10785, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1120:21178:10785, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1120:21178:10785, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1120:21178:10785, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1121:3689:72122, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1121:3689:72122, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1121:3689:72122, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1121:3689:72122, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1121:3710:72193, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1121:3710:72193, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1121:3710:72193, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1121:3710:72193, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1122:27390:43519, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1122:27390:43519, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1122:27390:43519, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1122:27390:43519, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1124:27430:18203, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1124:27430:18203, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1124:27430:18203, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1124:27430:18203, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1124:8531:38808, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1124:8531:38808, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1124:8531:38808, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1124:8531:38808, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1201:16570:19118, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1201:16570:19118, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1201:16570:19118, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1201:16570:19118, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1201:7922:18731, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1201:7922:18731, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1201:7922:18731, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1201:7922:18731, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1202:3659:45523, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1202:3659:45523, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1202:3659:45523, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1202:3659:45523, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1202:8653:47703, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1202:8653:47703, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1202:8653:47703, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1202:8653:47703, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:10835:40548, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:10835:40548, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:10835:40548, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:10835:40548, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:10916:40267, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:10916:40267, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:10916:40267, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:10916:40267, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:3730:49690, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:3730:49690, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:3730:49690, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:3730:49690, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1204:24314:57742, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1204:24314:57742, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1204:24314:57742, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1204:24314:57742, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1205:6745:62119, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1205:6745:62119, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1205:6745:62119, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1205:6745:62119, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1205:6765:62084, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1205:6765:62084, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1205:6765:62084, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1205:6765:62084, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1206:11931:3524, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1206:11931:3524, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1206:11931:3524, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1206:11931:3524, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1206:12215:1801, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1206:12215:1801, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1206:12215:1801, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1206:12215:1801, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1207:6755:65477, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1207:6755:65477, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1207:6755:65477, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1207:6755:65477, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1207:8561:65828, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1207:8561:65828, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1207:8561:65828, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1207:8561:65828, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:12104:72843, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:12104:72843, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:12104:72843, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:12104:72843, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:13159:53048, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:13159:53048, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:13159:53048, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:13159:53048, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:17940:44240, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:17940:44240, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:17940:44240, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:17940:44240, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:3456:7233, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:3456:7233, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:3456:7233, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:3456:7233, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:3476:7163, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:3476:7163, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:3476:7163, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:3476:7163, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1211:16671:69221, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1211:16671:69221, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1211:16671:69221, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1211:16671:69221, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:24913:36628, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:24913:36628, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:24913:36628, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:24913:36628, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:24923:36645, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:24923:36645, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:24923:36645, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:24923:36645, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:25461:63807, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:25461:63807, A record is missing a read group Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: Maximum output of [100] errors reached. Maximum output of [100] errors reached. Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ValidateSamFileTest.test[4](bad/missing-rg-info.sam, 2) STANDARD_ERROR [Tue Jul 02 12:04:34 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method test[4](bad/missing-rg-info.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: INFO 2024-07-02 12:04:34 ValidateSamFile Gradle suite > Gradle test > picard.sam.ValidateSamFileTest.test[5](bad/missing-rg-info-v1.6.sam, 2) STANDARD_ERROR INFO 2024-07-02 12:04:34 ValidateSamFile Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ValidateSamFile -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/bad/missing-rg-info-v1.6.sam ********** ValidateSamFile -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/bad/missing-rg-info-v1.6.sam Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.639 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:34.639 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.639 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:34.639 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.639 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:34.639 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.639 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:34.639 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] ValidateSamFile INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/bad/missing-rg-info-v1.6.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:34 GMT+14:00 2024] ValidateSamFile INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/bad/missing-rg-info-v1.6.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING 2024-07-02 12:04:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:04:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: ERROR::MISSING_READ_GROUP:Read groups is empty Gradle suite > Gradle test > picard.sam.ValidateSamFileTest.test[5](bad/missing-rg-info-v1.6.sam, 2) STANDARD_OUT ERROR::MISSING_READ_GROUP:Read groups is empty Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1101:17727:54981, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1101:17727:54981, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1101:17727:54981, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1101:17727:54981, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1101:32434:62066, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1101:32434:62066, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1101:32434:62066, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1101:32434:62066, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1106:24872:23759, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1106:24872:23759, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1106:24872:23759, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1106:24872:23759, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1106:7526:7884, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1106:7526:7884, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1106:7526:7884, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1106:7526:7884, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1107:25837:52503, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1107:25837:52503, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1107:25837:52503, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1107:25837:52503, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1107:27907:56933, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1107:27907:56933, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1107:27907:56933, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1107:27907:56933, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:10114:61099, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:10114:61099, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:10114:61099, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:10114:61099, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:8135:38509, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:8135:38509, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:8135:38509, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:8135:38509, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:8247:38350, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:8247:38350, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:8247:38350, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1108:8247:38350, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1109:8978:18203, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1109:8978:18203, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1109:8978:18203, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1109:8978:18203, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1110:18092:66233, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1110:18092:66233, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1110:18092:66233, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1110:18092:66233, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1111:15413:71999, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1111:15413:71999, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1111:15413:71999, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1111:15413:71999, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1111:9434:70997, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1111:9434:70997, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1111:9434:70997, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1111:9434:70997, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1112:6602:11066, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1112:6602:11066, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1112:6602:11066, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1112:6602:11066, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1112:8237:10380, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1112:8237:10380, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1112:8237:10380, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1112:8237:10380, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1113:22233:39194, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1113:22233:39194, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1113:22233:39194, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1113:22233:39194, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1113:24071:73353, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1113:24071:73353, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1113:24071:73353, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1113:24071:73353, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1115:5527:12050, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1115:5527:12050, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1115:5527:12050, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1115:5527:12050, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1115:9282:41761, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1115:9282:41761, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1115:9282:41761, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1115:9282:41761, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1118:29359:28119, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1118:29359:28119, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1118:29359:28119, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1118:29359:28119, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1119:14560:61627, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1119:14560:61627, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1119:14560:61627, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1119:14560:61627, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1120:21178:10785, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1120:21178:10785, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1120:21178:10785, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1120:21178:10785, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1121:3689:72122, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1121:3689:72122, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1121:3689:72122, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1121:3689:72122, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1121:3710:72193, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1121:3710:72193, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1121:3710:72193, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1121:3710:72193, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1122:27390:43519, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1122:27390:43519, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1122:27390:43519, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1122:27390:43519, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1124:27430:18203, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1124:27430:18203, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1124:27430:18203, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1124:27430:18203, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1124:8531:38808, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1124:8531:38808, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1124:8531:38808, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1124:8531:38808, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1201:16570:19118, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1201:16570:19118, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1201:16570:19118, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1201:16570:19118, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1201:7922:18731, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1201:7922:18731, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1201:7922:18731, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1201:7922:18731, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1202:3659:45523, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1202:3659:45523, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1202:3659:45523, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1202:3659:45523, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1202:8653:47703, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1202:8653:47703, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1202:8653:47703, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1202:8653:47703, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:10835:40548, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:10835:40548, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:10835:40548, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:10835:40548, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:10916:40267, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:10916:40267, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:10916:40267, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:10916:40267, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:3730:49690, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:3730:49690, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:3730:49690, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1203:3730:49690, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1204:24314:57742, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1204:24314:57742, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1204:24314:57742, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1204:24314:57742, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1205:6745:62119, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1205:6745:62119, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1205:6745:62119, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1205:6745:62119, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1205:6765:62084, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1205:6765:62084, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1205:6765:62084, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1205:6765:62084, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1206:11931:3524, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1206:11931:3524, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1206:11931:3524, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1206:11931:3524, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1206:12215:1801, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1206:12215:1801, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1206:12215:1801, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1206:12215:1801, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1207:6755:65477, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1207:6755:65477, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1207:6755:65477, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1207:6755:65477, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1207:8561:65828, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1207:8561:65828, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1207:8561:65828, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1207:8561:65828, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:12104:72843, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:12104:72843, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:12104:72843, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:12104:72843, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:13159:53048, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:13159:53048, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:13159:53048, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:13159:53048, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:17940:44240, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:17940:44240, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:17940:44240, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:17940:44240, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:3456:7233, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:3456:7233, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:3456:7233, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:3456:7233, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:3476:7163, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:3476:7163, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:3476:7163, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1210:3476:7163, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1211:16671:69221, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1211:16671:69221, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1211:16671:69221, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1211:16671:69221, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:24913:36628, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:24913:36628, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:24913:36628, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:24913:36628, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:24923:36645, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:24923:36645, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:24923:36645, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:24923:36645, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:25461:63807, A record is missing a read group WARNING::RECORD_MISSING_READ_GROUP:Read name H0164ALXX140820:2:1213:25461:63807, A record is missing a read group Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: Maximum output of [100] errors reached. Maximum output of [100] errors reached. Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ValidateSamFileTest.test[5](bad/missing-rg-info-v1.6.sam, 2) STANDARD_ERROR [Tue Jul 02 12:04:34 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method test[5](bad/missing-rg-info-v1.6.sam, 2)(picard.sam.ValidateSamFileTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method test[6](bad/sorted-pair-missing-rg.sam, 1)(picard.sam.ValidateSamFileTest) Test: Test method test[6](bad/sorted-pair-missing-rg.sam, 1)(picard.sam.ValidateSamFileTest) produced standard out/err: INFO 2024-07-02 12:04:34 ValidateSamFile Gradle suite > Gradle test > picard.sam.ValidateSamFileTest.test[6](bad/sorted-pair-missing-rg.sam, 1) STANDARD_ERROR INFO 2024-07-02 12:04:34 ValidateSamFile Test: Test method test[6](bad/sorted-pair-missing-rg.sam, 1)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method test[6](bad/sorted-pair-missing-rg.sam, 1)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method test[6](bad/sorted-pair-missing-rg.sam, 1)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method test[6](bad/sorted-pair-missing-rg.sam, 1)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method test[6](bad/sorted-pair-missing-rg.sam, 1)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method test[6](bad/sorted-pair-missing-rg.sam, 1)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method test[6](bad/sorted-pair-missing-rg.sam, 1)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method test[6](bad/sorted-pair-missing-rg.sam, 1)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method test[6](bad/sorted-pair-missing-rg.sam, 1)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ValidateSamFile -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/bad/sorted-pair-missing-rg.sam ********** ValidateSamFile -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/bad/sorted-pair-missing-rg.sam Test: Test method test[6](bad/sorted-pair-missing-rg.sam, 1)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method test[6](bad/sorted-pair-missing-rg.sam, 1)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method test[6](bad/sorted-pair-missing-rg.sam, 1)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method test[6](bad/sorted-pair-missing-rg.sam, 1)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.734 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:34.734 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method test[6](bad/sorted-pair-missing-rg.sam, 1)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.734 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:34.734 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method test[6](bad/sorted-pair-missing-rg.sam, 1)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.734 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:34.734 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method test[6](bad/sorted-pair-missing-rg.sam, 1)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.734 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:34.734 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method test[6](bad/sorted-pair-missing-rg.sam, 1)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] ValidateSamFile INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/bad/sorted-pair-missing-rg.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:34 GMT+14:00 2024] ValidateSamFile INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/sam/ValidateSamFile/bad/sorted-pair-missing-rg.sam MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method test[6](bad/sorted-pair-missing-rg.sam, 1)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method test[6](bad/sorted-pair-missing-rg.sam, 1)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING 2024-07-02 12:04:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:04:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method test[6](bad/sorted-pair-missing-rg.sam, 1)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING::RECORD_MISSING_READ_GROUP:Read name bar:record:1, A record is missing a read group Gradle suite > Gradle test > picard.sam.ValidateSamFileTest.test[6](bad/sorted-pair-missing-rg.sam, 1) STANDARD_OUT WARNING::RECORD_MISSING_READ_GROUP:Read name bar:record:1, A record is missing a read group Test: Test method test[6](bad/sorted-pair-missing-rg.sam, 1)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ValidateSamFileTest.test[6](bad/sorted-pair-missing-rg.sam, 1) STANDARD_ERROR [Tue Jul 02 12:04:34 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method test[6](bad/sorted-pair-missing-rg.sam, 1)(picard.sam.ValidateSamFileTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method test[6](bad/sorted-pair-missing-rg.sam, 1)(picard.sam.ValidateSamFileTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: INFO 2024-07-02 12:04:34 SortSam Gradle suite > Gradle test > picard.sam.ValidateSamFileTest.testIndex[0](index_test_b.bam, 0) STANDARD_ERROR INFO 2024-07-02 12:04:34 SortSam Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** SortSam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test.sam -O /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test_b.bam -SORT_ORDER coordinate ********** SortSam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test.sam -O /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test_b.bam -SORT_ORDER coordinate Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.746 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:34.746 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.747 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:34.747 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.747 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:34.747 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.747 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:34.747 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] SortSam INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test.sam OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test_b.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:34 GMT+14:00 2024] SortSam INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test.sam OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test_b.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: INFO 2024-07-02 12:04:34 SortSam Finished reading inputs, merging and writing to output now. INFO 2024-07-02 12:04:34 SortSam Finished reading inputs, merging and writing to output now. Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:04:34 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.00 minutes. Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: INFO 2024-07-02 12:04:34 ValidateSamFile INFO 2024-07-02 12:04:34 ValidateSamFile Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ValidateSamFile -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test_b.bam -IGNORE MISSING_PLATFORM_VALUE -IGNORE MISMATCH_MATE_ALIGNMENT_START -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test_b.bam -IGNORE MISSING_PLATFORM_VALUE -IGNORE MISMATCH_MATE_ALIGNMENT_START -IGNORE MISSING_TAG_NM Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.815 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:34.815 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.815 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:34.815 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.815 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:34.815 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.815 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:34.815 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] ValidateSamFile INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test_b.bam IGNORE=[MISSING_PLATFORM_VALUE, MISMATCH_MATE_ALIGNMENT_START, MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:34 GMT+14:00 2024] ValidateSamFile INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test_b.bam IGNORE=[MISSING_PLATFORM_VALUE, MISMATCH_MATE_ALIGNMENT_START, MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING 2024-07-02 12:04:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:04:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING: BAM index file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test_b.bam.bai is older than BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test_b.bam WARNING: BAM index file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test_b.bam.bai is older than BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test_b.bam Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ValidateSamFileTest.testIndex[0](index_test_b.bam, 0) STANDARD_OUT No errors found Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ValidateSamFileTest.testIndex[0](index_test_b.bam, 0) STANDARD_ERROR [Tue Jul 02 12:04:34 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testIndex[0](index_test_b.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: INFO 2024-07-02 12:04:34 SortSam Gradle suite > Gradle test > picard.sam.ValidateSamFileTest.testIndex[1](index_test_c.bam, 0) STANDARD_ERROR INFO 2024-07-02 12:04:34 SortSam Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** SortSam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test.sam -O /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test_c.bam -SORT_ORDER coordinate ********** SortSam -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test.sam -O /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test_c.bam -SORT_ORDER coordinate Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.824 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:34.824 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.824 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:34.824 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.825 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:34.825 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.825 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:34.825 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] SortSam INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test.sam OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test_c.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:34 GMT+14:00 2024] SortSam INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test.sam OUTPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test_c.bam SORT_ORDER=coordinate VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: INFO 2024-07-02 12:04:34 SortSam Finished reading inputs, merging and writing to output now. INFO 2024-07-02 12:04:34 SortSam Finished reading inputs, merging and writing to output now. Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:04:34 GMT+14:00 2024] picard.sam.SortSam done. Elapsed time: 0.00 minutes. Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: INFO 2024-07-02 12:04:34 ValidateSamFile INFO 2024-07-02 12:04:34 ValidateSamFile Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ValidateSamFile -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test_c.bam -IGNORE MISSING_PLATFORM_VALUE -IGNORE MISMATCH_MATE_ALIGNMENT_START -IGNORE MISSING_TAG_NM ********** ValidateSamFile -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test_c.bam -IGNORE MISSING_PLATFORM_VALUE -IGNORE MISMATCH_MATE_ALIGNMENT_START -IGNORE MISSING_TAG_NM Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: ********** ********** Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.875 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:34.875 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.875 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:34.875 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.875 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:34.875 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: 12:04:34.875 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:34.875 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] ValidateSamFile INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test_c.bam IGNORE=[MISSING_PLATFORM_VALUE, MISMATCH_MATE_ALIGNMENT_START, MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:34 GMT+14:00 2024] ValidateSamFile INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test_c.bam IGNORE=[MISSING_PLATFORM_VALUE, MISMATCH_MATE_ALIGNMENT_START, MISSING_TAG_NM] MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 SKIP_MATE_VALIDATION=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING 2024-07-02 12:04:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. WARNING 2024-07-02 12:04:34 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: WARNING: BAM index file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test_c.bam.csi is older than BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test_c.bam WARNING: BAM index file /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test_c.bam.csi is older than BAM /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/indices/index_test_c.bam Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: No errors found Gradle suite > Gradle test > picard.sam.ValidateSamFileTest.testIndex[1](index_test_c.bam, 0) STANDARD_OUT No errors found Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Gradle suite > Gradle test > picard.sam.ValidateSamFileTest.testIndex[1](index_test_c.bam, 0) STANDARD_ERROR [Tue Jul 02 12:04:34 GMT+14:00 2024] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Test: Test method testIndex[1](index_test_c.bam, 0)(picard.sam.ValidateSamFileTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testCombinationOne(picard.vcf.VariantContextComparatorTest) Running Test: Test method testCombinationTwo(picard.vcf.VariantContextComparatorTest) Running Test: Test method testContigs(picard.vcf.VariantContextComparatorTest) Running Test: Test method testIdentical(picard.vcf.VariantContextComparatorTest) Running Test: Test method testPositions(picard.vcf.VariantContextComparatorTest) Running Test: Test method testThrowsOnDuplicateContig(picard.vcf.VariantContextComparatorTest) Running Test: Test method ensureOverlapExclusionTest(picard.vcf.processor.VcfFileSegmentGeneratorTest) Running Test: Test method testBcfToBcf(picard.vcf.VcfFormatConverterTest) Test: Test method testBcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: INFO 2024-07-02 12:04:34 VcfFormatConverter Gradle suite > Gradle test > picard.vcf.VcfFormatConverterTest.testBcfToBcf STANDARD_ERROR INFO 2024-07-02 12:04:34 VcfFormatConverter Test: Test method testBcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: Test: Test method testBcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testBcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testBcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testBcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** VcfFormatConverter -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/vcfFormatTest.bcf -OUTPUT /tmp/likeTest5599078219607552947.bcf ********** VcfFormatConverter -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/vcfFormatTest.bcf -OUTPUT /tmp/likeTest5599078219607552947.bcf Test: Test method testBcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testBcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: Test: Test method testBcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: Test: Test method testBcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:34.951 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:34.951 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:34.951 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:34.951 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:34.951 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:34.951 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:34.951 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:34.951 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] VcfFormatConverter INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/vcfFormatTest.bcf OUTPUT=/tmp/likeTest5599078219607552947.bcf REQUIRE_INDEX=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:34 GMT+14:00 2024] VcfFormatConverter INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/vcfFormatTest.bcf OUTPUT=/tmp/likeTest5599078219607552947.bcf REQUIRE_INDEX=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: [Tue Jul 02 12:04:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:34 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: [Tue Jul 02 12:04:35 GMT+14:00 2024] picard.vcf.VcfFormatConverter done. Elapsed time: 0.01 minutes. [Tue Jul 02 12:04:35 GMT+14:00 2024] picard.vcf.VcfFormatConverter done. Elapsed time: 0.01 minutes. Test: Test method testBcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: INFO 2024-07-02 12:04:35 VcfFormatConverter Gradle suite > Gradle test > picard.vcf.VcfFormatConverterTest.testBcfToVcf STANDARD_ERROR INFO 2024-07-02 12:04:35 VcfFormatConverter Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** VcfFormatConverter -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/vcfFormatTest.bcf -OUTPUT /tmp/backAndForth660236410152220354.vcf ********** VcfFormatConverter -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/vcfFormatTest.bcf -OUTPUT /tmp/backAndForth660236410152220354.vcf Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:35.756 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:35.756 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:35.756 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:35.756 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:35.758 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:35.758 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:35.758 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:35.758 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: [Tue Jul 02 12:04:35 GMT+14:00 2024] VcfFormatConverter INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/vcfFormatTest.bcf OUTPUT=/tmp/backAndForth660236410152220354.vcf REQUIRE_INDEX=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:35 GMT+14:00 2024] VcfFormatConverter INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/vcfFormatTest.bcf OUTPUT=/tmp/backAndForth660236410152220354.vcf REQUIRE_INDEX=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: [Tue Jul 02 12:04:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:35 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: [Tue Jul 02 12:04:36 GMT+14:00 2024] picard.vcf.VcfFormatConverter done. Elapsed time: 0.01 minutes. [Tue Jul 02 12:04:36 GMT+14:00 2024] picard.vcf.VcfFormatConverter done. Elapsed time: 0.01 minutes. Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: INFO 2024-07-02 12:04:36 VcfFormatConverter INFO 2024-07-02 12:04:36 VcfFormatConverter Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** VcfFormatConverter -INPUT /tmp/backAndForth660236410152220354.vcf -OUTPUT /tmp/backAndForth13547578326112097723.bcf ********** VcfFormatConverter -INPUT /tmp/backAndForth660236410152220354.vcf -OUTPUT /tmp/backAndForth13547578326112097723.bcf Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:36.639 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:36.639 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:36.639 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:36.639 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:36.639 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:36.639 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:36.639 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:36.639 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: [Tue Jul 02 12:04:36 GMT+14:00 2024] VcfFormatConverter INPUT=/tmp/backAndForth660236410152220354.vcf OUTPUT=/tmp/backAndForth13547578326112097723.bcf REQUIRE_INDEX=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:36 GMT+14:00 2024] VcfFormatConverter INPUT=/tmp/backAndForth660236410152220354.vcf OUTPUT=/tmp/backAndForth13547578326112097723.bcf REQUIRE_INDEX=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: [Tue Jul 02 12:04:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:36 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: [Tue Jul 02 12:04:37 GMT+14:00 2024] picard.vcf.VcfFormatConverter done. Elapsed time: 0.02 minutes. [Tue Jul 02 12:04:37 GMT+14:00 2024] picard.vcf.VcfFormatConverter done. Elapsed time: 0.02 minutes. Test: Test method testBcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: INFO 2024-07-02 12:04:37 VcfFormatConverter Gradle suite > Gradle test > picard.vcf.VcfFormatConverterTest.testVcfToBcf STANDARD_ERROR INFO 2024-07-02 12:04:37 VcfFormatConverter Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** VcfFormatConverter -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/vcfFormatTest.vcf -OUTPUT /tmp/backAndForth6943065687353127969.bcf ********** VcfFormatConverter -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/vcfFormatTest.vcf -OUTPUT /tmp/backAndForth6943065687353127969.bcf Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:37.686 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:37.686 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:37.686 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:37.686 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:37.686 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:37.686 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:37.686 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:37.686 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: [Tue Jul 02 12:04:37 GMT+14:00 2024] VcfFormatConverter INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/vcfFormatTest.vcf OUTPUT=/tmp/backAndForth6943065687353127969.bcf REQUIRE_INDEX=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:37 GMT+14:00 2024] VcfFormatConverter INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/vcfFormatTest.vcf OUTPUT=/tmp/backAndForth6943065687353127969.bcf REQUIRE_INDEX=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: [Tue Jul 02 12:04:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:37 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: [Tue Jul 02 12:04:38 GMT+14:00 2024] picard.vcf.VcfFormatConverter done. Elapsed time: 0.01 minutes. [Tue Jul 02 12:04:38 GMT+14:00 2024] picard.vcf.VcfFormatConverter done. Elapsed time: 0.01 minutes. Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: INFO 2024-07-02 12:04:38 VcfFormatConverter INFO 2024-07-02 12:04:38 VcfFormatConverter Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** VcfFormatConverter -INPUT /tmp/backAndForth6943065687353127969.bcf -OUTPUT /tmp/backAndForth2132986482233868537.vcf ********** VcfFormatConverter -INPUT /tmp/backAndForth6943065687353127969.bcf -OUTPUT /tmp/backAndForth2132986482233868537.vcf Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:38.385 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:38.385 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:38.385 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:38.385 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:38.385 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:38.385 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:38.385 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:38.385 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: [Tue Jul 02 12:04:38 GMT+14:00 2024] VcfFormatConverter INPUT=/tmp/backAndForth6943065687353127969.bcf OUTPUT=/tmp/backAndForth2132986482233868537.vcf REQUIRE_INDEX=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:38 GMT+14:00 2024] VcfFormatConverter INPUT=/tmp/backAndForth6943065687353127969.bcf OUTPUT=/tmp/backAndForth2132986482233868537.vcf REQUIRE_INDEX=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: [Tue Jul 02 12:04:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:38 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: [Tue Jul 02 12:04:39 GMT+14:00 2024] picard.vcf.VcfFormatConverter done. Elapsed time: 0.01 minutes. [Tue Jul 02 12:04:39 GMT+14:00 2024] picard.vcf.VcfFormatConverter done. Elapsed time: 0.01 minutes. Test: Test method testVcfToBcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testVcfToVcf(picard.vcf.VcfFormatConverterTest) Test: Test method testVcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: INFO 2024-07-02 12:04:39 VcfFormatConverter Gradle suite > Gradle test > picard.vcf.VcfFormatConverterTest.testVcfToVcf STANDARD_ERROR INFO 2024-07-02 12:04:39 VcfFormatConverter Test: Test method testVcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: Test: Test method testVcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testVcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testVcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testVcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testVcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testVcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testVcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testVcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** VcfFormatConverter -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/vcfFormatTest.vcf -OUTPUT /tmp/likeTest17490877929471299934.vcf ********** VcfFormatConverter -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/vcfFormatTest.vcf -OUTPUT /tmp/likeTest17490877929471299934.vcf Test: Test method testVcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testVcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: Test: Test method testVcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: Test: Test method testVcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:39.278 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:39.278 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:39.278 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:39.278 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:39.278 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:39.278 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:39.278 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:39.278 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: [Tue Jul 02 12:04:39 GMT+14:00 2024] VcfFormatConverter INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/vcfFormatTest.vcf OUTPUT=/tmp/likeTest17490877929471299934.vcf REQUIRE_INDEX=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:39 GMT+14:00 2024] VcfFormatConverter INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/vcfFormatTest.vcf OUTPUT=/tmp/likeTest17490877929471299934.vcf REQUIRE_INDEX=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testVcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: [Tue Jul 02 12:04:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:39 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testVcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: [Tue Jul 02 12:04:40 GMT+14:00 2024] picard.vcf.VcfFormatConverter done. Elapsed time: 0.02 minutes. [Tue Jul 02 12:04:40 GMT+14:00 2024] picard.vcf.VcfFormatConverter done. Elapsed time: 0.02 minutes. Test: Test method testVcfToVcf(picard.vcf.VcfFormatConverterTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: INFO 2024-07-02 12:04:40 VcfFormatConverter Gradle suite > Gradle test > picard.vcf.VcfFormatConverterTest.testVcfToVcfGz STANDARD_ERROR INFO 2024-07-02 12:04:40 VcfFormatConverter Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** VcfFormatConverter -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/vcfFormatTest.vcf -OUTPUT /tmp/backAndForth4455356225813298922.vcf.gz -CREATE_INDEX false ********** VcfFormatConverter -INPUT /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/vcfFormatTest.vcf -OUTPUT /tmp/backAndForth4455356225813298922.vcf.gz -CREATE_INDEX false Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:40.504 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:40.504 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:40.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:40.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:40.504 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:40.504 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:40.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:40.504 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: [Tue Jul 02 12:04:40 GMT+14:00 2024] VcfFormatConverter INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/vcfFormatTest.vcf OUTPUT=/tmp/backAndForth4455356225813298922.vcf.gz CREATE_INDEX=false REQUIRE_INDEX=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:40 GMT+14:00 2024] VcfFormatConverter INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/vcfFormatTest.vcf OUTPUT=/tmp/backAndForth4455356225813298922.vcf.gz CREATE_INDEX=false REQUIRE_INDEX=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: [Tue Jul 02 12:04:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: [Tue Jul 02 12:04:40 GMT+14:00 2024] picard.vcf.VcfFormatConverter done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:04:40 GMT+14:00 2024] picard.vcf.VcfFormatConverter done. Elapsed time: 0.00 minutes. Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: INFO 2024-07-02 12:04:40 VcfFormatConverter INFO 2024-07-02 12:04:40 VcfFormatConverter Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** VcfFormatConverter -INPUT /tmp/backAndForth4455356225813298922.vcf.gz -OUTPUT /tmp/backAndForth5336718726125242860.vcf -REQUIRE_INDEX false ********** VcfFormatConverter -INPUT /tmp/backAndForth4455356225813298922.vcf.gz -OUTPUT /tmp/backAndForth5336718726125242860.vcf -REQUIRE_INDEX false Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: ********** ********** Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:40.790 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:40.790 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:40.790 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:40.790 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:40.790 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:40.790 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: 12:04:40.790 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:40.790 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: [Tue Jul 02 12:04:40 GMT+14:00 2024] VcfFormatConverter INPUT=/tmp/backAndForth4455356225813298922.vcf.gz OUTPUT=/tmp/backAndForth5336718726125242860.vcf REQUIRE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:40 GMT+14:00 2024] VcfFormatConverter INPUT=/tmp/backAndForth4455356225813298922.vcf.gz OUTPUT=/tmp/backAndForth5336718726125242860.vcf REQUIRE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: [Tue Jul 02 12:04:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:40 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: [Tue Jul 02 12:04:41 GMT+14:00 2024] picard.vcf.VcfFormatConverter done. Elapsed time: 0.02 minutes. [Tue Jul 02 12:04:41 GMT+14:00 2024] picard.vcf.VcfFormatConverter done. Elapsed time: 0.02 minutes. Test: Test method testVcfToVcfGz(picard.vcf.VcfFormatConverterTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testVcfToAdpc[0]([testdata/picard/arrays/illumina/TestVcfToAdpc.vcf], testdata/picard/arrays/illumina/TestVcfToAdpc.adpc.bin, testdata/picard/arrays/illumina/TestVcfToAdpc.samples.txt, testdata/picard/arrays/illumina/TestVcfToAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) Test: Test method testVcfToAdpc[0]([testdata/picard/arrays/illumina/TestVcfToAdpc.vcf], testdata/picard/arrays/illumina/TestVcfToAdpc.adpc.bin, testdata/picard/arrays/illumina/TestVcfToAdpc.samples.txt, testdata/picard/arrays/illumina/TestVcfToAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: 12:04:41.786 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.arrays.illumina.VcfToAdpcTest.testVcfToAdpc[0]([testdata/picard/arrays/illumina/TestVcfToAdpc.vcf], testdata/picard/arrays/illumina/TestVcfToAdpc.adpc.bin, testdata/picard/arrays/illumina/TestVcfToAdpc.samples.txt, testdata/picard/arrays/illumina/TestVcfToAdpc.num_markers.txt) STANDARD_ERROR 12:04:41.786 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVcfToAdpc[0]([testdata/picard/arrays/illumina/TestVcfToAdpc.vcf], testdata/picard/arrays/illumina/TestVcfToAdpc.adpc.bin, testdata/picard/arrays/illumina/TestVcfToAdpc.samples.txt, testdata/picard/arrays/illumina/TestVcfToAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: 12:04:41.786 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:41.786 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVcfToAdpc[0]([testdata/picard/arrays/illumina/TestVcfToAdpc.vcf], testdata/picard/arrays/illumina/TestVcfToAdpc.adpc.bin, testdata/picard/arrays/illumina/TestVcfToAdpc.samples.txt, testdata/picard/arrays/illumina/TestVcfToAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: 12:04:41.786 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:41.786 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVcfToAdpc[0]([testdata/picard/arrays/illumina/TestVcfToAdpc.vcf], testdata/picard/arrays/illumina/TestVcfToAdpc.adpc.bin, testdata/picard/arrays/illumina/TestVcfToAdpc.samples.txt, testdata/picard/arrays/illumina/TestVcfToAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: 12:04:41.786 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:41.786 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVcfToAdpc[0]([testdata/picard/arrays/illumina/TestVcfToAdpc.vcf], testdata/picard/arrays/illumina/TestVcfToAdpc.adpc.bin, testdata/picard/arrays/illumina/TestVcfToAdpc.samples.txt, testdata/picard/arrays/illumina/TestVcfToAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: [Tue Jul 02 12:04:41 GMT+14:00 2024] VcfToAdpc VCF=[testdata/picard/arrays/illumina/TestVcfToAdpc.vcf] OUTPUT=/tmp/testIlluminaAdpcFileWriter.7843445104181950662.adpc.bin SAMPLES_FILE=/tmp/testIlluminaAdpcFileWriter.14770744999080051052.samples.txt NUM_MARKERS_FILE=/tmp/testIlluminaAdpcFileWriter.17156449516565965500.num_markers.txt VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:41 GMT+14:00 2024] VcfToAdpc VCF=[testdata/picard/arrays/illumina/TestVcfToAdpc.vcf] OUTPUT=/tmp/testIlluminaAdpcFileWriter.7843445104181950662.adpc.bin SAMPLES_FILE=/tmp/testIlluminaAdpcFileWriter.14770744999080051052.samples.txt NUM_MARKERS_FILE=/tmp/testIlluminaAdpcFileWriter.17156449516565965500.num_markers.txt VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testVcfToAdpc[0]([testdata/picard/arrays/illumina/TestVcfToAdpc.vcf], testdata/picard/arrays/illumina/TestVcfToAdpc.adpc.bin, testdata/picard/arrays/illumina/TestVcfToAdpc.samples.txt, testdata/picard/arrays/illumina/TestVcfToAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: [Tue Jul 02 12:04:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testVcfToAdpc[0]([testdata/picard/arrays/illumina/TestVcfToAdpc.vcf], testdata/picard/arrays/illumina/TestVcfToAdpc.adpc.bin, testdata/picard/arrays/illumina/TestVcfToAdpc.samples.txt, testdata/picard/arrays/illumina/TestVcfToAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: INFO 2024-07-02 12:04:41 VcfToAdpc Processing sample: 203078500006_R01C01 from VCF: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/arrays/illumina/TestVcfToAdpc.vcf INFO 2024-07-02 12:04:41 VcfToAdpc Processing sample: 203078500006_R01C01 from VCF: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/arrays/illumina/TestVcfToAdpc.vcf Test: Test method testVcfToAdpc[0]([testdata/picard/arrays/illumina/TestVcfToAdpc.vcf], testdata/picard/arrays/illumina/TestVcfToAdpc.adpc.bin, testdata/picard/arrays/illumina/TestVcfToAdpc.samples.txt, testdata/picard/arrays/illumina/TestVcfToAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: [Tue Jul 02 12:04:41 GMT+14:00 2024] picard.arrays.VcfToAdpc done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:04:41 GMT+14:00 2024] picard.arrays.VcfToAdpc done. Elapsed time: 0.00 minutes. Test: Test method testVcfToAdpc[0]([testdata/picard/arrays/illumina/TestVcfToAdpc.vcf], testdata/picard/arrays/illumina/TestVcfToAdpc.adpc.bin, testdata/picard/arrays/illumina/TestVcfToAdpc.samples.txt, testdata/picard/arrays/illumina/TestVcfToAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testVcfToAdpc[1]([testdata/picard/arrays/illumina/TestAdpc1.vcf], testdata/picard/arrays/illumina/TestAdpc1.adpc.bin, testdata/picard/arrays/illumina/TestAdpc1.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) Test: Test method testVcfToAdpc[1]([testdata/picard/arrays/illumina/TestAdpc1.vcf], testdata/picard/arrays/illumina/TestAdpc1.adpc.bin, testdata/picard/arrays/illumina/TestAdpc1.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: 12:04:41.803 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.arrays.illumina.VcfToAdpcTest.testVcfToAdpc[1]([testdata/picard/arrays/illumina/TestAdpc1.vcf], testdata/picard/arrays/illumina/TestAdpc1.adpc.bin, testdata/picard/arrays/illumina/TestAdpc1.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt) STANDARD_ERROR 12:04:41.803 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVcfToAdpc[1]([testdata/picard/arrays/illumina/TestAdpc1.vcf], testdata/picard/arrays/illumina/TestAdpc1.adpc.bin, testdata/picard/arrays/illumina/TestAdpc1.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: 12:04:41.803 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:41.803 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVcfToAdpc[1]([testdata/picard/arrays/illumina/TestAdpc1.vcf], testdata/picard/arrays/illumina/TestAdpc1.adpc.bin, testdata/picard/arrays/illumina/TestAdpc1.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: 12:04:41.803 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:41.803 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVcfToAdpc[1]([testdata/picard/arrays/illumina/TestAdpc1.vcf], testdata/picard/arrays/illumina/TestAdpc1.adpc.bin, testdata/picard/arrays/illumina/TestAdpc1.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: 12:04:41.803 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:41.803 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVcfToAdpc[1]([testdata/picard/arrays/illumina/TestAdpc1.vcf], testdata/picard/arrays/illumina/TestAdpc1.adpc.bin, testdata/picard/arrays/illumina/TestAdpc1.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: [Tue Jul 02 12:04:41 GMT+14:00 2024] VcfToAdpc VCF=[testdata/picard/arrays/illumina/TestAdpc1.vcf] OUTPUT=/tmp/testIlluminaAdpcFileWriter.8958803538704615992.adpc.bin SAMPLES_FILE=/tmp/testIlluminaAdpcFileWriter.8140490161665662890.samples.txt NUM_MARKERS_FILE=/tmp/testIlluminaAdpcFileWriter.1867541253656624680.num_markers.txt VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:41 GMT+14:00 2024] VcfToAdpc VCF=[testdata/picard/arrays/illumina/TestAdpc1.vcf] OUTPUT=/tmp/testIlluminaAdpcFileWriter.8958803538704615992.adpc.bin SAMPLES_FILE=/tmp/testIlluminaAdpcFileWriter.8140490161665662890.samples.txt NUM_MARKERS_FILE=/tmp/testIlluminaAdpcFileWriter.1867541253656624680.num_markers.txt VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testVcfToAdpc[1]([testdata/picard/arrays/illumina/TestAdpc1.vcf], testdata/picard/arrays/illumina/TestAdpc1.adpc.bin, testdata/picard/arrays/illumina/TestAdpc1.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: [Tue Jul 02 12:04:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testVcfToAdpc[1]([testdata/picard/arrays/illumina/TestAdpc1.vcf], testdata/picard/arrays/illumina/TestAdpc1.adpc.bin, testdata/picard/arrays/illumina/TestAdpc1.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: INFO 2024-07-02 12:04:41 VcfToAdpc Processing sample: 203469020115_R01C01 from VCF: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/arrays/illumina/TestAdpc1.vcf INFO 2024-07-02 12:04:41 VcfToAdpc Processing sample: 203469020115_R01C01 from VCF: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/arrays/illumina/TestAdpc1.vcf Test: Test method testVcfToAdpc[1]([testdata/picard/arrays/illumina/TestAdpc1.vcf], testdata/picard/arrays/illumina/TestAdpc1.adpc.bin, testdata/picard/arrays/illumina/TestAdpc1.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: [Tue Jul 02 12:04:41 GMT+14:00 2024] picard.arrays.VcfToAdpc done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:04:41 GMT+14:00 2024] picard.arrays.VcfToAdpc done. Elapsed time: 0.00 minutes. Test: Test method testVcfToAdpc[1]([testdata/picard/arrays/illumina/TestAdpc1.vcf], testdata/picard/arrays/illumina/TestAdpc1.adpc.bin, testdata/picard/arrays/illumina/TestAdpc1.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testVcfToAdpc[2]([testdata/picard/arrays/illumina/TestAdpc23.vcf], testdata/picard/arrays/illumina/TestAdpc23.adpc.bin, testdata/picard/arrays/illumina/TestAdpc23.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) Test: Test method testVcfToAdpc[2]([testdata/picard/arrays/illumina/TestAdpc23.vcf], testdata/picard/arrays/illumina/TestAdpc23.adpc.bin, testdata/picard/arrays/illumina/TestAdpc23.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: 12:04:41.816 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.arrays.illumina.VcfToAdpcTest.testVcfToAdpc[2]([testdata/picard/arrays/illumina/TestAdpc23.vcf], testdata/picard/arrays/illumina/TestAdpc23.adpc.bin, testdata/picard/arrays/illumina/TestAdpc23.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt) STANDARD_ERROR 12:04:41.816 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVcfToAdpc[2]([testdata/picard/arrays/illumina/TestAdpc23.vcf], testdata/picard/arrays/illumina/TestAdpc23.adpc.bin, testdata/picard/arrays/illumina/TestAdpc23.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: 12:04:41.816 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:41.816 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVcfToAdpc[2]([testdata/picard/arrays/illumina/TestAdpc23.vcf], testdata/picard/arrays/illumina/TestAdpc23.adpc.bin, testdata/picard/arrays/illumina/TestAdpc23.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: 12:04:41.817 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:41.817 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVcfToAdpc[2]([testdata/picard/arrays/illumina/TestAdpc23.vcf], testdata/picard/arrays/illumina/TestAdpc23.adpc.bin, testdata/picard/arrays/illumina/TestAdpc23.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: 12:04:41.817 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:41.817 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVcfToAdpc[2]([testdata/picard/arrays/illumina/TestAdpc23.vcf], testdata/picard/arrays/illumina/TestAdpc23.adpc.bin, testdata/picard/arrays/illumina/TestAdpc23.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: [Tue Jul 02 12:04:41 GMT+14:00 2024] VcfToAdpc VCF=[testdata/picard/arrays/illumina/TestAdpc23.vcf] OUTPUT=/tmp/testIlluminaAdpcFileWriter.12990163306122926120.adpc.bin SAMPLES_FILE=/tmp/testIlluminaAdpcFileWriter.9341440057274545390.samples.txt NUM_MARKERS_FILE=/tmp/testIlluminaAdpcFileWriter.6746685106525723595.num_markers.txt VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:41 GMT+14:00 2024] VcfToAdpc VCF=[testdata/picard/arrays/illumina/TestAdpc23.vcf] OUTPUT=/tmp/testIlluminaAdpcFileWriter.12990163306122926120.adpc.bin SAMPLES_FILE=/tmp/testIlluminaAdpcFileWriter.9341440057274545390.samples.txt NUM_MARKERS_FILE=/tmp/testIlluminaAdpcFileWriter.6746685106525723595.num_markers.txt VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testVcfToAdpc[2]([testdata/picard/arrays/illumina/TestAdpc23.vcf], testdata/picard/arrays/illumina/TestAdpc23.adpc.bin, testdata/picard/arrays/illumina/TestAdpc23.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: [Tue Jul 02 12:04:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testVcfToAdpc[2]([testdata/picard/arrays/illumina/TestAdpc23.vcf], testdata/picard/arrays/illumina/TestAdpc23.adpc.bin, testdata/picard/arrays/illumina/TestAdpc23.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: INFO 2024-07-02 12:04:41 VcfToAdpc Processing sample: 203469020115_R02C01 from VCF: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/arrays/illumina/TestAdpc23.vcf INFO 2024-07-02 12:04:41 VcfToAdpc Processing sample: 203469020115_R02C01 from VCF: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/arrays/illumina/TestAdpc23.vcf Test: Test method testVcfToAdpc[2]([testdata/picard/arrays/illumina/TestAdpc23.vcf], testdata/picard/arrays/illumina/TestAdpc23.adpc.bin, testdata/picard/arrays/illumina/TestAdpc23.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: INFO 2024-07-02 12:04:41 VcfToAdpc Processing sample: 203469020115_R03C01 from VCF: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/arrays/illumina/TestAdpc23.vcf INFO 2024-07-02 12:04:41 VcfToAdpc Processing sample: 203469020115_R03C01 from VCF: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/arrays/illumina/TestAdpc23.vcf Test: Test method testVcfToAdpc[2]([testdata/picard/arrays/illumina/TestAdpc23.vcf], testdata/picard/arrays/illumina/TestAdpc23.adpc.bin, testdata/picard/arrays/illumina/TestAdpc23.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: [Tue Jul 02 12:04:41 GMT+14:00 2024] picard.arrays.VcfToAdpc done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:04:41 GMT+14:00 2024] picard.arrays.VcfToAdpc done. Elapsed time: 0.00 minutes. Test: Test method testVcfToAdpc[2]([testdata/picard/arrays/illumina/TestAdpc23.vcf], testdata/picard/arrays/illumina/TestAdpc23.adpc.bin, testdata/picard/arrays/illumina/TestAdpc23.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testVcfToAdpc[3]([testdata/picard/arrays/illumina/TestAdpc1.vcf, testdata/picard/arrays/illumina/TestAdpc23.vcf], testdata/picard/arrays/illumina/TestAdpc1_23.adpc.bin, testdata/picard/arrays/illumina/TestAdpc1_23.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) Test: Test method testVcfToAdpc[3]([testdata/picard/arrays/illumina/TestAdpc1.vcf, testdata/picard/arrays/illumina/TestAdpc23.vcf], testdata/picard/arrays/illumina/TestAdpc1_23.adpc.bin, testdata/picard/arrays/illumina/TestAdpc1_23.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: 12:04:41.862 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.arrays.illumina.VcfToAdpcTest.testVcfToAdpc[3]([testdata/picard/arrays/illumina/TestAdpc1.vcf, testdata/picard/arrays/illumina/TestAdpc23.vcf], testdata/picard/arrays/illumina/TestAdpc1_23.adpc.bin, testdata/picard/arrays/illumina/TestAdpc1_23.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt) STANDARD_ERROR 12:04:41.862 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVcfToAdpc[3]([testdata/picard/arrays/illumina/TestAdpc1.vcf, testdata/picard/arrays/illumina/TestAdpc23.vcf], testdata/picard/arrays/illumina/TestAdpc1_23.adpc.bin, testdata/picard/arrays/illumina/TestAdpc1_23.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: 12:04:41.862 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:41.862 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVcfToAdpc[3]([testdata/picard/arrays/illumina/TestAdpc1.vcf, testdata/picard/arrays/illumina/TestAdpc23.vcf], testdata/picard/arrays/illumina/TestAdpc1_23.adpc.bin, testdata/picard/arrays/illumina/TestAdpc1_23.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: 12:04:41.863 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:41.863 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVcfToAdpc[3]([testdata/picard/arrays/illumina/TestAdpc1.vcf, testdata/picard/arrays/illumina/TestAdpc23.vcf], testdata/picard/arrays/illumina/TestAdpc1_23.adpc.bin, testdata/picard/arrays/illumina/TestAdpc1_23.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: 12:04:41.863 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:41.863 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVcfToAdpc[3]([testdata/picard/arrays/illumina/TestAdpc1.vcf, testdata/picard/arrays/illumina/TestAdpc23.vcf], testdata/picard/arrays/illumina/TestAdpc1_23.adpc.bin, testdata/picard/arrays/illumina/TestAdpc1_23.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: [Tue Jul 02 12:04:41 GMT+14:00 2024] VcfToAdpc VCF=[testdata/picard/arrays/illumina/TestAdpc1.vcf, testdata/picard/arrays/illumina/TestAdpc23.vcf] OUTPUT=/tmp/testIlluminaAdpcFileWriter.3778573397284078637.adpc.bin SAMPLES_FILE=/tmp/testIlluminaAdpcFileWriter.11122538116134712569.samples.txt NUM_MARKERS_FILE=/tmp/testIlluminaAdpcFileWriter.1000683342993354554.num_markers.txt VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:41 GMT+14:00 2024] VcfToAdpc VCF=[testdata/picard/arrays/illumina/TestAdpc1.vcf, testdata/picard/arrays/illumina/TestAdpc23.vcf] OUTPUT=/tmp/testIlluminaAdpcFileWriter.3778573397284078637.adpc.bin SAMPLES_FILE=/tmp/testIlluminaAdpcFileWriter.11122538116134712569.samples.txt NUM_MARKERS_FILE=/tmp/testIlluminaAdpcFileWriter.1000683342993354554.num_markers.txt VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testVcfToAdpc[3]([testdata/picard/arrays/illumina/TestAdpc1.vcf, testdata/picard/arrays/illumina/TestAdpc23.vcf], testdata/picard/arrays/illumina/TestAdpc1_23.adpc.bin, testdata/picard/arrays/illumina/TestAdpc1_23.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: [Tue Jul 02 12:04:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testVcfToAdpc[3]([testdata/picard/arrays/illumina/TestAdpc1.vcf, testdata/picard/arrays/illumina/TestAdpc23.vcf], testdata/picard/arrays/illumina/TestAdpc1_23.adpc.bin, testdata/picard/arrays/illumina/TestAdpc1_23.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: INFO 2024-07-02 12:04:41 VcfToAdpc Processing sample: 203469020115_R01C01 from VCF: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/arrays/illumina/TestAdpc1.vcf INFO 2024-07-02 12:04:41 VcfToAdpc Processing sample: 203469020115_R01C01 from VCF: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/arrays/illumina/TestAdpc1.vcf Test: Test method testVcfToAdpc[3]([testdata/picard/arrays/illumina/TestAdpc1.vcf, testdata/picard/arrays/illumina/TestAdpc23.vcf], testdata/picard/arrays/illumina/TestAdpc1_23.adpc.bin, testdata/picard/arrays/illumina/TestAdpc1_23.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: INFO 2024-07-02 12:04:41 VcfToAdpc Processing sample: 203469020115_R02C01 from VCF: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/arrays/illumina/TestAdpc23.vcf INFO 2024-07-02 12:04:41 VcfToAdpc Processing sample: 203469020115_R02C01 from VCF: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/arrays/illumina/TestAdpc23.vcf Test: Test method testVcfToAdpc[3]([testdata/picard/arrays/illumina/TestAdpc1.vcf, testdata/picard/arrays/illumina/TestAdpc23.vcf], testdata/picard/arrays/illumina/TestAdpc1_23.adpc.bin, testdata/picard/arrays/illumina/TestAdpc1_23.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: INFO 2024-07-02 12:04:41 VcfToAdpc Processing sample: 203469020115_R03C01 from VCF: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/arrays/illumina/TestAdpc23.vcf INFO 2024-07-02 12:04:41 VcfToAdpc Processing sample: 203469020115_R03C01 from VCF: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/arrays/illumina/TestAdpc23.vcf Test: Test method testVcfToAdpc[3]([testdata/picard/arrays/illumina/TestAdpc1.vcf, testdata/picard/arrays/illumina/TestAdpc23.vcf], testdata/picard/arrays/illumina/TestAdpc1_23.adpc.bin, testdata/picard/arrays/illumina/TestAdpc1_23.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: [Tue Jul 02 12:04:41 GMT+14:00 2024] picard.arrays.VcfToAdpc done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:04:41 GMT+14:00 2024] picard.arrays.VcfToAdpc done. Elapsed time: 0.00 minutes. Test: Test method testVcfToAdpc[3]([testdata/picard/arrays/illumina/TestAdpc1.vcf, testdata/picard/arrays/illumina/TestAdpc23.vcf], testdata/picard/arrays/illumina/TestAdpc1_23.adpc.bin, testdata/picard/arrays/illumina/TestAdpc1_23.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testVcfToAdpc[4]([testdata/picard/arrays/illumina/TestAdpc23.vcf, testdata/picard/arrays/illumina/TestAdpc1.vcf], testdata/picard/arrays/illumina/TestAdpc23_1.adpc.bin, testdata/picard/arrays/illumina/TestAdpc23_1.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) Test: Test method testVcfToAdpc[4]([testdata/picard/arrays/illumina/TestAdpc23.vcf, testdata/picard/arrays/illumina/TestAdpc1.vcf], testdata/picard/arrays/illumina/TestAdpc23_1.adpc.bin, testdata/picard/arrays/illumina/TestAdpc23_1.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: 12:04:41.892 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.arrays.illumina.VcfToAdpcTest.testVcfToAdpc[4]([testdata/picard/arrays/illumina/TestAdpc23.vcf, testdata/picard/arrays/illumina/TestAdpc1.vcf], testdata/picard/arrays/illumina/TestAdpc23_1.adpc.bin, testdata/picard/arrays/illumina/TestAdpc23_1.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt) STANDARD_ERROR 12:04:41.892 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVcfToAdpc[4]([testdata/picard/arrays/illumina/TestAdpc23.vcf, testdata/picard/arrays/illumina/TestAdpc1.vcf], testdata/picard/arrays/illumina/TestAdpc23_1.adpc.bin, testdata/picard/arrays/illumina/TestAdpc23_1.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: 12:04:41.892 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:41.892 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVcfToAdpc[4]([testdata/picard/arrays/illumina/TestAdpc23.vcf, testdata/picard/arrays/illumina/TestAdpc1.vcf], testdata/picard/arrays/illumina/TestAdpc23_1.adpc.bin, testdata/picard/arrays/illumina/TestAdpc23_1.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: 12:04:41.894 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:41.894 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVcfToAdpc[4]([testdata/picard/arrays/illumina/TestAdpc23.vcf, testdata/picard/arrays/illumina/TestAdpc1.vcf], testdata/picard/arrays/illumina/TestAdpc23_1.adpc.bin, testdata/picard/arrays/illumina/TestAdpc23_1.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: 12:04:41.894 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:41.894 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVcfToAdpc[4]([testdata/picard/arrays/illumina/TestAdpc23.vcf, testdata/picard/arrays/illumina/TestAdpc1.vcf], testdata/picard/arrays/illumina/TestAdpc23_1.adpc.bin, testdata/picard/arrays/illumina/TestAdpc23_1.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: [Tue Jul 02 12:04:41 GMT+14:00 2024] VcfToAdpc VCF=[testdata/picard/arrays/illumina/TestAdpc23.vcf, testdata/picard/arrays/illumina/TestAdpc1.vcf] OUTPUT=/tmp/testIlluminaAdpcFileWriter.8156376304862895439.adpc.bin SAMPLES_FILE=/tmp/testIlluminaAdpcFileWriter.11221253896394290573.samples.txt NUM_MARKERS_FILE=/tmp/testIlluminaAdpcFileWriter.2119454688421951517.num_markers.txt VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:41 GMT+14:00 2024] VcfToAdpc VCF=[testdata/picard/arrays/illumina/TestAdpc23.vcf, testdata/picard/arrays/illumina/TestAdpc1.vcf] OUTPUT=/tmp/testIlluminaAdpcFileWriter.8156376304862895439.adpc.bin SAMPLES_FILE=/tmp/testIlluminaAdpcFileWriter.11221253896394290573.samples.txt NUM_MARKERS_FILE=/tmp/testIlluminaAdpcFileWriter.2119454688421951517.num_markers.txt VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testVcfToAdpc[4]([testdata/picard/arrays/illumina/TestAdpc23.vcf, testdata/picard/arrays/illumina/TestAdpc1.vcf], testdata/picard/arrays/illumina/TestAdpc23_1.adpc.bin, testdata/picard/arrays/illumina/TestAdpc23_1.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: [Tue Jul 02 12:04:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testVcfToAdpc[4]([testdata/picard/arrays/illumina/TestAdpc23.vcf, testdata/picard/arrays/illumina/TestAdpc1.vcf], testdata/picard/arrays/illumina/TestAdpc23_1.adpc.bin, testdata/picard/arrays/illumina/TestAdpc23_1.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: INFO 2024-07-02 12:04:41 VcfToAdpc Processing sample: 203469020115_R02C01 from VCF: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/arrays/illumina/TestAdpc23.vcf INFO 2024-07-02 12:04:41 VcfToAdpc Processing sample: 203469020115_R02C01 from VCF: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/arrays/illumina/TestAdpc23.vcf Test: Test method testVcfToAdpc[4]([testdata/picard/arrays/illumina/TestAdpc23.vcf, testdata/picard/arrays/illumina/TestAdpc1.vcf], testdata/picard/arrays/illumina/TestAdpc23_1.adpc.bin, testdata/picard/arrays/illumina/TestAdpc23_1.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: INFO 2024-07-02 12:04:41 VcfToAdpc Processing sample: 203469020115_R03C01 from VCF: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/arrays/illumina/TestAdpc23.vcf INFO 2024-07-02 12:04:41 VcfToAdpc Processing sample: 203469020115_R03C01 from VCF: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/arrays/illumina/TestAdpc23.vcf Test: Test method testVcfToAdpc[4]([testdata/picard/arrays/illumina/TestAdpc23.vcf, testdata/picard/arrays/illumina/TestAdpc1.vcf], testdata/picard/arrays/illumina/TestAdpc23_1.adpc.bin, testdata/picard/arrays/illumina/TestAdpc23_1.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: INFO 2024-07-02 12:04:41 VcfToAdpc Processing sample: 203469020115_R01C01 from VCF: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/arrays/illumina/TestAdpc1.vcf INFO 2024-07-02 12:04:41 VcfToAdpc Processing sample: 203469020115_R01C01 from VCF: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/arrays/illumina/TestAdpc1.vcf Test: Test method testVcfToAdpc[4]([testdata/picard/arrays/illumina/TestAdpc23.vcf, testdata/picard/arrays/illumina/TestAdpc1.vcf], testdata/picard/arrays/illumina/TestAdpc23_1.adpc.bin, testdata/picard/arrays/illumina/TestAdpc23_1.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: [Tue Jul 02 12:04:41 GMT+14:00 2024] picard.arrays.VcfToAdpc done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:04:41 GMT+14:00 2024] picard.arrays.VcfToAdpc done. Elapsed time: 0.00 minutes. Test: Test method testVcfToAdpc[4]([testdata/picard/arrays/illumina/TestAdpc23.vcf, testdata/picard/arrays/illumina/TestAdpc1.vcf], testdata/picard/arrays/illumina/TestAdpc23_1.adpc.bin, testdata/picard/arrays/illumina/TestAdpc23_1.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt)(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: 12:04:41.923 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Gradle suite > Gradle test > picard.arrays.illumina.VcfToAdpcTest.testVcfToAdpcFailOnDifferingNumberOfLoci STANDARD_ERROR 12:04:41.923 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: 12:04:41.923 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:41.923 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: 12:04:41.923 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:41.923 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: 12:04:41.923 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:41.923 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: [Tue Jul 02 12:04:41 GMT+14:00 2024] VcfToAdpc VCF=[testdata/picard/arrays/illumina/TestVcfToAdpc.vcf, testdata/picard/arrays/illumina/TestAdpc1.vcf] OUTPUT=/tmp/testIlluminaAdpcFileWriter.17367226944104382539.adpc.bin SAMPLES_FILE=/tmp/testIlluminaAdpcFileWriter.1789221765215825674.samples.txt NUM_MARKERS_FILE=/tmp/testIlluminaAdpcFileWriter.12340105935716010042.num_markers.txt VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:41 GMT+14:00 2024] VcfToAdpc VCF=[testdata/picard/arrays/illumina/TestVcfToAdpc.vcf, testdata/picard/arrays/illumina/TestAdpc1.vcf] OUTPUT=/tmp/testIlluminaAdpcFileWriter.17367226944104382539.adpc.bin SAMPLES_FILE=/tmp/testIlluminaAdpcFileWriter.1789221765215825674.samples.txt NUM_MARKERS_FILE=/tmp/testIlluminaAdpcFileWriter.12340105935716010042.num_markers.txt VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: [Tue Jul 02 12:04:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: INFO 2024-07-02 12:04:41 VcfToAdpc Processing sample: 203078500006_R01C01 from VCF: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/arrays/illumina/TestVcfToAdpc.vcf INFO 2024-07-02 12:04:41 VcfToAdpc Processing sample: 203078500006_R01C01 from VCF: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/arrays/illumina/TestVcfToAdpc.vcf Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: INFO 2024-07-02 12:04:41 VcfToAdpc Processing sample: 203469020115_R01C01 from VCF: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/arrays/illumina/TestAdpc1.vcf INFO 2024-07-02 12:04:41 VcfToAdpc Processing sample: 203469020115_R01C01 from VCF: /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/arrays/illumina/TestAdpc1.vcf Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: ERROR 2024-07-02 12:04:41 VcfToAdpc ERROR 2024-07-02 12:04:41 VcfToAdpc Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: picard.PicardException: VCFs have differing number of loci picard.PicardException: VCFs have differing number of loci Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at picard.arrays.VcfToAdpc.doWork(VcfToAdpc.java:144) at picard.arrays.VcfToAdpc.doWork(VcfToAdpc.java:144) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:304) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at picard.arrays.illumina.VcfToAdpcTest.testVcfToAdpcFailOnDifferingNumberOfLoci(VcfToAdpcTest.java:92) at picard.arrays.illumina.VcfToAdpcTest.testVcfToAdpcFailOnDifferingNumberOfLoci(VcfToAdpcTest.java:92) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1129) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.testng.TestRunner.privateRun(TestRunner.java:746) at org.testng.TestRunner.privateRun(TestRunner.java:746) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.testng.TestRunner.run(TestRunner.java:600) at org.testng.TestRunner.run(TestRunner.java:600) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) at org.testng.SuiteRunner.runTest(SuiteRunner.java:366) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.testng.SuiteRunner.run(SuiteRunner.java:268) at org.testng.SuiteRunner.run(SuiteRunner.java:268) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) at org.testng.TestNG.runSuitesLocally(TestNG.java:1189) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.testng.TestNG.runSuites(TestNG.java:1104) at org.testng.TestNG.runSuites(TestNG.java:1104) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.testng.TestNG.run(TestNG.java:1076) at org.testng.TestNG.run(TestNG.java:1076) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:129) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:88) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at com.sun.proxy.$Proxy3.stop(Unknown Source) at com.sun.proxy.$Proxy3.stop(Unknown Source) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) at org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:119) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at java.base/java.lang.reflect.Method.invoke(Method.java:566) at java.base/java.lang.reflect.Method.invoke(Method.java:566) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:146) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) at org.gradle.internal.remote.internal.hub.MessageHubBackedObjectConnection$DispatchWrapper.dispatch(MessageHubBackedObjectConnection.java:128) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) at org.gradle.internal.remote.internal.hub.MessageHub$Handler.run(MessageHub.java:404) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:63) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:46) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:55) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: at java.base/java.lang.Thread.run(Thread.java:829) at java.base/java.lang.Thread.run(Thread.java:829) Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: [Tue Jul 02 12:04:41 GMT+14:00 2024] picard.arrays.VcfToAdpc done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:04:41 GMT+14:00 2024] picard.arrays.VcfToAdpc done. Elapsed time: 0.00 minutes. Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Test: Test method testVcfToAdpcFailOnDifferingNumberOfLoci(picard.arrays.illumina.VcfToAdpcTest) produced standard out/err: To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp Running Test: Test method testExcludingFiltered[0](testdata/picard/vcf/small_m2_more_variants.vcf, false, true, 9)(picard.vcf.VcfToIntervalListTest) Test: Test method testExcludingFiltered[0](testdata/picard/vcf/small_m2_more_variants.vcf, false, true, 9)(picard.vcf.VcfToIntervalListTest) produced standard out/err: INFO 2024-07-02 12:04:41 VcfToIntervalList Gradle suite > Gradle test > picard.vcf.VcfToIntervalListTest.testExcludingFiltered[0](testdata/picard/vcf/small_m2_more_variants.vcf, false, true, 9) STANDARD_ERROR INFO 2024-07-02 12:04:41 VcfToIntervalList Test: Test method testExcludingFiltered[0](testdata/picard/vcf/small_m2_more_variants.vcf, false, true, 9)(picard.vcf.VcfToIntervalListTest) produced standard out/err: Test: Test method testExcludingFiltered[0](testdata/picard/vcf/small_m2_more_variants.vcf, false, true, 9)(picard.vcf.VcfToIntervalListTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testExcludingFiltered[0](testdata/picard/vcf/small_m2_more_variants.vcf, false, true, 9)(picard.vcf.VcfToIntervalListTest) produced standard out/err: ********** ********** Test: Test method testExcludingFiltered[0](testdata/picard/vcf/small_m2_more_variants.vcf, false, true, 9)(picard.vcf.VcfToIntervalListTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testExcludingFiltered[0](testdata/picard/vcf/small_m2_more_variants.vcf, false, true, 9)(picard.vcf.VcfToIntervalListTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testExcludingFiltered[0](testdata/picard/vcf/small_m2_more_variants.vcf, false, true, 9)(picard.vcf.VcfToIntervalListTest) produced standard out/err: ********** ********** Test: Test method testExcludingFiltered[0](testdata/picard/vcf/small_m2_more_variants.vcf, false, true, 9)(picard.vcf.VcfToIntervalListTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testExcludingFiltered[0](testdata/picard/vcf/small_m2_more_variants.vcf, false, true, 9)(picard.vcf.VcfToIntervalListTest) produced standard out/err: ********** ********** Test: Test method testExcludingFiltered[0](testdata/picard/vcf/small_m2_more_variants.vcf, false, true, 9)(picard.vcf.VcfToIntervalListTest) produced standard out/err: ********** VcfToIntervalList -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/small_m2_more_variants.vcf -O /tmp/vcftointervallist_3179760921328499254.interval_list -VARIANT_ID_METHOD USE_FIRST ********** VcfToIntervalList -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/small_m2_more_variants.vcf -O /tmp/vcftointervallist_3179760921328499254.interval_list -VARIANT_ID_METHOD USE_FIRST Test: Test method testExcludingFiltered[0](testdata/picard/vcf/small_m2_more_variants.vcf, false, true, 9)(picard.vcf.VcfToIntervalListTest) produced standard out/err: ********** ********** Test: Test method testExcludingFiltered[0](testdata/picard/vcf/small_m2_more_variants.vcf, false, true, 9)(picard.vcf.VcfToIntervalListTest) produced standard out/err: Test: Test method testExcludingFiltered[0](testdata/picard/vcf/small_m2_more_variants.vcf, false, true, 9)(picard.vcf.VcfToIntervalListTest) produced standard out/err: Test: Test method testExcludingFiltered[0](testdata/picard/vcf/small_m2_more_variants.vcf, false, true, 9)(picard.vcf.VcfToIntervalListTest) produced standard out/err: 12:04:41.971 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:41.971 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testExcludingFiltered[0](testdata/picard/vcf/small_m2_more_variants.vcf, false, true, 9)(picard.vcf.VcfToIntervalListTest) produced standard out/err: 12:04:41.971 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:41.971 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testExcludingFiltered[0](testdata/picard/vcf/small_m2_more_variants.vcf, false, true, 9)(picard.vcf.VcfToIntervalListTest) produced standard out/err: 12:04:41.971 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:41.971 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testExcludingFiltered[0](testdata/picard/vcf/small_m2_more_variants.vcf, false, true, 9)(picard.vcf.VcfToIntervalListTest) produced standard out/err: 12:04:41.971 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:41.971 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testExcludingFiltered[0](testdata/picard/vcf/small_m2_more_variants.vcf, false, true, 9)(picard.vcf.VcfToIntervalListTest) produced standard out/err: [Tue Jul 02 12:04:41 GMT+14:00 2024] VcfToIntervalList INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/small_m2_more_variants.vcf OUTPUT=/tmp/vcftointervallist_3179760921328499254.interval_list VARIANT_ID_METHOD=USE_FIRST INCLUDE_FILTERED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:41 GMT+14:00 2024] VcfToIntervalList INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/small_m2_more_variants.vcf OUTPUT=/tmp/vcftointervallist_3179760921328499254.interval_list VARIANT_ID_METHOD=USE_FIRST INCLUDE_FILTERED=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testExcludingFiltered[0](testdata/picard/vcf/small_m2_more_variants.vcf, false, true, 9)(picard.vcf.VcfToIntervalListTest) produced standard out/err: [Tue Jul 02 12:04:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:41 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testExcludingFiltered[0](testdata/picard/vcf/small_m2_more_variants.vcf, false, true, 9)(picard.vcf.VcfToIntervalListTest) produced standard out/err: [Tue Jul 02 12:04:41 GMT+14:00 2024] picard.vcf.VcfToIntervalList done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:04:41 GMT+14:00 2024] picard.vcf.VcfToIntervalList done. Elapsed time: 0.00 minutes. Test: Test method testExcludingFiltered[0](testdata/picard/vcf/small_m2_more_variants.vcf, false, true, 9)(picard.vcf.VcfToIntervalListTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testExcludingFiltered[1](testdata/picard/vcf/small_m2_more_variants.vcf, true, false, 10)(picard.vcf.VcfToIntervalListTest) Test: Test method testExcludingFiltered[1](testdata/picard/vcf/small_m2_more_variants.vcf, true, false, 10)(picard.vcf.VcfToIntervalListTest) produced standard out/err: INFO 2024-07-02 12:04:42 VcfToIntervalList Gradle suite > Gradle test > picard.vcf.VcfToIntervalListTest.testExcludingFiltered[1](testdata/picard/vcf/small_m2_more_variants.vcf, true, false, 10) STANDARD_ERROR INFO 2024-07-02 12:04:42 VcfToIntervalList Test: Test method testExcludingFiltered[1](testdata/picard/vcf/small_m2_more_variants.vcf, true, false, 10)(picard.vcf.VcfToIntervalListTest) produced standard out/err: Test: Test method testExcludingFiltered[1](testdata/picard/vcf/small_m2_more_variants.vcf, true, false, 10)(picard.vcf.VcfToIntervalListTest) produced standard out/err: ********** NOTE: Picard's command line syntax is changing. ********** NOTE: Picard's command line syntax is changing. Test: Test method testExcludingFiltered[1](testdata/picard/vcf/small_m2_more_variants.vcf, true, false, 10)(picard.vcf.VcfToIntervalListTest) produced standard out/err: ********** ********** Test: Test method testExcludingFiltered[1](testdata/picard/vcf/small_m2_more_variants.vcf, true, false, 10)(picard.vcf.VcfToIntervalListTest) produced standard out/err: ********** For more information, please see: ********** For more information, please see: Test: Test method testExcludingFiltered[1](testdata/picard/vcf/small_m2_more_variants.vcf, true, false, 10)(picard.vcf.VcfToIntervalListTest) produced standard out/err: ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) ********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition) Test: Test method testExcludingFiltered[1](testdata/picard/vcf/small_m2_more_variants.vcf, true, false, 10)(picard.vcf.VcfToIntervalListTest) produced standard out/err: ********** ********** Test: Test method testExcludingFiltered[1](testdata/picard/vcf/small_m2_more_variants.vcf, true, false, 10)(picard.vcf.VcfToIntervalListTest) produced standard out/err: ********** The command line looks like this in the new syntax: ********** The command line looks like this in the new syntax: Test: Test method testExcludingFiltered[1](testdata/picard/vcf/small_m2_more_variants.vcf, true, false, 10)(picard.vcf.VcfToIntervalListTest) produced standard out/err: ********** ********** Test: Test method testExcludingFiltered[1](testdata/picard/vcf/small_m2_more_variants.vcf, true, false, 10)(picard.vcf.VcfToIntervalListTest) produced standard out/err: ********** VcfToIntervalList -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/small_m2_more_variants.vcf -O /tmp/vcftointervallist_17447899701614725577.interval_list -IF true -VARIANT_ID_METHOD CONCAT_ALL ********** VcfToIntervalList -I /build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/small_m2_more_variants.vcf -O /tmp/vcftointervallist_17447899701614725577.interval_list -IF true -VARIANT_ID_METHOD CONCAT_ALL Test: Test method testExcludingFiltered[1](testdata/picard/vcf/small_m2_more_variants.vcf, true, false, 10)(picard.vcf.VcfToIntervalListTest) produced standard out/err: ********** ********** Test: Test method testExcludingFiltered[1](testdata/picard/vcf/small_m2_more_variants.vcf, true, false, 10)(picard.vcf.VcfToIntervalListTest) produced standard out/err: Test: Test method testExcludingFiltered[1](testdata/picard/vcf/small_m2_more_variants.vcf, true, false, 10)(picard.vcf.VcfToIntervalListTest) produced standard out/err: Test: Test method testExcludingFiltered[1](testdata/picard/vcf/small_m2_more_variants.vcf, true, false, 10)(picard.vcf.VcfToIntervalListTest) produced standard out/err: 12:04:42.004 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:42.004 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testExcludingFiltered[1](testdata/picard/vcf/small_m2_more_variants.vcf, true, false, 10)(picard.vcf.VcfToIntervalListTest) produced standard out/err: 12:04:42.004 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:42.004 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testExcludingFiltered[1](testdata/picard/vcf/small_m2_more_variants.vcf, true, false, 10)(picard.vcf.VcfToIntervalListTest) produced standard out/err: 12:04:42.004 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib 12:04:42.004 WARN NativeLibraryLoader - OVERRIDE DEFAULT: Loading libgkl_compression.so from /usr/java/packages/lib:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib Test: Test method testExcludingFiltered[1](testdata/picard/vcf/small_m2_more_variants.vcf, true, false, 10)(picard.vcf.VcfToIntervalListTest) produced standard out/err: 12:04:42.004 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null 12:04:42.004 WARN NativeLibraryLoader - LD_LIBRARY_PATH = null Test: Test method testExcludingFiltered[1](testdata/picard/vcf/small_m2_more_variants.vcf, true, false, 10)(picard.vcf.VcfToIntervalListTest) produced standard out/err: [Tue Jul 02 12:04:42 GMT+14:00 2024] VcfToIntervalList INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/small_m2_more_variants.vcf OUTPUT=/tmp/vcftointervallist_17447899701614725577.interval_list VARIANT_ID_METHOD=CONCAT_ALL INCLUDE_FILTERED=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false [Tue Jul 02 12:04:42 GMT+14:00 2024] VcfToIntervalList INPUT=/build/reproducible-path/picard-tools-2.24.1+dfsg/testdata/picard/vcf/small_m2_more_variants.vcf OUTPUT=/tmp/vcftointervallist_17447899701614725577.interval_list VARIANT_ID_METHOD=CONCAT_ALL INCLUDE_FILTERED=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=2279706 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false Test: Test method testExcludingFiltered[1](testdata/picard/vcf/small_m2_more_variants.vcf, true, false, 10)(picard.vcf.VcfToIntervalListTest) produced standard out/err: [Tue Jul 02 12:04:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null [Tue Jul 02 12:04:42 GMT+14:00 2024] Executing as pbuilder2@i-capture-the-hostname on Linux 6.1.0-22-amd64 amd64; OpenJDK 64-Bit Server VM 11.0.23+9-post-Debian-1deb11u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: null Test: Test method testExcludingFiltered[1](testdata/picard/vcf/small_m2_more_variants.vcf, true, false, 10)(picard.vcf.VcfToIntervalListTest) produced standard out/err: [Tue Jul 02 12:04:42 GMT+14:00 2024] picard.vcf.VcfToIntervalList done. Elapsed time: 0.00 minutes. [Tue Jul 02 12:04:42 GMT+14:00 2024] picard.vcf.VcfToIntervalList done. Elapsed time: 0.00 minutes. Test: Test method testExcludingFiltered[1](testdata/picard/vcf/small_m2_more_variants.vcf, true, false, 10)(picard.vcf.VcfToIntervalListTest) produced standard out/err: Runtime.totalMemory()=1168113664 Runtime.totalMemory()=1168113664 Running Test: Test method testHeaderVersion(picard.sam.ViewSamTest) Running Test: Test method testIntervals(picard.sam.ViewSamTest) Running Test: Test method testForExitAfter(picard.analysis.WgsMetricsProcessorImplTest) Running Test: Test method testForFilteredBases(picard.analysis.WgsMetricsProcessorImplTest) Running Test: Test method testForProcessFile(picard.analysis.WgsMetricsProcessorImplTest) Running Test: Test method testMergeOverlappingIntervals(picard.analysis.WgsMetricsTest) Running Test: Test method testWgsMetricsMerge[0](GENOME_TERRITORY 0 MEAN_COVERAGE ? SD_COVERAGE -0 MEDIAN_COVERAGE 0 MAD_COVERAGE 0 PCT_EXC_ADAPTER 0 PCT_EXC_MAPQ 0 PCT_EXC_DUPE 0 PCT_EXC_UNPAIRED 0 PCT_EXC_BASEQ 0 PCT_EXC_OVERLAP 0 PCT_EXC_CAPPED 0 PCT_EXC_TOTAL 0 PCT_1X ? PCT_5X ? PCT_10X ? PCT_15X ? PCT_20X ? PCT_25X ? PCT_30X ? PCT_40X ? PCT_50X ? PCT_60X ? PCT_70X ? PCT_80X ? PCT_90X ? PCT_100X ? FOLD_80_BASE_PENALTY 0 FOLD_90_BASE_PENALTY 0 FOLD_95_BASE_PENALTY 0 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 , GENOME_TERRITORY 0 MEAN_COVERAGE ? SD_COVERAGE -0 MEDIAN_COVERAGE 0 MAD_COVERAGE 0 PCT_EXC_ADAPTER 0 PCT_EXC_MAPQ 0 PCT_EXC_DUPE 0 PCT_EXC_UNPAIRED 0 PCT_EXC_BASEQ 0 PCT_EXC_OVERLAP 0 PCT_EXC_CAPPED 0 PCT_EXC_TOTAL 0 PCT_1X ? PCT_5X ? PCT_10X ? PCT_15X ? PCT_20X ? PCT_25X ? PCT_30X ? PCT_40X ? PCT_50X ? PCT_60X ? PCT_70X ? PCT_80X ? PCT_90X ? PCT_100X ? FOLD_80_BASE_PENALTY 0 FOLD_90_BASE_PENALTY 0 FOLD_95_BASE_PENALTY 0 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 , GENOME_TERRITORY 0 MEAN_COVERAGE ? SD_COVERAGE -0 MEDIAN_COVERAGE 0 MAD_COVERAGE 0 PCT_EXC_ADAPTER 0 PCT_EXC_MAPQ 0 PCT_EXC_DUPE 0 PCT_EXC_UNPAIRED 0 PCT_EXC_BASEQ 0 PCT_EXC_OVERLAP 0 PCT_EXC_CAPPED 0 PCT_EXC_TOTAL 0 PCT_1X ? PCT_5X ? PCT_10X ? PCT_15X ? PCT_20X ? PCT_25X ? PCT_30X ? PCT_40X ? PCT_50X ? PCT_60X ? PCT_70X ? PCT_80X ? PCT_90X ? PCT_100X ? FOLD_80_BASE_PENALTY 0 FOLD_90_BASE_PENALTY 0 FOLD_95_BASE_PENALTY 0 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 )(picard.analysis.WgsMetricsTest) Running Test: Test method testWgsMetricsMerge[1](GENOME_TERRITORY 0 MEAN_COVERAGE ? SD_COVERAGE -0 MEDIAN_COVERAGE 0 MAD_COVERAGE 0 PCT_EXC_ADAPTER 0 PCT_EXC_MAPQ 0 PCT_EXC_DUPE 0 PCT_EXC_UNPAIRED 0 PCT_EXC_BASEQ 0 PCT_EXC_OVERLAP 0 PCT_EXC_CAPPED 0 PCT_EXC_TOTAL 0 PCT_1X ? PCT_5X ? PCT_10X ? PCT_15X ? PCT_20X ? PCT_25X ? PCT_30X ? PCT_40X ? PCT_50X ? PCT_60X ? PCT_70X ? PCT_80X ? PCT_90X ? PCT_100X ? FOLD_80_BASE_PENALTY 0 FOLD_90_BASE_PENALTY 0 FOLD_95_BASE_PENALTY 0 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 , GENOME_TERRITORY 100000 MEAN_COVERAGE 1 SD_COVERAGE 0 MEDIAN_COVERAGE 1 MAD_COVERAGE 0 PCT_EXC_ADAPTER 0.00005 PCT_EXC_MAPQ 0.0001 PCT_EXC_DUPE 0.0002 PCT_EXC_UNPAIRED 0.0003 PCT_EXC_BASEQ 0.0004 PCT_EXC_OVERLAP 0.0005 PCT_EXC_CAPPED 0.0006 PCT_EXC_TOTAL 0.002145 PCT_1X 1 PCT_5X 0 PCT_10X 0 PCT_15X 0 PCT_20X 0 PCT_25X 0 PCT_30X 0 PCT_40X 0 PCT_50X 0 PCT_60X 0 PCT_70X 0 PCT_80X 0 PCT_90X 0 PCT_100X 0 FOLD_80_BASE_PENALTY 1 FOLD_90_BASE_PENALTY 1 FOLD_95_BASE_PENALTY 1 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 , GENOME_TERRITORY 100000 MEAN_COVERAGE 1 SD_COVERAGE 0 MEDIAN_COVERAGE 1 MAD_COVERAGE 0 PCT_EXC_ADAPTER 0.00005 PCT_EXC_MAPQ 0.0001 PCT_EXC_DUPE 0.0002 PCT_EXC_UNPAIRED 0.0003 PCT_EXC_BASEQ 0.0004 PCT_EXC_OVERLAP 0.0005 PCT_EXC_CAPPED 0.0006 PCT_EXC_TOTAL 0.002145 PCT_1X 1 PCT_5X 0 PCT_10X 0 PCT_15X 0 PCT_20X 0 PCT_25X 0 PCT_30X 0 PCT_40X 0 PCT_50X 0 PCT_60X 0 PCT_70X 0 PCT_80X 0 PCT_90X 0 PCT_100X 0 FOLD_80_BASE_PENALTY 1 FOLD_90_BASE_PENALTY 1 FOLD_95_BASE_PENALTY 1 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 )(picard.analysis.WgsMetricsTest) Running Test: Test method testWgsMetricsMerge[2](GENOME_TERRITORY 100000 MEAN_COVERAGE 1 SD_COVERAGE 0 MEDIAN_COVERAGE 1 MAD_COVERAGE 0 PCT_EXC_ADAPTER 0.00005 PCT_EXC_MAPQ 0.0001 PCT_EXC_DUPE 0.0002 PCT_EXC_UNPAIRED 0.0003 PCT_EXC_BASEQ 0.0004 PCT_EXC_OVERLAP 0.0005 PCT_EXC_CAPPED 0.0006 PCT_EXC_TOTAL 0.002145 PCT_1X 1 PCT_5X 0 PCT_10X 0 PCT_15X 0 PCT_20X 0 PCT_25X 0 PCT_30X 0 PCT_40X 0 PCT_50X 0 PCT_60X 0 PCT_70X 0 PCT_80X 0 PCT_90X 0 PCT_100X 0 FOLD_80_BASE_PENALTY 1 FOLD_90_BASE_PENALTY 1 FOLD_95_BASE_PENALTY 1 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 , GENOME_TERRITORY 0 MEAN_COVERAGE ? SD_COVERAGE -0 MEDIAN_COVERAGE 0 MAD_COVERAGE 0 PCT_EXC_ADAPTER 0 PCT_EXC_MAPQ 0 PCT_EXC_DUPE 0 PCT_EXC_UNPAIRED 0 PCT_EXC_BASEQ 0 PCT_EXC_OVERLAP 0 PCT_EXC_CAPPED 0 PCT_EXC_TOTAL 0 PCT_1X ? PCT_5X ? PCT_10X ? PCT_15X ? PCT_20X ? PCT_25X ? PCT_30X ? PCT_40X ? PCT_50X ? PCT_60X ? PCT_70X ? PCT_80X ? PCT_90X ? PCT_100X ? FOLD_80_BASE_PENALTY 0 FOLD_90_BASE_PENALTY 0 FOLD_95_BASE_PENALTY 0 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 , GENOME_TERRITORY 100000 MEAN_COVERAGE 1 SD_COVERAGE 0 MEDIAN_COVERAGE 1 MAD_COVERAGE 0 PCT_EXC_ADAPTER 0.00005 PCT_EXC_MAPQ 0.0001 PCT_EXC_DUPE 0.0002 PCT_EXC_UNPAIRED 0.0003 PCT_EXC_BASEQ 0.0004 PCT_EXC_OVERLAP 0.0005 PCT_EXC_CAPPED 0.0006 PCT_EXC_TOTAL 0.002145 PCT_1X 1 PCT_5X 0 PCT_10X 0 PCT_15X 0 PCT_20X 0 PCT_25X 0 PCT_30X 0 PCT_40X 0 PCT_50X 0 PCT_60X 0 PCT_70X 0 PCT_80X 0 PCT_90X 0 PCT_100X 0 FOLD_80_BASE_PENALTY 1 FOLD_90_BASE_PENALTY 1 FOLD_95_BASE_PENALTY 1 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 )(picard.analysis.WgsMetricsTest) Running Test: Test method testWgsMetricsMerge[3](GENOME_TERRITORY 100000 MEAN_COVERAGE 1 SD_COVERAGE 0 MEDIAN_COVERAGE 1 MAD_COVERAGE 0 PCT_EXC_ADAPTER 0.00005 PCT_EXC_MAPQ 0.0001 PCT_EXC_DUPE 0.0002 PCT_EXC_UNPAIRED 0.0003 PCT_EXC_BASEQ 0.0004 PCT_EXC_OVERLAP 0.0005 PCT_EXC_CAPPED 0.0006 PCT_EXC_TOTAL 0.002145 PCT_1X 1 PCT_5X 0 PCT_10X 0 PCT_15X 0 PCT_20X 0 PCT_25X 0 PCT_30X 0 PCT_40X 0 PCT_50X 0 PCT_60X 0 PCT_70X 0 PCT_80X 0 PCT_90X 0 PCT_100X 0 FOLD_80_BASE_PENALTY 1 FOLD_90_BASE_PENALTY 1 FOLD_95_BASE_PENALTY 1 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 , GENOME_TERRITORY 100000 MEAN_COVERAGE 1 SD_COVERAGE 0 MEDIAN_COVERAGE 1 MAD_COVERAGE 0 PCT_EXC_ADAPTER 0.00005 PCT_EXC_MAPQ 0.0001 PCT_EXC_DUPE 0.0002 PCT_EXC_UNPAIRED 0.0003 PCT_EXC_BASEQ 0.0004 PCT_EXC_OVERLAP 0.0005 PCT_EXC_CAPPED 0.0006 PCT_EXC_TOTAL 0.002145 PCT_1X 1 PCT_5X 0 PCT_10X 0 PCT_15X 0 PCT_20X 0 PCT_25X 0 PCT_30X 0 PCT_40X 0 PCT_50X 0 PCT_60X 0 PCT_70X 0 PCT_80X 0 PCT_90X 0 PCT_100X 0 FOLD_80_BASE_PENALTY 1 FOLD_90_BASE_PENALTY 1 FOLD_95_BASE_PENALTY 1 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 , GENOME_TERRITORY 200000 MEAN_COVERAGE 1 SD_COVERAGE 0 MEDIAN_COVERAGE 1 MAD_COVERAGE 0 PCT_EXC_ADAPTER 0.00005 PCT_EXC_MAPQ 0.0001 PCT_EXC_DUPE 0.0002 PCT_EXC_UNPAIRED 0.0003 PCT_EXC_BASEQ 0.0004 PCT_EXC_OVERLAP 0.0005 PCT_EXC_CAPPED 0.0006 PCT_EXC_TOTAL 0.002145 PCT_1X 1 PCT_5X 0 PCT_10X 0 PCT_15X 0 PCT_20X 0 PCT_25X 0 PCT_30X 0 PCT_40X 0 PCT_50X 0 PCT_60X 0 PCT_70X 0 PCT_80X 0 PCT_90X 0 PCT_100X 0 FOLD_80_BASE_PENALTY 1 FOLD_90_BASE_PENALTY 1 FOLD_95_BASE_PENALTY 1 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 )(picard.analysis.WgsMetricsTest) Running Test: Test method testWgsMetricsMerge[4](GENOME_TERRITORY 100000 MEAN_COVERAGE 1 SD_COVERAGE 0 MEDIAN_COVERAGE 1 MAD_COVERAGE 0 PCT_EXC_ADAPTER 0.00005 PCT_EXC_MAPQ 0.0001 PCT_EXC_DUPE 0.0002 PCT_EXC_UNPAIRED 0.0003 PCT_EXC_BASEQ 0.0004 PCT_EXC_OVERLAP 0.0005 PCT_EXC_CAPPED 0.0006 PCT_EXC_TOTAL 0.002145 PCT_1X 1 PCT_5X 0 PCT_10X 0 PCT_15X 0 PCT_20X 0 PCT_25X 0 PCT_30X 0 PCT_40X 0 PCT_50X 0 PCT_60X 0 PCT_70X 0 PCT_80X 0 PCT_90X 0 PCT_100X 0 FOLD_80_BASE_PENALTY 1 FOLD_90_BASE_PENALTY 1 FOLD_95_BASE_PENALTY 1 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 , GENOME_TERRITORY 200000 MEAN_COVERAGE 1 SD_COVERAGE 0 MEDIAN_COVERAGE 1 MAD_COVERAGE 0 PCT_EXC_ADAPTER 0.00005 PCT_EXC_MAPQ 0.0001 PCT_EXC_DUPE 0.0002 PCT_EXC_UNPAIRED 0.0003 PCT_EXC_BASEQ 0.0004 PCT_EXC_OVERLAP 0.0005 PCT_EXC_CAPPED 0.0006 PCT_EXC_TOTAL 0.002145 PCT_1X 1 PCT_5X 0 PCT_10X 0 PCT_15X 0 PCT_20X 0 PCT_25X 0 PCT_30X 0 PCT_40X 0 PCT_50X 0 PCT_60X 0 PCT_70X 0 PCT_80X 0 PCT_90X 0 PCT_100X 0 FOLD_80_BASE_PENALTY 1 FOLD_90_BASE_PENALTY 1 FOLD_95_BASE_PENALTY 1 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 , GENOME_TERRITORY 300000 MEAN_COVERAGE 1 SD_COVERAGE 0 MEDIAN_COVERAGE 1 MAD_COVERAGE 0 PCT_EXC_ADAPTER 0.00005 PCT_EXC_MAPQ 0.0001 PCT_EXC_DUPE 0.0002 PCT_EXC_UNPAIRED 0.0003 PCT_EXC_BASEQ 0.0004 PCT_EXC_OVERLAP 0.0005 PCT_EXC_CAPPED 0.0006 PCT_EXC_TOTAL 0.002145 PCT_1X 1 PCT_5X 0 PCT_10X 0 PCT_15X 0 PCT_20X 0 PCT_25X 0 PCT_30X 0 PCT_40X 0 PCT_50X 0 PCT_60X 0 PCT_70X 0 PCT_80X 0 PCT_90X 0 PCT_100X 0 FOLD_80_BASE_PENALTY 1 FOLD_90_BASE_PENALTY 1 FOLD_95_BASE_PENALTY 1 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 )(picard.analysis.WgsMetricsTest) Running Test: Test method testWgsMetricsMerge[5](GENOME_TERRITORY 100000 MEAN_COVERAGE 1 SD_COVERAGE 0 MEDIAN_COVERAGE 1 MAD_COVERAGE 0 PCT_EXC_ADAPTER 0.00005 PCT_EXC_MAPQ 0.0001 PCT_EXC_DUPE 0.0002 PCT_EXC_UNPAIRED 0.0003 PCT_EXC_BASEQ 0.0004 PCT_EXC_OVERLAP 0.0005 PCT_EXC_CAPPED 0.0006 PCT_EXC_TOTAL 0.002145 PCT_1X 1 PCT_5X 0 PCT_10X 0 PCT_15X 0 PCT_20X 0 PCT_25X 0 PCT_30X 0 PCT_40X 0 PCT_50X 0 PCT_60X 0 PCT_70X 0 PCT_80X 0 PCT_90X 0 PCT_100X 0 FOLD_80_BASE_PENALTY 1 FOLD_90_BASE_PENALTY 1 FOLD_95_BASE_PENALTY 1 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 , GENOME_TERRITORY 100000 MEAN_COVERAGE 1 SD_COVERAGE 0 MEDIAN_COVERAGE 1 MAD_COVERAGE 0 PCT_EXC_ADAPTER 0.00005 PCT_EXC_MAPQ 0.0001 PCT_EXC_DUPE 0.0002 PCT_EXC_UNPAIRED 0.0003 PCT_EXC_BASEQ 0.0004 PCT_EXC_OVERLAP 0.0005 PCT_EXC_CAPPED 0.0006 PCT_EXC_TOTAL 0.002145 PCT_1X 1 PCT_5X 0 PCT_10X 0 PCT_15X 0 PCT_20X 0 PCT_25X 0 PCT_30X 0 PCT_40X 0 PCT_50X 0 PCT_60X 0 PCT_70X 0 PCT_80X 0 PCT_90X 0 PCT_100X 0 FOLD_80_BASE_PENALTY 1 FOLD_90_BASE_PENALTY 1 FOLD_95_BASE_PENALTY 1 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 , GENOME_TERRITORY 200000 MEAN_COVERAGE 1 SD_COVERAGE 0 MEDIAN_COVERAGE 1 MAD_COVERAGE 0 PCT_EXC_ADAPTER 0.00005 PCT_EXC_MAPQ 0.0001 PCT_EXC_DUPE 0.0002 PCT_EXC_UNPAIRED 0.0003 PCT_EXC_BASEQ 0.0004 PCT_EXC_OVERLAP 0.0005 PCT_EXC_CAPPED 0.0006 PCT_EXC_TOTAL 0.002145 PCT_1X 1 PCT_5X 0 PCT_10X 0 PCT_15X 0 PCT_20X 0 PCT_25X 0 PCT_30X 0 PCT_40X 0 PCT_50X 0 PCT_60X 0 PCT_70X 0 PCT_80X 0 PCT_90X 0 PCT_100X 0 FOLD_80_BASE_PENALTY 1 FOLD_90_BASE_PENALTY 1 FOLD_95_BASE_PENALTY 1 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 )(picard.analysis.WgsMetricsTest) Running Test: Test method testWgsMetricsMerge[6](GENOME_TERRITORY 100000 MEAN_COVERAGE 1 SD_COVERAGE 0 MEDIAN_COVERAGE 1 MAD_COVERAGE 0 PCT_EXC_ADAPTER 0.00005 PCT_EXC_MAPQ 0.0001 PCT_EXC_DUPE 0.0002 PCT_EXC_UNPAIRED 0.0003 PCT_EXC_BASEQ 0.0004 PCT_EXC_OVERLAP 0.0005 PCT_EXC_CAPPED 0.0006 PCT_EXC_TOTAL 0.002145 PCT_1X 1 PCT_5X 0 PCT_10X 0 PCT_15X 0 PCT_20X 0 PCT_25X 0 PCT_30X 0 PCT_40X 0 PCT_50X 0 PCT_60X 0 PCT_70X 0 PCT_80X 0 PCT_90X 0 PCT_100X 0 FOLD_80_BASE_PENALTY 1 FOLD_90_BASE_PENALTY 1 FOLD_95_BASE_PENALTY 1 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 , GENOME_TERRITORY 100000 MEAN_COVERAGE 2 SD_COVERAGE 0 MEDIAN_COVERAGE 2 MAD_COVERAGE 0 PCT_EXC_ADAPTER 0.00005 PCT_EXC_MAPQ 0.0001 PCT_EXC_DUPE 0.0002 PCT_EXC_UNPAIRED 0.0003 PCT_EXC_BASEQ 0.0004 PCT_EXC_OVERLAP 0.0005 PCT_EXC_CAPPED 0.0006 PCT_EXC_TOTAL 0.002145 PCT_1X 1 PCT_5X 0 PCT_10X 0 PCT_15X 0 PCT_20X 0 PCT_25X 0 PCT_30X 0 PCT_40X 0 PCT_50X 0 PCT_60X 0 PCT_70X 0 PCT_80X 0 PCT_90X 0 PCT_100X 0 FOLD_80_BASE_PENALTY 1 FOLD_90_BASE_PENALTY 1 FOLD_95_BASE_PENALTY 1 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 , GENOME_TERRITORY 200000 MEAN_COVERAGE 1.5 SD_COVERAGE 0.500001 MEDIAN_COVERAGE 1.5 MAD_COVERAGE 0.5 PCT_EXC_ADAPTER 0.00005 PCT_EXC_MAPQ 0.0001 PCT_EXC_DUPE 0.0002 PCT_EXC_UNPAIRED 0.0003 PCT_EXC_BASEQ 0.0004 PCT_EXC_OVERLAP 0.0005 PCT_EXC_CAPPED 0.0006 PCT_EXC_TOTAL 0.002145 PCT_1X 1 PCT_5X 0 PCT_10X 0 PCT_15X 0 PCT_20X 0 PCT_25X 0 PCT_30X 0 PCT_40X 0 PCT_50X 0 PCT_60X 0 PCT_70X 0 PCT_80X 0 PCT_90X 0 PCT_100X 0 FOLD_80_BASE_PENALTY 1.5 FOLD_90_BASE_PENALTY 1.5 FOLD_95_BASE_PENALTY 1.5 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 )(picard.analysis.WgsMetricsTest) Running Test: Test method testWgsMetricsMerge[7](GENOME_TERRITORY 200000 MEAN_COVERAGE 1.5 SD_COVERAGE 0.500001 MEDIAN_COVERAGE 1.5 MAD_COVERAGE 0.5 PCT_EXC_ADAPTER 0.00005 PCT_EXC_MAPQ 0.0001 PCT_EXC_DUPE 0.0002 PCT_EXC_UNPAIRED 0.0003 PCT_EXC_BASEQ 0.0004 PCT_EXC_OVERLAP 0.0005 PCT_EXC_CAPPED 0.0006 PCT_EXC_TOTAL 0.002145 PCT_1X 1 PCT_5X 0 PCT_10X 0 PCT_15X 0 PCT_20X 0 PCT_25X 0 PCT_30X 0 PCT_40X 0 PCT_50X 0 PCT_60X 0 PCT_70X 0 PCT_80X 0 PCT_90X 0 PCT_100X 0 FOLD_80_BASE_PENALTY 1.5 FOLD_90_BASE_PENALTY 1.5 FOLD_95_BASE_PENALTY 1.5 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 , GENOME_TERRITORY 200000 MEAN_COVERAGE 1.5 SD_COVERAGE 0.500001 MEDIAN_COVERAGE 1.5 MAD_COVERAGE 0.5 PCT_EXC_ADAPTER 0.00005 PCT_EXC_MAPQ 0.0001 PCT_EXC_DUPE 0.0002 PCT_EXC_UNPAIRED 0.0003 PCT_EXC_BASEQ 0.0004 PCT_EXC_OVERLAP 0.0005 PCT_EXC_CAPPED 0.0006 PCT_EXC_TOTAL 0.002145 PCT_1X 1 PCT_5X 0 PCT_10X 0 PCT_15X 0 PCT_20X 0 PCT_25X 0 PCT_30X 0 PCT_40X 0 PCT_50X 0 PCT_60X 0 PCT_70X 0 PCT_80X 0 PCT_90X 0 PCT_100X 0 FOLD_80_BASE_PENALTY 1.5 FOLD_90_BASE_PENALTY 1.5 FOLD_95_BASE_PENALTY 1.5 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 , GENOME_TERRITORY 400000 MEAN_COVERAGE 1.5 SD_COVERAGE 0.500001 MEDIAN_COVERAGE 1.5 MAD_COVERAGE 0.5 PCT_EXC_ADAPTER 0.00005 PCT_EXC_MAPQ 0.0001 PCT_EXC_DUPE 0.0002 PCT_EXC_UNPAIRED 0.0003 PCT_EXC_BASEQ 0.0004 PCT_EXC_OVERLAP 0.0005 PCT_EXC_CAPPED 0.0006 PCT_EXC_TOTAL 0.002145 PCT_1X 1 PCT_5X 0 PCT_10X 0 PCT_15X 0 PCT_20X 0 PCT_25X 0 PCT_30X 0 PCT_40X 0 PCT_50X 0 PCT_60X 0 PCT_70X 0 PCT_80X 0 PCT_90X 0 PCT_100X 0 FOLD_80_BASE_PENALTY 1.5 FOLD_90_BASE_PENALTY 1.5 FOLD_95_BASE_PENALTY 1.5 HET_SNP_SENSITIVITY 0 HET_SNP_Q 0 )(picard.analysis.WgsMetricsTest) Running Test: Test method testForVcf(picard.vcf.processor.WidthLimitingDecoratorTest) Gradle Test Executor 1 finished executing tests. Results: SUCCESS (4977 tests, 4977 successes, 0 failures, 0 skipped) Finished generating test XML results (0.723 secs) into: /build/reproducible-path/picard-tools-2.24.1+dfsg/build/test-results/test Generating HTML test report... Finished generating test html results (0.804 secs) into: /build/reproducible-path/picard-tools-2.24.1+dfsg/build/reports/tests/test :test (Thread[Task worker for ':',5,main]) completed. Took 45 mins 40.119 secs. BUILD SUCCESSFUL in 46m 3s 5 actionable tasks: 3 executed, 2 up-to-date make[1]: Leaving directory '/build/reproducible-path/picard-tools-2.24.1+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=gradle dh_prep -O--buildsystem=gradle rm -f -- debian/picard-tools.substvars debian/libpicard-java.substvars debian/libpicard-java-doc.substvars rm -fr -- debian/.debhelper/generated/picard-tools/ debian/picard-tools/ debian/tmp/ debian/.debhelper/generated/libpicard-java/ debian/libpicard-java/ debian/.debhelper/generated/libpicard-java-doc/ debian/libpicard-java-doc/ dh_auto_install -O--buildsystem=gradle install -d /build/reproducible-path/picard-tools-2.24.1\+dfsg/debian/tmp dh_install -O--buildsystem=gradle install -d debian/picard-tools/usr/bin cp --reflink=auto -a ./debian/bin/PicardCommandLine debian/picard-tools/usr/bin/ install -d debian/.debhelper/generated/picard-tools install -d debian/.debhelper/generated/libpicard-java install -d debian/.debhelper/generated/libpicard-java-doc jh_installjavadoc -O--buildsystem=gradle Installing javadoc from build/docs/javadoc into package libpicard-java-doc install -d debian/libpicard-java-doc/usr/share/doc/libpicard-java cp -r build/docs/javadoc debian/libpicard-java-doc/usr/share/doc/libpicard-java/api cat > debian/libpicard-java-doc.doc-base.javadoc dh_installdocs -O--buildsystem=gradle install -d debian/picard-tools/usr/share/doc/picard-tools cp --reflink=auto -a ./testdata/picard/sam/unmapped.sam debian/picard-tools/usr/share/doc/picard-tools cp --reflink=auto -a ./testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.sam debian/picard-tools/usr/share/doc/picard-tools cp --reflink=auto -a ./testdata/picard/analysis/artifacts/CollectSequencingArtifactMetrics/test.fasta debian/picard-tools/usr/share/doc/picard-tools cp --reflink=auto -a ./testdata/picard/vcf/mini.vcf debian/picard-tools/usr/share/doc/picard-tools cp --reflink=auto -a ./testdata/picard/vcf/mini.vcf.idx debian/picard-tools/usr/share/doc/picard-tools cp --reflink=auto -a ./debian/README.test debian/picard-tools/usr/share/doc/picard-tools cp --reflink=auto -a ./debian/tests/run-unit-test debian/picard-tools/usr/share/doc/picard-tools chmod -R u\+rw,go=rX debian/picard-tools/usr/share/doc install -p -m0644 debian/copyright debian/picard-tools/usr/share/doc/picard-tools/copyright install -d debian/libpicard-java/usr/share/doc/libpicard-java install -p -m0644 debian/copyright debian/libpicard-java/usr/share/doc/libpicard-java/copyright install -d debian/libpicard-java-doc/usr/share/doc/libpicard-java-doc install -p -m0644 debian/copyright debian/libpicard-java-doc/usr/share/doc/libpicard-java-doc/copyright install -d debian/libpicard-java-doc/usr/share/doc-base/ install -p -m0644 debian/libpicard-java-doc.doc-base.javadoc debian/libpicard-java-doc/usr/share/doc-base/libpicard-java-doc dh_installchangelogs -O--buildsystem=gradle install -p -m0644 debian/changelog debian/picard-tools/usr/share/doc/picard-tools/changelog.Debian install -p -m0644 debian/changelog debian/libpicard-java/usr/share/doc/libpicard-java/changelog.Debian install -p -m0644 debian/changelog debian/libpicard-java-doc/usr/share/doc/libpicard-java-doc/changelog.Debian dh_installman -O--buildsystem=gradle install -d debian/picard-tools/usr/share/man/man1/ install -p -m0644 ./debian/PicardCommandLine.1 debian/picard-tools/usr/share/man/man1/PicardCommandLine.1 man-recode --to-code UTF-8 --suffix .dh-new debian/picard-tools/usr/share/man/man1/PicardCommandLine.1 mv debian/picard-tools/usr/share/man/man1/PicardCommandLine.1.dh-new debian/picard-tools/usr/share/man/man1/PicardCommandLine.1 chmod 0644 -- debian/picard-tools/usr/share/man/man1/PicardCommandLine.1 dh_installsystemduser -O--buildsystem=gradle dh_perl -O--buildsystem=gradle rm -f debian/libpicard-java-doc.debhelper.log debian/libpicard-java.debhelper.log debian/picard-tools.debhelper.log debian/rules override_dh_link make[1]: Entering directory '/build/reproducible-path/picard-tools-2.24.1+dfsg' rm -f debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/jquery/external/jquery/jquery.js dh_link install -d debian/picard-tools/usr/share/debian-med/bin rm -f debian/picard-tools/usr/share/debian-med/bin/picard ln -s ../../../bin/PicardCommandLine debian/picard-tools/usr/share/debian-med/bin/picard rm -f debian/picard-tools/usr/share/man/man1/picard-tools.1 ln -s PicardCommandLine.1 debian/picard-tools/usr/share/man/man1/picard-tools.1 rm -f debian/picard-tools/usr/bin/picard-tools ln -s PicardCommandLine debian/picard-tools/usr/bin/picard-tools rm -f debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/jquery/external/jquery/jquery.js ln -s ../../../../../../javascript/jquery/jquery.min.js debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/jquery/external/jquery/jquery.js make[1]: Leaving directory '/build/reproducible-path/picard-tools-2.24.1+dfsg' jh_installlibs -O--buildsystem=gradle install -d debian/libpicard-java/usr/share/java install -p -m0644 ./build/libs/picard-2.24.1.jar debian/libpicard-java/usr/share/java/picard-2.24.1.jar rm -f debian/libpicard-java/usr/share/java/picard.jar ln -s picard-2.24.1.jar debian/libpicard-java/usr/share/java/picard.jar jh_classpath -O--buildsystem=gradle jh_manifest -ppicard-tools "--classpath=/usr/share/java/htsjdk.jar /usr/share/java/guava.jar /usr/lib/jvm/default-java/lib/tools.jar /usr/share/java/commons-lang3.jar /usr/share/java/gkl.jar /usr/share/java/gatk-native-bindings.jar /usr/share/java/barclay.jar" debian/libpicard-java/usr/share/java/picard.jar Updating symlinked /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/libpicard-java/usr/share/java/picard-2.24.1.jar (via debian/libpicard-java/usr/share/java/picard.jar) Reading manifest from /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/libpicard-java/usr/share/java/picard-2.24.1.jar Updating manifest in /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/libpicard-java/usr/share/java/picard-2.24.1.jar jh_manifest -O--buildsystem=gradle find debian/picard-tools -name '*.jar' find debian/libpicard-java -name '*.jar' Found usr/share/java/picard-2.24.1.jar Found symlink usr/share/java/picard.jar Updating symlinked /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/libpicard-java/usr/share/java/picard-2.24.1.jar (using manifest for usr/share/java/picard.jar) Reading manifest from /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/libpicard-java/usr/share/java/picard-2.24.1.jar Updating manifest in /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/libpicard-java/usr/share/java/picard-2.24.1.jar find debian/libpicard-java-doc -name '*.jar' jh_exec -O--buildsystem=gradle jh_depends -O--buildsystem=gradle Searching /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/picard-tools for picard-tools Searching Found Jars: Found Debs: Adding substvars: java:Depends= java:Recommends= Searching /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/libpicard-java for libpicard-java Searching /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/libpicard-java/usr/share/java/picard-2.24.1.jar Found Jars: /usr/lib/jvm/default-java/lib/tools.jar /usr/share/java/barclay.jar /usr/share/java/commons-lang3.jar /usr/share/java/gatk-native-bindings.jar /usr/share/java/gkl.jar /usr/share/java/guava.jar /usr/share/java/htsjdk.jar Checking: /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/picard-tools/usr/lib/jvm/default-java/lib/tools.jar Checking: /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/libpicard-java/usr/lib/jvm/default-java/lib/tools.jar Checking: /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/libpicard-java-doc/usr/lib/jvm/default-java/lib/tools.jar Checking: /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/picard-tools/usr/share/java/barclay-2.1.0.jar Checking: /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/libpicard-java/usr/share/java/barclay-2.1.0.jar Checking: /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/libpicard-java-doc/usr/share/java/barclay-2.1.0.jar Checking: /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/picard-tools/usr/share/java/commons-lang3.jar Checking: /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/libpicard-java/usr/share/java/commons-lang3.jar Checking: /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/libpicard-java-doc/usr/share/java/commons-lang3.jar Checking: /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/picard-tools/usr/share/java/gatk-native-bindings-1.0.0.jar Checking: /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/libpicard-java/usr/share/java/gatk-native-bindings-1.0.0.jar Checking: /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/libpicard-java-doc/usr/share/java/gatk-native-bindings-1.0.0.jar Checking: /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/picard-tools/usr/share/java/gkl-0.8.7.jar Checking: /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/libpicard-java/usr/share/java/gkl-0.8.7.jar Checking: /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/libpicard-java-doc/usr/share/java/gkl-0.8.7.jar Checking: /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/picard-tools/usr/share/java/guava.jar Checking: /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/libpicard-java/usr/share/java/guava.jar Checking: /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/libpicard-java-doc/usr/share/java/guava.jar Checking: /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/picard-tools/usr/share/java/htsjdk-2.23.0.jar Checking: /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/libpicard-java/usr/share/java/htsjdk-2.23.0.jar Checking: /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/libpicard-java-doc/usr/share/java/htsjdk-2.23.0.jar Found Debs: libbarclay-java libcommons-lang3-java libgatk-native-bindings-java libgkl-java libguava-java libhtsjdk-java Adding substvars: java:Depends=libbarclay-java, libcommons-lang3-java, libgatk-native-bindings-java, libgkl-java, libguava-java, libhtsjdk-java java:Recommends= Searching /build/reproducible-path/picard-tools-2.24.1+dfsg/debian/libpicard-java-doc for libpicard-java-doc Searching Found Jars: Found Debs: Adding substvars: java:Depends= java:Recommends= mh_installpoms -O--buildsystem=gradle mh_linkjars --skip-clean-poms -O--buildsystem=gradle dh_strip_nondeterminism -O--buildsystem=gradle Using 1611816462 as canonical time Normalizing debian/libpicard-java/usr/share/java/picard-2.24.1.jar using File::StripNondeterminism::handlers::jar Using 1611816462 as canonical time Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/IlluminaAdpcFileWriter.Record.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/InfiniumTransformation.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/IlluminaManifestRecord.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/InfiniumGTCFile.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/Build37ExtendedIlluminaManifestRecord.Flag.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/arrays/illumina/Build37ExtendedIlluminaManifest.html using File::StripNondeterminism::handlers::javadoc Normalizing 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debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/CommandLineDefaults.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/ClassFinder.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/package-summary.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/PicardCommandLine.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/StandardOptionDefinitions.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/CommandLineProgram.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/CommandLineSyntaxTranslater.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/programgroups/package-tree.html using File::StripNondeterminism::handlers::javadoc Normalizing debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/picard/cmdline/programgroups/GenotypingArraysProgramGroup.html using File::StripNondeterminism::handlers::javadoc dh_compress -O--buildsystem=gradle cd debian/picard-tools cd debian/libpicard-java cd debian/libpicard-java-doc chmod a-x usr/share/doc/libpicard-java/changelog.Debian gzip -9nf usr/share/doc/libpicard-java/changelog.Debian chmod a-x usr/share/doc/picard-tools/changelog.Debian usr/share/doc/picard-tools/mini.vcf usr/share/man/man1/PicardCommandLine.1 chmod a-x usr/share/doc/libpicard-java-doc/changelog.Debian usr/share/doc/libpicard-java/api/legal/jszip.md gzip -9nf usr/share/doc/libpicard-java-doc/changelog.Debian usr/share/doc/libpicard-java/api/legal/jszip.md cd '/build/reproducible-path/picard-tools-2.24.1+dfsg' gzip -9nf usr/share/doc/picard-tools/changelog.Debian usr/share/doc/picard-tools/mini.vcf usr/share/man/man1/PicardCommandLine.1 cd '/build/reproducible-path/picard-tools-2.24.1+dfsg' cd '/build/reproducible-path/picard-tools-2.24.1+dfsg' rm -f debian/picard-tools/usr/share/man/man1/picard-tools.1 debian/picard-tools/usr/share/man/man1/picard-tools.1.gz ln -s PicardCommandLine.1.gz debian/picard-tools/usr/share/man/man1/picard-tools.1.gz dh_fixperms -O--buildsystem=gradle find debian/picard-tools ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libpicard-java ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libpicard-java-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/picard-tools/usr/share/doc -type f -a -true -a ! -regex 'debian/picard-tools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libpicard-java/usr/share/doc -type f -a -true -a ! -regex 'debian/libpicard-java/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/picard-tools/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libpicard-java-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/libpicard-java-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libpicard-java/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/picard-tools/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libpicard-java -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libpicard-java-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/picard-tools -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/picard-tools/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/libpicard-java-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 dh_missing -O--buildsystem=gradle dh_installdeb -O--buildsystem=gradle install -d debian/picard-tools/DEBIAN install -d debian/libpicard-java/DEBIAN install -d debian/libpicard-java-doc/DEBIAN rm -f debian/libpicard-java-doc.debhelper.log debian/libpicard-java.debhelper.log debian/picard-tools.debhelper.log debian/rules override_dh_gencontrol make[1]: Entering directory '/build/reproducible-path/picard-tools-2.24.1+dfsg' cat debian/control \ | sed -e '/^Build-.*Depends:/,/^[^[:space:]#]/{s/^Build-.*Depends:/ /;p};d' \ | grep '^[[:space:]]' \ | tr ',' '\n' \ > debian/bd-temp-substvars echo -n "bd:libhtsjdk-java=" > debian/bd.substvars grep 'libhtsjdk-java ' debian/bd-temp-substvars \ | tr "\n" "," \ | sed -e 's/[[:space:]]\+/ /g;s/,$/\n/' \ >> debian/bd.substvars echo -n "bd:libguava-java=" >> debian/bd.substvars grep 'libguava-java ' debian/bd-temp-substvars \ | tr "\n" "," \ | sed -e 's/[[:space:]]\+/ /g;s/,$/\n/' \ >> debian/bd.substvars dh_gencontrol -O--buildsystem=gradle -- -Tdebian/bd.substvars echo misc:Depends= >> debian/picard-tools.substvars echo misc:Pre-Depends= >> debian/picard-tools.substvars dpkg-gencontrol -ppicard-tools -ldebian/changelog -Tdebian/picard-tools.substvars -Pdebian/picard-tools -Tdebian/bd.substvars echo misc:Depends= >> debian/libpicard-java.substvars echo misc:Pre-Depends= >> debian/libpicard-java.substvars dpkg-gencontrol -plibpicard-java -ldebian/changelog -Tdebian/libpicard-java.substvars -Pdebian/libpicard-java -Tdebian/bd.substvars echo misc:Depends= >> debian/libpicard-java-doc.substvars echo misc:Pre-Depends= >> debian/libpicard-java-doc.substvars dpkg-gencontrol -plibpicard-java-doc -ldebian/changelog -Tdebian/libpicard-java-doc.substvars -Pdebian/libpicard-java-doc -Tdebian/bd.substvars dpkg-gencontrol: warning: package picard-tools: substitution variable ${bd:libhtsjdk-java} unused, but is defined chmod 0644 -- debian/picard-tools/DEBIAN/control dpkg-gencontrol: warning: package libpicard-java: substitution variable ${java:Depends} unused, but is defined chmod 0644 -- debian/libpicard-java/DEBIAN/control dpkg-gencontrol: warning: package libpicard-java-doc: substitution variable ${bd:libhtsjdk-java} unused, but is defined chmod 0644 -- debian/libpicard-java-doc/DEBIAN/control make[1]: Leaving directory '/build/reproducible-path/picard-tools-2.24.1+dfsg' dh_md5sums -O--buildsystem=gradle cd debian/libpicard-java >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/picard-tools >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libpicard-java-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/picard-tools/DEBIAN/md5sums chmod 0644 -- debian/libpicard-java/DEBIAN/md5sums chmod 0644 -- debian/libpicard-java-doc/DEBIAN/md5sums dh_builddeb -O--buildsystem=gradle dpkg-deb --root-owner-group --build debian/picard-tools .. dpkg-deb --root-owner-group --build debian/libpicard-java-doc .. dpkg-deb --root-owner-group --build debian/libpicard-java .. dpkg-deb: building package 'picard-tools' in '../picard-tools_2.24.1+dfsg-1_all.deb'. dpkg-deb: building package 'libpicard-java-doc' in '../libpicard-java-doc_2.24.1+dfsg-1_all.deb'. dpkg-deb: building package 'libpicard-java' in '../libpicard-java_2.24.1+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../picard-tools_2.24.1+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3151990/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3151990/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3151990 and its subdirectories I: Current time: Tue Jul 2 12:06:13 +14 2024 I: pbuilder-time-stamp: 1719871573